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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35,160 | Multi-Seq: my notes from the lab | null | dx.doi.org/10.17504/protocols.io.bejyjcpw | https://www.protocols.io/view/multi-seq-my-notes-from-the-lab-bejyjcpw | Luciano Martelotto | TITLE: Multi-Seq: my notes from the lab
AUTHORS: Luciano Martelotto
[DESCRIPTION]
<div class = "text-blocks"><table border><tr style = "text-align:center;"><td> </td><td>A</td></tr><tr><td style = "text-align:center;">1</td><td rowspan = "" colspan = "" style ="display : table-cell;">Please note these are just my not... | ["First thing to do is to get very clean nuclei preps. You may start with less clean nuclei if you like but it is likely that CMO will bind to the debris, and that is not good (just a thought). So, if you work with cell lines, iPSCs, PBMCs or some of the ‘liquid’ cancers then nuclei will be pretty clean, but depending ... |
null | null | null | dx.doi.org/10.17504/protocols.io.tqdems6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Immunocytochemistry for morphology analysis. Staining of cell culture in order to obtain fluorescence images of the culture.
[STEPS]
SECTION: Cell fix
?.
SECTION: Staining
?.
SECTION: Permeabilization
?.
SECTION: Block
?.
SECTION: Primary antibody incubation
?.
SECTION: Se... | ["[Cell fix] {\"blocks\":[{\"key\":\"bq65e\",\"text\":\"1. Wash the culture twice in a phosphate buffered saline (PBS);\",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[],\"entityRanges\":[],\"data\":[]},{\"key\":\"6g3ps\",\"text\":\"2. Fix with 4% paraformaldehyde (Merck) for 10 min , then put it in PBS unti... |
5,602 | Transformation of E.coli with pGem-T Easy | null | dx.doi.org/10.17504/protocols.io.hqab5se | null | Gustaf Degen | TITLE: Transformation of E.coli with pGem-T Easy
AUTHORS: Gustaf Degen
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. [A-tailing procedure (Day 1)]
Because the Phusion polymerase will remove the A-overhangs, adding these with
Taq DNA Polymerase is necessary, as this is required for cloningMix the followi... | ["[A-tailing procedure (Day 1)]\nBecause the Phusion polymerase will remove the A-overhangs, adding these with \nTaq DNA Polymerase is necessary, as this is required for cloningMix the following reagents: AB1PCR Product1-7µl210x Taq Buffer1µl3ATP to 0.2mM1µl4Taq DNA Pol 5U1µl5dH2Oto 10µlIncubate for 30 min at 70°CIdea... |
null | null | null | dx.doi.org/10.17504/protocols.io.nwmdfc6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Testing antibacterial activity of bacteriophages on hard surfaces</p>
[BEFORE_START]
<p> </p>
<p>The following materials are needed:</p>
<p>- individual pure bacterial cultures</p>
<p>- bacteriophage preparation (either commercial or home-prepared)</p>
<p>- bacterial growth ... | [] |
94,282 | α-Synuclein sedimentation assay | 4 | dx.doi.org/10.17504/protocols.io.6qpvr3nwpvmk/v1 | https://www.protocols.io/view/synuclein-sedimentation-assay-c8bizske | arpine.sokratian | TITLE: α-Synuclein sedimentation assay
AUTHORS: arpine.sokratian
[DESCRIPTION]
The protocol describes step-by-step instructions on how to set a sedimentation assay to monitor the aggregation of alpha-synuclein over time. The protocol allows for precise quantification of fibril formation kinetics using SDS-PAGE. This ... | ["[Amplification set-up] Thaw down a-syn monomer and/or sonicated fibril aliquots. Use water-bath.\nDo not generate bubbles by pipetting or shaking", "[Amplification set-up] Measure monomer concentration via Nanodrop\nAdd Amount of 5x, 10x or 20x diluted aliquots in PBS onto nanodrop piedestal; \nParameters: other pro... |
null | null | null | dx.doi.org/10.17504/protocols.io.dzs76d | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
The following procedure is an adaptation of the original FLVP protocol from Hennes et al. (1995) for use with SYBR Green I stain. Normally, this protocol will take 2 days given that the softening of the viral pellet is an overnight step. However, if the viral pellet redissolves ... | [] |
62,255 | Keto Start ACV Gummies - Most Effective Weight Loss Gummies - Best Gummies For Weight Loss?( 2022 Update) | 3 | dx.doi.org/10.17504/protocols.io.q26g74drqgwz/v1 | https://www.protocols.io/view/keto-start-acv-gummies-most-effective-weight-loss-b82prydn | Keto Start ACV Gummies | TITLE: Keto Start ACV Gummies - Most Effective Weight Loss Gummies - Best Gummies For Weight Loss?( 2022 Update)
AUTHORS: Keto Start ACV Gummies
[DESCRIPTION]
Keto Start ACV Gummies
[STEPS] | [] |
53,826 | Crosslinking assay to study a specific cargo-coat interaction through a transmembrane receptor in the secretory pathway | 4 | dx.doi.org/10.17504/protocols.io.bytapwie | https://www.protocols.io/view/crosslinking-assay-to-study-a-specific-cargo-coat-bytapwie | Javier Manzano-Lopez †, Sofia Rodriguez-Gallardo †, Susana Sabido-Bozo, Ana Maria Perez-Linero, Rafael Lucena, Antonio Cordones-Romero, Sergio Lopez, Auxiliadora Aguilera-Romero, Manuel Muñiz | TITLE: Crosslinking assay to study a specific cargo-coat interaction through a transmembrane receptor in the secretory pathway
AUTHORS: Javier Manzano-Lopez †, Sofia Rodriguez-Gallardo †, Susana Sabido-Bozo, Ana Maria Perez-Linero, Rafael Lucena, Antonio C... | ["[Yeast growth and culture] Transform the yeast strain genomically expressing Lst1-mCherry with a centromeric plasmid expressing GFP-tagged Gas1 under control of its own promoter (pRS416-GAS1-GFP).", "[Cell lysis] Quick thaw the cell pellets and immediately place on ice.", "[Cell lysis] Resuspend each cell pellet with... |
63,519 | Reverse transcription, primer pools preparation and multiplex PCR steps for DENV2 serotype | 4 | dx.doi.org/10.17504/protocols.io.4r3l2ob2pv1y/v1 | https://www.protocols.click/view/reverse-transcription-primer-pools-preparation-and-b997r99n | Laís Ceschini, Carla Julia da Silva Pessoa Vieira, Gustavo Lima, Luisa Maria Inácio da Silva, Raul Emídio Lima, Tiago Graf, Gabriel Wallau | TITLE: Reverse transcription, primer pools preparation and multiplex PCR steps for DENV2 serotype
AUTHORS: Laís Ceschini, Carla Julia da Silva Pessoa Vieira, Gustavo Lima, Luisa Maria Inácio da Silva, Raul Emídio Lima, Tiago Graf, Gabriel Wallau
[DESCRIPTION]
This step-by-step protocol describes the cDNA synthesis, pr... | ["[Reverse transcription] Using a 2mL tube prepare the Mix 1 described below for 96 samples:\n\n \n \n \n Mix 1Reverse transcriptionVol. (1x)96 samples (+2 = 98 to keep some extra due to pipetting issues)Random Hexamers (50µM)1µL98µLdNTPs mix (10mM cada)1µL98µLTotal2µL194µL", "[Reverse transcription] Using 0,2mL PCR ... |
58,078 | Protocol of a systematic review with meta-analysis: The effects of physical exercise/activity on body composition of individuals with cardiometabolic multimorbidity | 1 | dx.doi.org/10.17504/protocols.io.b4x6qxre | https://www.protocols.io/view/protocol-of-a-systematic-review-with-meta-analysis-b4x6qxre | Juliene Gonçalves Costa, Igor Mariano, Victor Hugo Carrijo, Priccila Zuchinalli, Guilherme Morais Puga, Paula Aver Bretanha Ribeiro | TITLE: Protocol of a systematic review with meta-analysis: The effects of physical exercise/activity on body composition of individuals with cardiometabolic multimorbidity
AUTHORS: Juliene Gonçalves Costa, Igor Mariano, Victor Hugo Carrijo, Priccila Zuchinalli, Guilherme Morais Puga, Paula Aver Bretanha Ribeiro
... | ["[Background] Background \n\n Worldwide, more than 60% of the adult population has at least one chronic disease and 20% to 30% are affected by two or more chronic diseases, with cardiometabolic diseases being the most frequent and the main causes of death in the world. People with multiple chronic diseases have a... |
37,956 | HTAPP_TST- Nuclei isolation from frozen tissue | 1 | dx.doi.org/10.17504/protocols.io.bhbcj2iw | https://www.protocols.io/view/htapp-tst-nuclei-isolation-from-frozen-tissue-bhbcj2iw | Eugene Drokhlyansky, Nicholas Van Wittenberghe, Michal Slyper, Julia Waldman, Asa Segerstolpe, Orit Rozenblatt-Rosen, Aviv Regev | TITLE: HTAPP_TST- Nuclei isolation from frozen tissue
AUTHORS: Eugene Drokhlyansky, Nicholas Van Wittenberghe, Michal Slyper, Julia Waldman, Asa Segerstolpe, Orit Rozenblatt-Rosen, Aviv Regev
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol describes a method based on work by </sp... | ["[Nuclei isolation]\nUsing forceps, place tissue in the pre-filled well of the 6-well plate on ice (containing the 1 ml of TST; Step 1) and chop tissue for 10 minutes in the buffer using spring scissors.\n[On ice]", "[Nuclei isolation]\nWith a 1 ml pipette transfer the suspension from the 6-well plate to a 40 µm filte... |
91,694 | Deepwell Reusual Protocol | 1 | dx.doi.org/10.17504/protocols.io.j8nlko2x6v5r/v2 | https://www.protocols.io/view/deepwell-reusual-protocol-c5sny6de | Morris Jack | TITLE: Deepwell Reusual Protocol
AUTHORS: Morris Jack
[DESCRIPTION]
This is a protocol to reuse deepwells for sustainability practices
[STEPS]
SECTION: Growing cultures in a deep well
1. Cover a deep well with two layers of aluminium foil and tape the front and back to hold it securely. The tape also turns the alumi... | ["[Growing cultures in a deep well] Cover a deep well with two layers of aluminium foil and tape the front and back to hold it securely. The tape also turns the aluminium foil into a lid for the deep well by temporarily peeling off the front tape.", "[Growing cultures in a deep well] Autoclave at 120C for 20min. After ... |
103,679 | In-Silico Validation of Biomarkers using ROC and AUC Curve Analysis in R: A Comprehensive Protocol | 0 | dx.doi.org/10.17504/protocols.io.q26g713qqgwz/v1 | https://www.protocols.io/view/in-silico-validation-of-biomarkers-using-roc-and-a-dhg733zn | Adarsh V, Shreya Satyanarayan Bhat, Vidya Niranjan | TITLE: In-Silico Validation of Biomarkers using ROC and AUC Curve Analysis in R: A Comprehensive Protocol
AUTHORS: Adarsh V, Shreya Satyanarayan Bhat, Vidya Niranjan
[DESCRIPTION]
Biomarkers are essential for the early detection, diagnosis, and management of diseases, particularly in complex conditions like Alzheimer'... | ["[Introduction] Biomarkers play a crucial role in the early detection, diagnosis, and management of various diseases. However, the development and validation of reliable biomarkers is a complex and challenging process that requires rigorous evaluation of their analytical and clinical performance. Biomarker validation ... |
43,696 | PCR | 4 | dx.doi.org/10.17504/protocols.io.bnwqmfdw | https://www.protocols.io/view/pcr-bnwqmfdw | Zhujun Wei | TITLE: PCR
AUTHORS: Zhujun Wei
[STEPS]
?. Add the following reagent to a PCR tube.(50 μl). AB12×high Taq Master Mix (Enzyme)25 μl2Template2 μl3Forward Primer (10 μM)2 μl4Reverse Primer (10 μM)2 μl5ddH2O19 μl
AB12×high Taq Master Mix (Enzyme)25 μl2Template2 μl3Forward Primer (10 μM)2 μl4Reverse Primer (10 μM)2 μl5ddH2... | ["Add the following reagent to a PCR tube.(50 μl). AB12×high Taq Master Mix (Enzyme)25 μl2Template2 μl3Forward Primer (10 μM)2 μl4Reverse Primer (10 μM)2 μl5ddH2O19 μl\nAB12×high Taq Master Mix (Enzyme)25 μl2Template2 μl3Forward Primer (10 μM)2 μl4Reverse Primer (10 μM)2 μl5ddH2O19 μl", "Program the thermocycler as fo... |
29,278 | Minimal sample metadata for healthy liver tissue | null | dx.doi.org/10.17504/protocols.io.8t6hwre | null | Lenny Teytelman | TITLE: Minimal sample metadata for healthy liver tissue
AUTHORS: Lenny Teytelman
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is just a draft. Please feel free to revise and comment, but try to keep the total fields to a maximum of 20.</div></div>
[STEPS] | [] |
56,243 | Total Starch Enzymatic Digestion | 1 | dx.doi.org/10.17504/protocols.io.b26tqhen | https://www.protocols.io/view/total-starch-enzymatic-digestion-b26tqhen | Lynn Doran, Amanda P. De Souza | TITLE: Total Starch Enzymatic Digestion
AUTHORS: Lynn Doran, Amanda P. De Souza
[DESCRIPTION]
Enzymatic digestion of total soluble starch to glucose in plant tissue extracts for preparation for quantification via the GOD-POD Method (NZYtech).
