id float64 1.55k 110k ⌀ | title stringlengths 1 256 ⌀ | template_id float64 0 6 ⌀ | doi stringlengths 39 49 ⌀ | url stringlengths 40 92 ⌀ | authors stringlengths 1 933 ⌀ | protocol_text stringlengths 34 1.08M | steps_list stringlengths 2 269k |
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46,230 | NOMe-seq of fixed cells | 1 | null | https://www.protocols.io/view/nome-seq-of-fixed-cells-brdwm27e | Florian Noack, Boyan Bonev | TITLE: NOMe-seq of fixed cells
AUTHORS: Florian Noack, Boyan Bonev
[DESCRIPTION]
Protocol is based on the NOMe-seq protocol (Kelly et al.; 2012) with major modifications in the incubation times to work with fixed cells (Nordström et al.; 2019) and at the library preparation step.
[STEPS]
SECTION: Prepare control DN... | ["[Prepare control DNA] NOTE: Control DNA has to prepared only once and can be reused. \n\nTo prepare GpC methylated control DNA, mix 10µl of CpG methylated pUC19 DNA (Zymo Research, Cat. N.: D5017) with 10µl of unmethylated lambda DNA (Promega, Cat. N.: D1521).", "[Prepare control DNA] Perform GpC methylation by mixin... |
105,191 | A simple and quick protocol for isolating human IgM antibodies from plasma using magnetic beads | 0 | dx.doi.org/10.17504/protocols.io.4r3l2qbbxl1y/v1 | https://www.protocols.io/view/a-simple-and-quick-protocol-for-isolating-human-ig-diyf4ftn | Sudhir Bhatia, Gudrun Baersch | TITLE: A simple and quick protocol for isolating human IgM antibodies from plasma using magnetic beads
AUTHORS: Sudhir Bhatia, Gudrun Baersch
[DESCRIPTION]
Magnetic beads are used in various applications, e.g. cell isolation, nucleic acid analysis and endotoxin elimination. Numerous groups are actively involved in the... | ["Performing of the isolation:\nThe user should use 30µl magnetic beads for the isolation of IgM from 2000µl plasma (or corresponding ratios). The user should use the plasma in a 1:4 dilution (add 1500µl buffer solution to 500µl plasma (Tube B).", "Leave the mixture at room temperature for 30 minutes in dark. Shake occ... |
40,281 | Automation Protocol for DNA Barcode Sequencing Library Preparation | 4 | dx.doi.org/10.17504/protocols.io.bjjzkkp6 | https://www.protocols.io/view/automation-protocol-for-dna-barcode-sequencing-lib-bjjzkkp6 | Nina Alperovich, Drew S Tack, Olga Vasilyeva, Sasha F Levy, David Ross | TITLE: Automation Protocol for DNA Barcode Sequencing Library Preparation
AUTHORS: Nina Alperovich, Drew S Tack, Olga Vasilyeva, Sasha F Levy, David Ross
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Here, we describe a protocol for automated library preparation for DNA barcode sequencing. The ... | ["[Preparation of Magnetic Bead/PEG-NaCl Stock]\nAdd 9 g PEG-8000 to a new 50 mL sterile conical tube.", "[Preparation of Magnetic Bead/PEG-NaCl Stock]\nAdd 10 mL 5 mol/L NaCl.", "[Preparation of Magnetic Bead/PEG-NaCl Stock]\nAdd 500 µL 1 mol/L Tris-HCl, pH8.", "[Preparation of Magnetic Bead/PEG-NaCl Stock]\nAdd 500 µ... |
78,457 | Ai14 Genotyping | 1 | dx.doi.org/10.17504/protocols.io.81wgbywy1vpk/v1 | https://www.protocols.io/view/ai14-genotyping-cquzvwx6 | Ronald.zegarra | TITLE: Ai14 Genotyping
AUTHORS: Ronald.zegarra
[DESCRIPTION]
genotyping
[STEPS]
1. Thaw reagent on ice for10 min
2. Prepare :
3. Pipette 19 µL of into 0.2 mL Tube
4. Lightly Vortex DNA sample for 30 s
5. Add 1 µL of DNA to each tube
6. Select "Ai14" PCR protocol on the thermocycler
7. Run 15 uL of PC... | ["Thaw reagent on ice for10 min", "Prepare :", "Pipette 19 µL of into 0.2 mL Tube", "Lightly Vortex DNA sample for 30 s", "Add 1 µL of DNA to each tube", "Select \"Ai14\" PCR protocol on the thermocycler", "Run 15 uL of PCR samples and a DNA ladder on a \n \n at 120 V for 60 min or until the dye is somewhat in the m... |
25,614 | 04 Transformation | null | dx.doi.org/10.17504/protocols.io.49ngz5e | null | TJUSLS China | TITLE: 04 Transformation
AUTHORS: TJUSLS China
[STEPS]
?. Preparation of competent cells1.Streak out the E.coli strain on an LBM plate (no ampicillin!) to isolate colonies and incubate at 37 degrees C overnight (16-20 hours).2. Use a sterile inoculating loop to collect cells from a single colony and inoculate 50 ml... | ["Preparation of competent cells1.Streak out the E.coli strain on an LBM plate (no ampicillin!) to isolate colonies and incubate at 37 degrees C overnight (16-20 hours).2. Use a sterile inoculating loop to collect cells from a single colony and inoculate 50 ml sterile 1X LBM Grow at 37 degrees C overnight (16-20 hou... |
96,676 | Processing of pediatric nasal and bronchial brushing samples for single cell analysis | 0 | dx.doi.org/10.17504/protocols.io.5jyl8p379g2w/v1 | https://www.protocols.io/view/processing-of-pediatric-nasal-and-bronchial-brushi-danc2daw | Liam Gubbels, Shivanthan Shanthikumar, Melanie R Neeland | TITLE: Processing of pediatric nasal and bronchial brushing samples for single cell analysis
AUTHORS: Liam Gubbels, Shivanthan Shanthikumar, Melanie R Neeland
[DESCRIPTION]
This protocol describes the collection, processing, and cryopreservation of pediatric nasal and bronchial brushing samples for downstream single-c... | ["[COLLECTION OF NASAL AND BRONCHIAL BRUSHINGS] Prepare collection tubes for nasal and bronchial brushing samples by adding 5mL of pre-chilled RPMI supplemented with 2% heat-inactivated fetal calf serum (referred to as RPMI 2% FCS) to a 15mL tube labelled with the study/patient ID.", "[PROCESSING OF NASAL AND BRONCHIAL... |
70,458 | Assay for PhosphoRab activation of LRRK2 Kinase | 4 | dx.doi.org/10.17504/protocols.io.6qpvr4o8zgmk/v1 | https://www.protocols.io/view/assay-for-phosphorab-activation-of-lrrk2-kinase-cg22tyge | Claire Y Chiang, Suzanne R Pfeffer | TITLE: Assay for PhosphoRab activation of LRRK2 Kinase
AUTHORS: Claire Y Chiang, Suzanne R Pfeffer
[DESCRIPTION]
MST kinase phosphorylates Rab proteins at the same site as LRRK2 and has been used to phosphorylate Rab8A and Rab10 quantitatively. This protocol includes a method to produce phosphoRab8A protein and remov... | ["[A. Phosphorylate Rab8A and remove MST3 kinase] To cleave the HIS tag from MST3, bind GST-PreScission protease (50 µg) to 100 µL glutathione agarose slurry (pre-washed and pelleted) 120 min at 4 °Cin a total volume of 500 µL. Wash the resin 3X with 1 mL reaction buffer. Add His-MST3 kinase (0.5 mg) and incubate o... |
33,090 | Protocolo para PFA 4% | null | dx.doi.org/10.17504/protocols.io.bcjaiuie | null | Hector Silva | TITLE: Protocolo para PFA 4%
AUTHORS: Hector Silva
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Solução para fixar tecidos</div></div>
[STEPS]
?. Aquecer a Água destilada até 70°C, no misturador, colocar a “pulga” (imã) e liga-lo, acrescentando aos poucos o PFA
?. Jogar duas pedrinhas ou mais de... | ["Aquecer a Água destilada até 70°C, no misturador, colocar a “pulga” (imã) e liga-lo, acrescentando aos poucos o PFA", "Jogar duas pedrinhas ou mais de NaOH até a mistura ficar clara e homogênea. Por último, acrescentar a solução de PB 0,2M"] |
61,106 | Karnovsky’s Modified Fixative | 6 | dx.doi.org/10.17504/protocols.io.261genwoog47/v1 | https://www.protocols.click/view/karnovsky-s-modified-fixative-b7wsrpee | Mason Mackey, Mark Ellisman, Marianne Martone | TITLE: Karnovsky’s Modified Fixative
AUTHORS: Mason Mackey, Mark Ellisman, Marianne Martone
[DESCRIPTION]
Fixative for mice and rat tissues to be used during perfusion and immersion fixation.
[BEFORE_START]
Make sure heating plate for dissolving paraformaldehyde is between 60-70° C.
[GUIDELINES]
Preparing Fix sol... | ["Add 2.0 grams paraformaldehyde to a 100mL Erlenmeyer flask.", "Add 35mL of DDH2O to 100mL to a Erlenmeyer flask.", "Heat paraformaldehyde in DDH2O to 60-70ºC. Use stir bar to mix.", "Add 2-3 drops 1N NaOH.", "Filter solution with #1 Whatman filter into a 100mL graduated cylinder.", "Add 10.0 ml of 25% glutaraldehyde... |
61,549 | scRNA-seq Data Processing (Cell Ranger, v6.0.0) | 5 | dx.doi.org/10.17504/protocols.io.j8nlkk3q6l5r/v1 | https://www.protocols.io/view/scrna-seq-data-processing-cell-ranger-v6-0-0-b8cmrsu6 | molmer , Martin Lotz, Padmaja Natarajan, Steven Head | TITLE: scRNA-seq Data Processing (Cell Ranger, v6.0.0)
AUTHORS: molmer , Martin Lotz, Padmaja Natarajan, Steven Head
[DESCRIPTION]
scRNA-seq data are analyzed using Cell Ranger from 10X Genomics.
