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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null | null | null | dx.doi.org/10.17504/protocols.io.g6bbzan | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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33,520 | Plasmid Cloning | null | dx.doi.org/10.17504/protocols.io.bcyqixvw | null | Ken Christensen | TITLE: Plasmid Cloning
AUTHORS: Ken Christensen
[STEPS] | [] |
79,708 | Canine Respiratory Pathogen Detection Assays | 1 | dx.doi.org/10.17504/protocols.io.kxygx9x7zg8j/v1 | https://www.protocols.io/view/canine-respiratory-pathogen-detection-assays-cr34v8qw | Come J Thieulent, Mariano Carossino, Laura Peak, Udeni B. R. Balasuriya | TITLE: Canine Respiratory Pathogen Detection Assays
AUTHORS: Come J Thieulent, Mariano Carossino, Laura Peak, Udeni B. R. Balasuriya
[DESCRIPTION]
The Canine Respiratory Pathogen (CRP) Detection Assays is intended as an in vitro veterinary reagent set, based on Reverse Transcription quantitative PCR (RT-qPCR), for the... | ["[Reaction Setup] Thaw all reagents on ice.", "[Reaction Setup] Centrifuge all reagents on a benchtop centrifuge to ensure no liquid is in cap and keep on ice", "[Programming the Thermocycler] The following fluorescence channels should be selected: ABYTM, FAMTM, JUNTM, and VICTM.", "[Programming the Thermocycler] ROXT... |
69,932 | Cylinder behavioral test (mice version) | 4 | dx.doi.org/10.17504/protocols.io.j8nlkw58dl5r/v2 | https://www.protocols.io/view/cylinder-behavioral-test-mice-version-cgiktucw | miquel.vila | TITLE: Cylinder behavioral test (mice version)
AUTHORS: miquel.vila
[DESCRIPTION]
Cylinder behavioral test for left and right forepaw use in mice
[BEFORE_START]
All behavioral tests have to be performed during the light cycle by an investigator blinded to the experimental groups.
[GUIDELINES]
Important: Rats that pr... | ["First allow mice to habituate to the experimental room for at least 1 h before each test", "Put animals individually in a glass cylinder and the total number of left and right forepaw touches performed within 5 min was counted", "Clean behavioral equipment with 70% ethanol after each animal has been tested to avoid o... |
40,444 | Sandwich ELISA for investigating the binding of Protein-LG (SpLG) to avian immunoglobulins using anti-IgY-peroxidase as conjugate. | 6 | dx.doi.org/10.17504/protocols.io.bjq4kmyw | https://www.protocols.io/view/sandwich-elisa-for-investigating-the-binding-of-pr-bjq4kmyw | Angel Justiz-Vaillant, Monica F. Smikle | TITLE: Sandwich ELISA for investigating the binding of Protein-LG (SpLG) to avian immunoglobulins using anti-IgY-peroxidase as conjugate.