[BEFORE_START]
Extract and dry total starch pellet from plant tissue p... | ["Prepare fresh daily 120 U/mL α-amylase in MOPS buffer. 1 mL per sample will be needed. Initial concentration of α-amylase is 1000 U/mL. Use C1V1 = C2V2 to calculate the volume of α-amylase and MOPS buffer to use.", "Prepare fresh daily 30 U/mL amyloglucosidase in acetate buffer. 1 mL per sample will be needed. Initi... |
77,893 | Characterization of the VKORC1 and CYP2C9 genotypes | 1 | dx.doi.org/10.17504/protocols.io.kxygx9edzg8j/v3 | https://www.protocols.io/view/characterization-of-the-vkorc1-and-cyp2c9-genotype-cqbdvsi6 | Mirsada Causevic, Edin Begic | TITLE: Characterization of the VKORC1 and CYP2C9 genotypes
AUTHORS: Mirsada Causevic, Edin Begic
[DESCRIPTION]
Vitamin K antagonists (e.g. warfarin) are anticoagulants which represent widely prescribed drugs for prevention and treatment of thromboembolic disorders.
Warfarin's molecular target is vitamin K epoxide re... | ["[Genomic DNA extraction] Patients' whole blood was collected in ethylenediaminetetraacetic acid (EDTA)-containing tubes and stored at -20°C until use. Genomic DNA extraction from the human whole blood, that is, leukocytes, was carried out according to the protocol described by Subbarayan PR and colleagues (doi: 10.21... |
53,570 | Conducting Online Research With Infants | 1 | null | https://www.protocols.io/view/conducting-online-research-with-infants-byjapuie | ajthomas | TITLE: Conducting Online Research With Infants
AUTHORS: ajthomas
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a step-by-step process for running synchronous online studies with infants: studies in which you meet parents and infants via video chat. This method is meant to be very similar ... | ["[Stimuli Set Up]\nMake videos of stimuli by using keynote or powerpoint. Once you have the stimuli you want to use. You can use keynote or powerpoint to make a long video that includes attention getters etc. Make your keynote file that includes videos and attention getters in the order you want them. Then select File... |
98,082 | Spatial N-glycomics with MALDI-MSI for human kidney tissue | 1 | dx.doi.org/10.17504/protocols.io.8epv5j1m4l1b/v3 | https://www.protocols.io/view/spatial-n-glycomics-with-maldi-msi-for-human-kidn-db2a2qae | Dusan Velickovic, Kumar Sharma, Theodore Alexandrov, Chris Anderton | TITLE: Spatial N-glycomics with MALDI-MSI for human kidney tissue
AUTHORS: Dusan Velickovic, Kumar Sharma, Theodore Alexandrov, Chris Anderton
[DESCRIPTION]
This protocol describes the procedure to obtain high quality MALDI mass spectrometry images of N-linked glycans from formalin-fixed paraffin embedded tissue. Thi... | ["[Scope] This protocol describes the procedure to obtain high quality MALDI mass spectrometry images of N-linked glycans from formalin-fixed paraffin embedded tissue.", "[Health and Safety] Wear nitrile gloves and safety glasses. Follow standard laboratory safety procedures.", "[Equipment] Equipment Required:", "[Equi... |
88,667 | Village Nuclei Isolation With Myelin Removal | 4 | dx.doi.org/10.17504/protocols.io.n2bvj3dxblk5/v2 | https://www.protocols.io/view/village-nuclei-isolation-with-myelin-removal-c2t3yeqn | Steve McCarroll, Emi Ling, Melissa Goldman, Nora Reed | TITLE: Village Nuclei Isolation With Myelin Removal
AUTHORS: Steve McCarroll, Emi Ling, Melissa Goldman, Nora Reed
[DESCRIPTION]
Isolation of nuclei from fresh-frozen brain tissue from sets of multiple (typically 2-20) human donors for analysis as a “cell village” (Wells et al., PMID 36796362) in which nuclei from all... | ["[Before Starting] Gather Supplies\nRazor Blades\nGlass slides\nSyringes with needles (3 mL syringe with 26 1⁄2 gauge needle)\nMyelin removal beads (cat # 130-096-731) https://www.miltenyibiotec.com/US-en/products/myelin-removal-beads-ii-human-mouse-rat.html#gref \nEppendorf tubes (1.5 mL and 5 mL)\nEppendorf or Raini... |
28,384 | MojoSort™ Isolation Kits Protocol - 4 | null | dx.doi.org/10.17504/protocols.io.7x8hprw | null | Sam Li | TITLE: MojoSort™ Isolation Kits Protocol - 4
AUTHORS: Sam Li
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Product description and procedure summary:</span></div><div class = "text-block"><span>Target cells are depleted by incubating your sample with the biotin an... | ["Prepare cells from your tissue of interest or blood without lysing erythrocytes. Kits for human samples have been optimized for PBMCs, please prepare the cells using a suitable method.", "In the final wash of your sample preparation, resuspend the cells in MojoSort™ Buffer by adding up to 4mL in a 5 mL (12 x 75 mm) p... |
21,670 | Chlamydia trachomatis PCR | null | dx.doi.org/10.17504/protocols.io.zeef3be | null | Ana Ximena Kiguen, Jessica Paola Mosmann, Raul Fernando Venezuela, Cecilia Gabriela Cuffini | TITLE: Chlamydia trachomatis PCR
AUTHORS: Ana Ximena Kiguen, Jessica Paola Mosmann, Raul Fernando Venezuela, Cecilia Gabriela Cuffini
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:justify"><span>OmpA gene PCR: PCR DNA extract (5 μl) was used to amplify a ... | ["Pre Amplification Mix( NRO/NLO for ompA gene, and CTP1/CTP2 for cryptic Plasmid)\n[Mint Master Mix]\n[Agua ultrapura]\n[each primer]", "Add Extracted DNA\n[DNA]", "In a thermocycler , incubate as follows for ompA gene:49 amplification cycles as follows:Incubate as follows for Cryptic Plasmid:35 amplification cycles a... |
28,962 | Viral Preparation | null | dx.doi.org/10.17504/protocols.io.8iahuae | null | Aditya Mohan | TITLE: Viral Preparation
AUTHORS: Aditya Mohan
[STEPS]
?. [Day 1]
Coat the plates with 1% Poly-L-Lysine solution and leave in dry incubator overnight.