[STEPS]
1. The "cellranger mkfastq" pipeline is used to demultiplex the raw Illumina base call files (BCL) into fastq ... | ["The \"cellranger mkfastq\" pipeline is used to demultiplex the raw Illumina base call files (BCL) into fastq format for further analysis. This pipeline uses a custom-built wrapper around Illumina’s bcl2fastq to demultiplex raw BCL files.", "Differentially expressed genes identified between clusters of interest are fu... |
101,656 | Consensus standard operating procedure for collection of tongue swabs for TB diagnostics | 0 | dx.doi.org/10.17504/protocols.io.kxygxyw54l8j/v1 | https://www.protocols.io/view/consensus-standard-operating-procedure-for-collect-dfhy3j7w | Alfred Andama, Amy E Steadman, Charlotte Ahls, Gerard Cangelosi, Anura David, Margaretha de Vos, Karen Heichman, Midori Kato-Maeda, Adam Penn-Nicholson, Alaina Olson, Lesley Scott, Lindsey Turnbull, Rachel Wood, Kris Weigel, Adithya Cattamanchi | TITLE: Consensus standard operating procedure for collection of tongue swabs for TB diagnostics
AUTHORS: Alfred Andama, Amy E Steadman, Charlotte Ahls, Gerard Cangelosi, Anura David, Margaretha de Vos, Karen Heichman, Midori Kato-Maeda, Adam Penn-Nicholson, Alaina Olson, Lesley Scott, Lindsey Turnbull, Rachel Wood, Kri... | ["[Collection Method] Prior to collection, label transport tube as per standard practice.", "[Collection Method] Place the collection tube in an upright position in a tube rack. Loosen the cap on the collection tube to facilitate ease of handling during swab insertion. Keep the cap on the collection tube until it is ti... |
63,313 | DAB-quant | 5 | dx.doi.org/10.17504/protocols.io.b93rr8m6 | https://www.protocols.io/view/dab-quant-b93rr8m6 | Sneh Patel, Sara Fridovich-Keil, Shauna Rasmussen, and Judith L Fridovich-Keil | TITLE: DAB-quant
AUTHORS: Sneh Patel, Sara Fridovich-Keil, Shauna Rasmussen, and Judith L Fridovich-Keil
[DESCRIPTION]
Here we describe DAB-quant, a new system that facilitates quantitation of large numbers of scanned tissue slides stained via immunohistochemistry with 3,3′-Diaminobenzidine (DAB). The python cod... | ["Here we provide DAB-quant, a new system that facilitates quantitation of large numbers of scanned tissue slides stained via immunohistochemistry with 3,3′-Diaminobenzidine (DAB). The python code, instructions, license, and a link to example scans for analysis are all available at:\n https://github.com/sarafridov/DAB-... |
23,894 | Neuropathy Phentoyping Protocols - Immunofluorescence Method for 8DG Localizaiton | null | dx.doi.org/10.17504/protocols.io.3jwgkpe | null | Eva Feldman | TITLE: Neuropathy Phentoyping Protocols - Immunofluorescence Method for 8DG Localizaiton
AUTHORS: Eva Feldman
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span></div><div class = "text-block"><span style = "font-weight:bold;">Phenotyping of Rodents for ... | ["Deparaffinize slides by soaking in Hemo-D overnight in rocker oven. If using cryosections, thaw on warm plate 10 min, ring with PAP pen.", "Re-hydrate through EtOH 100% -50% dH²O.", "Equilibrate sections in Tris. (10 mM, pH 7.5, 1 mM EDTA, 0.4 M NaCl)", "Incubate with RNase in Tris, 100 µg/ml, 37ºC, 1 hour.", "Rinse ... |
null | null | null | dx.doi.org/10.17504/protocols.io.ch2t8d | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Cas9 Nuclease, <em>S. pyogenes </em>(Cas9), is a double-stranded DNA endonuclease that is guided to its target by sequence complementarity of a small RNA loaded into the protein. This protocol describes how to digest double-stranded DNA in vitro using Cas9 an... | [] |
99,357 | WATER PRODUCTION FOR AWARE (Total Coliforms, Fecal Enterococci and Escherichia coli:) | 0 | dx.doi.org/10.17504/protocols.io.4r3l22xxxl1y/v2 | https://www.protocols.io/view/water-production-for-aware-total-coliforms-fecal-e-dc952z86 | Celia Manaia | TITLE: WATER PRODUCTION FOR AWARE (Total Coliforms, Fecal Enterococci and Escherichia coli:)
AUTHORS: Celia Manaia
[DESCRIPTION]
The protocol summarises the procedures used for analytical control. The protocol describes the
Standard Operating Procedure (SOP) for the optimization of advanced tertiary treatment of water... | ["[Methods: The section below summarises the procedures used for analytical control – detailed protocols are annexed to this protocol.] Total Coliforms, Fecal Enterococci and Escherichia coli:", "[Methods: The section below summarises the procedures used for analytical control – detailed protocols are annexed to this p... |
49,894 | Study Protocol: The Association of Postoperative Opioid Prescribing and Persistent Opioid Use | 1 | dx.doi.org/10.17504/protocols.io.buyenxte | https://www.protocols.io/view/study-protocol-the-association-of-postoperative-op-buyenxte | rhow , Vidhya Gunaseelan, mbicket | TITLE: Study Protocol: The Association of Postoperative Opioid Prescribing and Persistent Opioid Use
AUTHORS: rhow , Vidhya Gunaseelan, mbicket
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This retrospective cohort study will investigate the incidence of new persistent opioid use between patient... | ["[Data Sources]\nMichigan Surgical Quality Collaborative (MSQC) Clinical Registry: The MSQC maintains a clinical registry that collects patient demographics, perioperative processes, and 30-day outcomes for patients undergoing surgery in Michigan. Specifically, the MSQC captures whether patients were prescribed opioid... |
16,406 | Single-nuclei suspensions from primary human esophagus tissue | 1 | dx.doi.org/10.17504/protocols.io.t9wer7e | https://www.protocols.io/view/single-nuclei-suspensions-from-primary-human-esoph-t9wer7e | Lucy Kimbley, Rachel Parker, Jack Harrington, Rob Walker, Annette Hayden, Jonathan West, Peter Johnson, TIm Underwood, Matthew Rose-Zerilli | TITLE: Single-nuclei suspensions from primary human esophagus tissue
AUTHORS: Lucy Kimbley, Rachel Parker, Jack Harrington, Rob Walker, Annette Hayden, Jonathan West, Peter Johnson, TIm Underwood, Matthew Rose-Zerilli
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">A protocol to dissociate frozen es... | ["Pre-chill Dounce homogenizer with pestle B, containing 2 ml of ice-cold Nuclei EZ lysis buffer.", "Remove tissue from storage (-20°C in RNALater-ICE) and hold in a petri dish on wet ice. If not utilizing all of the frozen tissue, sever off the amount of tissue required (using a cold scalpel) and return the remainder ... |
70,407 | Aureococcus anophagefferens population count, and relative size (Violet SSC) by flow cytometry (CytoFLEX S Flow Cytometer Beckman Coulter) | 1 | dx.doi.org/10.17504/protocols.io.q26g7yby9gwz/v1 | https://www.protocols.io/view/aureococcus-anophagefferens-population-count-and-r-cgzftx3n | Emily E. Chase, Alex Truchon, Steven W Wilhelm | TITLE: Aureococcus anophagefferens population count, and relative size (Violet SSC) by flow cytometry (CytoFLEX S Flow Cytometer Beckman Coulter)
AUTHORS: Emily E. Chase, Alex Truchon, Steven W Wilhelm
[DESCRIPTION]
A method for obtaining relative cell size, population density, etc., of the brown tide algae Aureococco... | ["[CytoFLEX Experiment Setup] Create a new experiment with sample acquisition settings as follows: \nFSC 200\nSSC 40\nVioSSC 75\nFITC 200\nPerCP 150\nPB450 1 [placeholder; this could be set for a different dye than Pacific Blue shown here, this will not change the results]\nThreshold: (manual) PerCP 5000\n\nSet the flo... |
null | null | null | dx.doi.org/10.17504/protocols.io.pxmdpk6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div>
<p>Laboratory protocols for preparation of blood smears, reporting of malaria parasites, processing of blood samples using malaria rdt (hrp-2), blood grouping and design of questionnaire, employed in this study are briefly described.</p>
</div>
<div> </div>
[STEPS]
?.
?.... | [] |
53,889 | Titan-gc SARS-CoV-2 Strain Characterization Workflow for Bioconda | 1 | null | https://www.protocols.io/view/titan-gc-sars-cov-2-strain-characterization-workfl-byu9pwz6 | Michelle Su, Robert A Petit III, Technical Outreach and Assistance for States Team | TITLE: Titan-gc SARS-CoV-2 Strain Characterization Workflow for Bioconda
AUTHORS: Michelle Su, Robert A Petit III, Technical Outreach and Assistance for States Team
[DESCRIPTION]
This protocol covers the process of using Titan on the command-line, which was developed by Robert Petit at Wyoming Public Heath Laborato... | ["[Set up conda environment] The Titan workflow and its dependencies can be installed using the Conda package manager and the Bioconda channel for bioinformatics software. To install Conda, follow the instructions in Step 1.1. To update an existing Conda installation, go to Step 1.2. To add the Bioconda channel, go to ... |
null | null | null | dx.doi.org/10.17504/protocols.io.fgbbjsn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Satinsky, Brandon M., et al. 'Use of internal standards for quantitative metatranscriptome and metagenome analysis.' <em>Methods in enzymology</em> 531 (2012): 237-250.</p>
[GUIDELINES]
<p>DNA standards can be prepared by purchasing or extracting genomic DNA from a cultured ... | [] |
102,344 | Simulation of cardiac arrhythmias in human induced pluripotent stem cell-derived cardiomyocytes | 0 | dx.doi.org/10.17504/protocols.io.kqdg32k1qv25/v1 | https://www.protocols.io/view/simulation-of-cardiac-arrhythmias-in-human-induced-df7g3rjw | Thea Bommer, Maria Knierim, Julia Unsöld, Dominic Riedl, Laura Stengel, Michael Paulus, Thomas Körtl, Norman Liaw, Lars S. Maier, Katrin Streckfuss-Bömeke, Samuel Sossalla, Steffen Pabel | TITLE: Simulation of cardiac arrhythmias in human induced pluripotent stem cell-derived cardiomyocytes
AUTHORS: Thea Bommer, Maria Knierim, Julia Unsöld, Dominic Riedl, Laura Stengel, Michael Paulus, Thomas Körtl, Norman Liaw, Lars S. Maier, Katrin Streckfuss-Bömeke, Samuel Sossalla, Steffen Pabel
[DESCRIPTION]
The ef... | ["[Differentiation of ventricular and atrial hiPSC-CM] Differentiation of hiPSC-CM was performed as previously described [1,2]. Briefly, hiPSCs were cultured feeder-free and adherent on cell culture dishes in the presence of chemically defined medium E8.", "[Differentiation of ventricular and atrial hiPSC-CM] Cardiac d... |
75,379 | Modified beetle rearing medium | 1 | null | https://www.protocols.io/view/modified-beetle-rearing-medium-cmutu6wn | 孟筠 陳 | TITLE: Modified beetle rearing medium
AUTHORS: 孟筠 陳
[DESCRIPTION]
Modified beetle rearing medium
[STEPS]
SECTION: Start making the medium!
1.
First, Add the dry ingredients
SECTION: Start making the medium!
2. Second, add the wet ingredients
SECTION: Start making the medium!