AUTHORS: Angel Justiz-Vaillant, Monica F. Smikle
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. This ELISA is used to study the interaction of protein-LG (SpLG) with... | ["This ELISA is used to study the interaction of protein-LG (SpLG) with diverse avian immunoglobulins.", "The 96 well microtitre plate is coated overnight at 4°C with 2 µg/µl per well of recombinant SpLG or a mixture of SpL with SpG in carbonate-bicarbonate buffer pH 9.6.", "Then plate is treated with bovine serum albu... |
50,294 | Study Design (Part 3 of Safety and Efficacy of Imatinib for Preserving Beta-Cell Function in New-onset Type 1 Diabetes Mellitus) | 1 | dx.doi.org/10.17504/protocols.io.bvcwn2xe | https://www.protocols.io/view/study-design-part-3-of-safety-and-efficacy-of-imat-bvcwn2xe | Stephen.Gitelman , Jeffrey A. Bluestone | TITLE: Study Design (Part 3 of Safety and Efficacy of Imatinib for Preserving Beta-Cell Function in New-onset Type 1 Diabetes Mellitus)
AUTHORS: Stephen.Gitelman , Jeffrey A. Bluestone
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is Part 3 of "Safety and Efficacy of Imatinib for Preserving ... | [] |
26,212 | Bleaching a population of C. elegans nematode worm in a tube | null | dx.doi.org/10.17504/protocols.io.5ucg6sw | null | Cristian Riccio | TITLE: Bleaching a population of C. elegans nematode worm in a tube
AUTHORS: Cristian Riccio
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is the C. elegans population bleaching protocol.</div></div>
[STEPS]
?. 1. Use C. elegans plates that have many gravid hermaphrodites (only the eggs will... | ["1. Use C. elegans plates that have many gravid hermaphrodites (only the eggs will resist to the bleach treatment). Wash the plates with M9 solution: pipet M9 solution across the plate several times to loosen worms and eggs that are stuck in the bacteria. Collect the M9+worms solution in a 15 ml Falcon tube. Top up th... |
null | null | null | dx.doi.org/10.17504/protocols.io.khgct3w | null | null | TITLE: No Title
AUTHORS:
[STEPS] | [] |
103,190 | Generation of pLKO.1 Plasmids Containing shRNA | 0 | dx.doi.org/10.17504/protocols.io.36wgqnm4ygk5/v1 | https://www.protocols.io/view/generation-of-plko-1-plasmids-containing-shrna-dgzw3x7e | Shiyi Wang | TITLE: Generation of pLKO.1 Plasmids Containing shRNA
AUTHORS: Shiyi Wang
[DESCRIPTION]
Generation of pLKO.1 Plasmids Containing shRNA
[STEPS]
1. **Obtain shRNA Plasmids**
1.1. - Obtain pLKO.1 Puro plasmids containing shRNA sequences against mouse/rat Lrrk2 (shLrrk2: TRCN0000322193) and mouse/rat Atg7 (shAtg7: TRCN00... | ["**Obtain shRNA Plasmids**", "- Obtain pLKO.1 Puro plasmids containing shRNA sequences against mouse/rat Lrrk2 (shLrrk2: TRCN0000322193) and mouse/rat Atg7 (shAtg7: TRCN0000092163) from the RNAi Consortium (TRC) via Dharmacon.", "**Synthesize Scrambled shRNA Sequences**", "- Generate two scrambled shRNA sequences: GTT... |
83,744 | Fungal Culture Long-term Storage (Dry Filter Paper Technique) | 4 | null | https://www.protocols.click/view/fungal-culture-long-term-storage-dry-filter-paper-cvz8w79w | Anuar Morales | TITLE: Fungal Culture Long-term Storage (Dry Filter Paper Technique)
AUTHORS: Anuar Morales
[DESCRIPTION]
Culture collections are expensive to support, as they require special equipment and continuous attention in order to maintain fungal cultures without losing their pathogenicity or virulence. Two examples of the... | ["[Initial Isolation] A pinch of pure fungal culture is taken from insect or plant host and added to culture medium in a Petri dish.\nSelective media PARP5 can be used or general PDA. Additives include chloramphenicol, lactic acid, ampicillin, streptomycin, etc.", "[Initial Isolation] Filter papers (1 x 1 cm) cut and s... |
93,363 | WIPI2d puncta formation assay | 1 | dx.doi.org/10.17504/protocols.io.n2bvj3myxlk5/v1 | https://www.protocols.io/view/wipi2d-puncta-formation-assay-c7etzjen | Dan Tudorica | TITLE: WIPI2d puncta formation assay
AUTHORS: Dan Tudorica
[DESCRIPTION]
Labels sites of autophagosome generation.