?. [Day 2 ]
Plate 6E6 HEK293 T cells overnight in DMEM media
?. [Day 3]
In 2 1.5 mL epindorph tube add 150 uL of OptiMEM. In one of them add 15 uL of lipofectamine. In ... | ["[Day 1]\nCoat the plates with 1% Poly-L-Lysine solution and leave in dry incubator overnight.", "[Day 2 ]\nPlate 6E6 HEK293 T cells overnight in DMEM media", "[Day 3]\nIn 2 1.5 mL epindorph tube add 150 uL of OptiMEM. In one of them add 15 uL of lipofectamine. In the other add 10 uL of packaging plasmid and 10 uL of ... |
81,048 | Size selection (Purification) | 1 | dx.doi.org/10.17504/protocols.io.bp2l695eklqe/v1 | https://www.protocols.io/view/size-selection-purification-ctdywi7w | Tsu-Chun Hung | TITLE: Size selection (Purification)
AUTHORS: Tsu-Chun Hung
[DESCRIPTION]
Size selection (Purification)
[STEPS]
1. Prepare 20 µL sample and 9 µL magnetic beads in 1.5 mL eppendorf tube.
2. Mix sample and beads gently by flicking then flash spin the tube. Put on the regular rack for 5mins 5 min.
3. Transfer the... | ["Prepare 20 µL sample and 9 µL magnetic beads in 1.5 mL eppendorf tube.", "Mix sample and beads gently by flicking then flash spin the tube. Put on the regular rack for 5mins 5 min.", "Transfer the tube to the magnetic rack. After most of the magnetic beads attach to the wall, remove the supernant.", "Add 300 µL 75% e... |
45,161 | 3.1 Preparation of Monocellular Lung Suspension from a Mouse Lung Lobe | 4 | dx.doi.org/10.17504/protocols.io.bqchmst6 | https://www.protocols.io/view/3-1-preparation-of-monocellular-lung-suspension-fr-bqchmst6 | Helen Graves, Steven Evans, Michael Fauler, Manfred Frick, Sterghios A. Moschos | TITLE: 3.1 Preparation of Monocellular Lung Suspension from a Mouse Lung Lobe
AUTHORS: Helen Graves, Steven Evans, Michael Fauler, Manfred Frick, Sterghios A. Moschos
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The clinical potential of DNA and RNA-targeting therapeutics for airways diseas... | ["[3.1 Preparation of Monocellular Lung Suspension from a Mouse Lung Lobe]\nRinse the fresh, perfused mouse lung, with sterile PBS to eliminate any blood.", "[3.1 Preparation of Monocellular Lung Suspension from a Mouse Lung Lobe]\nTransfer the lung lobe to in a sterile tissue vial (ensure full tissue submersion) and ... |
43,142 | Stranded Transcript Count Table Generation from Long Reads | 1 | dx.doi.org/10.17504/protocols.io.bndema3e | https://www.protocols.io/view/stranded-transcript-count-table-generation-from-lo-bndema3e | David Eccles | TITLE: Stranded Transcript Count Table Generation from Long Reads
AUTHORS: David Eccles
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is for comparing different samples at the transcript level, using long reads that are mapped to transcripts.</div><div class = "text-block"><span styl... | ["[Demultiplex Reads ]\nDemultiplex and orient reads as per the protocol Preparing Reads for Stranded Mapping. It is expected that these demultiplexed reads will be split up in the current directory, and coupled with a 'barcode_counts.txt' file. If that's the case, the following should work:for bc in $(awk '{print $... |
61,694 | Antibiotic Sensitivity Assay for Heterometopus palaeformis (strain RAJCA) | 4 | dx.doi.org/10.17504/protocols.io.x54v9y3mzg3e/v1 | https://www.protocols.io/view/antibiotic-sensitivity-assay-for-heterometopus-pal-b8g6rtze | Fatma Gomaa, Johana Rotterova, Roxanne Berinate, Maria Pachiadaki, Virginia Edgcomb | TITLE: Antibiotic Sensitivity Assay for Heterometopus palaeformis (strain RAJCA)
AUTHORS: Fatma Gomaa, Johana Rotterova, Roxanne Berinate, Maria Pachiadaki, Virginia Edgcomb
[DESCRIPTION]
Goal: To determine the optimal concentration of three antibiotics, Puromycin, Geneticin (G418) and Blasticidin, that will effec... | [] |
103,236 | SANGER Sequencing EFGL | 0 | dx.doi.org/10.17504/protocols.io.yxmvmew25g3p/v1 | https://www.protocols.io/view/sanger-sequencing-efgl-dg3c3yiw | EagleFish GeneticsLab | TITLE: SANGER Sequencing EFGL
AUTHORS: EagleFish GeneticsLab
[DESCRIPTION]
This protocol describes how the Eagle Fish Genetics Lab (EFGL) prepares extracted DNA samples for the ABI 3500xL Genetic Analyzer, and how we run and collect data from this machine. This process is achieved by PCR amplification, ExoSAP-IT purif... | ["[PCR Amplification of Target Sequence] Materials needed: \n• Forward and reverse primers\n• Heat Seal\n• 1.5mL vials \n• PCR master mix reagents/kits \n• DNA tray(s) \n• Unskirted PCR plate(s)\n• Pipette and tip", "[SECTION 1 – PCR Purification with ExoSAP-IT] Materials needed: \n• ExoSAP-IT Express reagent (pre-al... |
86,328 | Reverse transcription, primer pools preparation and multiplex PCR steps for DENV1 serotype for genomic sequencing | 4 | dx.doi.org/10.17504/protocols.io.5jyl8pjyrg2w/v1 | https://www.protocols.io/view/reverse-transcription-primer-pools-preparation-and-cyiyxufw | Laís Ceschini, Carla Julia da Silva Pessoa Vieira, Luisa Maria Inácio da Silva, Gustavo Lima, Raul Emídio, Tiago Graf, Gabriel Luz Wallau | TITLE: Reverse transcription, primer pools preparation and multiplex PCR steps for DENV1 serotype for genomic sequencing
AUTHORS: Laís Ceschini, Carla Julia da Silva Pessoa Vieira, Luisa Maria Inácio da Silva, Gustavo Lima, Raul Emídio, Tiago Graf, Gabriel Luz Wallau
[DESCRIPTION]
This step-by-step protocol describes ... | ["[Reverse transcription] Using a 2mL tube prepare the Mix 1 described below for 96 samples:", "[Reverse transcription] Using 0,2mL PCR tubes or 96 wells plates add 11-16µL of extracted RNA from\nRT-PCR positive samples. Add 2µL of Mix 1 to the tube/well and take it to the\nthermocycler with the following set up\n\n65º... |
28,807 | Lentiviral transduction of iPSCs with sgRNAs and sgRNA libraries | null | dx.doi.org/10.17504/protocols.io.8dfhs3n | null | Ruilin Tian, Jason Hong, Sydney Sattler, Martin Kampmann | TITLE: Lentiviral transduction of iPSCs with sgRNAs and sgRNA libraries
AUTHORS: Ruilin Tian, Jason Hong, Sydney Sattler, Martin Kampmann
[STEPS]
?. [Day 0: Seeding]
18 – 24 hours before transfection, seed 293T cells into a 6 well plate or other format with a density that will make the cells 80 – 95 % confluent on the... | ["[Day 0: Seeding]\n18 – 24 hours before transfection, seed 293T cells into a 6 well plate or other format with a density that will make the cells 80 – 95 % confluent on the day of transfection. Refer to a seeding chart if necessary to seed appropriate density.", "[Day 0: Seeding]\nIncubate overnight.", "[Day 1: Transf... |
90,731 | Isothermal Titration Calorimetry of the Rubicon RH domain and Rab7 | 4 | dx.doi.org/10.17504/protocols.io.q26g7pwd3gwz/v1 | https://www.protocols.io/view/isothermal-titration-calorimetry-of-the-rubicon-rh-c4ujywun | Dan Tudorica | TITLE: Isothermal Titration Calorimetry of the Rubicon RH domain and Rab7
AUTHORS: Dan Tudorica
[DESCRIPTION]
1:1 binding of Rubicon and Rab7
[STEPS]
SECTION: Protein prep
1. On day prior to experiment, codialyze both binding partners to use in the the same beaker.
SECTION: Protein prep
2. Prepare 2 L of 50 mM HEPES ... | ["[Protein prep] On day prior to experiment, codialyze both binding partners to use in the the same beaker.", "[Protein prep] Prepare 2 L of 50 mM HEPES 7.5, 150 mM NaCl, 10 mM TCEP, and degas thoroughly at room temperature under vacuum with stir bar agitation, then chill in fridge until ready for dialysis.", "[Protein... |
null | null | null | dx.doi.org/10.17504/protocols.io.ftybnpw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>A protocol used to generate a PDMS microfluidic chip. Work was funded by Cambridge Synthetic Biology Strategic Research Initative (SRI) SynBio Fund.</p>
<p>http://www.synbio.cam.ac.uk/synbiofund</p>
<p> </p>
[BEFORE_START]
<ol>
<li><span style="line-height: 16px;">Use AutoDe... | [] |
24,123 | Biochemical Measures of Neuropathy - Western Blot Stripping | null | dx.doi.org/10.17504/protocols.io.3s3gngn | null | Eva Feldman | TITLE: Biochemical Measures of Neuropathy - Western Blot Stripping
AUTHORS: Eva Feldman
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span></div><div class = "text-block">Oxidative stress is highly correlated with the metabolic changes caused by hypergly... | ["[Performing assay:]\nRainbow markers do not withstand stripping, so if you don’t have a biotinylated marker on your blot, be sure to mark the location of the rainbow markers with a pen or pencil before stripping 1. Incubate your blot for 10-20 min at 70ºC. to strip. (10 min. for 20-40 µg protein and 15-20 min. for lo... |
83,400 | S. aureus biofilm removal multi-assay | 6 | dx.doi.org/10.17504/protocols.io.bp2l6xk6klqe/v1 | https://www.protocols.click/view/s-aureus-biofilm-removal-multi-assay-cvpgw5jw | Tomasz Swebocki | TITLE: S. aureus biofilm removal multi-assay
AUTHORS: Tomasz Swebocki
[DESCRIPTION]
The following protocol describes culture and treatment of the S.aureus-based biofilm and techniques that can be used to asses its eradication/removal. The protocol covers basic preparation and three techniques, namely: growth control, ... | ["[Biofilm culture] Culture bacteria strains in TSB at 35 °C for approximately 240 min in order to reach mid-log phase (OD600 0.5-0.6).", "[Biofilm culture] Pellet the cells by centrifugation (4500 rpm, 5 min, 20 °C) then wash twice with potassium phosphate buffer (PPB; 100 millimolar (mM), pH 7).\n\nFor washing, redis... |
null | null | null | dx.doi.org/10.17504/protocols.io.ihncb5e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Please contact Dr. Steven Wilhelm (wilhelm@utk.edu) for additional information regarding this protocol.</p>
[STEPS]
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50,982 | Cross-linking/MS-analysis of Thr72-phosphorylated Rab8A and PPM1H (D288A) complex | 1 | dx.doi.org/10.17504/protocols.io.bv2en8be | https://www.protocols.io/view/cross-linking-ms-analysis-of-thr72-phosphorylated-bv2en8be | Pawel Lis, Pui Yiu Lam, Axel Knebel , Kerryn Berndsen, Dario Alessi | TITLE: Cross-linking/MS-analysis of Thr72-phosphorylated Rab8A and PPM1H (D288A) complex
AUTHORS: Pawel Lis, Pui Yiu Lam, Axel Knebel , Kerryn Berndsen, Dario Alessi
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">A subset of Rab proteins, including Rab8A, have been identified as substrates of the L... | ["[Protein buffer exchange]\nPrepare a beaker containing of HEPES , NaCl, MgCl2 buffer and a magnetic stir bar. Set the beaker on a magnetic stirrer with gentle stirring, at .\nAs the cross-linking reaction can be inhibited by amine containing buffers, a buffer exchange step for both, PPM1H and pRab8A protein solut... |
73,800 | Eggs injections | 4 | null | https://www.protocols.io/view/eggs-injections-ckbgusjw | FishFloorUCL | TITLE: Eggs injections
AUTHORS: FishFloorUCL
[DESCRIPTION]
Protocol for microinjections of 0-dpf eggs @FishFloorUCL.