3. MIx all of the ingredien... | ["[Start making the medium!] First, Add the dry ingredients", "[Start making the medium!] Second, add the wet ingredients", "[Start making the medium!] MIx all of the ingredients in the box and fill into the tube for 3/4 full (about 75ml)", "[Start making the medium!] Cut the tin foil into small pieces and fold it twic... |
53,159 | Transformation using electroporation | 4 | dx.doi.org/10.17504/protocols.io.bx6fprbn | https://www.protocols.io/view/transformation-using-electroporation-bx6fprbn | Ashwinuday | TITLE: Transformation using electroporation
AUTHORS: Ashwinuday
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">For transforming cells with the DNA of interest using electroporation as the tool.</div></div>
[STEPS]
?. To an electroporation cuvette add electro-competent cells of the required strai... | ["To an electroporation cuvette add electro-competent cells of the required strain, of DNA of interest and of autoclaved ultrapure water (milliQ)\n50 µl\n70 ng\n50 µl", "Keep the cuvette in ice for", "Pulse the cuvette using a pulser using the bacteria setting at 2.5keV\nEnsure that there is no sparking", "To the cuv... |
94,335 | Protocol for long read sequencing of dorsal root ganglia from human organ donors | 1 | dx.doi.org/10.17504/protocols.io.n92ldmxenl5b/v1 | https://www.protocols.io/view/protocol-for-long-read-sequencing-of-dorsal-root-g-c8c7zszn | Asta Arendt-Tranholm, Juliet M. Mwirigi, Theodore Price | TITLE: Protocol for long read sequencing of dorsal root ganglia from human organ donors
AUTHORS: Asta Arendt-Tranholm, Juliet M. Mwirigi, Theodore Price
[DESCRIPTION]
In this protocol, we describe how to extract RNA from dorsal root ganglia sourced from human organ donors, and subsequently perform long read sequencing... | ["[Harvesting and storing human dorsal root ganglia] Lumbar dorsal root ganglia (DRGs) are recovered from human organ donors with no known history of chronic pain, through a collaboration with the Southwest Transplant Alliance. DRGs are recovered within 4 hours of cross-clamp and immediately frozen in powdered dry ice.... |
50,834 | Human CD34+ cell isolation from fetal liver, and fetal thymus preparation | 4 | dx.doi.org/10.17504/protocols.io.bvvsn66e | https://www.protocols.io/view/human-cd34-cell-isolation-from-fetal-liver-and-fet-bvvsn66e | Austin Chen, Mohsen Khosravi-Maharlooei, Markus Holzl, Nichole Danzl, Chris Parks, Elizabeth Waffarn, Megan Sykes | TITLE: Human CD34+ cell isolation from fetal liver, and fetal thymus preparation
AUTHORS: Austin Chen, Mohsen Khosravi-Maharlooei, Markus Holzl, Nichole Danzl, Chris Parks, Elizabeth Waffarn, Megan Sykes
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol details the steps for isolating hu... | ["[Digestion method for CD34+ isolation]\nStart water bath and heat to if not already on.\n37 °C", "[Digestion method for CD34+ isolation]\nSpray the fetal organ test tube before putting it into the hood", "[Digestion method for CD34+ isolation]\nFill beaker w/ 70% EtOH. Soak your tools in this.", "[Digestion method ... |
77,503 | SEcuRe 2.0 – A simple and economic protocol for efficient in vitro fertilization using cryopreserved mouse sperm | 4 | dx.doi.org/10.17504/protocols.io.261ge4j3yv47/v4 | https://www.protocols.io/view/secure-2-0-a-simple-and-economic-protocol-for-effi-cpw7vphn | Magdalena Wigger, Branko Zevnik, Simon E Tröder | TITLE: SEcuRe 2.0 – A simple and economic protocol for efficient in vitro fertilization using cryopreserved mouse sperm
AUTHORS: Magdalena Wigger, Branko Zevnik, Simon E Tröder
[DESCRIPTION]
The advent of genome editing tools like CRISPR/Cas has substantially increased the number of genetically engineered mouse models... | ["[Sperm cryopreservation] Prepare 20 straws for 2 sacrificed males of the same line. Use of a single male is possible as well, but the number of straws and volume of media used needs to be reduced by 50%", "[Sperm cryopreservation] Mark the straws at 2.3 cm and 4.0 cm at the open end and label them at the other end (c... |
53,113 | RNA TRIzol isolation of Datura spp. | 6 | dx.doi.org/10.17504/protocols.io.bx4zpqx6 | https://www.protocols.io/view/rna-trizol-isolation-of-datura-spp-bx4zpqx6 | Eunice Kariñho-Betancourt, rtapia | TITLE: RNA TRIzol isolation of Datura spp.
AUTHORS: Eunice Kariñho-Betancourt, rtapia
[DESCRIPTION]
We present the TRIzol protocol for RNA extraction. We employed leaf tissue from vegetative and reproductive plants from four solanaceous species of the genus Datura; D. stramonium, D. pruinosa, D. inoxia and D. wrightii... | ["[REAGENTS] Reagents\n\nChloroform:Isoamyl alcohol (24:1) 100ml\n 96 ml Chloroform\n 4 ml Isoamyl alcohol\n\nSaline solution 500 ml \n 0.8M Sodium Citrate\n 1.2 M NaCl\n Distilled water\n\n75% ethanol 100 ml\n 75 ml of ethanol molecular biology grade (100%)\n 25 ml of Distilled water\n\nIsopropyl ... |
55,475 | Quant-iT™ PicoGreen® dsDNA Quantification | 1 | dx.doi.org/10.17504/protocols.io.b2etqben | https://www.protocols.io/view/quant-it-picogreen-dsdna-quantification-b2etqben | Roey Angel, Eva Petrova | TITLE: Quant-iT™ PicoGreen® dsDNA Quantification
AUTHORS: Roey Angel, Eva Petrova
[DESCRIPTION]
The following protocol is intended for the quantification of double-stranded DNA using Quant-iT™PicoGreen® dsDNA Assay Kit (ThermoFisher). This protocol is a simplified and condensed version of the full protocol from the ... | ["[Prepare reaction] Take out all reagents from the fridge and bring them to room temperature.\nTake out the DNA samples from the freezer. DNA samples should be slowly thawed on ice.", "[Prepare reaction] Prepare 22 ml 1X TE buffer by pipetting 1.1 ml of 20X TE buffer into 20.9 ml of nuclease-free water into a sterile ... |
51,211 | Investigating Invalid DOIs in COCI - Protocol | 5 | dx.doi.org/10.17504/protocols.io.bv9jn94n | https://www.protocols.io/view/investigating-invalid-dois-in-coci-protocol-bv9jn94n | Sara Coppini, Nooshin Shahidzadeh, Alessia Cioffi, Arianna Moretti | TITLE: Investigating Invalid DOIs in COCI - Protocol
AUTHORS: Sara Coppini, Nooshin Shahidzadeh, Alessia Cioffi, Arianna Moretti
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">A preliminary note</span></div><div class = "text-block"><span>This protocol illustrates ... | ["[Presenting the Input Material]\nFirst we read the input CSV file of the invalid DOIs, containing all the invalid cited DOIs in one column and their valid citing counterparts in another, using csv_reader.", "[Reading the CSV Data]\nFirst we read the input CSV file of the invalid DOIs, containing all the invalid cited... |
98,709 | RNA extraction and PCR protocol | 0 | dx.doi.org/10.17504/protocols.io.81wgbz7r3gpk/v1 | https://www.protocols.io/view/rna-extraction-and-pcr-protocol-dcmv2u66 | Enrico Bagnoli, Miratul Muqit | TITLE: RNA extraction and PCR protocol
AUTHORS: Enrico Bagnoli, Miratul Muqit
[DESCRIPTION]
This protocol details the extraction of RNA and PCR analysis.
[STEPS] | [] |
104,986 | KAPP-Sen TMC: Pancreas Donor Acceptance Criteria | 1 | dx.doi.org/10.17504/protocols.io.j8nlkokddv5r/v2 | https://www.protocols.io/view/kapp-sen-tmc-pancreas-donor-acceptance-criteria-dir24d8e | Cristina Aguayo-Mazzucato, Kanako Iwasaki | TITLE: KAPP-Sen TMC: Pancreas Donor Acceptance Criteria
AUTHORS: Cristina Aguayo-Mazzucato, Kanako Iwasaki
[DESCRIPTION]
Pancreas Donor Acceptance Criteria
[STEPS]
SECTION: Inclusion Criteria
1. Both sexes
Age > 18 years
All ethnicities
SECTION: Exclusion Criteria
2. HTN with end-organ damage
BMI > 35
GFR < 60 ml/min... | ["[Inclusion Criteria] Both sexes\nAge > 18 years\nAll ethnicities", "[Exclusion Criteria] HTN with end-organ damage\nBMI > 35\nGFR < 60 ml/min/1.73 m2\nKnown cardiovascular disease\nPancreatitis\nActive malignancy\nChronic pulmonary, hepatic, infectious, gastrointestinal, endocrine, neurologic, or inflammatory disease... |
14,000 | Using a Peristaltic Pump to Flow Buffer Through a Nanoporous Membrane in Filter Holder Assembly | 1 | dx.doi.org/10.17504/protocols.io.rwqd7dw | https://www.protocols.io/view/using-a-peristaltic-pump-to-flow-buffer-through-a-rwqd7dw | Harley King | TITLE: Using a Peristaltic Pump to Flow Buffer Through a Nanoporous Membrane in Filter Holder Assembly
AUTHORS: Harley King
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol provides steps for seating and flowing liquid through a 50 μm, 13mm round membrane containing a hexagonal arrangem... | ["[Mount the Membrane in the Filter Assembly]\nInsert a teflon ring into the luer-lock end half of the filter assembly. Without a membrane, connect both halves of filter assembly. A tight connection ensure the teflon ring is properly seated in the luer-lock end. Connect assembly to a peristaltic pump so that the flow i... |
76,242 | Quantification of various SARS-CoV-2 variant mutations (characteristic of Alpha, Beta, Gamma, Delta, Omicron and Omicron sublineages) in settled solids using digital RT-PCR | 1 | dx.doi.org/10.17504/protocols.io.14egnzrrzg5d/v11 | https://www.protocols.io/view/quantification-of-various-sars-cov-2-variant-mutat-cnpsvdne | Bridgette Hughes, Bradley J. White, Marlene K. Wolfe, Alexandria B Boehm | TITLE: Quantification of various SARS-CoV-2 variant mutations (characteristic of Alpha, Beta, Gamma, Delta, Omicron and Omicron sublineages) in settled solids using digital RT-PCR
AUTHORS: Bridgette Hughes, Bradley J. White, Marlene K. Wolfe, Alexandria B Boehm
[DESCRIPTION]
This process instruction describes the step... | ["[Preparation] Retrieve all kit components from the One-Step RT-ddPCR advanced kit for probes from the -20 °C freezer and thaw the components on ice.", "[Preparation] Retrieve ddPCR positive control aliquots (50 copies per uL gRNA) from the -80 °C freezer and thaw on ice", "[Preparation] For re-running frozen plates o... |
66,038 | Experimental setup for network based analysis of Drosophila melanogaster groups | 1 | dx.doi.org/10.17504/protocols.io.e6nvwk7q2vmk/v1 | https://www.protocols.io/view/experimental-setup-for-network-based-analysis-of-ccqwsvxe | Milan Petrović, Ana Meštrović, Ana Filošević Vujnović, Rozi Andretić Waldowski | TITLE: Experimental setup for network based analysis of Drosophila melanogaster groups
AUTHORS: Milan Petrović, Ana Meštrović, Ana Filošević Vujnović, Rozi Andretić Waldowski
[DESCRIPTION]
This protocol describes the breeding procedure of Dtosophila melanogaster for the purpose of studying group behavior. The ste... | ["Cultivation of flies on cornmeal media without separation male from female.", "Cornmeal food \n\nCornmeal food is used for breeding large amount of flies repeatedly collected and used during several days in road. \n\nTABLE 1. Ingrediens for different final volumes of cornmeal food.\n \n VolumeIngredient:1 L750 mL... |
28,701 | Th1 Polarization of Mouse CD4+ Cells | null | dx.doi.org/10.17504/protocols.io.795hr86 | null | Sam Li | TITLE: Th1 Polarization of Mouse CD4+ Cells
AUTHORS: Sam Li
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. [Isolation of CD4+ Cells From Lymph Nodes]
Harvest lymph nodes (superficial cervical, mandibular, axillary, inguinal, and mesenteric) from mice.
