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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68,080 | PLATERO: A Calibration Protocol for Plate Reader Green Fluorescence Measurements | 4 | dx.doi.org/10.17504/protocols.io.kxygxzjz4v8j/v1 | https://www.protocols.io/view/platero-a-calibration-protocol-for-plate-reader-gr-ceqqtdvw | Alejandro Vignoni, Yadira Boada | TITLE: PLATERO: A Calibration Protocol for Plate Reader Green Fluorescence Measurements
AUTHORS: Alejandro Vignoni, Yadira Boada
[DESCRIPTION]
One of the most common sources of information in Synthetic Biology is the data
coming from plate reader fluorescence measurements. These experiments provide a measure of
the l... | ["[Stock Reference Solution] Start from at least1 mL of10 micromolar (µM) solution in", "[Stock Reference Solution] [OPTIONAL] If you have access to a spectrophotometer, you can calculate the concentration of your Fluorescein reference stock solution even more accurately using the Beer-Lambert law.", "[Prepare the s... |
76,970 | Missed Opportunities in the Prevention and Diagnosis of Pediatric Tuberculosis; a scope review | 1 | dx.doi.org/10.17504/protocols.io.x54v9dwwmg3e/v1 | https://www.protocols.io/view/missed-opportunities-in-the-prevention-and-diagnos-cpeivjce | Daniela Russo | TITLE: Missed Opportunities in the Prevention and Diagnosis of Pediatric Tuberculosis; a scope review
AUTHORS: Daniela Russo
[DESCRIPTION]
Despite its ancient origins, tuberculosis (TB) remains a major public health problem. In the pediatric population, the prevention and diagnosis of TB is considered a major challeng... | ["Oportunidades perdidas na prevenção e diagnóstico da tuberculose pediátrica; uma revisão de escopo"] |
44,069 | The efficacy of albumin with diuretics in the mechanically ventilated patients with hypoalbuminemia : systematic review and meta-analysis | 1 | dx.doi.org/10.17504/protocols.io.bpadmia6 | https://www.protocols.io/view/the-efficacy-of-albumin-with-diuretics-in-the-mech-bpadmia6 | Yuki Itagaki, Naofumi Yoshida, Kohei Yamada, Masahiro Banno, Ryo Momosaki, Mineji Hayakawa, Yuki Kataoka | TITLE: The efficacy of albumin with diuretics in the mechanically ventilated patients with hypoalbuminemia : systematic review and meta-analysis
AUTHORS: Yuki Itagaki, Naofumi Yoshida, Kohei Yamada, Masahiro Banno, Ryo Momosaki, Mineji Hayakawa, Yuki Kataoka
[DESCRIPTION]
<div ... | [] |
19,433 | MRI pilot | null | dx.doi.org/10.17504/protocols.io.w8hfht6 | null | Lukas Snoek, Tinka Beemsterboer | TITLE: MRI pilot
AUTHORS: Lukas Snoek, Tinka Beemsterboer
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Run an MRI pilot at Spinoza REC.</span></div><div class = "text-block"><span style = "font-weight:bold;">This protocol will help you running your pilot. </span>... | ["Name your scans appriopriately.If you're using the centre's QC/preprocessing service, it is very important to name your scans (and thus the resulting MRI files) according to the BIDS-format.If you're not using the centre's QC/preprocessing service, you may give whatever name to your scans/files and skip the rest of t... |
93,725 | Collection 1 | 2 | dx.doi.org/10.17504/protocols.io.j8nlkop1wv5r/v1 | https://www.protocols.io/view/collection-1-c7r5zm86 | Mitt Coats | TITLE: Collection 1
AUTHORS: Mitt Coats
[DESCRIPTION]
A collection
[STEPS] | [] |
61,936 | Linker Design and Optimization | 6 | dx.doi.org/10.17504/protocols.io.yxmvmnw5bg3p/v1 | https://www.protocols.io/view/linker-design-and-optimization-b8qqrvvw | boc.protac | TITLE: Linker Design and Optimization
AUTHORS: boc.protac
[DESCRIPTION]
The linker is responsible for linking two key domains of PROTAC: the domain that specifically binds to the target protein that needs to be degraded, and the domain that binds to the E3 ubiquitin ligase. To date, several types of connectors have ... | [] |
25,181 | Clarification of cheese whey for microalgae cultivation | null | dx.doi.org/10.17504/protocols.io.4t5gwq6 | null | Bruna Emerenciano, Maria Izabel P Batista, Adriano H N Rangel | TITLE: Clarification of cheese whey for microalgae cultivation
AUTHORS: Bruna Emerenciano, Maria Izabel P Batista, Adriano H N Rangel
[STEPS]
?. Collect the cheese whey from dairy industry as a by-product of cheese production and put it in clean and dry bottles.
?. If the cheese whey is not be clarified after collect,... | ["Collect the cheese whey from dairy industry as a by-product of cheese production and put it in clean and dry bottles.", "If the cheese whey is not be clarified after collect, it should be frozen in a freezer at -20 °C.", "For clarification, defrost the cheese whey in a refrigerator at 5 ° C.", "Then sterilize the che... |
105,958 | Tomogram Reconstruction and Gold Fiducial Removal with Warp, Etomo, and Fidder | 0 | dx.doi.org/10.17504/protocols.io.6qpvr8qbblmk/v1 | https://www.protocols.io/view/tomogram-reconstruction-and-gold-fiducial-removal-djqe4mte | Connor Garrels, Benjamin Barad, Steve Reichow | TITLE: Tomogram Reconstruction and Gold Fiducial Removal with Warp, Etomo, and Fidder
AUTHORS: Connor Garrels, Benjamin Barad, Steve Reichow
[DESCRIPTION]
While gold nanoparticle fiducials greatly improve tilt-series alignment in cryo-electron tomography data, they can cause artifacts during later image processing ste... | ["[Install Software] Make sure you have these packages installed.\n\n- IMOD\n- Warp (technically WarpTools on linux)\n- Fidder", "[Warp Preprocessing] We will be using Warp for the bulk of our processing. This section follows this warp tutorial. \n\nValues shown are data-specific (i.e. exposure, pixel size, paths), so ... |
53,350 | Collection from Wastewater Treatment Plant, Transportation, and Storage of Raw Wastewater | 4 | dx.doi.org/10.17504/protocols.io.bycepste | https://www.protocols.io/view/collection-from-wastewater-treatment-plant-transpo-bycepste | Kevin Calci, Kevin Calci | TITLE: Collection from Wastewater Treatment Plant, Transportation, and Storage of Raw Wastewater
AUTHORS: Kevin Calci, Kevin Calci
[DESCRIPTION]
This method was developed at the FDA’s Center for Food Safety and Applied Nutrition for GenomeTrakr’s pandemic response project, monitoring SARS-CoV-2 variants in wastewa... | ["[Sample Storage] If samples cannot be processed immediately, samples should be stored at 2-8 °C for up to 7 days.", "[Composite Sample Collection] Composite samples can be collected as flow-paced or time-paced. Follow manufacturer's instructions for proper programming of the ISCO and then initiate collection.", "[Com... |
91,655 | CRISPRa tiling screens | 4 | null | https://www.protocols.io/view/crispra-tiling-screens-c5rfy53n | Andrea R Daniel | TITLE: CRISPRa tiling screens
AUTHORS: Andrea R Daniel
[DESCRIPTION]
This protocols describes methods for characterizing the activity of dSaCas9 as a activator using promoter tiling guide RNA screens in Jurkat cells.
[STEPS]
SECTION: Construction of CRISPRa Jurkat lines
1. Polyclonal dSaCas9VP64 and VP64dSaCas9VP64 ... | ["[Construction of CRISPRa Jurkat lines] Polyclonal dSaCas9VP64 and VP64dSaCas9VP64 Jurkat cell lines were generated by transducing Jurkat cells with lentivirus encoding for either dSaCas9VP64–2A–PuroR or VP64dSaCas9VP64–2A–PuroR.", "[Construction of CRISPRa Jurkat lines] Cells were selected for 5 days using 0.5 µg ml−... |
null | null | null | dx.doi.org/10.17504/protocols.io.eszbef6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
For use in <a href="https://www.protocols.io/view/CviRI-Purification-From-XZ-6E-Virus-Infected-NC64A-er4bd8w" target="_blank">CviRI Purification From XZ-6E Virus Infected NC64A Chlorella</a>.
[STEPS]
?.
?.
?.
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.uview4e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This cloning protocol refers to the Marburg Collection
[BEFORE_START]
Before start, the resistance and ori parts have to be digested with BsaI and purified!
[GUIDELINES]
This cloning protocol refers to the Marburg Collection
[STEPS]
SECTION: Predigestion
?.