[STEPS]
SECTION: Set-up breeding pairs
1. Set up the breeding pairs the night before or order them from the fish facility. Arrive early in the morning, 9AM for single cell, 9:30 for fish facility injec... | ["[Set-up breeding pairs] Set up the breeding pairs the night before or order them from the fish facility. Arrive early in the morning, 9AM for single cell, 9:30 for fish facility injections.\n\nMake sure to book the injector in advance.", "[Calibrate the needle] Open the red valve for your injector, you should see the... |
102,735 | Chromogenic in situ hybridisation | 4 | null | https://www.protocols.io/view/chromogenic-in-situ-hybridisation-dgjp3umn | Stephen Carter | TITLE: Chromogenic in situ hybridisation
AUTHORS: Stephen Carter
[DESCRIPTION]
The protocol for performing chromogenic in situ hybridisations in zebrafish embryos and larvae in the Wilson lab.
[STEPS]
SECTION: Probe synthesis
2. If the template DNA is a plasmid, it must first be linearised by restriction enzyme dige... | ["[Probe synthesis] If the template DNA is a plasmid, it must first be linearised by restriction enzyme digestion. If it is a PCR product, it can be used directly. \n\nPrepare probe synthesis reaction mix\n\nTemplate DNA (PCR product or plasmid) -0.5-1 µg\n10x DIG RNA mix (Roche) - 2 µL\n10x transcription buffer - 2 µL... |
98,415 | The Parkinson’s Progression Markers Initiative (PPMI) Clinical - Establishing a Deeply Phenotyped PD Cohort AM 3.2 | 1 | dx.doi.org/10.17504/protocols.io.n92ldmw6ol5b/v2 | https://www.protocols.io/view/the-parkinson-s-progression-markers-initiative-ppm-dccp2svn | Kenneth Marek | TITLE: The Parkinson’s Progression Markers Initiative (PPMI) Clinical - Establishing a Deeply Phenotyped PD Cohort AM 3.2
AUTHORS: Kenneth Marek
[DESCRIPTION]
This protocol details the Parkinson’s Progression Markers Initiative (PPMI) Clinical - establishing a deeply phenotyped PD cohort.
[GUIDELINES]
APPENDIX 1 – He... | ["[PURPOSE OF STUDY] Primary Objectives of PPMI Clinical:\nThe primary objectives include to:", "[PURPOSE OF STUDY] Establish standardized protocols for acquisition, transfer and analysis of clinical, digital, imaging, biologic and genetic data that can be used by the PD research community. This protocol will build on ... |
37,343 | Targeted ExSeq -- Sequencing Library Preparation | 1 | dx.doi.org/10.17504/protocols.io.bgp7jvrn | https://www.protocols.io/view/targeted-exseq-sequencing-library-preparation-bgp7jvrn | Anubhav Sinha, Asmamaw T. Wassie, Fei Chen, Yi Cui, Ed Boyden | TITLE: Targeted ExSeq -- Sequencing Library Preparation
AUTHORS: Anubhav Sinha, Asmamaw T. Wassie, Fei Chen, Yi Cui, Ed Boyden
[DESCRIPTION]
This protocol accompanies Expansion Sequencing (ExSeq), describing the process of targeted ExSeq library preparation for a sample that has been processed according ... | ["[Padlock Probe Hybridization] Padlock Probe Hybridization\n\nThe first step of library preparation is to hybridize padlock probes to the RNA transcripts of interest within the expanded samples.", "[Universal Amplicon Detection Hybridization] Amplicon Detection Hybridization\n\nA rapid quality control assay for the li... |
98,529 | Carrier-assisted One-pot Sample Preparation for Targeted Proteomics Analysis of Small Numbers of Human Cells | 4 | dx.doi.org/10.17504/protocols.io.4r3l24zbjg1y/v2 | https://www.protocols.io/view/carrier-assisted-one-pot-sample-preparation-for-ta-dcf92tr6 | Kendall Martin, Tong Zhang, William B. Chrisler, Fillmore L. Thomas, WEI-JUN QIAN, Tujin Shi | TITLE: Carrier-assisted One-pot Sample Preparation for Targeted Proteomics Analysis of Small Numbers of Human Cells
AUTHORS: Kendall Martin, Tong Zhang, William B. Chrisler, Fillmore L. Thomas, WEI-JUN QIAN, Tujin Shi
[DESCRIPTION]
Protein analysis of small numbers of human cells is primarily achieved by targeted prot... | ["[PROCEDURE] Pretreatment of PCR tubes", "[PROCEDURE] Add 100 µL of nonhuman (e.g., Shewanella oneidensis)cell lysate digests at 0.2 µg/µL to PCR tubes. Incubate at room temperature for overnight to coat PCR tube surface.", "[PROCEDURE] Remove the cell lysate digests by pipetting, rinse PCR tubes with HPLC-grade water... |
null | null | null | dx.doi.org/10.17504/protocols.io.pmxdk7n | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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107,243 | A Protocol for Assessing Open Data Practices: Honours Students Can Lead the Way. | 0 | dx.doi.org/10.17504/protocols.io.kxygxyxmdl8j/v2 | https://www.protocols.io/view/a-protocol-for-assessing-open-data-practices-honou-dkyj4xun | Haya Deeb, Tomasz Zieliński, Andrew J. Millar | TITLE: A Protocol for Assessing Open Data Practices: Honours Students Can Lead the Way.
AUTHORS: Haya Deeb, Tomasz Zieliński, Andrew J. Millar
[DESCRIPTION]
Introduction
The culture of scientific research is increasingly recognising the importance of Open Data. Open Data practices involve making research data freely ... | ["[Sampling Framework and Selection Process] Research groups within the biosciences at the University of Edinburgh were selected for study based on the educational interests of the undergraduate honours student researchers. Articles from each group were retrieved from the University’s public Edinburgh Research Explorer... |
95,715 | MycoEd Lab: CU Denver Protocols | 0 | dx.doi.org/10.17504/protocols.io.n2bvj3k6xlk5/v1 | https://www.protocols.io/view/mycoed-lab-cu-denver-protocols-c9qbz5sn | Andrew W. Wilson, sara.branco | TITLE: MycoEd Lab: CU Denver Protocols
AUTHORS: Andrew W. Wilson, sara.branco
[DESCRIPTION]
These lab protocols were written for the Fall 2023 Mycology course at University of Colorado Denver, Department of Integrative Biology instructed by Sara Branco and Andrew Wilson. The course is designed to guide students throug... | [] |
65,237 | Oprah Winfrey Keto Gummies | 1 | dx.doi.org/10.17504/protocols.io.dm6gpb13jlzp/v1 | https://www.protocols.io/view/oprah-winfrey-keto-gummies-cbxvspn6 | jamshruckz | TITLE: Oprah Winfrey Keto Gummies
AUTHORS: jamshruckz
[DESCRIPTION]
Progressing to ketosis is certainly not a speedy cycle. It requires investment for your body to become accustomed to this better approach for living. Certain individuals experience a ton of desires, weariness, and other upsetting incidental effects... | ["➢Official Link:- https://www.facebook.com/OprahWinfreyGummies/\n➢ Product Name —Oprah Winfrey Keto Gummies\n➢ Composition—NATURAL\n➢ Side-Effects— NA\n➢ Availability— Online\n➢ Rating— ⭐⭐⭐⭐⭐\n➢ Official Website (Sale Is Live) —\nShop Now:- https://topcbdoilmart.com/oprah-winfrey-keto-gummies/\n\nOprah Winfrey Keto Gu... |
39,056 | teste | 1 | dx.doi.org/10.17504/protocols.io.bidqka5w | https://www.protocols.io/view/teste-bidqka5w | Nancy Sotero | TITLE: teste
AUTHORS: Nancy Sotero
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">teste teste teste</div></div>
[STEPS]
?. testei
?. testei | ["testei", "testei"] |
27,848 | Tranformation of Thalassiosira pseudonana via bacterial conjugation | null | dx.doi.org/10.17504/protocols.io.7fghjjw | null | Ana Cristina Jaramillo Madrid, Justin Ashworth | TITLE: Tranformation of Thalassiosira pseudonana via bacterial conjugation
AUTHORS: Ana Cristina Jaramillo Madrid, Justin Ashworth
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol has been successfully used to express nourseothricin resistance gene, mVenus fluorescence protein and... | ["[Growth and preparation of E. coli donor]\nInoculate 5 mL LB medium (gentamicin+antibiotic 2) with bacterial colonies from the gentamicin +antibiotic 2 plates. Grow overnight.", "[Growth and preparation of E. coli donor]\nStart a 150 mL LB subculture with the 5 mL overnight culture (recommended starting OD600 either ... |
61,760 | Final QC, Pooling and Sequencing | 4 | dx.doi.org/10.17504/protocols.io.yxmvmnw29g3p/v1 | https://www.protocols.io/view/final-qc-pooling-and-sequencing-b8i8ruhw | Katarina A Cohen, Khai-Minh H Nguyen, Oksana Polesskaya, Abraham Palmer | TITLE: Final QC, Pooling and Sequencing
AUTHORS: Katarina A Cohen, Khai-Minh H Nguyen, Oksana Polesskaya, Abraham Palmer
[DESCRIPTION]
This protocol is conducted after a set of libraries are completed and ready to quantify and pool. This protocol outlines the final steps before submitting for sequencing.