?. [Isolation of CD4+ Cells From Lymph Nodes]
Tease ly... | ["[Isolation of CD4+ Cells From Lymph Nodes]\nHarvest lymph nodes (superficial cervical, mandibular, axillary, inguinal, and mesenteric) from mice.", "[Isolation of CD4+ Cells From Lymph Nodes]\nTease lymph nodes through a sterile 70-µm nylon cell strainer to obtain single-cell suspensions incomplete RPMI containing 10... |
50,752 | Pyruvate and Urea preparation for dissolution DNP | 3 | dx.doi.org/10.17504/protocols.io.5jyl858m8l2w/v1 | https://www.protocols.io/view/pyruvate-and-urea-preparation-for-dissolution-dnp-bvs8n6hw | Dave Korenchan, Hikari Yoshihara, Sukumar Subramaniam, Romelyn DeLos Santos, Renuka Sriram, John Kurhanewicz | TITLE: Pyruvate and Urea preparation for dissolution DNP
AUTHORS: Dave Korenchan, Hikari Yoshihara, Sukumar Subramaniam, Romelyn DeLos Santos, Renuka Sriram, John Kurhanewicz
[DESCRIPTION]
This document codifies the probe preparation of pyruvate and urea for dissolution dynamic nuclear polarization. Additionally, th... | [] |
66,540 | Functionality test (10x PCR buffer) | 4 | null | https://www.protocols.io/view/functionality-test-10x-pcr-buffer-cc8kszuw | Nadine Mowoh, Stephane Fadanka | TITLE: Functionality test (10x PCR buffer)
AUTHORS: Nadine Mowoh, Stephane Fadanka
[DESCRIPTION]
In this protocol we describe how to test the functionality of the BenBio 10x PCR buffer by showing that the buffer is able to provide a suitable condition for DNA polymerase to amplify a DNA template in a PCR reaction ... | ["[Functionality test of 10x PCR buffer] Mixing\n\nHold the tubes up and gently flick the tubes to mix the components and place the tubes in a thermocycler.", "[Functionality test of 10x PCR buffer] Thermocycling\n\nInput the cycling parameters as indicated in the table below and run. (The amplification/running time wi... |
93,505 | Transformation of Diplonema papillatum by electroporation | 1 | dx.doi.org/10.17504/protocols.io.4r3l28e1xl1y/v3 | https://www.protocols.io/view/transformation-of-diplonema-papillatum-by-electrop-c7i9zkh6 | Matus Valach, Gertraud Burger | TITLE: Transformation of Diplonema papillatum by electroporation
AUTHORS: Matus Valach, Gertraud Burger
[DESCRIPTION]
Variant protocol for transformation of Diplonema papillatum by electroporation using a "home-made" transformation buffer. The procedure was devised based on previously published protocols by Kaur et al... | ["Prepare the transformation (cytomix-like) buffer.", "Inoculate Diplonema cells at 1–2×105 /mL into 100 mL OSS medium supplemented with 0.05% tryptone and let them grow for 2–3 days.", "Harvest the cells while they are in the late exponential phase (optimal density 8×106–2×107 /mL). Wash twice with OS (i.e., medium wi... |
12,971 | Sequencing and data quality control | null | dx.doi.org/10.17504/protocols.io.qwjdxcn | null | Adriana Alberti, Julie Poulain, Stefan Engelen, Karine Labadie, Sarah Romac, Isabel Ferrera, Guillaume Albini, Jean-Marc Aury, Caroline Belser, Alexis Bertrand, Corinne Cruaud, Corinne Da Silva, Carole Dossat, Frédéric Gavory, Shahinaz Gas, Julie Guy, Maud Haquelle, E'krame Jacoby, Olivier Jaillon, Arnaud Lemainque, E... | TITLE: Sequencing and data quality control
AUTHORS: Adriana Alberti, Julie Poulain, Stefan Engelen, Karine Labadie, Sarah Romac, Isabel Ferrera, Guillaume Albini, Jean-Marc Aury, Caroline Belser, Alexis Bertrand, Corinne Cruaud, Corinne Da Silva, Carole Dossat, Frédéric Gavory, Shahinaz Gas, Julie Guy, Maud Haquelle, ... | ["[Filtering]\nRemove the sequences of the Illumina adapters and primers used during library construction from the whole reads. Remove low quality nucleotides with quality value\nThese trimming steps are achieved using fastx_clean (Code availability 3), a software based on the FASTX library (Code availability 4).", "[F... |
52,357 | Shape and color analysis at wing-size and wing-pattern levels | 5 | dx.doi.org/10.17504/protocols.io.81wgb783qvpk/v1 | https://www.protocols.io/view/shape-and-color-analysis-at-wing-size-and-wing-pat-bxddpi26 | Wei-Ping Chan | TITLE: Shape and color analysis at wing-size and wing-pattern levels
AUTHORS: Wei-Ping Chan
[DESCRIPTION]
Details could be found in the Supplementary Information of "A high-throughput multispectral imaging system for museum specimens"
[STEPS]
1. Inspect all specimens before running the dorsal-ventral analysis
5. Dow... | ["Inspect all specimens before running the dorsal-ventral analysis", "Download group summary materials to local machine", "Multispectral reflectance at the wing-pattern level & Visualization according to summarized groups.", "Download all images in Shape_analysis/wing_segmentation to your local disk. Make sure all segm... |
81,065 | SARS-CoV-2 nsp3 Mac1 macrodomain TR-FRET Peptide displacement Assay | 1 | null | https://www.protocols.io/view/sars-cov-2-nsp3-mac1-macrodomain-tr-fret-peptide-d-ctehwjb6 | Haim Barr, Noa Lahav | TITLE: SARS-CoV-2 nsp3 Mac1 macrodomain TR-FRET Peptide displacement Assay
AUTHORS: Haim Barr, Noa Lahav
[DESCRIPTION]
This is a HTRF-based peptide displacement assay
-------------------------------------------------------
Experiment Concentrations (From Stock to Assay)
ReagentStockLoaded into CombiFinal in assa... | ["[Prepare Reagents] PREPARE all of the reagents/buffers required for this experiment.\n\nReagents\n \n\nDetection Solution\n \nMAC1 Buffer\n \nHTRF PPI Europium Detection Buffer\n \nAssay Buffer", "[Prepare 384-well Plate] PRIME Multi-Drop Combi Tube Dispensing Cassette MAC1 Buffer by selecting the PRIME button on the... |
84,183 | Chocolate Chip Cookies (CCCOOCI) | 1 | dx.doi.org/10.17504/protocols.io.n92ldmy9nl5b/v1 | https://www.protocols.io/view/chocolate-chip-cookies-cccooci-cwfxxbpn | Richard J Acton | TITLE: Chocolate Chip Cookies (CCCOOCI)
AUTHORS: Richard J Acton
[DESCRIPTION]
A recipe for chocolate cookies
By running this protocol and supplying your results you will be particpating in CCCOOCI (chocolate chip cookie optimisation open colaborative initiative) to learn more visit the project page: https://renkulab... | ["[Ingredients] 175 g Plain Flour \n3 g bicabonate of soda \n3 g Salt \n113 g Butter\n\nThree Sugar Variant:\n58 g Caster sugar\n58 g Soft light brown sugar\n58 g Soft Dark Brown Sugar (Muscovado)\n\nTwo Sugar Variant:\n88 g Caster sugar\n88 g Soft brown sugar\n\n5 g Vanilla extract\n1 eggs\n200 g Dark chocolate ... |
40,486 | Universal Immunoblot analysis for investigating Protein-AG (SpAG)-binding to avian and mammalian immunoglobulins. | 6 | dx.doi.org/10.17504/protocols.io.bjseknbe | https://www.protocols.io/view/universal-immunoblot-analysis-for-investigating-pr-bjseknbe | Angel Justiz-Vaillant | TITLE: Universal Immunoblot analysis for investigating Protein-AG (SpAG)-binding to avian and mammalian immunoglobulins.
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">A protein that combines the binding capacity of SpA and SpG is not comercially available. It can b... | ["Aliquots of egg yolks, animal sera or 2 µg/µl of purified immunoglobulins from birds, laboratory, wild, farm animals and pets are applied to the gels of SDS-PAGE as described elsewhere.", "Gels are transferred to nitrocellulose membranes (Immobilon-Nc, pore size 0.45 µm, Sigma-Aldrich Co, St Louis, Missouri) during 7... |
null | null | null | dx.doi.org/10.17504/protocols.io.hw2b7ge | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol describes an ELISA assay for measurement of FAS ligand (FASL, CD95L) in supernatants collected from T cell dependent cytotoxicity (TDCC) cultures after BiTE® treatment.</p>
[STEPS]
?.
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null | null | null | dx.doi.org/10.17504/protocols.io.r72d9qe | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Be the Banksy-Monat love child you've always wanted to be.</p>
[GUIDELINES]
<p>Materials needed: sharpened pencil, eraser, at least a 4 inch by 4 inch piece of unlined paper</p>
[STEPS]
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null | null | null | dx.doi.org/10.17504/protocols.io.gsnbwde | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>RNA extraction of plant tissues (in our case Bauhinia leaves) using a pBIOZOL/CTAB lysis buffer</p>
[STEPS]
?.
?.
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?.
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?. | [] |
102,337 | General Total Protein Sample Preparation Protocol for the Immunodetection of Auxenochlorella protothecoides Proteins. | 0 | dx.doi.org/10.17504/protocols.io.dm6gpzdm8lzp/v1 | https://www.protocols.io/view/general-total-protein-sample-preparation-protocol-df693rh6 | Dimitrios Camacho, Sabeeha S. Merchant | TITLE: General Total Protein Sample Preparation Protocol for the Immunodetection of Auxenochlorella protothecoides Proteins.