[STEPS]
1. Target cells are cultured until they reach 80% confluence on cell-culture treated, chambered confocal slide, and then transfect cells with a WIPI2d-Halo mammalian expression plasmid using lipo... | ["Target cells are cultured until they reach 80% confluence on cell-culture treated, chambered confocal slide, and then transfect cells with a WIPI2d-Halo mammalian expression plasmid using lipofectamine 3000 (Thermo Fisher). Calculate DNA amount to use via the manufacturer instructions, scale DNA according to culture ... |
85,447 | RNAlater preparation | 1 | dx.doi.org/10.17504/protocols.io.eq2lyjn6wlx9/v1 | https://www.protocols.click/view/rnalater-preparation-cxpfxmjn | Tsu-Chun Hung | TITLE: RNAlater preparation
AUTHORS: Tsu-Chun Hung
[DESCRIPTION]
RNAlater preparation
[STEPS]
SECTION: DEPC-treated water prepartion
1. Prepare 0.1% DEPC-treated water and autocleave it
SECTION: RNAlater preparation
2. Add these component in 1L bottle in order
SECTION: RNAlater preparation
3. Put the bottle on... | ["[DEPC-treated water prepartion] Prepare 0.1% DEPC-treated water and autocleave it", "[RNAlater preparation] Add these component in 1L bottle in order", "[RNAlater preparation] Put the bottle on the stirring hot plate, stir till the mixture clear", "[RNAlater preparation] After cool down, add 8.96 mL 1M sulfuric acid ... |
87,159 | Polychromatic UV Fluence (Dose) Response Determination | 1 | dx.doi.org/10.17504/protocols.io.n92ldzqoov5b/v3 | https://www.protocols.io/view/polychromatic-uv-fluence-dose-response-determinati-czcxx2xn | Daniel Ma, NATALIE HULL | TITLE: Polychromatic UV Fluence (Dose) Response Determination
AUTHORS: Daniel Ma, NATALIE HULL
[DESCRIPTION]
The purpose of this protocol is to document the steps used for determination of UV doses for polychromatic UV sources such as UV LEDs, excimer lamps, medium pressure mercury lamps. The method is not limited to ... | ["[UV Dose Spreadsheet] UV Dose Spreadsheet: \n\nHere is an example spreadsheet filled out with radiometer factors, absorbance scan of sample, UV emission spectra of a low pressure mercury lamp, and sample geometry: \n\nThis protocol will guide users through important parts of the UV Dose Spreadsheet.", "[Performin... |
70,150 | Midbrain organoid differentiation in spinner flasks. | 1 | null | https://www.protocols.io/view/midbrain-organoid-differentiation-in-spinner-flask-cgretv3e | gustavo.parfitt | TITLE: Midbrain organoid differentiation in spinner flasks.
AUTHORS: gustavo.parfitt
[DESCRIPTION]
Midbrain differentiation protocol using spinner flasks.
[STEPS]
SECTION: iPSCs aggregation in spinner flasks
1. Passage iPSC lines to four 10-cm dishes to generate 40X106 cells.
SECTION: iPSCs aggregation in spinner fl... | ["[iPSCs aggregation in spinner flasks] Passage iPSC lines to four 10-cm dishes to generate 40X106 cells.", "[iPSCs aggregation in spinner flasks] Wait for the cells to reach 80% confluence and seed iPSC 40X106 cells into a spinner flask.", "[iPSCs aggregation in spinner flasks] Prepare 120 mL of StemFlex per flask wi... |
90,570 | MRI Imaging of the Gut | 4 | null | https://www.protocols.io/view/mri-imaging-of-the-gut-c4piyvke | Santiago Unda, rar, Michael G. Kaplitt | TITLE: MRI Imaging of the Gut
AUTHORS: Santiago Unda, rar, Michael G. Kaplitt
[DESCRIPTION]
This test is used measure peristaltic activity in the upper portion of the gut.