[BEFORE_ST... | ["[Library QC] Quantify purity and concentration of library with Nanodrop and a Qubit Assay\nObtain average fragment size of library with Tapestation (D1000 Assay)", "[Pooling] Download", "[Pooling] Increase \"Target Vol (uL) per Sample\" if any Sample Vol is lower than 1ul\nUse when adding water to final pool", "[Ch... |
86,984 | Tissue clearing of human cardiac tissues using modified iDISCO+ protocol | 4 | dx.doi.org/10.17504/protocols.io.yxmvm3eo9l3p/v1 | https://www.protocols.io/view/tissue-clearing-of-human-cardiac-tissues-using-mod-cy7gxzjw | Peter Hanna, Kalyanam Shivkumar, Shumpei Mori, Olujimi Ajijola | TITLE: Tissue clearing of human cardiac tissues using modified iDISCO+ protocol
AUTHORS: Peter Hanna, Kalyanam Shivkumar, Shumpei Mori, Olujimi Ajijola
[DESCRIPTION]
The purpose of this protocol is to evaluate the myocardial innervation of the human heart. Using donor hearts rejected for human transplantation, imaging... | ["[Tissue Fixation] Donor human hearts are obtained from the organ procurement organization and undergo perfusion fixation.", "[Tissue Fixation] Suture three of the pulmonary veins and the inferior vena cava closed. One pulmonary vein and the superior vena cava are left patent as outflow of perfusate.", "[Tissue Fixati... |
72,742 | High-throughput Assay for Screening Fungal Isolates against Polyphenolic Compounds | 4 | null | https://www.protocols.io/view/high-throughput-assay-for-screening-fungal-isolate-cjaeuibe | Jana M U'Ren, Megan Nickerson | TITLE: High-throughput Assay for Screening Fungal Isolates against Polyphenolic Compounds
AUTHORS: Jana M U'Ren, Megan Nickerson
[DESCRIPTION]
This protocol was developed for the screening of fungal isolates against polyphenolic compounds to test their capacity for detoxification.
[STEPS]
SECTION: Media and Solutio... | ["[Media and Solution Preparation- Aspergillus nidulans Defined Media plus Carrageenan] Combine:\n- 900mL nanopure water\n-50mL 20X Sodium nitrate salts\n-1mL Trace elements", "[Media and Solution Preparation- Aspergillus nidulans Defined Media plus Carrageenan] Bring the pH to 6.5.", "[Media and Solution Preparation- ... |
null | null | null | dx.doi.org/10.17504/protocols.io.c4gytv | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Must be made fresh before experiment because of the Sucrose. <br />For 20 mL solutions.
[BEFORE_START]
Prepare solution with sterile milliQ water and filter sterilize or autoclave before use.
[GUIDELINES]
Final Concentration of Lysis Buffer<br />40 mM EDTA<br />50 mM Tris (pH ... | [] |
97,849 | Solid Growth Medium - Yeast | 0 | dx.doi.org/10.17504/protocols.io.j8nlk85x5l5r/v1 | https://www.protocols.io/view/solid-growth-medium-yeast-dbsz2nf6 | Mathias Hammer, Ammeret Rossouw, Azra Lari, Ben Montpetit, David Grunwald | TITLE: Solid Growth Medium - Yeast
AUTHORS: Mathias Hammer, Ammeret Rossouw, Azra Lari, Ben Montpetit, David Grunwald
[DESCRIPTION]
This protocol describes the steps to prepare solid culture medium for Saccharomyces cerevisiae.
[BEFORE_START]
Have the following solutions premixed:
Glucose 20% 500 ml solution:
Concen... | ["[Preparation of ~20 agar plates of yeast growth medium] Compound medium for autoclave", "[Preparation of ~20 agar plates of yeast growth medium] Fill a 500 ml flask with 449 mLddH2O. \nAdd a magnetic stirring bar and place the flask on a stirring hot plate.", "[Preparation of ~20 agar plates of yeast growth medium] A... |
49,629 | Pneumonia Associated with Invasive and Noninvasive Oxygenation Strategies for Acute Hypoxemic Respiratory Failure in Adults: A Systematic Review and Network Meta-analysis Protocol | 1 | dx.doi.org/10.17504/protocols.io.bup5nvq6 | https://www.protocols.io/view/pneumonia-associated-with-invasive-and-noninvasive-bup5nvq6 | Satoshi Hokari, Shunsuke Kimata, Masaaki Sakuraya, Hiromu Okano, Tomoyuki Masuyama | TITLE: Pneumonia Associated with Invasive and Noninvasive Oxygenation Strategies for Acute Hypoxemic Respiratory Failure in Adults: A Systematic Review and Network Meta-analysis Protocol
AUTHORS: Satoshi Hokari, Shunsuke Kimata, Masaaki Sakuraya, Hiromu Okano, Tomoyuki Masuyama
[DESCRIPTION]
<div class = "text-blocks"... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.h2db8a6 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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71,559 | Interventions promoting physical activity among adolescents in Sub-Saharan Africa: a scoping review protocol | 1 | dx.doi.org/10.17504/protocols.io.n92ldpzpnl5b/v1 | https://www.protocols.io/view/interventions-promoting-physical-activity-among-ad-ch5ft83n | Cécile Longchamps, Oumar Bassoum, Adama Faye, Valéry Ridde | TITLE: Interventions promoting physical activity among adolescents in Sub-Saharan Africa: a scoping review protocol
AUTHORS: Cécile Longchamps, Oumar Bassoum, Adama Faye, Valéry Ridde
[DESCRIPTION]
Objective: To describe the existing health promotion interventions that aim to promote physical activity among adolescent... | ["[Introduction] Non-communicable diseases (NCDs) cause 41 million deaths annually in the world, representing 71% of all deaths, and more than three quarters of these deaths take place in lower-middle-income countries (LMIC)1. The African region is undergoing an epidemiological transition with a double burden of commun... |
null | null | null | dx.doi.org/10.17504/protocols.io.e7gbhjw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Picking colonies from TCBS Agar plates to 96 well plates for growth</p>
[STEPS]
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21,294 | Quantifying Fluorescent Cells in Mammalian Cell Tissue Culture | null | dx.doi.org/10.17504/protocols.io.y2nfyde | null | Harley King | TITLE: Quantifying Fluorescent Cells in Mammalian Cell Tissue Culture
AUTHORS: Harley King
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Quantifying the change in fluorescent status of cells over time can be an important data point in experimental analysis. Optimally, quantification can be accomp... | ["[Preparation and Transfection of Cells]\nA six-well plate is seeded with cells at a typical pre-transfection density. The following day cells are transfected.", "[Capture Plate Images]\nImages can be taken of the plate 24 twenty-four hours post transfection (hpt). Depending on the vector and the promoter, fluorescenc... |
107,688 | DDNS Data analysis and quality control checks | 0 | dx.doi.org/10.17504/protocols.io.5qpvok4jxl4o/v1 | https://www.protocols.io/view/ddns-data-analysis-and-quality-control-checks-dmeg43bw | Alex Shaw, Joyce Akello, Catherine Troman, Aine OToole, c.ansley, Catherine Pratt, Erika Bujaki, Zoe Vance, rachel.colquhoun, Andrew Rambaut, Javier Martin, Nick Grassly | TITLE: DDNS Data analysis and quality control checks
AUTHORS: Alex Shaw, Joyce Akello, Catherine Troman, Aine OToole, c.ansley, Catherine Pratt, Erika Bujaki, Zoe Vance, rachel.colquhoun, Andrew Rambaut, Javier Martin, Nick Grassly
[DESCRIPTION]
This standard operating procedure indicates how to perform data analysis... | ["[Post Sequencing Run Checks] Perform the post sequencing run checks by confirming the following points manually\n a. Did the sequencing run complete its full run duration (check the\nMinKNOW run report). \n b. Was there no sudden reduction in pore numbers i.e. pores numbers did not fall beneath 400 (or 25% of total p... |
64,975 | In situ high-speed brightfield imaging for studies of aquatic organisms | 4 | dx.doi.org/10.17504/protocols.io.kxygxz4ykv8j/v2 | https://www.protocols.io/view/in-situ-high-speed-brightfield-imaging-for-studies-cbppsmmn | Sean P. Colin, Brad J. Gemmell, John H. Costello, Kelly R R Sutherland | TITLE: In situ high-speed brightfield imaging for studies of aquatic organisms
AUTHORS: Sean P. Colin, Brad J. Gemmell, John H. Costello, Kelly R R Sutherland
[DESCRIPTION]
Behavioral measurements of fragile aquatic organisms require specialized in situ techniques.We developed an in situ brightfield camera set-up ... | ["[Select field site] This system is lightweight, compact and portable and can be used SCUBA diving from shore, docks or boats.The camera system can also potentially be towed vertically from a research vessel.", "[Assemble equipment] The brightfield camera system relies entirely on available off the shelf components an... |
24,068 | Thawing and Seeding Frozen Cells | null | dx.doi.org/10.17504/protocols.io.3rcgm2w | null | Kenneth Schackart | TITLE: Thawing and Seeding Frozen Cells
AUTHORS: Kenneth Schackart
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">How to thaw cells from the liquid nitrogen storage and seed into a tissue culture flask</div></div>
[STEPS]
?. [Thaw Cells]
Thaw cells by suspending cryotube in water bath until compl... | ["[Thaw Cells]\nThaw cells by suspending cryotube in water bath until completely thawed, but no longer than necessary", "[Transfer cell suspension]\nWithin biosafety cabinet, transfer cell suspension to 15 mL centrifuge tube using 1000 μL pipette.", "[Dilute freezing medium]\nAdd warmed cell culture medium to cell su... |
41,590 | Cloning of Bacillus mycoides | 1 | dx.doi.org/10.17504/protocols.io.bkuwkwxe | https://www.protocols.io/view/cloning-of-bacillus-mycoides-bkuwkwxe | Andreea S | TITLE: Cloning of Bacillus mycoides
AUTHORS: Andreea S
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:left"><span style = "font-weight:bold;">Introducing NLP14a in the genome of B. mycoides: </span><span> In order to create plasmid pYCR-gamyNLP, the backb... | ["[Making electro competent cells]\nPick 1 colony of B. mycoides M2E_15 and inoculate it in BHIS", "[Making electro competent cells]\nWhen OD600nm reached 0.85 add 2% glycine and 2% threonine in order to weaken the cell wall.", "[Making electro competent cells]\nGrow the cells overnight at\n30 33", "[Making electro com... |
82,448 | Regular maintenance of human pluripotent stem cells | 4 | dx.doi.org/10.17504/protocols.io.bp2l69obdlqe/v1 | https://www.protocols.click/view/regular-maintenance-of-human-pluripotent-stem-cell-curqwv5w | Narayana Yadavalli, Shawn M. Ferguson | TITLE: Regular maintenance of human pluripotent stem cells
AUTHORS: Narayana Yadavalli, Shawn M. Ferguson
[DESCRIPTION]
This protocol describes the regular maintenance and passaging human iPSCs.