AUTHORS: Dimitrios Camacho, Sabeeha S. Merchant
[DESCRIPTION]
This protocol describes a general method for quickly preparing and storing protein samples for the immunodetection of Auxenochlorell... | ["Collect 108 - 109 cells by centrifugation (10000 x g, 2 min, 4 °C) using Globe Scientific metal free 15 mL or 50 mL tubes. Discard the supernatant.", "Optional: Flash freeze cell suspension in liquid nitrogen and store in -80 °C", "Resuspend the cells in 300 µL of trace metal grade 10 millimolar (mM) sodium-phosphate... |
54,584 | ZooScan Protocol | 1 | dx.doi.org/10.17504/protocols.io.yxmvmk8j9g3p/v1 | https://www.protocols.io/view/zooscan-protocol-bziyp4fw | Laëtitia Jalabert, Marc Picheral, Corinne Desnos, Amanda Elineau | TITLE: ZooScan Protocol
AUTHORS: Laëtitia Jalabert, Marc Picheral, Corinne Desnos, Amanda Elineau
[DESCRIPTION]
The ZooScan (HYDROPTIC Inc.) is an imaging system for the measurement and classification of organisms and particles (150 µm to 5 cm) present in a liquid. It is suitable for meso- and macro-planktonic organi... | ["[IMPORTANT NOTE about the ZOOPROCESS VERSION] This protocol applies for the Zooprocess 7.27 version and above. The images are issued from versions up to 8.12.\nDO UPGRADE Zooprocess as often as it is updated on the PIQv website.\nThe PIQv would assist you only if you use the latest available update of Zooprocess.\nTh... |
62,778 | SMARTerV4 (0.5x) Amplification for single-cell or single-nuclei RNASeq Protocol | 1 | dx.doi.org/10.17504/protocols.io.8epv517xdl1b/v2 | https://www.protocols.io/view/smarterv4-0-5x-amplification-for-single-cell-or-si-b9i2r4ge | Zeng | TITLE: SMARTerV4 (0.5x) Amplification for single-cell or single-nuclei RNASeq Protocol
AUTHORS: Zeng
[DESCRIPTION]
Protocol to generate full-length cDNA from single cells, or nuclei, using Takara SMARTer V4.
[STEPS] | [] |
74,993 | P14 PROCEDIMIENTO DE RECLAMACIONES | 1 | dx.doi.org/10.17504/protocols.io.ewov1oznklr2/v1 | https://www.protocols.io/view/p14-procedimiento-de-reclamaciones-cmgru3v6 | cgarcia | TITLE: P14 PROCEDIMIENTO DE RECLAMACIONES
AUTHORS: cgarcia
[DESCRIPTION]
Las reclamaciones y sugerencias serán presentadas por los doctorandos, directores y/o tutores o agentes externos que tengan relación con la EIDUCAM en la Secretaría Técnica de la EIDUCAM (eiducam@ucam.edu).
Para realizar una reclamación/sugerenc... | ["[P14 PROCEDIMIENTO DE RECLAMACIONES] Rellenar el formulario presente en la página web de la EIDUCAM (enlace).", "[P14 PROCEDIMIENTO DE RECLAMACIONES] La Secretaría Técnica de la EIDUCAM recepciona, registra y estudia las reclamaciones y sugerencias que le sean presentadas y, posteriormente las trasmite al Secretario ... |
26,635 | Protocol for mouse perfusion with dye, DAPI staining, and slide preparation | null | dx.doi.org/10.17504/protocols.io.59jg94n | null | Boaz Mohar, Monique Copeland | TITLE: Protocol for mouse perfusion with dye, DAPI staining, and slide preparation
AUTHORS: Boaz Mohar, Monique Copeland
[STEPS]
?. Add 50-100 ul of 1mM dye stock to of 4% paraformaldehyde in .1M PB
[per mouse]
?. [Set-up hood for perfusion]
Set up fume hood with:
?. [Prepare dye and fix]
Add of DMSO to lyophilized... | ["Add 50-100 ul of 1mM dye stock to of 4% paraformaldehyde in .1M PB\n[per mouse]", "[Set-up hood for perfusion]\nSet up fume hood with:", "[Prepare dye and fix]\nAdd of DMSO to lyophilized dye (100nmol) and Pipette up and down ~20 times to get 1mM concentration stock.\n100 µl", "Mix further using a vortex machine t... |
41,700 | COVIDscanDX mScanner Protocol (Confidential) | 4 | dx.doi.org/10.17504/protocols.io.bkyckxsw | https://www.protocols.io/view/covidscandx-mscanner-protocol-confidential-bkyckxsw | don.cooper | TITLE: COVIDscanDX mScanner Protocol (Confidential)
AUTHORS: don.cooper
[STEPS]
?. [COVIDscanDX mScanner Instructions for Use]
For iOS iPad and iPhone devices newer than 2018 use the following procedure. To scan the result of the developed test open the Safari browser on the iPad or iPhone device and navigate to www... | ["[COVIDscanDX mScanner Instructions for Use]\nFor iOS iPad and iPhone devices newer than 2018 use the following procedure. To scan the result of the developed test open the Safari browser on the iPad or iPhone device and navigate to www.register.covidscandx.com.For Android Samsung Galaxy Tab A 10.1 inch (2019) use th... |
33,447 | Hybridization chain reaction (HCR) protocol for Gastruloids (ESC aggregates) | 1 | dx.doi.org/10.17504/protocols.io.bcwfixbn | https://www.protocols.io/view/hybridization-chain-reaction-hcr-protocol-for-gast-bcwfixbn | Stefano Vianello, Jisoo Park, Matthias Lutolf | TITLE: Hybridization chain reaction (HCR) protocol for Gastruloids (ESC aggregates)
AUTHORS: Stefano Vianello, Jisoo Park, Matthias Lutolf
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol is for the in situ hybridization chain reaction (HCR) of Gastruloids (3D aggregates of mouse ... | ["[Day 1: Recovery and fixation of samples ]\nPrecoat a well of a 6well plate with 2mL serum solution (e.g. PBSFT: PBS+10%FBS+0.2%Triton-X100), for around 30min. Remove the serum solution and replace with with 2mL 4% formaldehyde ( 37% formaldehyde diluted to with PBS).To recover samples, use a cut P1000 pipette to pi... |
50,207 | Streaking bacteria on a Petri Plate from -70C frozen culture | 4 | dx.doi.org/10.17504/protocols.io.q26g7898qlwz/v1 | https://www.protocols.io/view/streaking-bacteria-on-a-petri-plate-from-70c-froze-bu97nz9n | Emma Tollafield, Dibyendu Dutta, Wolfram Moebius | TITLE: Streaking bacteria on a Petri Plate from -70C frozen culture
AUTHORS: Emma Tollafield, Dibyendu Dutta, Wolfram Moebius
[DESCRIPTION]
This protocol describes how to obtain isolated single colonies of any bacterial strain by streak plating, from a -70C frozen stock culture.
[STEPS]
SECTION: Creating a streak pla... | ["[Creating a streak plate] Label bottom of LB agar plate with name, date, E. coli strain, and any additional contents such as antibiotics.", "[Creating a streak plate] Working aseptically, use inoculation loop to take E. coli from the frozen stock by swirling loop on surface of stock until slushy.", "[Creating a strea... |
87,946 | Absorbance assay from an M2P flower plate | 1 | dx.doi.org/10.17504/protocols.io.x54v9pr51g3e/v1 | https://www.protocols.io/view/absorbance-assay-from-an-m2p-flower-plate-cz5ix84e | Tijana Radivojevic, Matthew Incha, Apostolos Zournas, vblayroger, Stephen Tan, Hector Garcia Martin | TITLE: Absorbance assay from an M2P flower plate
AUTHORS: Tijana Radivojevic, Matthew Incha, Apostolos Zournas, vblayroger, Stephen Tan, Hector Garcia Martin
[DESCRIPTION]
This protocol explains the steps for preparing samples and taking OD600 and OD340 measurements from a BioLector plate.
[BEFORE_START]
Make sure ... | ["[Required equipment/labware] Destination plate:\n\n \n\nWater plate:\n \nSupernatant plate:", "[Required equipment/labware] Liquid handler:\n \n\nPipette tips needed (available at Robotics lab):\ntips s200 (green box)\ntips p1000 (yellow box)\n\nSpectrophotometer/plate-reader:\nMolecular Devices SpectraMax M2\nor any... |
50,594 | Bioluminescence-based Minimum Inhibitory Concentration (MIC) testing of fungal extracts against Mycobacterium marinum | 1 | dx.doi.org/10.17504/protocols.io.bvnan5ae | https://www.protocols.io/view/bioluminescence-based-minimum-inhibitory-concentra-bvnan5ae | Siouxsie Wiles, Alex Grey | TITLE: Bioluminescence-based Minimum Inhibitory Concentration (MIC) testing of fungal extracts against Mycobacterium marinum
AUTHORS: Siouxsie Wiles, Alex Grey
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>There is a real and urgent need for new antibiotics which are able to kill Mycobacteri... | ["[Preparing 96 well plates]\nWe test doubling dilutions of each extract fraction in duplicate with a maximum concentration of 1000 µg/mL (Fig. 1A). Each round of screening also requires control wells containing a series of dilutions of the solvent used (we use DMSO), an antibiotic(we use rifampicin at a maximum concen... |
25,733 | Text Mining Approach for Adapting a School-Based Sexual Health Promotion Program in Colombia | null | dx.doi.org/10.17504/protocols.io.5ddg226 | null | Pablo Vallejo-Medina, Juan C. Correa, Mayra Gómez-Lugo, Diego Alejandro Saavedra, Eileen García-Montaño, Diana Pérez-Pedraza, Janivys Niebles-Charris, Paola García-Roncallo, Daniella Abello-Luque, José Pedro Espada, Alexandra Morales | TITLE: Text Mining Approach for Adapting a School-Based Sexual Health Promotion Program in Colombia
AUTHORS: Pablo Vallejo-Medina, Juan C. Correa, Mayra Gómez-Lugo, Diego Alejandro Saavedra, Eileen García-Montaño, Diana Pérez-Pedraza, Janivys Niebles-Charris, Paola García-Roncallo, Daniella Abello-Luque, José Pedro Esp... | ["Download the following five txt-formatted files. and put these files inside a folder with the name \"COMPAS\".", "If you are using a Linux distro, you can put that folder in the following path: \"/home/juan/Documents/COMPAS\". In Windows, you can put it in the following path: \"C:\\Users\\juan\\Documents\\COMPAS\\\""... |
58,851 | Preparing 1x PCR Master Mix | 4 | null | https://www.protocols.io/view/preparing-1x-pcr-master-mix-b5qbq5sn | Jenny Molloy, Stephane Fadanka, Nadine Mowoh, Cordellia Cordellia Fulai | TITLE: Preparing 1x PCR Master Mix
AUTHORS: Jenny Molloy, Stephane Fadanka, Nadine Mowoh, Cordellia Cordellia Fulai
[DESCRIPTION]
This protocol documents the production of BenBio 1X PCR Master Mix "Wet" and "Dry" formulations including ‘the different colors of the Wet formulations (Rubis or oink and Saphir or... | ["[Functionality test] Remove the enzymes from storage, reconstitute and test for functionality as described in the BenBio protocol using the specific test that apply for cellular reagents (OpenVent enzyme).", "[Preparation of 1x PCR Master mix formulations] Pipetting components to make up the \"Wet\" mix\n\nPipette th... |
null | null | null | dx.doi.org/10.17504/protocols.io.nutdewn | null | null | TITLE: No Title
AUTHORS:
[BEFORE_START]
<ol>
<li>Clean all surfaces and pipettors to remove DNA</li>
<li>Label Plates
<ul>
<li>Plate #1 – 1ml collection plate</li>
<li>Plate #2 – 1ml collection plate</li>
<li>Plate #3 – 1ml collection plate</li>
<li>Plate #4 – 1ml collection plate</li>
<li>Plate #5 – 2ml collection p... | [] |
70,511 | LTEE Media Recipes | 1 | dx.doi.org/10.17504/protocols.io.n92ldpy5ol5b/v1 | https://www.protocols.click/view/ltee-media-recipes-cg4ptyvn | Jesus E Chavarria-Palma, Jeffrey E Barrick | TITLE: LTEE Media Recipes
AUTHORS: Jesus E Chavarria-Palma, Jeffrey E Barrick
[DESCRIPTION]
Growth media used by the long-term E. coli evolution experiment.