SECTION: Prediges... | ["[Predigestion] Before start, digest the Resistance and Ori plasmide with BsaI.", "[Predigestion] Purify the Fragments with PCR Cleanup.", "[Reaction Setup on ice:] 1. Add 20 fmol of TU’s.", "[Reaction Setup on ice:] 2. Add 0.5 µL BsmBI.", "[Reaction Setup on ice:] 3. Add 0.5 µL T7-Ligase.", "[Reaction Setup on ice:] ... |
89,972 | Immobilizing cells for live imaging | 1 | dx.doi.org/10.17504/protocols.io.bp2l6xr15lqe/v1 | https://www.protocols.io/view/immobilizing-cells-for-live-imaging-c34uyqww | Tara Essock-Burns, David Matus | TITLE: Immobilizing cells for live imaging
AUTHORS: Tara Essock-Burns, David Matus
[DESCRIPTION]
This protocol covers the sample preparation for high-resolution confocal microscopy to visualize algal cells and their organelles (chloroplasts and mitochondria) by immobilizing them in agarose. The sample preparation incl... | ["[Prepare low-melt agarose in appropriate medium] To make 1.25% low-melt agarose in TAP medium (which we use for Chlamydomonas cells), measure 3.75 mg of low-melt agarose and dissolve into 3 mL of TAP medium in a glass culture tube, then place it on a heat block set to 100 °C until the agarose dissolves.", "[Prepare l... |
null | null | null | dx.doi.org/10.17504/protocols.io.mycc7sw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p style="margin-bottom: 0in; font-weight: normal; line-height: 100%;">One remarkable issue in mitochondrial DNA sequencing and variant detection is heavy nuclear DNA contamination persistent throughout the commonly used mitochondria enrichment protocols including differential a... | [] |
93,201 | Micro-CT scanning and fiber localization | 1 | dx.doi.org/10.17504/protocols.io.j8nlko1jdv5r/v1 | https://www.protocols.io/view/micro-ct-scanning-and-fiber-localization-c69rzh56 | Mai-Anh Vu, mwhowe | TITLE: Micro-CT scanning and fiber localization
AUTHORS: Mai-Anh Vu, mwhowe
[DESCRIPTION]
We have developed a new micro-fiber array approach capable of chronically measuring and optogenetically manipulating local dynamics across over 100 targeted locations simultaneously in head-fixed and freely moving mice, enabling ... | ["[Perfusion and dissection] Mice were injected intraperitoneally with 400-500 mg/kg Euthasol (Covetrus Euthanasia III), and then perfused transcardially with 20mL 1% phosphate buffered saline (PBS, Fisher), followed by 20mL 4% paraformaldehyde in 1% PBS.", "[Perfusion and dissection] After perfusion and decapitation, ... |
93,921 | Cryo-electron microscopy and helical reconstructions of α-synuclein fibrils | 1 | dx.doi.org/10.17504/protocols.io.ewov1qwy2gr2/v1 | https://www.protocols.io/view/cryo-electron-microscopy-and-helical-reconstructio-c7x9zpr6 | Arpine Sokratian, Nilakshee Bhattacharya, Elizabeth Viverette, Yezhou867 | TITLE: Cryo-electron microscopy and helical reconstructions of α-synuclein fibrils
AUTHORS: Arpine Sokratian, Nilakshee Bhattacharya, Elizabeth Viverette, Yezhou867
[DESCRIPTION]
This protocol describes how to create cryo-EM grids for α-synuclein fibril image collection. It also includes the specific settings for the ... | ["[Freezing alpha-synuclein onto AuFoil grids] Preparation of α-synuclein protein is described here:", "[Freezing alpha-synuclein onto AuFoil grids] Preparation of α-synuclein fibrils is described here:", "[Freezing alpha-synuclein onto AuFoil grids] Generated purified fraction of full-length fibrils removed from any s... |
53,524 | Total RNA and DNA in Microalgae | 1 | null | https://www.protocols.io/view/total-rna-and-dna-in-microalgae-byhupt6w | Yingyu Hu, Zoe V Finkel | TITLE: Total RNA and DNA in Microalgae
AUTHORS: Yingyu Hu, Zoe V Finkel
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Here we describe a protocol for extracting and quantifying bulk RNA and DNA from microalgae, which is adapted from Berdalet E. et al. (2005).</div><br/><div class = "text-block">RN... | ["[Day 1: Freeze-dry samples]\nFreeze dry samples and blank filters. Freeze at until processed.\n-80 °C\nFreeze-drying should be as short as possible to reduce sample degradation.The exact duration of freeze-drying depends on size of filter, quantity of sample and the size of container.", "[Day 1: Prepare primary sol... |
18,021 | Optical density measurement for Bacterial solution (Worm Food) | null | dx.doi.org/10.17504/protocols.io.vude6s6 | null | Priota Islam | TITLE: Optical density measurement for Bacterial solution (Worm Food)
AUTHORS: Priota Islam
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Before the OP50 solution is aliquoted into small falcon tubes, it is always better to check the OD by using a spectrophotometer, for documentation purposes.</di... | ["Pre-measurement Clean the disposable cuvettes with ethanol and lint free paper Aliquot small amount of LB broth into a falcon tube (For Blank) Fill about 1ml of the LB broth into a clean cuvette Mix/Vortex the tube containing the stock bacteria to achieve a homogenized solution Take three aliquots from the same tube ... |
48,191 | Chimeric Protein-LA and Protein LAG sandwich ELISA | 1 | dx.doi.org/10.17504/protocols.io.bta7nihn | https://www.protocols.io/view/chimeric-protein-la-and-protein-lag-sandwich-elisa-bta7nihn | Angel Justiz-Vaillant | TITLE: Chimeric Protein-LA and Protein LAG sandwich ELISA
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This ELISA was used to study the interactions between protein LA (SpLA) and protein-LAG (PLAG) with different immunoglobulin preparations from mammalian and avia... | ["This ELISA was used to study the interactions between protein LA (SpLA) and protein-LAG (PLAG) with different immunoglobulin preparations from mammalian and avian species. The 96 well microtiter plate was coated overnight at 4°C with 2 µg/µl per well of SpLA in carbonate-bicarbonate buffer pH 9.6.", "The plate was th... |
92,957 | EVTrap non-antibody affinity bead protocol for EV isolation from urine, compatible with SiMOA assays | 4 | dx.doi.org/10.17504/protocols.io.81wgbxonylpk/v1 | https://www.protocols.io/view/evtrap-non-antibody-affinity-bead-protocol-for-ev-c6z5zf86 | andrew.west, yuan.yuan | TITLE: EVTrap non-antibody affinity bead protocol for EV isolation from urine, compatible with SiMOA assays
AUTHORS: andrew.west, yuan.yuan
[DESCRIPTION]
A modified protocol using EVTrap beads (Tymora Analytical) to isolate EVs from human urine, and subsequent processing, for detection of proteins using SiMOA or compa... | ["[Preparation of Urine] Prechill the AVANTI centrifuge, add adapters (Prechilled).", "[Preparation of Urine] Thaw the urine in a shaking water bath at 42 °C 100 rpm . Leave the urine tubes on ice.", "[Preparation of Urine] Aliquot 250uL of urine into labeled 1.5mL tubes for creatinine measurements.", "[Preparation of ... |
75,367 | eDNA water sampling in remote rocky shore environments | 4 | null | https://www.protocols.io/view/edna-water-sampling-in-remote-rocky-shore-environm-cmufu6tn | Dina-Leigh Simons, Helen Hipperson, Tom Webb, Nova Mieszkowska | TITLE: eDNA water sampling in remote rocky shore environments
AUTHORS: Dina-Leigh Simons, Helen Hipperson, Tom Webb, Nova Mieszkowska
[DESCRIPTION]
This is a protocol to collect marine environmental DNA samples from remote rocky intertidal sites by filtering on-site using Sterivex filtering units and a syringe/sealant... | ["[Cleaning and packing equipment (pre-sampling)] Submerge 1L Nalgene bottles in 20% bleach solution (see solution preparation below) for at least 10-minutes. Be sure to completely expose all surfaces to bleach. If excessive dirt present, scrub with soap and water before submerging in bleach. If previous labelling is p... |
103,073 | Arthrospira platensis Growth Media Stock Solution Preparation | 0 | dx.doi.org/10.17504/protocols.io.j8nlk83z1l5r/v1 | https://www.protocols.io/view/arthrospira-platensis-growth-media-stock-solution-dgv93w96 | Victor vmr Rodriguez | TITLE: Arthrospira platensis Growth Media Stock Solution Preparation
AUTHORS: Victor vmr Rodriguez
[DESCRIPTION]
The purpose of this protocol is to prepare a growth media for
spirulina (Arthrospira platensis). Arthrospira
platensis is a cyanobacterium species usually found in alkali
environments rich with carbonate an... | ["[Materials Needed] 500 ml media bottle", "[Materials Needed] magnetic stir bar", "[Materials Needed] Weight boat", "[Equipment Needed] UV Sanitizer", "[Materials Needed] P1000 pipettor", "[Materials Needed] P1000 pipette tips", "[Materials Needed] Roll of labeling tape", "[Materials Needed] Magnetic stir bar remover ... |
47,413 | Biospecimen Aliquotting | 4 | dx.doi.org/10.17504/protocols.io.dm6gpwyz5lzp/v1 | https://www.protocols.io/view/biospecimen-aliquotting-bsivnce6 | Clemens Scherzer, Bradley Hyman, Charles Jennings | TITLE: Biospecimen Aliquotting
AUTHORS: Clemens Scherzer, Bradley Hyman, Charles Jennings
[DESCRIPTION]
This protocol explains the Standard Operating Protocol for aliquotting Bio-Specimens.