[STEPS]
SECTION: Day 1
1. Pre coat a 6 well dish with Matrigel matrix for 1440 min or 1 hour.
SECTION: Day 1
2. Thaw the f... | ["[Day 1] Pre coat a 6 well dish with Matrigel matrix for 1440 min or 1 hour.", "[Day 1] Thaw the frozen iPSCs by placing the vial in 37 °C water bath for 2 min.", "[Day 1] After thawing, spray the tube with 70% ethanol and place in biosafety cabinet.", "[Day 1] Aspirate the cells into 15 ml falcon tube and add 4 mL co... |
19,997 | U Mass - Aspartate Transferase | null | dx.doi.org/10.17504/protocols.io.xr5fm86 | null | Jason Kim | TITLE: U Mass - Aspartate Transferase
AUTHORS: Jason Kim
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span><span style = "font-weight:bold;"> </span></div><div class = "text-block">This experiment involves a spectrophotometric measurement using Roche Co... | ["Perform daily quality control assessment of instrumentation before analysis.", "Load each sample into a specialized micro-sample cup for the clinical chemistry analyzer.", "Select Aspartate Transferase test on display and run the analysis.", "Collect and analyze the data."] |
68,486 | cDNA Library Preparation for scRNA-seq of Human Meniscus (10x Genomics) | 5 | dx.doi.org/10.17504/protocols.io.e6nvwkw32vmk/v1 | https://www.protocols.io/view/cdna-library-preparation-for-scrna-seq-of-human-me-ce5etg3e | molmer, Martin Lotz, Tony Mondala, Steven Head | TITLE: cDNA Library Preparation for scRNA-seq of Human Meniscus (10x Genomics)
AUTHORS: molmer, Martin Lotz, Tony Mondala, Steven Head
[DESCRIPTION]
Samples are processed using V2 barcoding chemistry kits of 10x Genomics. For each run, 10,000 cells from individual donors are labeled with distinct oligo-barcoded antib... | ["Single cells are isolated from human knee menicus using doi dx.doi.org/10.17504/protocols.io.n2bvj6k7blk5/v1.", "Single cell suspensions are multiplexed and converted to barcoded scRNAseq libraries using the Chromium Single Cell 3’ Library, Gel Bead and Chip Kit (10x Genomics), and the BD™ Hu Single Cell Sample Multi... |
null | null | null | dx.doi.org/10.17504/protocols.io.ssheeb6 | null | null | TITLE: No Title
AUTHORS:
[BEFORE_START]
<p>Clean the work area with 70% alcohol. Use all filters and autoclaved tips. Refrigerate your centrifuge to 4C.</p>
[STEPS]
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null | null | null | dx.doi.org/10.17504/protocols.io.jqicmue | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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28,533 | Preparing Reads for Stranded Mapping | null | dx.doi.org/10.17504/protocols.io.74vhqw6 | null | David A. Eccles | TITLE: Preparing Reads for Stranded Mapping
AUTHORS: David A. Eccles
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is for preparing long reads for stranded mapping, as an intermediate step for additional protocols:</div><div class = "text-block"><ul style = "list-style-type:disc;"><l... | ["[Index Preparation]\nPrepare transcript index (see Guidelines for data sources)lastdb Mus_musculus.GRCm38.cds.all.fa", "[Transcriptome Mapping]\nReads are mapped to the transcriptome with LAST.The results of that mapping can be piped through last-map-probs to exclude unlikely hits, then through 'maf-convert -n tab' t... |
54,185 | CoBG-11 preparation | 4 | dx.doi.org/10.17504/protocols.io.by6hpzb6 | https://www.protocols.io/view/cobg-11-preparation-by6hpzb6 | Arshshaikh | TITLE: CoBG-11 preparation
AUTHORS: Arshshaikh
[DESCRIPTION]
CoBG-11 is a coculture medium used to coculture cyanobacteria and E. coli by Zhang et al (2020). It is optimized for E. coli growth. Here are its components:
1. 150 mM NaCl,
2. 4 mM NH4Cl
3. 3 g/L 2-[[1,3-dihydroxy-2-(hydroxymethyl) propan-2-yl] amino] et... | ["Measure 0.88 g , 0.0214 g, and 0.3 g and add it to a 150mL flask.", "Add 50 mL to the flask and mix till contents dissolve. If salt persists, add 10mL more of BG-11 and mix well.", "Once contents dissolve, add BG-11 up to 95 mL.", "Adjust pH of the solution to 8.3 with NaOH.", "Fill BG-11 up to 100 mL measure pH and ... |
32,343 | Protocols for predicting Sphagnum bogs distributional pattern in China | null | dx.doi.org/10.17504/protocols.io.bbtxinpn | null | Mingyang Cong | TITLE: Protocols for predicting Sphagnum bogs distributional pattern in China
AUTHORS: Mingyang Cong
[STEPS]
?. Collect the center points of Sphagnum bogs. To collect the longitude and latitude for Sphagnum bogs’ central points across China, we principally consulted Swamps in China and Marshes in China and then extrac... | ["Collect the center points of Sphagnum bogs. To collect the longitude and latitude for Sphagnum bogs’ central points across China, we principally consulted Swamps in China and Marshes in China and then extracted occurrence data from the literature. For the records lacking specific geographic coordinates, we used Googl... |
93,523 | JMN-MSMP NIA Automated Histological Staining | 1 | dx.doi.org/10.17504/protocols.io.eq2lyjb6rlx9/v1 | https://www.protocols.io/view/jmn-msmp-nia-automated-histological-staining-c7jtzknn | ccherry | TITLE: JMN-MSMP NIA Automated Histological Staining
AUTHORS: ccherry
[DESCRIPTION]
SenNet aged mouse histological staining from NIA
[STEPS]
SECTION: Fixation
1. Take the whole carcass into a jar and fix in formalin for 24 hr
SECTION: Fixation
2. Wash the carcass with 70% EtOH and store in EtOH jar until histogrossing... | ["[Fixation] Take the whole carcass into a jar and fix in formalin for 24 hr", "[Fixation] Wash the carcass with 70% EtOH and store in EtOH jar until histogrossing", "[Tissue collection:] Take out the ovaries together with uterus and vagina from the female samples and put into a histology cassette.", "[Tissue collectio... |
81,475 | Duragel Application for Acute Electrophysiology Recordings | 1 | dx.doi.org/10.17504/protocols.io.14egn2dwqg5d/v1 | https://www.protocols.io/view/duragel-application-for-acute-electrophysiology-re-cttbwnin | anna.lakunina | TITLE: Duragel Application for Acute Electrophysiology Recordings
AUTHORS: anna.lakunina
[DESCRIPTION]
This protocol describes the process of coating an implant with duragel in preparation for in vivo electrophysiology experiments. Duragel seals and protects the surface of the brain while also being soft enough for si... | ["[Setup] Draw up the white and blue duragel components into separate 1 mL Luer lock syringes. Attach 20G needles.", "[Setup] Turn on microscope lights and heating pad.", "[Setup] Wrap heating pad in press ‘n’ seal.", "[Setup] Anesthetize the mouse (see section Prepare the anesthesia system and anesthetize the mouse (a... |
39,605 | SOLUTION- 08 - Türk solution | 3 | dx.doi.org/10.17504/protocols.io.biwvkfe6 | https://www.protocols.io/view/solution-08-t-rk-solution-biwvkfe6 | Marco Cosentino, Elisa Storelli, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Marco Ferrari, Franca Marino | TITLE: SOLUTION- 08 - Türk solution
AUTHORS: Marco Cosentino, Elisa Storelli, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Marco Ferrari, Franca Marino
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This recepe is used in the following protocols:</div><div class = "text-block"><span sty... | [] |
35,878 | Triage for critically ill patients under the limited medical resource capacity during the COVID-19 and other infectious disease pandemics: a scoping review. | null | dx.doi.org/10.17504/protocols.io.bfaejibe | https://www.protocols.io/view/triage-for-critically-ill-patients-under-the-limit-bfaejibe | Yusuke Tsutsumi, Yasushi Tsujimoto, Sei Takahashi, Asuka Tsuchiya, Ikuyo Tsutsumi | TITLE: Triage for critically ill patients under the limited medical resource capacity during the COVID-19 and other infectious disease pandemics: a scoping review.