TA: Tetrazolium Arabinose for distinguishing Ara- and Ara+ strains in most competition assays. Colonies of Ara- strains typically appear red on TA agar, while th... | ["[DM: Davis-Mingioli] To prepare 1 L of DM:", "[DM: Davis-Mingioli] Add distilled water to a final volume of 1 L", "[TA: Tetrazolium Arabinose] To prepare 1.5 L of TA:", "[DM: Davis-Mingioli] Autoclave using liquid program. Sterilization times are based on total volume:", "[DM: Davis-Mingioli] After autoclaving add t... |
39,097 | GWAS Self-Administration | 1 | null | https://www.protocols.io/view/gwas-self-administration-biezkbf6 | Sharona Sedighim, Olivier George | TITLE: GWAS Self-Administration
AUTHORS: Sharona Sedighim, Olivier George
[STEPS]
?. [Animal Arrival & Grouping]
When animals arrive at the lab, they will be left in a 2-week quarantine. During the end of this we will scan and mark the animals (prior to any testing or surgery).
?. [Animal Arrival & Grouping]
Animals s... | ["[Animal Arrival & Grouping]\nWhen animals arrive at the lab, they will be left in a 2-week quarantine. During the end of this we will scan and mark the animals (prior to any testing or surgery).", "[Animal Arrival & Grouping]\nAnimals separated into four groups, predetermined on the shipping sheet provided", "[Animal... |
59,577 | EPMotion - DNA Extraction | 4 | dx.doi.org/10.17504/protocols.io.8epv59reng1b/v1 | https://www.protocols.io/view/epmotion-dna-extraction-b6ezrbf6 | Khai-Minh H Nguyen, Katarina A Cohen, Oksana Polesskaya, Abraham Palmer | TITLE: EPMotion - DNA Extraction
AUTHORS: Khai-Minh H Nguyen, Katarina A Cohen, Oksana Polesskaya, Abraham Palmer
[DESCRIPTION]
This protocol is designed for Agencourt's DNAdvance Extraction kit on the EPmotion 5075. Samples are extracted in a 96 well plate. This is a continuation of the "Sample Cutting/Processing" P... | ["[Lysis Master Mix] Note: The following amounts will make a master mix for 96 samples.\n\nAdd 15.18 mL of to a new 50mL falcon tube.", "[Agencourt DNAdvance Reagent Preparation] Download the DNAdvance Handbook from Beckman Coulter Genomics. Google this - (PN B66866AC) or request from Beckman Coulter Group. \n\nPrepa... |
49,929 | Potency Test: Glucose Stimulated Insulin Release Assay | 1 | dx.doi.org/10.17504/protocols.io.buzhnx36 | https://www.protocols.io/view/potency-test-glucose-stimulated-insulin-release-as-buzhnx36 | Integrated Islet Distribution Program | TITLE: Potency Test: Glucose Stimulated Insulin Release Assay
AUTHORS: Integrated Islet Distribution Program
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The goal of the Integrated Islet Distribution Program (IIDP) is to develop a uniform standardized shipping method among all the subcontracted I... | ["[Culture Media Preparation]\nCulture media that is to be used for overnight culturing is prepared as described below.The Prodo Labs PIM(R) should be stored between 2° and 8°C upon receipt.The (heat inactivated) Gemini AB serum and the PIM(G) vials should be stored at -5° to -20°C.", "[Culture Media Preparation]\nThe... |
87,743 | DeRisi Lab Phage Immunoprecipitation Sequencing (PhIP-Seq) | 4 | dx.doi.org/10.17504/protocols.io.4r3l229qxl1y/v1 | https://www.protocols.io/view/derisi-lab-phage-immunoprecipitation-sequencing-ph-czw7x7hn | Hannah Kortbawi, Caleigh Mandell-Brehm, Brian O'Donovan, Saravazquez, Madhuraraghavan, Elze Rackaityte, Grace Wang, Aditi Saxena, David Yu, Joseph Derisi | TITLE: DeRisi Lab Phage Immunoprecipitation Sequencing (PhIP-Seq)
AUTHORS: Hannah Kortbawi, Caleigh Mandell-Brehm, Brian O'Donovan, Saravazquez, Madhuraraghavan, Elze Rackaityte, Grace Wang, Aditi Saxena, David Yu, Joseph Derisi
[DESCRIPTION]
This protocol describes the process of Phage Immunoprecipitation Sequencing ... | ["[Before Starting] Make buffers", "[Day 1] Prepare overnight E. coli (BLT5403) stock\n*This should be prepared from frozen for each day", "[Day 1] Add 20-25 mL LB-carb into an autoclaved 125 mL Erlenmeyer flask\n*Flame all flask and bottle openings upon opening and closing containers", "[Day 1] Using a sterile loop to... |
78,208 | YT medium | 4 | dx.doi.org/10.17504/protocols.io.kxygx9qx4g8j/v1 | https://www.protocols.io/view/yt-medium-cqk8vuzw | Andreas Sagen | TITLE: YT medium
AUTHORS: Andreas Sagen
[DESCRIPTION]
2xYT is a nutritionally rich liquid microbial growth medium used for propagation of recombinant strains of Escherichia coli and M13 bacteriophage or other filamentous single-stranded DNA bacteriophages.
[GUIDELINES]
Prepare enough for the necessary number of exper... | ["[500 mL 2x YT medium] Fill the bottle with 400 mL deionized water", "[500 mL 2x YT medium] Measure and add:\n 8 g Tryptone\n 5 g Yeast extract\n 2.5 g Sodium chloride\n\nPowdered compounds:", "[500 mL 2x YT medium] Adjust pH to pH 7.0 by adding drops of concentrated NaOH", "[500 mL 2x YT medium] Add deionize... |
76,701 | Generation of long-term genetically modified human T cells using Sleeping Beauty | 1 | dx.doi.org/10.17504/protocols.io.j8nlkw64xl5r/v1 | https://www.protocols.io/view/generation-of-long-term-genetically-modified-human-cn55vg86 | Zaki Molvi | TITLE: Generation of long-term genetically modified human T cells using Sleeping Beauty
AUTHORS: Zaki Molvi
[DESCRIPTION]
Genetic modification of T cells is an important step in T cell engineering for adoptive cellular therapy. Long-term T cell lines expressing a therapeutic antigen receptor, such as a chimeric antige... | ["[Introduction] Genetic modification of T cells is an important step in T cell engineering for adoptive cellular therapy. Long-term T cell lines expressing a therapeutic antigen receptor, such as a chimeric antigen receptor (CAR) or exogenous T cell receptor (TCR), are useful for in vitro and in vivo studies of antige... |
52,583 | Far East XL Male Enhancement | 1 | dx.doi.org/10.17504/protocols.io.bxkfpktn | https://www.protocols.io/view/far-east-xl-male-enhancement-bxkfpktn | health | TITLE: Far East XL Male Enhancement
AUTHORS: health
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Far East XL Male Enhancement is a medical formulation that uses spices and plant extracts to enhance sexual performance. GET IT FROM OFFICIAL WEBSITE AND GET HEAVY DISCOUNT</div></div>
[STEPS]
?. Fa... | ["Far East XL Male Enhancement Official Website: www.FarEastXL.comFar East XLReview:- It is possible to lose your sexual and physical endurance after you reach 40. These concerns can make it difficult to please your female partner. Low testosterone hormone production is the most common reason for sexual distress. N... |
95,292 | TaqMan qPCR INRAE eWHALE | 1 | dx.doi.org/10.17504/protocols.io.kqdg3xj87g25/v1 | https://www.protocols.io/view/taqman-qpcr-inrae-ewhale-c9a4z2gw | Teddy Urvois, Anne-Laure Besnard, Erwan Quéméré | TITLE: TaqMan qPCR INRAE eWHALE
AUTHORS: Teddy Urvois, Anne-Laure Besnard, Erwan Quéméré
[DESCRIPTION]
Protocol for the TaqMan assay used by INRAE team in eWHALE ring test study
[BEFORE_START]
Lab work:
Put all equipment (micropipettes, disposable tips, microtubes, molecular grade water, qPCR plate) in UV cabinet an... | ["[Master mix preparation] Determine the number of reactions, including negative controls and NTCs. Add 2-3 reactions to have margin for pipetting error.\nPrepare the Master mix according following this volume for 1 reaction :\n4 µL of Molecular Grade Water\n10 µL Master Mix environnemental TaqMan‱ 2.0\n1 µL Probe at 0... |
102,676 | Protocol for in situ sequencing (ISS) in mouse skeletal muscle | 0 | null | https://www.protocols.io/view/protocol-for-in-situ-sequencing-iss-in-mouse-skele-dghu3t6w | Ines Boehm | TITLE: Protocol for in situ sequencing (ISS) in mouse skeletal muscle
AUTHORS: Ines Boehm
[DESCRIPTION]
Protocol used to perform in situ sequencing (ISS) on mouse skeletal muscle.