[GUIDELINES]
FREEZER STORAGE
Freezers are divided into 4 shelves, with 6 racks per shelf, and 24 boxes that can be held in ea... | ["[1-2 days before aliquotting:] Order dry ice the night before, at the latest, for delivery at 9 am.", "[1-2 days before aliquotting:] Compile list of parent aliquots according to freezer position. Group aliquots from the same rack, column and box in the freezer.", "[1-2 days before aliquotting:] Pull parent aliquots ... |
28,446 | Isolation of cardiac myocytes and measurement of myocyte shortening | 1 | dx.doi.org/10.17504/protocols.io.7z6hp9e | https://www.protocols.io/view/isolation-of-cardiac-myocytes-and-measurement-of-m-7z6hp9e | Gustavo Marchini, Ismar N. Cestari, Idágene A. Cestari | TITLE: Isolation of cardiac myocytes and measurement of myocyte shortening
AUTHORS: Gustavo Marchini, Ismar N. Cestari, Idágene A. Cestari
[STEPS]
?. [Prepare solutions]
Prepare 400 mL of buffer solution. Adjust the pH to 7.4 with NaOH. ABCD1 Concentration
[mM] Molar
Mass [g/mol] Mass
[mg] 2 NaCl ... | ["[Prepare solutions]\nPrepare 400 mL of buffer solution. Adjust the pH to 7.4 with NaOH. ABCD1 Concentration\n [mM] Molar\n Mass [g/mol] Mass\n [mg] 2 NaCl 134 58,44 3132,38 3 KCl 4,0 74,56 119,30 4 NaH2PO4 1,2 156,01 74,88 5 HEPES 10 238,30 953,20 6 MgSO4 ... |
19,174 | Human colon tissue clearing and Immunohistochemistry | null | dx.doi.org/10.17504/protocols.io.wyeffte | null | Robert Heuckeroth, Silvia Huerta Lopez, Kahleb Graham, Rajarshi Sengupta | TITLE: Human colon tissue clearing and Immunohistochemistry
AUTHORS: Robert Heuckeroth, Silvia Huerta Lopez, Kahleb Graham, Rajarshi Sengupta
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">INTRODUCTION: Bowel pathology is routinely evaluated by sectioning tissue, staining, and light microscopy. Tis... | ["[Fresh tissue processing and fixation]\nTransport fresh tissue from human colon in cold sterile 1X phosphate buffered saline (PBS) on ice. Tissues placed in cold PBS within 1-2 hours of resection were used for imaging.", "[B. ImmunostainingThe following incubations are done in 24-well plates with approximately 500ul ... |
98,584 | Lifeplan Audio Recording Protocol | 1 | dx.doi.org/10.17504/protocols.io.kqdg3xbp1g25/v2 | https://www.protocols.io/view/lifeplan-audio-recording-protocol-dchy2t7w | Arielle M Farrell, Gaia Giedre Banelyte, Hanna M.K. Rogers, Petteri Lehikoinen, Deirdre Kerdraon, Bess Hardwick | TITLE: Lifeplan Audio Recording Protocol
AUTHORS: Arielle M Farrell, Gaia Giedre Banelyte, Hanna M.K. Rogers, Petteri Lehikoinen, Deirdre Kerdraon, Bess Hardwick
[DESCRIPTION]
Here we describe a protocol that is used for collecting audio recordings of birds and bats using an AudioMoth (AudioMoth | Open Acoustic Device... | ["[Site Selection and Placement] Site design\n\nThe Lifeplan equipment is deployed within a 1 hectare plot. We aim for an accuracy of 10 meters.\n\nThere are two design options to choose from depending on budget and site access. In Lifeplan, we started with Option 1 in 2021, and reduced to Option 2 in 2023 by removing ... |
null | null | null | dx.doi.org/10.17504/protocols.io.ha4b2gw | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.rwrd7d6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This is the protocol for making and running a 12% SDS-PAGE Western blot. Protocol starts from pouring gels all the way to reading the membrane. </p>
[BEFORE_START]
<p>Run a BCA assay before starting a Western Blot</p>
<p>Make 10% AP fresh each time you pour gels. Mix 0.1 gra... | [] |
86,889 | KAPP-Sen TMC: Nuclei Suspension Preparation for snPATHO-seq | 1 | dx.doi.org/10.17504/protocols.io.3byl4qqnzvo5/v1 | https://www.protocols.io/view/kapp-sen-tmc-nuclei-suspension-preparation-for-snp-cy4hxyt6 | Dylan Baker, Juliana Alcoforado Diniz, Jessica Garofalo, Paul Robson | TITLE: KAPP-Sen TMC: Nuclei Suspension Preparation for snPATHO-seq
AUTHORS: Dylan Baker, Juliana Alcoforado Diniz, Jessica Garofalo, Paul Robson
[DESCRIPTION]
This protocol for nuclei suspension preparation was adapted from Vallejo et al. (https://doi.org/10.1101/2022.08.23.505054) with minor changes. Once the suspens... | ["[Reagents and Consumables] Hyaluronidase: 0.5mg/ml\nLiberase TM: 1mg/ml\nCollagenase D: 1mg/ml", "[Nuclei isolation] Cut up to 2 ~25 μm-thick sections and place it in 1.5 mL Eppendorf tube. Store dry at 4°C if not used immediately. To keep it dry, you may use the cylinder containing silica beads that comes with 10x ... |
null | null | null | dx.doi.org/10.17504/protocols.io.nshdeb6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This is a protocol for sampling people in order to understand patterns of mobility and activity-space segregation at the scale of city-days. The goal is to obtain a representative sample of the space-time paths that exist in a given city. Sampling points and times are choosen... | [] |
20,537 | Screening Edited iPSC Clones | null | dx.doi.org/10.17504/protocols.io.yazfsf6 | null | Celeste Karch, Rita Martinez, Jacob Marsh | TITLE: Screening Edited iPSC Clones
AUTHORS: Celeste Karch, Rita Martinez, Jacob Marsh
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Screening Edited iPSC Clones</span></div><div class = "text-block"><span style = "font-weight:bold;">Expanding and gDNA Extraction ... | [] |
34,024 | Elisa_Protocols_Cytokines | 1 | dx.doi.org/10.17504/protocols.io.bdggi3tw | https://www.protocols.io/view/elisa-protocols-cytokines-bdggi3tw | Marcia Guimaraes da Silva, Jossimara Polettini | TITLE: Elisa_Protocols_Cytokines
AUTHORS: Marcia Guimaraes da Silva, Jossimara Polettini
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Immunoenzymatic test (enzyme-linked immunosorbent assay) for cytokines: Interleukin (IL)-1, IL-6, IL-8 and Tumor necrosis factor (TNF)-a</div></div>
[STEPS] | [] |
77,624 | Polymerase Chain Reaction for the Identification of a Plasmid | 4 | dx.doi.org/10.17504/protocols.io.bp2l69pwdlqe/v1 | https://www.protocols.io/view/polymerase-chain-reaction-for-the-identification-o-cp2yvqfw | SGD | TITLE: Polymerase Chain Reaction for the Identification of a Plasmid
AUTHORS: SGD
[DESCRIPTION]
Protocol for the identification of a plasmid by polymerase chain reaction followed by gel electrophoresis
[STEPS]
SECTION: Making the PCR mix
1. Add 1 ng of the target DNA,
5 µL of each primer,
25 µL of 2X PCR master mix... | ["[Making the PCR mix] Add 1 ng of the target DNA, \n5 µL of each primer, \n25 µL of 2X PCR master mix, \nand sufficient sterile water to make the volume up to 50 µL.", "[Thermocycling] Thermocycle on the following settings:", "[Making the Gel] Add 100 mL 1× TAE buffer and swirl gently to mix. Put an inverted small con... |
49,196 | PAS Staining of Fresh Frozen or Paraffin Embedded Human Kidney Tissue | 1 | dx.doi.org/10.17504/protocols.io.buaknscw | https://www.protocols.io/view/pas-staining-of-fresh-frozen-or-paraffin-embedded-buaknscw | Elizabeth Neumann, Jamie Allen, Jennifer Harvey, Maya Brewer, Carrie Romer, Mark De Caestecker, Jeff Spraggins | TITLE: PAS Staining of Fresh Frozen or Paraffin Embedded Human Kidney Tissue
AUTHORS: Elizabeth Neumann, Jamie Allen, Jennifer Harvey, Maya Brewer, Carrie Romer, Mark De Caestecker, Jeff Spraggins
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Scope:</div><div class = "text-block">The PAS stain is... | ["[Start with FFPE here:]\nAllow PAS “kit” to come to room temperature on the bench.", "[Start with FFPE here:]\nFor paraffin sections, deparaffinize in xylene, two changes, each.", "[Start with FFPE here:]\nHydrate through graded alcohols, each:100%, 100%, 95%, 70%, water", "[Start Frozen samples here:]\nRemove fr... |
83,889 | Active zone protein clusters and dopamine axons in striatal slices | 1 | dx.doi.org/10.17504/protocols.io.3byl4q21zvo5/v1 | https://www.protocols.click/view/active-zone-protein-clusters-and-dopamine-axons-in-cv6rw9d6 | Chuyu Chen | TITLE: Active zone protein clusters and dopamine axons in striatal slices
AUTHORS: Chuyu Chen
[DESCRIPTION]
This protocol detail the procedures for measuring the size and density of active zone proteins and axon terminals with Imaris software.