AUTHORS: Yusuke Tsutsumi, Yasushi Tsujimoto, Sei Takahashi, Asuka Tsuchiya, Ikuyo Tsutsumi
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-bloc... | [] |
96,908 | Mammalian cell culture and transfection for stable cell lines generation | 0 | dx.doi.org/10.17504/protocols.io.kxygxyk9dl8j/v1 | https://www.protocols.io/view/mammalian-cell-culture-and-transfection-for-stable-davk2e4w | Hina Ojha, Miratul M. K. Muqit | TITLE: Mammalian cell culture and transfection for stable cell lines generation
AUTHORS: Hina Ojha, Miratul M. K. Muqit
[DESCRIPTION]
Autosomal recessive mutations in PTEN-induced kinase 1 (PINK1) are linked to early-onset Parkinson's disease (PD) [1]. Upon mitochondrial depolarization, PINK1 activates through autopho... | ["[Cell Culture] Maintain cells at 37 °C in a 5% CO2 water-saturated incubator.", "[Generation of Stable Cell Lines:] Achieve doxycycline-induced, stable expression of exogenous protein using the Flp-In T-Rex system according to Invitrogen's instructions, utilizing CRISPR knock-out PINK1 KO HeLa Flp-In T-Rex cells [4].... |
88,334 | High-throughput analysis of products from deconstructed nylon-6 by UHPLC-MS/MS (dMRM) | 6 | dx.doi.org/10.17504/protocols.io.6qpvr3k92vmk/v1 | https://www.protocols.io/view/high-throughput-analysis-of-products-from-deconstr-c2hnyb5e | Kelsey J. Ramirez, Morgan A Ingraham, Elizabeth L. Bell, Gregg T. Beckham | TITLE: High-throughput analysis of products from deconstructed nylon-6 by UHPLC-MS/MS (dMRM)
AUTHORS: Kelsey J. Ramirez, Morgan A Ingraham, Elizabeth L. Bell, Gregg T. Beckham
[DESCRIPTION]
A 3 minute, high-throughput analysis method was developed for the quantitation of products produced by deconstruction of nylon-6 ... | ["[Preparation of Standards] By weight, create individual 2000 µg/mL stock solutions of all analytes listed below using ultrapure water (18.2MΩ⋅cm)(UPW) water as a diluent, except for 6-aminohexanoic acid cyclic-dimer in which methanol is used:\nɛ-Caprolactam\n6-Aminohexanoic acid\n6-Aminohexanoic acid dimer (6-(6-amin... |
28,729 | Nanopore Data Analysis | null | dx.doi.org/10.17504/protocols.io.8azhsf6 | null | David A. Eccles | TITLE: Nanopore Data Analysis
AUTHORS: David A. Eccles
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a collection of protocols that I use frequently for the analysis of long read data</div></div>
[STEPS] | [] |
44,236 | General Salts + Sodium Bicarbonate Solutions | 1 | dx.doi.org/10.17504/protocols.io.bpfkmjkw | https://www.protocols.io/view/general-salts-sodium-bicarbonate-solutions-bpfkmjkw | Ada de la Cruz | TITLE: General Salts + Sodium Bicarbonate Solutions
AUTHORS: Ada de la Cruz
[STEPS]
?. [General Salts Solution:]
For 1L of 10x salts solution:1 L nanopore water into 1 L bottle with lid55 g of MgCl2*6H2O5 g of NH4Cl1.4 g CaCl2*2H2O1 g KCl
?. [Sodium Bicarbonate]
For 1 L of NaHCO3 (sodium bicarbonate):1 L nanopore wat... | ["[General Salts Solution:]\nFor 1L of 10x salts solution:1 L nanopore water into 1 L bottle with lid55 g of MgCl2*6H2O5 g of NH4Cl1.4 g CaCl2*2H2O1 g KCl", "[Sodium Bicarbonate]\nFor 1 L of NaHCO3 (sodium bicarbonate):1 L nanopore water in a 1 L flask/bottle85 g of NaHCO3", "[General Salts Solution:]\nPour everything... |
null | null | null | dx.doi.org/10.17504/protocols.io.cq5vy5 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?. | [] |
45,442 | HuBMAP Donor and Tissue Eligibility Criteria Form v 1.0 | 1 | dx.doi.org/10.17504/protocols.io.bqmamu2e | https://www.protocols.io/view/hubmap-donor-and-tissue-eligibility-criteria-form-bqmamu2e | Yiing Lin, Shin Lin | TITLE: HuBMAP Donor and Tissue Eligibility Criteria Form v 1.0
AUTHORS: Yiing Lin, Shin Lin
[STEPS]
?. HuBMAP Donor and Tissue Eligibility Criteria FormVersion 1.0Effective Date: 1/1/2019 Inel... | ["HuBMAP Donor and Tissue Eligibility Criteria FormVersion 1.0Effective Date: 1/1/2019 Ineligible EligibleOverall eligibilityDoes the consent allow for research activities? ... |
43,671 | pYCR cloning strategy | 1 | dx.doi.org/10.17504/protocols.io.bnvxme7n | https://www.protocols.io/view/pycr-cloning-strategy-bnvxme7n | Andreea S | TITLE: pYCR cloning strategy
AUTHORS: Andreea S
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Introducing NLP14a in the genome of B. mycoides: </span><span> In order to create plasmid pYCR-gamyNLP, the backbone of Pycr will be digested with the PCR product of gam... | ["[Clone sgRNA sequence into pYCR]\nDesign sgRNA spacer sequence (~20 nts) using \"Benchling'\" and choose B. mycoides M2E_15 genomeChoose the gRNA with the highest on-target score and the lowest off-target score.", "[Clone sgRNA sequence into pYCR]\nOrder the 2 complementary oligos flanked by overhang containing BsaI ... |
54,234 | Cecret Workflow for SARS-CoV-2 Assembly and Lineage Classification | 5 | null | https://www.protocols.io/view/cecret-workflow-for-sars-cov-2-assembly-and-lineag-by72pzqe | Erin L Young, Technical Outreach and Assistance for States Team | TITLE: Cecret Workflow for SARS-CoV-2 Assembly and Lineage Classification
AUTHORS: Erin L Young, Technical Outreach and Assistance for States Team
[DESCRIPTION]
This protocol provides instructions to install and run the Cecret workflow as part of the StaPH-B Toolkit. Cecret produces SARS-CoV-2 consensus sequence ass... | ["[Software Dependencies] Load software dependencies\n \n\nWithin certain high-performance computing environments, these software can be loaded using GNU module commands similar to:", "[Installing StaPH-B Toolkit] The Cecret assembly workflow can be installed as part of the StaPH-B Toolkit using the following commands:... |
62,875 | Prima UK--Reviews-2022 | 1 | dx.doi.org/10.17504/protocols.io.14egn7nzqv5d/v1 | https://www.protocols.io/view/prima-uk-reviews-2022-b9m3r48n | prima | TITLE: Prima UK--Reviews-2022
AUTHORS: prima
[DESCRIPTION]
Prima UK--Reviews-2022
[STEPS]
SECTION: How does Prima UK Function?
1. hat's going on here?
The Prima Keto UK or "keto" diet is a low-carb, fat-rich eating plan that has been utilized for a really long time to treat explicit ailments. In the nineteenth 100 ... | ["[How does Prima UK Function?] hat's going on here?\nThe Prima Keto UK or \"keto\" diet is a low-carb, fat-rich eating plan that has been utilized for a really long time to treat explicit ailments. In the nineteenth 100 years, the Prima Keto UK was generally used to assist with controlling diabetes. In 1920 it was pre... |
87,626 | Sanger Tree of Life Sample Homogenisation: Cryogenic Bead Beating of Plants with FastPrep-96 | 4 | dx.doi.org/10.17504/protocols.io.rm7vzxk38gx1/v1 | https://www.protocols.io/view/sanger-tree-of-life-sample-homogenisation-cryogeni-cztix6ke | Benjamin Jackson, Caroline Howard | TITLE: Sanger Tree of Life Sample Homogenisation: Cryogenic Bead Beating of Plants with FastPrep-96
AUTHORS: Benjamin Jackson, Caroline Howard
[DESCRIPTION]
Disruption under cryogenic conditions is vital to interrupt the often tough, flexible and rigid structure of plant tissues whilst maintaining nucleic acid integri... | ["[Laboratory protocol] Prepare all necessary equipment prior to starting and place any applicable items (e.g. cold blocks, tools) onto dry ice.", "[Laboratory protocol] Add 3 x 3 mm sterile stainless steel beads (Qiagen PN 69997) to the required number of 1.9 mL Tri-coded FluidX tubes and place into a cold block on dr... |
null | null | null | dx.doi.org/10.17504/protocols.io.ke6cthe | null | null | TITLE: No Title
AUTHORS:
[STEPS] | [] |
85,705 | Protocol for Facially Guided Digital Diagnosis in Orthodontics | 1 | dx.doi.org/10.17504/protocols.io.8epv5x9q6g1b/v1 | https://www.protocols.io/view/protocol-for-facially-guided-digital-diagnosis-in-cxxhxpj6 | Rupert HG Kelley BSc, Álvaro Ferrando Cascales DDS,PhD, Raúl Ferrando Cascales DDS,MSc,PhD | TITLE: Protocol for Facially Guided Digital Diagnosis in Orthodontics
AUTHORS: Rupert HG Kelley BSc, Álvaro Ferrando Cascales DDS,PhD, Raúl Ferrando Cascales DDS,MSc,PhD
[DESCRIPTION]
As the digital age of dentistry continues to flourish, it has never been more important to have protocols to guide dentists through the... | ["[Treatment Planning] Records: NHP pictures, STL and DICOM files", "[Treatment Planning] Orientation and alignment of STL and DICOM files with photographs\n\nOnce all the records have been obtained, the digital impressions (STLs) can be superimposed onto the natural head position photographs using a software package s... |
41,232 | allele.variability | 1 | dx.doi.org/10.17504/protocols.io.bkhqkt5w | https://www.protocols.io/view/allele-variability-bkhqkt5w | Sara Beier, Sara Beier | TITLE: allele.variability
AUTHORS: Sara Beier, Sara Beier
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">A prerequisite to improve the predictability of microbial community dynamics is to understand their assembly mechanisms. To study factors that contribute to microbial community assembly, we exam... | ["removal of nextera adaptors (cutadapt v1.8.3)"] |
70,911 | Planktoscope protocol for plankton imaging | 1 | dx.doi.org/10.17504/protocols.io.bp2l6bq3zgqe/v2 | https://www.protocols.io/view/planktoscope-protocol-for-plankton-imaging-chg7t3zn | Lombard Fabien, Will Major, Anna Oddone, Clémence Clausse | TITLE: Planktoscope protocol for plankton imaging
AUTHORS: Lombard Fabien, Will Major, Anna Oddone, Clémence Clausse
[DESCRIPTION]
this protocol is for using planktoscope and collect usable result for quantitative imaging of plankton
see also https://www.planktoscope.org/
[BEFORE_START]
-Test the protocol before acq... | ["[Calibration] Pump calibration:", "[Calibration] -prepare a large volume of tap water and put in in the syringe targeting a total volume of e.g. 20ml\n-on the optic configuration tab: tell him that you want to pass 10ml and record the exact volume it finally ends to pass (eg. by looking on the graduation of the syrin... |
12,419 | AMPureXP purification | 1 | dx.doi.org/10.17504/protocols.io.4r3l2wy3l1y9/v1 | https://www.protocols.io/view/ampurexp-purification-qdbds2n | Eva Petrova, Roey Angel | TITLE: AMPureXP purification
AUTHORS: Eva Petrova, Roey Angel
[DESCRIPTION]
PCR-product purification with AMPureXP solution.
From the manual:
"The Agencourt AMPure XP system is a highly efficient, easily automated PCR purification system that delivers superior-quality DNA with no salt carryover. Requiring no centrif... | ["Shake the Agencourt AMPureXP bottle to fully resuspend magnetic particles.", "Add sample Vol µL × 1.8 (or less i.e. 0.8) of the Agencourt AMPure XP solution. Pipette mix 10 times, or vortex a few seconds.", "Incubate at room temperature for 5 minutes.\n5 min", "Place the reaction plate/tube onto an Agencourt SPRIPlat... |
60,289 | 2022 GenomeTrakr Proficiency Testing exercise (PulseNet Harmonized) | 1 | dx.doi.org/10.17504/protocols.io.e6nvw5m9dvmk/v4 | https://www.protocols.io/view/2022-genometrakr-proficiency-testing-exercise-puls-b649rgz6 | Maria Balkey, Ruth Timme, Julie Haendiges | TITLE: 2022 GenomeTrakr Proficiency Testing exercise (PulseNet Harmonized)
AUTHORS: Maria Balkey, Ruth Timme, Julie Haendiges
[DESCRIPTION]
This SOP outlines guidelines on how to process the isolates for the 2022 GenomeTrakr (GT) Proficiency Testing exercise.