[STEPS]
SECTION: Sectioning
3. Clean the cryostat with 70% EtOH. Clean the block with RNA-Zap, 70%EtOH and dry afterwards
SECTION: Section... | ["[Sectioning] Clean the cryostat with 70% EtOH. Clean the block with RNA-Zap, 70%EtOH and dry afterwards", "[Sectioning] Put the number of blades needed (as many as different tissues are being sectioned) on top of the block and turn on UV-lamp. Keep brushes and other tools that will be used also in the cryostat.\n\nCa... |
84,501 | Lung COVID | 1 | dx.doi.org/10.17504/protocols.io.j8nlkoeyxv5r/v1 | https://www.protocols.click/view/lung-covid-cwrvxd66 | Solos Jaturapisanukul | TITLE: Lung COVID
AUTHORS: Solos Jaturapisanukul
[DESCRIPTION]
Primary
objectives:
-To study the Chest CT and
pulmonary function tests in ESRD patients after recovered from COVID-19
Secondary objectives
- To study the factors affecting the
pulmonary sequalae after COVID-19 in CKD patientssuch as oxygen requirement,... | ["Follow-up Study of the Pulmonary Function and CT\nscan finding in Chronic Kidney Disease Patients After COVID-19 Infection"] |
48,937 | child document 1 7.4 | 3 | null | https://www.protocols.io/view/child-document-1-7-4-bt2hnqb6 | Mariia Guliakina | TITLE: child document 1 7.4
AUTHORS: Mariia Guliakina
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">test</div></div>
[STEPS] | [] |
64,429 | Nano-CUT&Tag for multimodal profiling of the chromatin | 4 | dx.doi.org/10.17504/protocols.io.8epv59o8dg1b/v1 | https://www.protocols.io/view/nano-cut-amp-tag-for-multimodal-profiling-of-the-c-ca6mshc6 | Marek Bartosovic, Goncalo Castelo-Branco | TITLE: Nano-CUT&Tag for multimodal profiling of the chromatin
AUTHORS: Marek Bartosovic, Goncalo Castelo-Branco
[DESCRIPTION]
Nano-CUT&Tag is a multimodal technology to profile several histone modifications at the same with single-cell resolution. Nano-CUT&Tag implements a novel Tn5 fusion proteins to anti-mous... | ["[Tn5 loading] Annealing adaptor sequences:\n\nTn5_MeA_P5_noBCD. \n5' TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG\n\nTn5_MeA_P5_bcdA. \t \n5'-TCGTCGGCAGCGTCT TATAGCCT GCGATCGAGGACGGCAGATGTGTATAAGAGACAG\n\nTn5_MeA_P5_bcdB\t \n5'-TCGTCGGCAGCGTCT ATAGAGGC GCGATCGAGGACGGCAGATGTGTATAAGAGACAG\n\nTn5_MeA_P5_bcdC\... |
null | null | null | dx.doi.org/10.17504/protocols.io.ey3bfyn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Separates molecules based on size. Great for checking DNA after a Restriction Digest.
[BEFORE_START]
Have a DNA Sample ready, typically either from PCR or a recently performed Restriction Digest. Dilute down the 50X TAE Buffer to 1X.
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?. ... | [] |
87,395 | Isolation of rest of the trypsinized stem cells from empty cell culture flasks with CD90 specific magnetic beads | 4 | dx.doi.org/10.17504/protocols.io.eq2lyjw5elx9/v1 | https://www.protocols.io/view/isolation-of-rest-of-the-trypsinized-stem-cells-fr-czkbx4sn | Sudhir Bhatia | TITLE: Isolation of rest of the trypsinized stem cells from empty cell culture flasks with CD90 specific magnetic beads
AUTHORS: Sudhir Bhatia
[DESCRIPTION]
In all laboratories working with the stem cells, it is common practice to isolate these cells with help pf trypsin solution because these cells are grown on the... | ["Grow the stem cells in the flask in cell culture media till they reach 80% confluency.", "Remove the cell culture media.", "Add 15 ml PBS to wash the cells and remove the solution. This is washing step, which is optional.", "Add trypsin solution to this. Usually it is 6 – 10 ml depending on the manufacturer.", "Keep ... |
69,012 | BICCN_DART-FISH | 4 | dx.doi.org/10.17504/protocols.io.yxmvmnd45g3p/v1 | https://www.protocols.io/view/biccn-dart-fish-cfmutk6w | Chien-Ju Chen | TITLE: BICCN_DART-FISH
AUTHORS: Chien-Ju Chen
[DESCRIPTION]
This protocol documents DART-FISH procedures used to generate spatial transcriptomic data from human brain section for BICCN.
[STEPS]
SECTION: preparation
2. Wash, dry and UV the silicone isolators. UV the EasyDip jars. Move away unused stuff from the bench ... | ["[preparation] Wash, dry and UV the silicone isolators. UV the EasyDip jars. Move away unused stuff from the bench and clean and undust the working area. Set the HybEZ oven 37C.", "[permeabilization] Prepare 75ml of 4% formaldehyde in 1x PBS. Requires two vials of 16% formaldehyde.", "[permeabilization] Take the secti... |
54,199 | SARS-CoV-2 McGill Nextera Flex sequencing protocol_Lunascript_ARTIC.V3_5uLRT | 1 | dx.doi.org/10.17504/protocols.io.by6xpzfn | https://www.protocols.io/view/sars-cov-2-mcgill-nextera-flex-sequencing-protocol-by6xpzfn | Sarah J Reiling, Marie-Michelle Simon, Anne-Marie Roy, Shu-Huang Chen, Ioannis Ragoussis | TITLE: SARS-CoV-2 McGill Nextera Flex sequencing protocol_Lunascript_ARTIC.V3_5uLRT
AUTHORS: Sarah J Reiling, Marie-Michelle Simon, Anne-Marie Roy, Shu-Huang Chen, Ioannis Ragoussis
[DESCRIPTION]
How the Nextera DNA Flex Assay Works
The Nextera DNA Flex library prep kit uses a bead-based transposome complex to ta... | ["[cDNA preparation] cDNA PREPARATION\n\n\n\nMix the following components in a 0.2 mL 8-strip tube or in a 96-well plate:\n\nComponent Volume\n\nLunaScript RT SuperMix (5x) 4 µL \nNuclease-free water 5 µL\nTemplate RNA ... |
58,247 | Conventional fixation method for Tetrahymena thermophila | 4 | null | https://www.protocols.io/view/conventional-fixation-method-for-tetrahymena-therm-b45fqy3n | miao.tian | TITLE: Conventional fixation method for Tetrahymena thermophila
AUTHORS: miao.tian
[DESCRIPTION]
A rapid and robust method for fixing Tetrahymena thermophila cells
[STEPS]
SECTION: General description of the method
1. It works for the IF of cytoplasm, nucleoplasm, and chromatin-bound proteins, FISH staining of rec... | ["[General description of the method] It works for the IF of cytoplasm, nucleoplasm, and chromatin-bound proteins, FISH staining of receptive sequences (e.g., telomeric repeats, TEs). Nuclear and cell morphology are nicely maintained.\n\nIt does not work for the IF of Cna1, γ-H2A.X, and tubulin.", "[Reagents] - 37% ... |
61,544 | Zebrafish 2021 Environmental Summary, Reptile & Aquatics, Stowers Institute for Medical Research | 1 | dx.doi.org/10.17504/protocols.io.kqdg3p8zql25/v1 | https://www.protocols.io/view/zebrafish-2021-environmental-summary-reptile-amp-a-b8cgrstw | Diana P Baumann, Adam Petrie | TITLE: Zebrafish 2021 Environmental Summary, Reptile & Aquatics, Stowers Institute for Medical Research
AUTHORS: Diana P Baumann, Adam Petrie
[DESCRIPTION]
Zebrafish are an established model organism in biomedical research, and we have maintained these fish at the Stowers Institute for Medical Research since 2006... | [] |
34,971 | Data Processing and Preparation of MALDI IMS data | null | dx.doi.org/10.17504/protocols.io.bed3ja8n | null | Nathan Heath Patterson, Elizabeth Neumann, Jamie Allen, Danielle Gutierrez, Jeff Spraggins | TITLE: Data Processing and Preparation of MALDI IMS data
AUTHORS: Nathan Heath Patterson, Elizabeth Neumann, Jamie Allen, Danielle Gutierrez, Jeff Spraggins
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Scope:</div><div class = "text-block">How to process a mass spectrometry imaging data into a fi... | ["For each spectrum in the data set, apply total ion current normalization by dividing the intensity values in the spectrum by the sum of the spectrum's intensity values.", "Generate a mean spectrum for the dataset by taking the mean of each mass bin of the dataset.", "Internally recalibrate the mean spectrum using wel... |
45,090 | HuBMAP TMC-Florida/Zurich Light Sheet Fluorescence Microscopy Modality Overview | 1 | dx.doi.org/10.17504/protocols.io.bqaamsae | https://www.protocols.io/view/hubmap-tmc-florida-zurich-light-sheet-fluorescence-bqaamsae | Jerelyn Nick, Marda Jorgensen, Seth Currlin | TITLE: HuBMAP TMC-Florida/Zurich Light Sheet Fluorescence Microscopy Modality Overview
AUTHORS: Jerelyn Nick, Marda Jorgensen, Seth Currlin
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is an overview of all of the protocols currently in use for the Light Sheet Fluorescence Microsco... | ["Process donor organs into samples for analysis. Lymph Node: dx.doi.org/10.17504/protocols.io.bbgnijveThymus: dx.doi.org/10.17504/protocols.io.bbgmiju6Spleen: dx.doi.org/10.17504/protocols.io.bc3kiykw", "Register organ donor, organs received and common coordinate region information in the HuBMAP UUID generator at http... |
null | null | null | dx.doi.org/10.17504/protocols.io.qykdxuw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol describes (1) how to amplify the genomic markers SCAR3, SCAR4, SCAR5 and SCAR7 (developed by Thornhill et al., 2013) from genomic DNA of Aiptasia<em>,</em> (2) how to use Gibson Assembly® to clone them into a (pCR<sup>™</sup>II-TOPO<sup>®</sup>-derived) plasmid ... | [] |
25,298 | TRIO tracing | null | dx.doi.org/10.17504/protocols.io.4xsgxne | null | Hongwei Dong | TITLE: TRIO tracing
AUTHORS: Hongwei Dong
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"> TRIO (Tracing the Relationship of Inputs and Outputs) experiments systematically inject complementary viruses into different target brain regions to monosynaptically label inputs to a specific projection neuro... | ["[Day 1 (after habituation)]\nInstruments are washed with soap, wiped down with alcohol and autoclaved for the first surgery. Instruments are wiped down with alcohol and sterilized via a glass bead sterilizer in between surgeries.", "[Day 1 (after habituation)]\nAnimal is deeply anesthetized. 4% lidocaine gel is appli... |
24,638 | Transposase injection mix protocol | null | dx.doi.org/10.17504/protocols.io.4a6gshe | null | Ben Matthews | TITLE: Transposase injection mix protocol
AUTHORS: Ben Matthews
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol details the steps necessary to generate injection mixes (comprised of plasmid DNA for integration and transposase mRNA) for transposon-mediated integration into </span>... | ["[Purifying injection-ready integration plasmid]\nPerform a midiprep of the integration plasmid from a overnight culture of your transposon integration plasmid.\n50 ml", "[Purifying injection-ready integration plasmid]\nFollow the kit protocol (if using recommended kit: Machery Nagel Nucleobond EF)\nBe sure to follow... |
67,816 | Physical property-Stability and pH (TBE and Borax Agarose electrophoresis buffer) | 4 | dx.doi.org/10.17504/protocols.io.kxygxz8j4v8j/v2 | https://www.protocols.io/view/physical-property-stability-and-ph-tbe-and-borax-a-ceggtbtw | Stephane Fadanka, Nadine Mowoh, Shalo Minette | TITLE: Physical property-Stability and pH (TBE and Borax Agarose electrophoresis buffer)