[STEPS]
SECTION: Visualization of active zoon proteins and dopamine axons... | ["[Visualization of active zoon proteins and dopamine axons] Stain and amplify fluorescent labeled axons with GFP, cherry, and bassoon antibodies.", "[Visualization of active zoon proteins and dopamine axons] Capture z-stack images with 100x oil lens (Nikon N-SIM Structured Illumination Super-Resolution Microscope), 4 ... |
106,592 | JAX-Sen: Mice selection criteria | 0 | dx.doi.org/10.17504/protocols.io.4r3l2q17pl1y/v2 | https://www.protocols.io/view/jax-sen-mice-selection-criteria-dkb84srw | Laura Robinson, Susan Sheehan, Gaven Garland, Ron Korstanje | TITLE: JAX-Sen: Mice selection criteria
AUTHORS: Laura Robinson, Susan Sheehan, Gaven Garland, Ron Korstanje
[DESCRIPTION]
We aim to select 12 mice (C57BL/6J), 6 male and 6 female at 6 and 24 months of age, 3 mice in each age and sex group. This number is for each analysis (scRNA-seq, snRNA-seq, bulkRNA-seq, and visiu... | [] |
107,134 | Species Molecular Barcode Analysis with Nanopore Sequence Data | 0 | dx.doi.org/10.17504/protocols.io.6qpvr8y1blmk/v1 | https://www.protocols.io/view/species-molecular-barcode-analysis-with-nanopore-s-dku64wze | Gideon Erkenswick, Mrinalini Watsa, Zane Libke, Pamela Sánchez-Vendizú, Stefan Prost | TITLE: Species Molecular Barcode Analysis with Nanopore Sequence Data
AUTHORS: Gideon Erkenswick, Mrinalini Watsa, Zane Libke, Pamela Sánchez-Vendizú, Stefan Prost
[DESCRIPTION]
End-to-end workflow to generate cleaned consensus sequences from multiplexed amplicons sequenced with Nanopore sequencing technology. Includ... | ["[Prepare Working Environment] Create a working directory", "[Basecalling Raw Sequence Data] This command will perform basecalling on all sequence files inside path/to/working/directory/1.all.pod5s\\\n\nMust select a basecalling model:\n- Fast (fast)\n- High Accurancy (hac) *RECOMMENDED FOR AMPLICON SEQUENCE DATA*\n- ... |
null | null | null | dx.doi.org/10.17504/protocols.io.eksbcwe | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p align="LEFT">This alternative adherent cell protocol utilizes a methanol based fixation which can be effective at reducing background fluorescence</p>
<p>under certain circumstances.</p>
[BEFORE_START]
<p align="LEFT">Storage Guidelines</p>
<p align="LEFT">Stellaris RNA FISH... | [] |
55,958 | A Supplemental Guide to Building the optoPlate-96 | 1 | dx.doi.org/10.17504/protocols.io.b2vwqe7e | https://www.protocols.io/view/a-supplemental-guide-to-building-the-optoplate-96-b2vwqe7e | Mary J Dunlop | TITLE: A Supplemental Guide to Building the optoPlate-96
AUTHORS: Mary J Dunlop
[DESCRIPTION]
The optoPlate-96 is a device that uses small LEDs to illuminate cell cultures in a 96-well plate. It was developed by Lukasz Bugaj and Wendell Lim. If you haven’t read the original optoPlate-96 paper and its Supplementary In... | ["[Introduction] Here is what the final design looks like:", "[The Parts List] THE PARTS LIST\n\nThe first thing you’ll need to do after reading Bugaj and Lim, Nature Protocols 2019 in detail is actually order the parts you will need. Most of this is straightforward since they’re nicely listed in the Materials section,... |
47,740 | Protein A- Protein A Sandwich ELISA | 1 | dx.doi.org/10.17504/protocols.io.bsu4neyw | https://www.protocols.io/view/protein-a-protein-a-sandwich-elisa-bsu4neyw | Angel Justiz-Vaillant | TITLE: Protein A- Protein A Sandwich ELISA
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This ELISA was used to study Staphylococcal protein-A (SpA) interactions with various mammalian and avian immunoglobulins.</div></div>
[STEPS]
?. This ELISA was used to study S... | ["This ELISA was used to study Staphylococcal protein-A (SpA) interactions with various mammalian and avian immunoglobulins. The 96 well microtiter plate was coated overnight at 4°C with 2 µg/µl per well of SpA in carbonate-bicarbonate buffer pH 9.6.", "The plate was then treated with bovine serum albumin solution and ... |
49,258 | The effectiveness of high intensity exercise therapy for improving bone density in postmenopausal women: a systematic review and meta-analysis protocol | 1 | dx.doi.org/10.17504/protocols.io.bucinsue | https://www.protocols.io/view/the-effectiveness-of-high-intensity-exercise-thera-bucinsue | Takashi Kitagawa, Kaede Hiraya, Homare Hirokawa, Takumi Denda, Nanako Otake, Yoshiki Saimon, Shuhei Yamamoto | TITLE: The effectiveness of high intensity exercise therapy for improving bone density in postmenopausal women: a systematic review and meta-analysis protocol
AUTHORS: Takashi Kitagawa, Kaede Hiraya, Homare Hirokawa, Takumi Denda, Nanako Otake, Yoshiki Saimon, Shuhei Yamamoto
[DESCRIPTION]
<div class = "text-blocks"><... | [] |
93,359 | Preparing 10X Genomics CytAssist FFPE Sections | 4 | dx.doi.org/10.17504/protocols.io.n92ldme3ol5b/v1 | https://www.protocols.io/view/preparing-10x-genomics-cytassist-ffpe-sections-c7epzjdn | YuHong Fu, Glenda Halliday | TITLE: Preparing 10X Genomics CytAssist FFPE Sections
AUTHORS: YuHong Fu, Glenda Halliday
[DESCRIPTION]
Designing and properly mounting FFPE sections on large-window CytAssist slides is important for downstream analysis and data quality. This protocol describes the key steps for this preparation.
[STEPS]
SECTION: Se... | ["[Set-up before cutting FFPE sections] Clean the surface of the bench area, microtome (HistoCore MULTICUT R, Leica), Water bath (HI1210, Leica), and tools (including forceps and blades) with 80% ethanol.", "[Set-up before cutting FFPE sections] Spray RNase ZapTM (Thermo Fisher Scientific) on the surface of the bench a... |
null | null | null | dx.doi.org/10.17504/protocols.io.quidwue | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Extraction of genomic DNA from Arabidopsis leaf material.</p>
[BEFORE_START]
<p>Make CTAB buffer:</p>
<p>- 2% (w/v) CTAB</p>
<p>- 1.4 M NaCl</p>
<p>- 0.1 M Tris-HLC pH 8</p>
<p> </p>
<p>Grind leaf tissue into fine powder using mortar and pestle or Qiagen tissue lyser (place ... | [] |
29,113 | HuBMAP - Tissue Processing with Paraffin Infiltration | null | dx.doi.org/10.17504/protocols.io.8nzhvf6 | null | Marda Jorgensen, Franchesca Farris, Jerelyn Nick | TITLE: HuBMAP - Tissue Processing with Paraffin Infiltration
AUTHORS: Marda Jorgensen, Franchesca Farris, Jerelyn Nick
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The purpose of this Standard Operating Procedure (SOP) is to outline procedures for the automated processing of formalin fixed HuBMAP... | ["[Processing Selection & Initial Steps]\nPlace dividers in processor sample basket and load cassettes. No more than 10 cassettes can be added to each partition. Cover the basket with the basket lid.\nPerform transfer of cassettes in the hood to avoid inhalation of the 70% ethanol that the cassettes are held in prior t... |
59,455 | Preparing Combined Indexed Primer Plates (IDT Standard) for the PacBio Sequel2 - Sequel Dual Indices | 4 | dx.doi.org/10.17504/protocols.io.q26g741y1gwz/v1 | https://www.protocols.io/view/preparing-combined-indexed-primer-plates-idt-stand-b6a7rahn | André M Comeau, Gina V Filloramo | TITLE: Preparing Combined Indexed Primer Plates (IDT Standard) for the PacBio Sequel2 - Sequel Dual Indices
AUTHORS: André M Comeau, Gina V Filloramo
[DESCRIPTION]
The preparation of diluted combined (F+R) IDT working primer stocks of PacBio Dual Index primers for use in IMR PCR preps.
[STEPS]
SECTION: Order Primers
... | ["[Order Primers] Use our Excel template ( ) to copy existing full-length 16S/18S/ITS primers or to design your own custom gene primers with the proper PacBio indices. No special synthesis type (unlike longer Illumina fusion primers) is needed for these primers as they are close to the length of standard PCR primers. O... |
106,879 | Pan-microbial metagenomics protocol | 0 | dx.doi.org/10.17504/protocols.io.q26g717w1gwz/v1 | https://www.protocols.io/view/pan-microbial-metagenomics-protocol-dkk74uzn | Adela Alcolea-Medina, Luke Blagdon Snell, Chris Alder, Rahul Batra | TITLE: Pan-microbial metagenomics protocol
AUTHORS: Adela Alcolea-Medina, Luke Blagdon Snell, Chris Alder, Rahul Batra
[DESCRIPTION]
DOI: 10.1038/s43856-024-00554-3
[STEPS]
SECTION: Preparation of quality controls:
2. Mix 300μL of control 1 and 300μL of control 2 in an Eppendorf. Label with date and LOT number.
SE... | ["[Preparation of quality controls:] Mix 300μL of control 1 and 300μL of control 2 in an Eppendorf. Label with date and LOT number.", "[Preparation of quality controls:] Vortex for 1 minute and Centrifuge at 1,200xg for 5min immediately prior to each use.", "[Preparation of quality controls:] Aliquot the volume specifi... |
null | null | null | dx.doi.org/10.17504/protocols.io.nwwdffe | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Description file for PLOS PONE-D-17-43572 - EMID:f954815f1ce44492</p>
<p>All speech samples are in samples.zip directory, all are 48kSa/s, 16 bit mono, to be played at -26dBoV corresponds to diotic 73dB SPL. Available at</p>
<p>https://www.dropbox.com/s/xme4tu1u9rhwvmx/sample... | [] |
93,629 | Guide Pratique sur l'Échantillonage des Animaux Vivants (Domestiques, Peridomestiques et Sauvages) pour la Surveillance des Maladies Infectieuses | 1 | dx.doi.org/10.17504/protocols.io.ewov1qb5pgr2/v2 | https://www.protocols.io/view/guide-pratique-sur-l-39-chantillonage-des-animaux-c7n5zmg6 | Stefano Catalano | TITLE: Guide Pratique sur l'Échantillonage des Animaux Vivants (Domestiques, Peridomestiques et Sauvages) pour la Surveillance des Maladies Infectieuses
AUTHORS: Stefano Catalano
[DESCRIPTION]
Les cas de maladies causées par des agents pathogènes particulièrement dangereux ou mal diagnostiquées présentent des risq... | [] |
36,612 | SPARC Cat - Sham Control Chronic Cat 2, Day 0 | 1 | dx.doi.org/10.17504/protocols.io.bfzcjp2w | https://www.protocols.io/view/sparc-cat-sham-control-chronic-cat-2-day-0-bfzcjp2w | Brett Hanzlicek, Margot Damaser | TITLE: SPARC Cat - Sham Control Chronic Cat 2, Day 0
AUTHORS: Brett Hanzlicek, Margot Damaser
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a procedure for a sham control chronic cat experiment (Day 0) for cystotomy (bladder surgery). The cystotomy is performed without UroMOCA implanta... | ["[Transport Cat]\nTransport cat from housing site to surgery site.", "[Animal Prep and catheter placement]\nAnimal is anesthetized and abdomen is shaved by the vet team. The cat is then moved into the surgery room and attached to monitors by the vet team.", "[Animal Prep and catheter placement]\nDrape animal and perf... |
34,622 | CUT&Tag@home | null | dx.doi.org/10.17504/protocols.io.bd26i8he | https://www.protocols.io/view/cut-amp-tag-home-bd26i8he | Steven Henikoff, Derek Janssens, Hatice Kaya-Okur, Jorja Henikoff, Kami Ahmad | TITLE: CUT&Tag@home
AUTHORS: Steven Henikoff, Derek Janssens, Hatice Kaya-Okur, Jorja Henikoff, Kami Ahmad
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">CUT&Tag@home uses a modification of Bench-top CUT&Tag which includes incubation in 0.1% SDS post-tagmentation for quantitative release of targete... | ["[ REAGENT SETUP (for up to 16 samples)]\nBinding buffer Mix 200 μL 1M HEPES-KOH pH 7.9, 100 μL 1M KCl, 10 μL 1M CaCl2 and 10 μL 1M MnCl2, and bring the final volume to 10 mL with dH2O. Store the buffer at 4 °C for up to several months.Wash buffer Mix 1 mL 1 M HEPES pH 7.5, 1.5 mL 5 M NaCl, 12.5 μL 2 M spermidine, bri... |
86,118 | Passaging of Organoids in Matrigel | 4 | null | https://www.protocols.io/view/passaging-of-organoids-in-matrigel-cycexste | Annika Fendler | TITLE: Passaging of Organoids in Matrigel
AUTHORS: Annika Fendler
[DESCRIPTION]
This protocol is for passaging prostate cancer organoids in matrigel. Protocol modified from Drost et al. (see citation below)
[STEPS]
SECTION: Before start
1. Prepare sufficient medium for passaging and prewarm immediately before use
SEC... | ["[Before start] Prepare sufficient medium for passaging and prewarm immediately before use", "[Before start] Thaw on ice o/n", "[Before start] Warm to 37°C before use", "[Before start] Coat 15 ml Falcons with 1% BSA o/n", "Coat tips before use in 1% BSA by pipetting up and down a few times", "[Dissociate organoids... |
null | null | null | dx.doi.org/10.17504/protocols.io.jy7cpzn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol presents a Gibson Assembly design for highly efficient construction of diatom episomes. We regularly observe >90% efficiency (efficiency = % of screened bacterial colonies containing the desired construct) following the steps presented here.</p>
[BEFORE_STAR... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.heyb3fw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>An easy to follow template for adding Golden Gate adapters to PCR primers. </p>
[STEPS]
?.