This SOP is applicable to all GenomeTrakr labs partici... | ["[Culture Preparation] Salmonella and Escherichia/Shigella Lyophilized cultures:\n\nDay 1\n\nDocument the isolate number(s) and the lyophilized date(s) for your records. Wipe the aluminum cover and outside of the vial with isopropyl alcohol. Using sturdy forceps, aseptically remove the aluminum cover and rubber stoppe... |
99,199 | Protocol (B): Zebrafish embedding and imaging (3 dpf) | 0 | dx.doi.org/10.17504/protocols.io.14egn6726l5d/v1 | https://www.protocols.io/view/protocol-b-zebrafish-embedding-and-imaging-3-dpf-dc472yzn | Désirée A. Schmitz, Tobias Wechsler, Hongwei Bran Li, Bjoern H. Menze, Rolf Kümmerli | TITLE: Protocol (B): Zebrafish embedding and imaging (3 dpf)
AUTHORS: Désirée A. Schmitz, Tobias Wechsler, Hongwei Bran Li, Bjoern H. Menze, Rolf Kümmerli
[DESCRIPTION]
This protocol details the zebrafish embedding and imaging.
[STEPS]
SECTION: Part 0: Material preparation
1. Prepare 1.5% low-melting point agarose by... | ["[Part 0: Material preparation] Prepare 1.5% low-melting point agarose by heating e.g. 1.5 g low-melting point agarose (Sigma, serial no: A9414) in 100 mL distilled water in a flask (minimal volume 150 mL) in 30 s bursts in the microwave.", "[Part 0: Material preparation] Once the solution is clear, i.e. no flocs or p... |
28,839 | Microfluidic Digital Logic Chip Assembly | 1 | dx.doi.org/10.17504/protocols.io.8efhtbn | https://www.protocols.io/view/microfluidic-digital-logic-chip-assembly-8efhtbn | Erik Werner, Elliot Hui [University Of California | TITLE: Microfluidic Digital Logic Chip Assembly
AUTHORS: Erik Werner, Elliot Hui [University Of California
[DESCRIPTION]
This protocol describes how to reversibly bond layers of poly(methyl methacrylate) (PMMA) and polydimethylsiloxane (PDMS) using thermo-compresison bonding. Usually, two layers of PMMA are sandwiched... | ["[Clean] Rinse all parts to be assembled under a stream of DI water to remove charred material or debris from machining.", "[Clean] Prepare a solution of ~1% Microsoap in DI water and fill each bag about half way", "[Clean] Insert each component of the Microfluidic device into a 3\" x 4\" zip loc bag.", "[Clean] Sonic... |
52,679 | Investigation_of_mitophagy_in_Hippo_neurons | 1 | dx.doi.org/10.17504/protocols.io.bxpfpmjn | https://www.protocols.io/view/investigation-of-mitophagy-in-hippo-neurons-bxpfpmjn | OLIVIA HARDING, Chantell S. Evans | TITLE: Investigation_of_mitophagy_in_Hippo_neurons
AUTHORS: OLIVIA HARDING, Chantell S. Evans
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">We developed a method for assessing mitochondrial clearance in primary hippocampal neurons. </div></div>
[STEPS]
?. [Plating and maintenance of hippocampal ... | ["[Plating and maintenance of hippocampal neurons]\nPlate primary hippocampal Sprague Dawley rat neurons (embryonic day 18) on 35 mm glass bottomed dishes at 250,00 cells per dish in MEM supplemented with 10% horse serum, 33 mM D-glucose, and 1 mM sodium pyruvate.", "[Plating and maintenance of hippocampal neurons]\nAd... |
25,252 | Loop L2 (even level) type IIS cloning - pCs-ye vectors | null | dx.doi.org/10.17504/protocols.io.4wcgxaw | null | Eftychis Frangedakis, Susana Sauret-Gueto, Anthony West, marta tomaselli, Nicola Patron, Marius Rebmann, Jim Haseloff | TITLE: Loop L2 (even level) type IIS cloning - pCs-ye vectors
AUTHORS: Eftychis Frangedakis, Susana Sauret-Gueto, Anthony West, marta tomaselli, Nicola Patron, Marius Rebmann, Jim Haseloff
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol based on</div><div class = "text-block"><a href="http:... | ["Determine DNA parts concentration with spectrophotometry (Nanodrop).", "Prepare aliquots for DNA parts to be assembled at a concentration of 15 nM and of the pCs-pe vector at a concentration of 7.5 nM.To calculate the concentration needed for each part to assemble (not the backbone) in ng/µL, divide the length of the... |
78,527 | A Systematic Review of Bullous Pemphigoid and HLA-DQA1 | 1 | dx.doi.org/10.17504/protocols.io.14egn2r6pg5d/v1 | https://www.protocols.io/view/a-systematic-review-of-bullous-pemphigoid-and-hla-cqw7vxhn | Dylan Thibaut, Roksana Hesari, Nina Schur, Shivani Thoutireddy, Ryan Witcher, Elyse Julian | TITLE: A Systematic Review of Bullous Pemphigoid and HLA-DQA1
AUTHORS: Dylan Thibaut, Roksana Hesari, Nina Schur, Shivani Thoutireddy, Ryan Witcher, Elyse Julian
[DESCRIPTION]
There is growing evidence suggesting that specific HLA-DQA1 alleles are associated with increased odds of developing bullous pemphigoid. Howeve... | ["[Administrative Information] Tilte:\n\n\"A Systematic Review of Bullous Pemphigoid and HLA-DQA1\"\n\nRegistrations:\n\nprotocols.io", "[Methods] Eligibility Criteria \n\nInclusion Criteria:\n1. Studies that investigate the association between HLA-DQA1 and bullous pemphigoid in human subjects.\n2. Studies published af... |
null | null | null | dx.doi.org/10.17504/protocols.io.s4regv6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Transformation of <em>Acanthamoeba castellanii </em>Neff (ATCC-30010) with plasmid DNA can be achieved with a modified version of the protocol described in Peng, Omaruddin, & Bateman (2005) using constructs from Bateman (2010). </p>
[BEFORE_START]
<p>Materials needed:</p... | [] |
50,824 | Nissl Staining | 1 | dx.doi.org/10.17504/protocols.io.bp2l6bz9zgqe/v1 | https://www.protocols.io/view/nissl-staining-bvvgn63w | Pranay Srivastava, Xiqun Chen | TITLE: Nissl Staining
AUTHORS: Pranay Srivastava, Xiqun Chen
[DESCRIPTION]
This protocol details the staining procedure and mounting procedure of Nissl staining.
[STEPS]
SECTION: Staining Procedure
1. Mount sections on positive charged plus slides. Air dry sections .
SECTION: Staining Procedure
2. Incubate the slid... | ["[Staining Procedure] Mount sections on positive charged plus slides. Air dry sections .", "[Staining Procedure] Incubate the slides directly into 1:1 ethanol/chloroform for 30 min.\n(All the steps mentioned should be done under the hood)", "[Staining Procedure] Incubate in 100% ethanol 2 min", "[Staining Procedure]... |
86,287 | W-2 WATER PROCESSING | 4 | dx.doi.org/10.17504/protocols.io.ewov1opwplr2/v1 | https://www.protocols.io/view/w-2-water-processing-cyhpxt5n | REDI-NET Consortium | TITLE: W-2 WATER PROCESSING
AUTHORS: REDI-NET Consortium
[DESCRIPTION]
This protocol details about water processing.
[BEFORE_START]
BEFORE START
Make sure the feeding tube and PTFE sinker for SolVac Filter are properly clean by using 70% ethanol and allowed to air dry.
For the samples stored at 4 °C, pour thre... | ["[1. VACUUM PUMP SET UP] Wipe the surfaces with 70% ethanol to remove contaminants.", "[1. VACUUM PUMP SET UP] Use tubing to connect a 3 liter Medi-Vac Canister with vacuum pump through the vacuum outlet on the lid.", "[1. VACUUM PUMP SET UP] Connect tubing with the 3 liter Medi-Vac Canister through the inlet on the l... |
85,912 | Typology of Physical Activity | 1 | dx.doi.org/10.17504/protocols.io.yxmvm32kbl3p/v1 | https://www.protocols.io/view/typology-of-physical-activity-cx5yxq7w | Christine Roberts | TITLE: Typology of Physical Activity
AUTHORS: Christine Roberts
[DESCRIPTION]
Different physical activity types vary in metabolic demand (intensity), but also in non-metabolic demand (balance, co-ordination, speed and flexibility), cognitive demand (attention, memory and decision making), and social demand (social int... | ["[Typology of Physical Activity] A TYPOLOGY OF PHYSICAL ACTIVITY", "[Typology of Physical Activity] Title: A Typology of Physical Activity", "[Typology of Physical Activity] Investigators: Chief Investigator: Christine Roberts, University of Aberdeen, Health Psychology, Health Sciences Building, Foresterhill, Aberdeen... |
27,805 | SMARTerV4 (0.5x) Amplification for single-cell or single-nuclei RNASeq Protocol | null | dx.doi.org/10.17504/protocols.io.7d5hi86 | null | ZengU19 BRAIN grant | TITLE: SMARTerV4 (0.5x) Amplification for single-cell or single-nuclei RNASeq Protocol
AUTHORS: ZengU19 BRAIN grant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol to generate full-length cDNA from single cells, or nuclei, using Takara SMARTer V4.</div></div>
[STEPS] | [] |
104,146 | Developing and Testing Framework for Assessing Quality of Facility Readiness for Clinical Teaching and Learning in Tanzania - A Mixed Method Study. | 0 | dx.doi.org/10.17504/protocols.io.x54v92kn1l3e/v1 | https://www.protocols.io/view/developing-and-testing-framework-for-assessing-qua-dhxs37ne | Jackson Karani Maira | TITLE: Developing and Testing Framework for Assessing Quality of Facility Readiness for Clinical Teaching and Learning in Tanzania - A Mixed Method Study.
AUTHORS: Jackson Karani Maira
[DESCRIPTION]
Background
Clinical education and clinical learning are important parts of nursing education, providing students with th... | ["[Developing and Testing Framework for Assessing Quality of Facility Readiness for Clinical Teaching and Learning in Tanzania - A Mixed Method Study.] ABSTRACT\nBackground\nClinical education and clinical learning are important parts of nursing education,\nproviding students with the hands-on experience and practical ... |
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