AUTHORS: Stephane Fadanka, Nadine Mowoh, Shalo Minette
[DESCRIPTION]
The pH check is important because changes in the pH might affect mobility of DNA in the agarose gel hence PCR result alteration and misinterpretation.... | ["[Confirming Stability and pH] To confirm the weight of the TBE powder buffer sachet:\n\nWeigh the individual buffer components that would make 500 mL of the 10x buffer as indicated in the table below (the individual powders could be pre-dried if necessary in an incubator with silica gel beads at 37 °C).\n\n \n\nPut t... |
98,204 | Differentiation of Mesenchymal Stromal Cells to Endothelial-like cells in Spheroidal Culture | 0 | dx.doi.org/10.17504/protocols.io.5jyl82m17l2w/v1 | https://www.protocols.io/view/differentiation-of-mesenchymal-stromal-cells-to-en-db542q8w | Simeng Li, Isabel Arias Quiros, Guenther Eissner | TITLE: Differentiation of Mesenchymal Stromal Cells to Endothelial-like cells in Spheroidal Culture
AUTHORS: Simeng Li, Isabel Arias Quiros, Guenther Eissner
[DESCRIPTION]
In this protocol, a easy and cost-friendly method to form mesenchymal stromal cell (MSC) spheroids was specified. The MSC spheroids would form in 1... | ["[Mesenchymal stromal cell spheroids formation] Split and resuspend MSC in fully-supplemented MesenCult-ACF plus medium.", "[Mesenchymal stromal cell spheroids formation] Count cells with Trypan blue and dilute cell to 3x10e5/ml or 12x10e5/ml. Cells need to be over 95% viable in order to form spheroids.", "[Mesenchyma... |
88,544 | Golden Gate Assembly | 4 | dx.doi.org/10.17504/protocols.io.kqdg3xknqg25/v1 | https://www.protocols.io/view/golden-gate-assembly-c2p8ydrw | NUS iGEM | TITLE: Golden Gate Assembly
AUTHORS: NUS iGEM
[DESCRIPTION]
2023 NUS-Singapore iGEM team followed this protocol to assemble DNA oligos containing Golden Gate restriction sites with a plasmid backbone that contains the same restriction sites. The restriction enzymes utilised in this protocol are the Type IIS restrictio... | ["[Golden Gate Assembly] Add the following reagents into a PCR tube:", "[Golden Gate Assembly] Prepare an ice box.", "[Golden Gate Assembly] Put the sample into the Thermal Cycler and run it with the following conditions: \n\n*Set \"Lid Temperature\" to 105 °C and set \"Volume\" to 20 µL", "[Golden Gate Assembly] Place... |
69,746 | Water sample collection and processing | 6 | null | https://www.protocols.io/view/water-sample-collection-and-processing-cgcstswe | isis.scott | TITLE: Water sample collection and processing
AUTHORS: isis.scott
[DESCRIPTION]
This protocol includes the guidelines for water sample collection and processing (CEAP samples)
[STEPS]
SECTION: SCOPE
1. This standard operating procedure (SOP) describes the procedure for the collection and processing of water samples i... | ["[SCOPE] This standard operating procedure (SOP) describes the procedure for the collection and processing of water samples in the Snake River Basin. Water samples are collected often for assessing water quality in the irrigation return flows to the Snake River. The samples are analyzed for pH, electrical conductivity... |
57,871 | Assembly: Chronic recoverable Neuropixels in mice | 1 | null | https://www.protocols.io/view/assembly-chronic-recoverable-neuropixels-in-mice-b4rpqv5n | Emily A Aery Jones | TITLE: Assembly: Chronic recoverable Neuropixels in mice
AUTHORS: Emily A Aery Jones
[DESCRIPTION]
This protocol collection explains how to build a low-cost, lightweight system to implant Neuropixels 1.0 probes into mice, record during freely moving behavior, then recover the probe for future use. This protocol explai... | ["[3D print components] Build a print file for the following pieces per mouse: 1 each of body piece, back and front flex cable holders, and dome, plus 2 wings. Print 1 headstage holder per recording rig. To re-use explanted probes, print everything except for the body piece, which is permanently affixed to the probe. F... |
76,681 | PFA treatment of OP50 | 1 | dx.doi.org/10.17504/protocols.io.81wgbyq71vpk/v1 | https://www.protocols.io/view/pfa-treatment-of-op50-cn5hvg36 | Bonnie Evans | TITLE: PFA treatment of OP50
AUTHORS: Bonnie Evans
[DESCRIPTION]
Paraformaldehyde (PFA), a polymer of formaldehyde, is an organic solution that permeabilizes bacterial cells making them no longer viable/metabolically active. However, PFA does not cause the lysis of inner cell structure, meaning the bacteria are still ... | ["[PFA treatment] Follow steps 1 to 12", "[PFA treatment] In the fume hood, add 16% PFA stock to the culture to give a 0.5% concentration", "[PFA treatment] Incubate culture for 2 hours at 37C 200rpm", "[PFA treatment] Divide culture into an even number of 50mL Falcons with equal volume", "[PFA treatment] Centrifuge fo... |
94,247 | Protocol5_HEK293T pSB-HygB-GADD34-K3L cells and extract preparation.pdf | 1 | dx.doi.org/10.17504/protocols.io.eq2lyjr2mlx9/v1 | https://www.protocols.io/view/protocol5-hek293t-psb-hygb-gadd34-k3l-cells-and-ex-c8afzsbn | angelica.gonzalez | TITLE: Protocol5_HEK293T pSB-HygB-GADD34-K3L cells and extract preparation.pdf
AUTHORS: angelica.gonzalez
[DESCRIPTION]
HEK293T pSB-HygB-GADD34-K3L cells and extract preparation
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.j9jcr4n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Proteins from the spinal ligament cells of wild-type and null mice were separated using two-dimensional gel electrophoresis and stained with Pro-Q Diamond phosphoprotein gel stain (Thermo Fisher Scientific, Waltham, MA, USA) followed by SYPRO Ruby protein gel stain (Thermo Fi... | [] |
100,674 | Seawater Filtration for Microbial or Environmental DNA | 1 | dx.doi.org/10.17504/protocols.io.rm7vzjxrrlx1/v1 | https://www.protocols.io/view/seawater-filtration-for-microbial-or-environmental-deja3cie | Colleen Kellogg | TITLE: Seawater Filtration for Microbial or Environmental DNA
AUTHORS: Colleen Kellogg
[DESCRIPTION]
This protocol describes water filtrations onto 0.22μl sterivex filters using a peristaltic pump. As part of the Hakai Institute Ocean Observing Program, biomolecular samples have been collected weekly, from 0 m to near... | ["[SETUP OF FILTRATION APPARATUS] Line counter with lab diapers.", "[SETUP OF FILTRATION APPARATUS] For extra cleanliness, you can place an autoclave or otherwise plastic bin on one side of the pump.", "[SETUP OF FILTRATION APPARATUS] Place the waste flask or container on the other side of the pump.", "[SETUP OF FILTRA... |
21,596 | Vandy - Biliopancreatic Diversion in Mice | null | dx.doi.org/10.17504/protocols.io.zb4f2qw | null | Vance L. Albaugh | TITLE: Vandy - Biliopancreatic Diversion in Mice
AUTHORS: Vance L. Albaugh
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">This is the protocol for the biliopancreatic diversion procedure in the mouse. This procedure i... | ["Preoperative Care1. All animals must be singly-housed, given Ensure 12 hours before surgery and have all bedding removed. 2. Preoperative pain medications should be administered: a. Ketoprofen (5 mg/kg) b. Saline is given at the end of surgery and a second dose is given 24 hours later. 3. Ensure adequacy of a... |
40,162 | Protocols for ZDF Study | 3 | dx.doi.org/10.17504/protocols.io.bjgakjse | https://www.protocols.io/view/protocols-for-zdf-study-bjgakjse | jlwebb , Amanda Bries | TITLE: Protocols for ZDF Study
AUTHORS: jlwebb , Amanda Bries
[STEPS] | [] |
42,311 | Chapter 6: Paralysis | 4 | null | https://www.protocols.io/view/chapter-6-paralysis-bmjfk4jn | Kerri Wolter | TITLE: Chapter 6: Paralysis
AUTHORS: Kerri Wolter
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Paralysis is commonly associated with traumatic injuries and poisoning (carbamate, organophosphate and lead) cases. </div><div class = "text-block">In respect of trauma – these are typically birds which... | ["[Assessment of paralysis cases]\nThe most important prognostic test is to check for a pain response. Use a pair of forceps to pinch a toe or skin on the leg.\nThe bird may well pull its leg up in an involuntary (automatic) response; this is called a spinal reflex. Whilst worth noting, this response only tells us abou... |
87,317 | Poliovirus direct detection and nanopore sequencing (DDNS) FAQs | 3 | dx.doi.org/10.17504/protocols.io.bp2l619ezvqe/v2 | https://www.protocols.io/view/poliovirus-direct-detection-and-nanopore-sequencin-czhvx366 | Alex Shaw, Catherine Troman, Joyce Akello, Erika Bujaki, Manasi Majumdar, Javier Martin, Nick Grassly | TITLE: Poliovirus direct detection and nanopore sequencing (DDNS) FAQs
AUTHORS: Alex Shaw, Catherine Troman, Joyce Akello, Erika Bujaki, Manasi Majumdar, Javier Martin, Nick Grassly
[DESCRIPTION]
This short FAQ document summarises the poliovirus direct detection and nanopore sequencing (DDNS) protocol, the equipment a... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.g6cbzaw | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
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105,308 | Cryopreservation of Neurons and ipSC. | 0 | dx.doi.org/10.17504/protocols.io.kxygxy2bdl8j/v1 | https://www.protocols.io/view/cryopreservation-of-neurons-and-ipsc-di344gqw | Kasandra Diaz, Gist Croft | TITLE: Cryopreservation of Neurons and ipSC.
AUTHORS: Kasandra Diaz, Gist Croft
[DESCRIPTION]
This protocol describes cryopreservation and thawing methods for iPSC and derived neural cell types, including postmitotic neurons. It is based on standard protocols and approaches but recommends critical working reagents, ti... | ["[Cryopreservation] Prelabel all tubes and thaw freezing medium (Embryomax 2x freezing medium, for ES cells, Millipore); KEEP ON ICE. *See guideline #1 for information on other freezing media recommendations.", "[Cryopreservation] Dissociate EBs/tissue/passage cells and resuspend cells at high density (5-20M cells/ml... |
21,286 | ddRADSeq in a Field Setting | null | dx.doi.org/10.17504/protocols.io.y2efybe | null | Mrinalini Watsa, Gideon Erkenswick, Aaron Pomerantz, Stefan Prost | TITLE: ddRADSeq in a Field Setting
AUTHORS: Mrinalini Watsa, Gideon Erkenswick, Aaron Pomerantz, Stefan Prost
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol begins with blood stored in Longmire's solution and has as its goal, the sequencing of genomic DNA from several individuals onto... | ["[P1 Adaptor Ligation]\nResuspend P1 oligos to 100uM in 0.5X AE Buffer (Qiagen), and follow instructions provided by supplier to do so if needed.", "[P1 Adaptor Ligation]\nIn a PCR strip tube, mix equal volumes of each oligo together to get a final concentration of 50uM of adapter. E.g. of P1F_X and l of P1R_X 11.\n2... |
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