?. | [] |
88,360 | Modified salting out method for high molecular weight gDNA extraction (oribatid mites) | 4 | dx.doi.org/10.17504/protocols.io.yxmvm3yybl3p/v1 | https://www.protocols.io/view/modified-salting-out-method-for-high-molecular-wei-c2igycbw | Hüsna Öztoprak, Jens Bast | TITLE: Modified salting out method for high molecular weight gDNA extraction (oribatid mites)
AUTHORS: Hüsna Öztoprak, Jens Bast
[DESCRIPTION]
This protocol describes a low-cost, high-molecular-weight genomic DNA extraction method for a single minuscule specimen (modified from Miller et al 1988). DNA extractions from ... | ["[Version i) High-molecular gDNA extraction: DNA Extraction] Submerge cleansed specimen in 195 µL TNES buffer and flash freeze by holding tube in liquid nitrogen.", "[Version i) High-molecular gDNA extraction: DNA Extraction] Using a sterile pestle, homogenize by applying pressure to grind the specimen between pestle\... |
null | null | null | dx.doi.org/10.17504/protocols.io.hrkb54w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><span style="color: #222222; font-family: arial, sans-serif; font-size: 12.8px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; w... | [] |
19,206 | Simulating colonic tissue mechanics using a structure-based material model in Abaqus | null | dx.doi.org/10.17504/protocols.io.wzeff3e | null | Bhavesh Patel | TITLE: Simulating colonic tissue mechanics using a structure-based material model in Abaqus
AUTHORS: Bhavesh Patel
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The structure-based material constitutive model typically used for the colon tissue (DOI:10.1016/j.jmbbm.2017.08.031, DOI:10.1016/j.jmbbm... | ["[Generate input file]\nOnce your model setup is completed (geometry definition, orientation assigment, meshing, etc.), go to the \"Job\" module and click on \"Create Job\".", "[Specify material parameters in input file]\nThe structure-based material constitutive model typically proposed for the colon is shown below. ... |
null | null | null | dx.doi.org/10.17504/protocols.io.gvwbw7e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Describes the library preparation for Nanopore sequencing from low input DNA according to the SQK-MAP006 protocol</p>
<p>It accompanies the <em>GigaScience</em> publication:</p>
<p> </p>
<p>Benjamin Istace, et al. (2017) De novo assembly and population genomic survey of natur... | [] |
21,285 | Yale - Blood and Urine Creatinine | null | dx.doi.org/10.17504/protocols.io.y2dfya6 | null | Gary Cline, John Stack | TITLE: Yale - Blood and Urine Creatinine
AUTHORS: Gary Cline, John Stack
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">Procedure followed to detect the concentration of creatinine in serum, plasma, and urine.</div></... | ["Fill 1.5mL eppendorf tubes with 80µL of acetonitrile.", "Add sample: a. Use 20µL of plasma or serum/tube b. Use 6 µL of urine/tube", "Add 6.5 µL of d3-creatinine (5mg/dl) to each tube.", "Vortex each sample for 5 seconds.", "Spin each sample at 4˚C for 10 minutes", "Transfer supernatant to LC/MS/MS vials.",... |
83,155 | Transcardiac Perfusion of Mouse for Brain Tissue | 1 | dx.doi.org/10.17504/protocols.io.q26g7pzmkgwz/v1 | https://www.protocols.click/view/transcardiac-perfusion-of-mouse-for-brain-tissue-cvftw3nn | Maryana Nissan, divya.darwinarulseeli | TITLE: Transcardiac Perfusion of Mouse for Brain Tissue
AUTHORS: Maryana Nissan, divya.darwinarulseeli
[DESCRIPTION]
Transcardiac perfusion is a method used for clearing blood and preserving the mouse brain for immunostaining.
[STEPS]
1. Add Neutralizing Agent to break down Paraformaldehyde [PFA] for proper disposa... | ["Add Neutralizing Agent to break down Paraformaldehyde [PFA] for proper disposal. We use HydeAway [CAT #2201 from Decon Labs]", "Turn on the perfusion apparatus and place the tube into 1X Phosphate-Buffered Saline [PBS]", "Wash the system for 1 round, until the tube is saturated with 1X PBS", "Saturate anesthetic cham... |
62,597 | Kelly Clarkson CBD gummies reviews: Is it fake or legit? Read pros & cons! | 1 | dx.doi.org/10.17504/protocols.io.j8nlkknywl5r/v1 | https://www.protocols.io/view/kelly-clarkson-cbd-gummies-reviews-is-it-fake-or-l-b9ddr226 | kellybealy | TITLE: Kelly Clarkson CBD gummies reviews: Is it fake or legit? Read pros & cons!
AUTHORS: kellybealy
[DESCRIPTION]
Kelly Clarkson CBD Gummies - The Gummy to a Complete Bone Health Regime!
The idea of torment is developing to a bigger scope consistently. Many individuals, are occupied with life nowadays and dep... | ["Kelly Clarkson CBD chewy candies - Important Things To Know!\n\nDo you struggle with managing pressure? Do you experience issues in circumstances where many individuals are near, making you apprehensive or terrified? Do you have ceaseless muscle compressions that you don't know why? Maybe the response is no different... |
87,550 | Prozedere Bacterial stabs in Kultur nehmen bis Übernachtkultur ernten | 1 | null | https://www.protocols.io/view/prozedere-bacterial-stabs-in-kultur-nehmen-bis-ber-czq6x5ze | Bettina Ergün | TITLE: Prozedere Bacterial stabs in Kultur nehmen bis Übernachtkultur ernten
AUTHORS: Bettina Ergün
[DESCRIPTION]
Das Protokoll beschreibt die In-Kulturnahme von Bacterial stabs zur Anreicherung einzelner Klone und zur Produktion von ausreichend Bakterien zur Gewinnung der gewünschten Plasmide mittels Maxi Prep.
[GUI... | ["[Before Start] Ampicillin:\n100 mg/ml in sterilem H2O lösen; sterilfiltrieren, aliq.; - 20 °C\n1:1000 zu dem Platten bzw. Medium => 100 µg/ml", "[Before Start] Agarplatten gießen:\n10 cm Greiner-Schalen\n1,5 g Agar auf 100 ml LB-Broth-Medium o. 3,5 g LB Agar auf 100 ml ddH2O\naufkochen, abkühlen auf 50 °C im Wasserba... |
54,922 | PanelsDB2, FMDB to manage CGP report xml data. | 5 | dx.doi.org/10.17504/protocols.io.bzvip64e | https://www.protocols.io/view/panelsdb2-fmdb-to-manage-cgp-report-xml-data-bzvip64e | Keita Fukuyama | TITLE: PanelsDB2, FMDB to manage CGP report xml data.
AUTHORS: Keita Fukuyama
[DESCRIPTION]
PanelsDB2, FMDB to manage CGP report xml data.
The descrition about DB usage.
[STEPS]
SECTION: introduction
1. Here I will show you here how to manage the report xml data for Foundation One CDx and NCC Oncopanels that have be... | ["[introduction] Here I will show you here how to manage the report xml data for Foundation One CDx and NCC Oncopanels that have been insured in Japan.\nIt is very difficult to manage patient mutation data as a pdf report, but in Japan this is provided as xml data, and if you read xml, you can manage this as structured... |
28,364 | Single Cell Dissociation of Fresh Lung Tissue | null | dx.doi.org/10.17504/protocols.io.7xkhpkw | null | Lance Peter, Mei-I Chung, Nicholas E. Banovich | TITLE: Single Cell Dissociation of Fresh Lung Tissue
AUTHORS: Lance Peter, Mei-I Chung, Nicholas E. Banovich
[STEPS]
?. [Lung Dissociation]
Transfer distal lung tissue to a cold petri dish and dissect into required pieces for the experiment
?. [Lung Dissociation]
One piece tissue (2cm3) blot dry on disposable underpad... | ["[Lung Dissociation]\nTransfer distal lung tissue to a cold petri dish and dissect into required pieces for the experiment", "[Lung Dissociation]\nOne piece tissue (2cm3) blot dry on disposable underpad and place to another cold petri dish. Mince the tissue into smaller pieces using scalpel. Transfer minced tissue to ... |
54,000 | How to Assign AMBER Parameters to Desmond-generated System with viparr4 | 5 | dx.doi.org/10.17504/protocols.io.byyqpxvw | https://www.protocols.io/view/how-to-assign-amber-parameters-to-desmond-generate-byyqpxvw | Thilo Mast, Dmitry Lupyan | TITLE: How to Assign AMBER Parameters to Desmond-generated System with viparr4
AUTHORS: Thilo Mast, Dmitry Lupyan
[DESCRIPTION]
This tutorial partially copies steps from How to Assign CHARMM Parameters to Desmond-generated System with viparr4 but differs in the parametrization steps.
You can use the Schrödinger so... | ["[Setting up a Schrödinger Python Environment] Set up a Python Virtual Environment\n\nIn order to avoid compatibility issues with the Python modules, and ensure interoperability with Schrödinger's Python modules, use the Schrödinger software to create a new virtual environment.", "[Setting up a Schrödinger Python Envi... |
59,374 | CODEX Staining Protocol For FFPE Tissue | 1 | dx.doi.org/10.17504/protocols.io.rm7vzyjn4lx1/v1 | https://www.protocols.io/view/codex-staining-protocol-for-ffpe-tissue-b58nq9ve | Kyung J Ahn, Shovik Bandyopadhyay, Anusha Thadi, Kai Tan | TITLE: CODEX Staining Protocol For FFPE Tissue
AUTHORS: Kyung J Ahn, Shovik Bandyopadhyay, Anusha Thadi, Kai Tan
[DESCRIPTION]
This protocol describes the method for antibody staining of FFPE tissues on coverslips using CODEX Barcoded Antibodies. The Akoya CODEX user manual was modified to include photoble... | ["[Tissue Pre-treatment] Heat sample coverslip on hot plate at 55°C with tissue facing up for 20-25 minutes until wax thoroughly melts.", "[Tissue Deparaffinization and Hydration] Immerse the staining rack in the container containing the following reagents for 5 minutes each: \n\na.Xylene\nb.Xylene\nc.100% Ethanol/Reag... |
101,716 | Transcriptome annotation | 0 | dx.doi.org/10.17504/protocols.io.5qpvok92bl4o/v1 | https://www.protocols.io/view/transcriptome-annotation-dfju3knw | Rafael Rodrigues Ferrari, Thiago Mafra Batista | TITLE: Transcriptome annotation
AUTHORS: Rafael Rodrigues Ferrari, Thiago Mafra Batista
[DESCRIPTION]
This protocol provides detailed, step-by-step instructions for students and researchers to annotate transcriptomes. In this tutorial, we will follow the Trinity -> TransDecoder -> Trinotate pipeline, using the SwissPr... | ["[FINDIG CODING REGIONS WITHIN TRANSCRIPTS] ****TransDecoder (https://github.com/TransDecoder/TransDecoder/wiki)****\n\n***Extracting the long open reading frames (ORFs)***\n\n**Prepare a .pbs file to run the analysis remotely on Sagarana**\n \n***Including homology searches as ORF retention criteria***\n\n**BlastP se... |
96,390 | CRISPR/Cas9-Mediated Knockdown in LUHMES Cells: Nucleofection and Validation Protocol | 0 | null | https://www.protocols.io/view/crispr-cas9-mediated-knockdown-in-luhmes-cells-nuc-dade2a3e | Mallory Wright, William J Buchser, Colin Kremitzki, Serena Elia, Graham Bachman, emanuel gerbi, Jason Waligorski, Nicholas Tu, Lina Mohammed Ali | TITLE: CRISPR/Cas9-Mediated Knockdown in LUHMES Cells: Nucleofection and Validation Protocol
AUTHORS: Mallory Wright, William J Buchser, Colin Kremitzki, Serena Elia, Graham Bachman, emanuel gerbi, Jason Waligorski, Nicholas Tu, Lina Mohammed Ali
[DESCRIPTION]
This protocol uses a CRISPR RNP complex and nucleofection ... | ["[Nucleofection Protocol] Maintain a cell confluency of 70–85%. Higher cell densities may lead to lower Nucleofection efficiencies.", "[Nucleofection Protocol] Coat a new 6-well plate freshly with poly-L-ornithine and fibronectin to facilitate LUHMES attachment.", "[Nucleofection Protocol] Rinse LUHMES cells with 1XPB... |
51,740 | Nuclear isolation and sequencing for mouse hypothalamus | 4 | dx.doi.org/10.17504/protocols.io.bwr4pd8w | https://www.protocols.io/view/nuclear-isolation-and-sequencing-for-mouse-hypotha-bwr4pd8w | Zhengzheng Sophia Liang, Eric Vaughn, Dhananjay Bambah-Mukku, Catherine Dulac | TITLE: Nuclear isolation and sequencing for mouse hypothalamus
AUTHORS: Zhengzheng Sophia Liang, Eric Vaughn, Dhananjay Bambah-Mukku, Catherine Dulac
[DESCRIPTION]
This protocol is intended for isolation of nuclei from fresh brain tissue in preparation for single-nuclei sequencing library using Chromium Single Cell... | ["[Buffer to prepare] Lysis Buffer (100mL, store @ 4 C):\n98.4mL Nuclease-free water\n1mL 1M Tris-HCl (10mM)\n200uL 5M NaCl (10mM)\n300uL 1M MgCl2(3mM)\n100uL NonIdet P40 (0.1%)", "[Nuclei isolation] Dissect out and separate anterior and posterior hypothalamic tissue, place in sterile 35 x 10 mm petri dishes with 1 mL ... |
55,948 | Observational monitoring of leaf-eating caterpillars and ants in oil palm plantations | 3 | null | https://www.protocols.io/view/observational-monitoring-of-leaf-eating-caterpilla-b2vkqe4w | A D Advento | TITLE: Observational monitoring of leaf-eating caterpillars and ants in oil palm plantations
AUTHORS: A D Advento
[DESCRIPTION]
the protocol to conduct for monitoring LEC and ants in oil palm plantations
[STEPS] | [] |
67,388 | Huuman CBD Gummies | 1 | dx.doi.org/10.17504/protocols.io.5qpvobzjzl4o/v1 | https://www.protocols.io/view/huuman-cbd-gummies-cd24s8gw | Huuman CBD Gummies | TITLE: Huuman CBD Gummies
AUTHORS: Huuman CBD Gummies
[DESCRIPTION]
Huuman CBD Gummies
[STEPS]
1. Huuman CBD Gummies Reviews - Trending 100% Pure Easy Solution For Pain Relief! Cost & Website
2. Huuman CBD Gummies are supplemented and further developed that could mitigate any optional impacts connected with physical ... | ["Huuman CBD Gummies Reviews - Trending 100% Pure Easy Solution For Pain Relief! Cost & Website", "Huuman CBD Gummies are supplemented and further developed that could mitigate any optional impacts connected with physical and mental agony. Making this CBD supplement in the Huuman CBD Gummies is valuable, as it allows a... |
30,791 | Plasma Preparation | 1 | null | https://www.protocols.io/view/plasma-preparation-babfiajn | Sierra Simpson, Olivier George | TITLE: Plasma Preparation
AUTHORS: Sierra Simpson, Olivier George
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol for preparing plasma for metabolomics studies / GWAS</div></div>
[STEPS]
?. Collect blood into the EDTA coated microvette tube. Once spun, about half will be plasma, half wil... | ["Collect blood into the EDTA coated microvette tube. Once spun, about half will be plasma, half will be whole blood. For initial harvest of blood, we use retro-orbital blood sampling. This is done under general anesthesia ( isofluorane ) - The tip of the capillary tube is placed at the medial canthus of the eye ... |
70,053 | Phosphorus Extraction - Olsen Method | 1 | dx.doi.org/10.17504/protocols.io.8epv5j6m4l1b/v1 | https://www.protocols.io/view/phosphorus-extraction-olsen-method-cgndtva6 | maggie.bowman | TITLE: Phosphorus Extraction - Olsen Method
AUTHORS: maggie.bowman
[DESCRIPTION]
The method is based on the extraction of phosphate from the soil by 0.5 N sodium bicarbonate solution adjusted to pH 8.5.
[STEPS]
1. Print the required labels needed for Bray extraction for each site, depth, and replicate.
2. Weigh out ... | ["Print the required labels needed for Bray extraction for each site, depth, and replicate.", "Weigh out 3 gof soil into labeled 50 mL centrifuge tubes.", "Add20 mL of Olsen Extract solution (in cabinet under hood in 1521) using the pipet and electronic pipettor.", "Cap the samples and shake to mix. Add samples to foam... |
26,051 | Sea Cucumber Sperm Extraction from Gonads | null | dx.doi.org/10.17504/protocols.io.5pbg5in | null | Jon Eilers | TITLE: Sea Cucumber Sperm Extraction from Gonads
AUTHORS: Jon Eilers
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">How to extract sperm and gonadal tissue from sea cucumber gonads</div></div>
[STEPS]
?. Secure mesh (panty hose or other mesh like material) to top of funnel and place funnel into a ... | ["Secure mesh (panty hose or other mesh like material) to top of funnel and place funnel into a falcon tube", "Place gonads onto mesh and begin gently mashing with surgical spatula\nAn opaque fluid should begin accumulating in the bottom of the tube"] |
99,941 | Setting and Customizing OT-2 for LAP Entries | 0 | dx.doi.org/10.17504/protocols.io.3byl49jxjgo5/v1 | https://www.protocols.io/view/setting-and-customizing-ot-2-for-lap-entries-ddud26s6 | Ana Mariya Anhel, Lorea Alejaldre, Ángel Goñi-Moreno | TITLE: Setting and Customizing OT-2 for LAP Entries
AUTHORS: Ana Mariya Anhel, Lorea Alejaldre, Ángel Goñi-Moreno
[DESCRIPTION]
Automation scripts such as those included in the LAP repository (https://www.laprepo.cbgp.upm.es/repository/) require set up steps that not directly part of the experimental process but are e... | ["[Preparing Robot OS] Check needed packages and versions of LAP entry\n\nIn the Requirements Section of each LAP Entry you can find that the protocol/entry needs more packages than the ones are installed in the OT-2 system", "[Preparing Robot OS] Check python packages of robot\n\nTo know which packages are needed to b... |
22,142 | Expansion of DENV stocks | null | dx.doi.org/10.17504/protocols.io.zu6f6ze | null | Fabio Gomes | TITLE: Expansion of DENV stocks
AUTHORS: Fabio Gomes
[STEPS]
?. [Expansion of Cell Culture]
Warm culture media and TrypLE at 37oC
?. [Expansion of Cell Culture]
From a 25cm2 bottle, remove media, wash with 2mL PBS and add 2mL TrypLE
?. [Expansion of Cell Culture]
Incubate for 10-15 min
?. [Expansion of Cell Culture]
A... | ["[Expansion of Cell Culture]\nWarm culture media and TrypLE at 37oC", "[Expansion of Cell Culture]\nFrom a 25cm2 bottle, remove media, wash with 2mL PBS and add 2mL TrypLE", "[Expansion of Cell Culture]\nIncubate for 10-15 min", "[Expansion of Cell Culture]\nAfter 10 minutes incubation, inspect for cell dettachment at... |
33,724 | Basic Molecular Biology | 2 | dx.doi.org/10.17504/protocols.io.bc64izgw | https://www.protocols.io/view/basic-molecular-biology-bc64izgw | Ken Christensen | TITLE: Basic Molecular Biology
AUTHORS: Ken Christensen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">A collection of public protocols used in the Christensen Lab.</div></div>
[STEPS] | [] |
108,828 | Crystallisation of Zika NS5 RdRp | 1 | dx.doi.org/10.17504/protocols.io.5jyl82746l2w/v1 | https://www.protocols.io/view/crystallisation-of-zika-ns5-rdrp-dnh45b8w | Anu V. Chandran, Peter Marples, Martin austin Walsh | TITLE: Crystallisation of Zika NS5 RdRp
AUTHORS: Anu V. Chandran, Peter Marples, Martin austin Walsh
[DESCRIPTION]
The main aim of this work was to identify small molecules that bind Zika NS5 RdRp (catalytic RNA-dependent RNA polymerase domain) through X-ray fragment-based screening. The Zika NS5 RDRP domain was clone... | ["[Crystallisation experiment] Protein and buffer requirements:\n28.8 µL5 mg/mL \n3.264 mL", "[Crystallisation experiment] Dispense 34 µL into SwissCI 3 lens plate reservoir wells using a 100 µl multi-channel pipette.\nDispense 100 nL5 mg/mL to each lens using the SPT mosquito.\nDispense 50 nL to each lens using t... |
34,944 | Sampling strategies and sample preservation Acropora | null | dx.doi.org/10.17504/protocols.io.bec8jazw | https://www.protocols.io/view/sampling-strategies-and-sample-preservation-acropo-bec8jazw | Iliana Baums | TITLE: Sampling strategies and sample preservation Acropora
AUTHORS: Iliana Baums
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol describes sampling strategies, perservation and shipping of Acropora samples for </div><div class = "text-block">Applied Biosystems™ Axiom™ Coral Genotyping Arra... | [] |
59,497 | JAX - 10x Genomics - NEXTGEM Multiome ATAC + Gene Expression | 1 | dx.doi.org/10.17504/protocols.io.j8nlkk885l5r/v1 | https://www.protocols.io/view/jax-10x-genomics-nextgem-multiome-atac-gene-expres-b6chrat6 | William F F F. Flynn | TITLE: JAX - 10x Genomics - NEXTGEM Multiome ATAC + Gene Expression
AUTHORS: William F F F. Flynn
[DESCRIPTION]
Standard 10x Genomics - NEXTGEM Multiome protocol used by the JAX Single Cell Biology lab for the simultaneous single nucleus chromatin accessibility and gene expression assay.
[STEPS]
1. Follow the 10x Gen... | ["Follow the 10x Genomics NEXTGEM Single Cell Multiome ATAC+Gene expression protocol (CG00338)."] |
63,884 | Attention! NextGen Pharma Keto Reviews : Scam Or Legit | Must Read! | 3 | dx.doi.org/10.17504/protocols.io.yxmvmnqr6g3p/v1 | https://www.protocols.io/view/attention-nextgen-pharma-keto-reviews-scam-or-leg-camksc4w | Warapen Treekitkarnmongkol | TITLE: Attention! NextGen Pharma Keto Reviews : Scam Or Legit | Must Read!
AUTHORS: Warapen Treekitkarnmongkol
[DESCRIPTION]
The easiest way to start losing weight today is to visit the official NextGen Pharma Keto website and grab a bottle for yourself. The company offers some discounts to people who purchase ... | [] |
27,735 | K/2 Ian / K-ET | null | dx.doi.org/10.17504/protocols.io.7bxhipn | null | Ian Probert | TITLE: K/2 Ian / K-ET
AUTHORS: Ian Probert
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Modified from K medium by Ian Probert</div><div class = "text-block">Reference </div><div class = "text-block">Keller, M.D., Selvin, R.C., Claus, W. & Guillard, R.R.L. 1987. Media for the culture of oceanic ul... | ["ABCD1Quantity\nCompound\nStock solution (sterile)\nFinal conc. in K medium\n20.5ml\nNaNO3\n48.9542g/litre H2O\n288µM\n30.5ml\nNH4Cl *\n0.535g/litre H2O\n5µM\n40.5ml\nKH2PO4\n4.8992g/litre H2O\n18µM\n50.5ml\nFeEDTA solution\n(see recipe below)\n(see below)\n60.5ml\nTrace metal solution\n(see recipe below)\n(see below)... |
41,180 | manu 2 | 1 | dx.doi.org/10.17504/protocols.io.bkf4ktqw | https://www.protocols.io/view/manu-2-bkf4ktqw | Monica Hassan | TITLE: manu 2
AUTHORS: Monica Hassan
[STEPS]
?. | [] |
14,101 | Phenol-chloroform extraction and ethanol precipitation of RNA | 1 | dx.doi.org/10.17504/protocols.io.rzvd766 | https://www.protocols.io/view/phenol-chloroform-extraction-and-ethanol-precipita-rzvd766 | Tomasz Suchan | TITLE: Phenol-chloroform extraction and ethanol precipitation of RNA
AUTHORS: Tomasz Suchan
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Based on the protocol form NEB HiScribeTM T7 High Yield RNA Synthesis Kit</div></div>
[STEPS]
?. Adjust the reaction volume to 180 μl by adding 160 μl nuclease... | ["Adjust the reaction volume to 180 μl by adding 160 μl nuclease-free water. Add 20 μl of 3 M sodium acetate, pH 5.2 or 20 μl of 5 M ammonium acetate (1/10 of the total volume), mix thoroughly.", "Extract with an equal volume (200 μl) of 1:1 phenol/chloroform mixture. Vortex and centrufugate at maximum speed for 5 min.... |
23,096 | 16S Amplicon PCR for the V3-V4 region for the MicroCOPD samples | null | dx.doi.org/10.17504/protocols.io.2sygefw | null | Tuyen Hoang, Harald Wiker, Tomas Mikal L. Eagan, Christine Drengenes | TITLE: 16S Amplicon PCR for the V3-V4 region for the MicroCOPD samples
AUTHORS: Tuyen Hoang, Harald Wiker, Tomas Mikal L. Eagan, Christine Drengenes
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is the protocol for DNA extraction, PCR, and MiSeq sample preparation for the microbiome samples f... | ["[Amplicon PCR]\nSelect and thaw DNA samples for PCR.", "[Amplicon PCR]\nCreate an overview excel sheet and a plate- and pipetting-layout for the PCR run.", "[Amplicon PCR]\nSpin DNA samples at 13000 x g for 1 minute at room temperature.", "[Amplicon PCR]\nPipette 5 μl of each DNA sample into a well on a PCR plate, fo... |
45,783 | Copy of COVID 19 testing using ATR spectrometer and AI. | 1 | dx.doi.org/10.17504/protocols.io.bqxxmxpn | https://www.protocols.io/view/copy-of-covid-19-testing-using-atr-spectrometer-an-bqxxmxpn | Driss LAHLOU KITANE, Salma LOUKMAN, Nabila Marchoudi, Nawfel Azami | TITLE: Copy of COVID 19 testing using ATR spectrometer and AI.
AUTHORS: Driss LAHLOU KITANE, Salma LOUKMAN, Nabila Marchoudi, Nawfel Azami
[STEPS]
?. [Sample collection and RNA extraction]
Sample collection A sample of saliva swab or Naso-pharyngeal swab is collected using only swab with a synthetic tip. Swab is immed... | ["[Sample collection and RNA extraction]\nSample collection A sample of saliva swab or Naso-pharyngeal swab is collected using only swab with a synthetic tip. Swab is immediately inserted into sterile tubes containing 1ml of viral transport mediathe VTM used is the VTM-N of Citoswab\n[Saliva Swab or NP Swab]", "[Sample... |
67,434 | Visisharp [SCAM & LEGIT] Reviews | 1 | dx.doi.org/10.17504/protocols.io.6qpvr6jezvmk/v1 | https://www.protocols.io/view/visisharp-scam-amp-legit-reviews-cd4is8ue | visisharpcan | TITLE: Visisharp [SCAM & LEGIT] Reviews
AUTHORS: visisharpcan
[DESCRIPTION]
Visisharpis a dietary equation that supports the eyes and safeguards them from harm. As indicated by the authority site it incites normal mending, utilizing plant-based that save the eye from super durable vision misfortune. It comes in ... | [] |
38,165 | Plate Preparation and Submission (Eurofins) | 5 | dx.doi.org/10.17504/protocols.io.3byl47yqjlo5/v1 | https://www.protocols.io/view/plate-preparation-and-submission-eurofins-bhhvj366 | Dakota Betz | TITLE: Plate Preparation and Submission (Eurofins)
AUTHORS: Dakota Betz
[DESCRIPTION]
This protocol details how to set up a plate for sequence submission, from the initial spreadsheet preparation and sample naming scheme, to physical plate preparation and submission to the eurofins website/shipping.
[STEPS]
SECTION: ... | ["[Spreadsheet Preparation] Log in (lab credentials) to eurofins.genomics.com. Navigate to Plate Sequencing and select Order Now for Standard Plates. Download the Excel spreadsheet by clicking on the icon.", "[Spreadsheet Preparation] If applicable: type the Plate Barcode (found on the sticker you will afix to the plat... |
87,572 | Mid-lumbar (L3) epidural stimulation effects on bladder and external urethral sphincter in non-injured and chronically transected urethane-anesthetized rats | 1 | dx.doi.org/10.17504/protocols.io.bp2l6xdk5lqe/v1 | https://www.protocols.io/view/mid-lumbar-l3-epidural-stimulation-effects-on-blad-czrux56w | Daniel Medina Aguinaga, Daniel Medina Aguinaga, Charles H. Hubscher, Natasha L. Wilkins, Robert Hoey, Jason Fell, Beatrice Ugiliweneza, Susan J. Harkema | TITLE: Mid-lumbar (L3) epidural stimulation effects on bladder and external urethral sphincter in non-injured and chronically transected urethane-anesthetized rats
AUTHORS: Daniel Medina Aguinaga, Daniel Medina Aguinaga, Charles H. Hubscher, Natasha L. Wilkins, Robert Hoey, Jason Fell, Beatrice Ugiliweneza, Susan J. Ha... | ["[Post-surgical care] After surgery, the rat's urinary bladder was manually emptied 3/day until voiding reflexively.", "[Terminal mapping - Electromyography and cystometrogram sensors surgical placement] The rat is placed on their ventrum throughout testing. The hindlimbs are taped down to the platform\nas the electri... |
44,317 | Dephosphorylation of Input RNA | 4 | dx.doi.org/10.17504/protocols.io.bph5mj86 | https://www.protocols.io/view/dephosphorylation-of-input-rna-bph5mj86 | Eric L. Van Nostrand, Thai B. Nguyen, Chelsea Gelboin-Burkhart, Ruth Wang, Steven M. Blue, Gabriel A. Pratt, Ashley L. Louie, Gene W. Yeo | TITLE: Dephosphorylation of Input RNA
AUTHORS: Eric L. Van Nostrand, Thai B. Nguyen, Chelsea Gelboin-Burkhart, Ruth Wang, Steven M. Blue, Gabriel A. Pratt, Ashley L. Louie, Gene W. Yeo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Profiling of RNA binding protein targets in vivo provides critical ... | ["[TAP Treat Input RNA]\nPrepare TAP master mix: AB1H2O10 μL210× TAP buffer2.5 μL3RNase Inhibitor0.5 μL4TAP enzyme2.5 μL\nAB1H2O10 μL210× TAP buffer2.5 μL3RNase Inhibitor0.5 μL4TAP enzyme2.5 μL", "[TAP Treat Input RNA]\nTo INPUT samples ONLY, add .\n[TAP master mix]", "[TAP Treat Input RNA]\nMix and incubate in Thermo... |
87,805 | Building a SpikeGLX Rig with camera: Chronic recoverable Neuropixels in mice | 1 | dx.doi.org/10.17504/protocols.io.kxygxzzxkv8j/v4 | https://www.protocols.io/view/building-a-spikeglx-rig-with-camera-chronic-recove-czy5x7y6 | Emily A Aery Jones | TITLE: Building a SpikeGLX Rig with camera: 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 1 Neuropixels 1.0 probe or 2 Neuropixels 2.0 probes into mice, record during freely moving behavior, the... | ["[Set up acquisition hardware] Load the PCIe module into your computer", "[Set up acquisition hardware] Load the PXIe modules and the IMEC module into the NIDAQ chassis", "[Set up acquisition hardware] Connect the PXIe modules to the BNC breakout board and the computer. Connect the IMEC SMA to the BNC board (analog sl... |
71,190 | Microscopy-based mtDNA turnover measurements in HeLa and iNeurons | 4 | dx.doi.org/10.17504/protocols.io.36wgqj4y3vk5/v1 | https://www.protocols.io/view/microscopy-based-mtdna-turnover-measurements-in-he-chrwt57e | Felix Kraus | TITLE: Microscopy-based mtDNA turnover measurements in HeLa and iNeurons
AUTHORS: Felix Kraus
[DESCRIPTION]
Protocol for microscopy-based mtDNA turnover measurements in HeLa and iNeurons
[STEPS]
SECTION: Seeding of Hela cells
1. Wash HeLa cells expressing doxycycline-inducible Parkin with 1x PBS
SECTION: Seeding of H... | ["[Seeding of Hela cells] Wash HeLa cells expressing doxycycline-inducible Parkin with 1x PBS", "[Seeding of Hela cells] Add Trypsin to cells for 5 min and incubate at 37°C to dissociate cells from plastic well", "[Seeding of Hela cells] Resuspend cells in 1 mL DMEM media", "[Seeding of Hela cells] Count cells", "[Seed... |
51,150 | Copy of NEBNext® ARTIC SARS-CoV-2 Library Prep Kit (Illumina®) (NEB #E7650S/L) Express Protocol without PCR Bead Cleanup | 1 | dx.doi.org/10.17504/protocols.io.bv7nn9me | https://www.protocols.io/view/copy-of-nebnext-artic-sars-cov-2-library-prep-kit-bv7nn9me | Isabel Gautreau | TITLE: Copy of NEBNext® ARTIC SARS-CoV-2 Library Prep Kit (Illumina®) (NEB #E7650S/L) Express Protocol without PCR Bead Cleanup
AUTHORS: Isabel Gautreau
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol details methods for the NEBNext® ARTIC SARS-CoV-2 Library Prep Kit (Illumina®), NEB #... | ["[cDNA Synthesis]\nGently mix and spin down the LunaScript RT SuperMix reagent. Prepare the cDNA synthesis reaction as described below:COMPONENT VOLUMERNA Sample8 µl(lilac) LunaScript RT SuperMix2 µlTotal Volume10 µlFor no template controls, mix the following components:COMPONENTVOLUME(white) Nuclease-free Water8 µl(l... |
null | null | null | dx.doi.org/10.17504/protocols.io.efmbbk6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><span style="color: #3c3c39;">Bioinformatic pipleine used to process all sequence reads. </span></p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
39,688 | An improved ChEC-seq method for mapping the genome-wide binding of S. cerevisiae transcription factors | 1 | dx.doi.org/10.17504/protocols.io.bizgkf3w | https://www.protocols.io/view/an-improved-chec-seq-method-for-mapping-the-genome-bizgkf3w | Rafal Donczew, Amélia Lalou, Steven Hahn | TITLE: An improved ChEC-seq method for mapping the genome-wide binding of S. cerevisiae transcription factors
AUTHORS: Rafal Donczew, Amélia Lalou, Steven Hahn
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">ChEC-seq and other nuclease-based methods such as Cut&Run map protein locations on DNA by ta... | ["[Cell harvest]\nGrow 50 ml of yeast cells in preferred conditions to OD600 = 0.5 – 0.7.", "[Cell harvest]\nWhen the culture approaches the desired OD600 set up a heat block or water bath to 30°C and prepare Buffer A.", "[Cell harvest]\nHarvest cells in a 50 ml tube (2000 x g, 3 min).", "[Cell harvest]\nResuspend cell... |
26,101 | Overview of the Application of Cytokines in Immunotherapy | null | dx.doi.org/10.17504/protocols.io.5qvg5w6 | null | susan wind | TITLE: Overview of the Application of Cytokines in Immunotherapy
AUTHORS: susan wind
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Cytokines are generally produced by stimulated cells, primarily immune cells. Cytokines are highly potent and can act in micromolar or even picomoles. The effect of a ... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.dq85zv | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
For use in "<a href="https://www.protocols.io/view/Isolation-of-cyanophages-by-liquid-enrichment-assa-dp65rd" target="_blank">Isolation of cyanophages by liquid enrichment assay</a>"
[STEPS]
?.
?.
?.
?.
?.
?. | [] |
45,472 | SEM gold coat protocol | 4 | null | https://www.protocols.io/view/sem-gold-coat-protocol-bqm8mu9w | Elizabeth Fozo | TITLE: SEM gold coat protocol
AUTHORS: Elizabeth Fozo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol for how to the gold coater for SEM samples</div></div>
[STEPS]
?. [This coater is in the lab sample prep room in JIAM.]
Lift glass unit – hold it together and set it to the side.
?. [This ... | ["[This coater is in the lab sample prep room in JIAM.]\nLift glass unit – hold it together and set it to the side.", "[This coater is in the lab sample prep room in JIAM.]\nAdd samples on the silicon chip and mounted post.", "[This coater is in the lab sample prep room in JIAM.]\nTurn pump on (switch on the left).", "... |
42,143 | Protocols for Primer Design | 2 | null | https://www.protocols.io/view/protocols-for-primer-design-bmd7k29n | TITLE: Protocols for Primer Design
AUTHORS:
[STEPS] | [] | |
28,375 | MojoSort™ Human CD41 Nanobeads Protocol | null | dx.doi.org/10.17504/protocols.io.7xxhppn | null | Sam Li | TITLE: MojoSort™ Human CD41 Nanobeads Protocol
AUTHORS: Sam Li
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Product description and procedure summary:</span><span> The cells targeted by the Nanobeads are either selected or depleted by incubating your sample with ... | ["Prepare cells from your tissue of interest or blood without lysing erythrocytes. If erythrocytes are lysed, the volume of Nanobeads may need to be adjusted. Please contact BioLegend Technical Service for guidance. Kits for human samples have been optimized for PBMCs, please prepare the cells using a suitable method."... |
54,718 | Virus Production and Administration | 4 | dx.doi.org/10.17504/protocols.io.bzn6p5he | https://www.protocols.io/view/virus-production-and-administration-bzn6p5he | Sarkis Mazmanian, Bryan Yoo, Jessica Griffiths | TITLE: Virus Production and Administration
AUTHORS: Sarkis Mazmanian, Bryan Yoo, Jessica Griffiths
[DESCRIPTION]
Protocol for virus production and administration to mice in Yoo et al 2021
[STEPS]
SECTION: Virus Production
4. Virus is precipitated from cells and supernatant with an 8% PEG solution (wt/vol), and pur... | ["[Virus Production] Virus is precipitated from cells and supernatant with an 8% PEG solution (wt/vol), and purified by ultracentrifugation using 15%, 25%, 40%, 60% stacked iodixanol gradients.", "[Virus Production] Briefly, human embryonic kidney (HEK293T) cells were triple-transfected with pUCmini-iCAP-AAV-PHP.S, pHe... |
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