[STEPS]
6. Localize the longitudinal axis of the stomach.
SECTION: Protocol
1. Habituate mice to eat Diet gel (Cat#DietGel Recovery, ClearH2O, ... | ["Localize the longitudinal axis of the stomach.", "[Protocol] Habituate mice to eat Diet gel (Cat#DietGel Recovery, ClearH2O, ME, USA) for at least a week.", "[Protocol] Fast mice for 12 to 18 hours.", "[Protocol] Prepare 10g of Diet gel mixed with 22.4mg of Gadolinium [Gd-DTPA powder] (Cat#381667, Sigma Aldrich, St. ... |
75,784 | Spatially selective stimulation of the pig vagus nerve to modulate target effect versus side effect | 1 | dx.doi.org/10.17504/protocols.io.yxmvm2wzbg3p/v1 | https://www.protocols.io/view/spatially-selective-stimulation-of-the-pig-vagus-n-cm9gu93w | Stephan L Blanz, Evan N Nicolai, Kip Ludwig | TITLE: Spatially selective stimulation of the pig vagus nerve to modulate target effect versus side effect
AUTHORS: Stephan L Blanz, Evan N Nicolai, Kip Ludwig
[DESCRIPTION]
This protocol was used to collect data now published in the Journal of Neural Engineering, Spatially selective stimulation of the pig vagus nerve... | ["[Animal preparation and initial administration of anaesthesia] What we did (approved by the University of Wisconsin-Madison IACUC):\n\nWeigh pig, and perform an IM injection of a mixture of telazol (6 mg/kg) and xylazine (2 mg/kg). Intubate and ventilate the pig and anesthetize using isoflurane gas (0.5-3% in room ai... |
62,439 | Ln-DAB2 Solutions | 1 | dx.doi.org/10.17504/protocols.io.n2bvj6zdblk5/v1 | https://www.protocols.io/view/ln-dab2-solutions-b88frztn | Stephen R. Adams, Mason R. Mackey, Roger Tsien, Mark Ellisman, Jeffrey D. Martell | TITLE: Ln-DAB2 Solutions
AUTHORS: Stephen R. Adams, Mason R. Mackey, Roger Tsien, Mark Ellisman, Jeffrey D. Martell
[DESCRIPTION]
We use multicolor EM (electron microscopy) to paint multiple cellular markers by locally depositing specific Ln3+ from prepared solutions of Ln-DAB2 by mSOG, APEX2 or HRP. Each Ln3+ is the... | ["To make 10 mL of a 2 mM Ln, Ce or Pr-DAB2 solution, 15.6 mg (20 μmol) of DTPA-DAB2 is suspended in 0.25 mL N,N Dimethylformamide (DMF) and gently heated to about 50C and sonicated/vortexed to dissolve.", "8.33 mL of DDH2O is added to give a cloudy solution that cleared on addition of LnCl3 aqueous solution (0.1 M of ... |
53,980 | Encoding Probe Design using PaintSHOP, SOP006.v1.1 | 1 | null | https://www.protocols.io/view/encoding-probe-design-using-paintshop-sop006-v1-1-byx4pxqw | Nicole Houchins, Rory Kruithoff, Douglas Shepherd | TITLE: Encoding Probe Design using PaintSHOP, SOP006.v1.1
AUTHORS: Nicole Houchins, Rory Kruithoff, Douglas Shepherd
[DESCRIPTION]
Document Summary: This document, SOP006 – Encoding Probe Design using PaintSHOP, describes how to construct RNA-targeting, DNA-based encoding probes with the open-source, interactive ap... | ["[Part 1 - Generating encoding probe sequences - Step 1: Determine gene/genes of interest] Determine a gene or list of genes of interest for your specific experimental design. Gene selection may require consideration of expression levels depending on the sample size and distribution of the expression of the selected... |
null | null | null | dx.doi.org/10.17504/protocols.io.hnzb5f6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol describes a method for screening transgenic lines of <em>Phaeodactylum</em>, specifically for those obtained via conjugation with episomal plasmids. The assay can also be used for screening genomic integrants obtained through biolistics. The assay uses patched... | [] |
46,880 | A bioinformatics pipeline for processing and analysis of whole transcriptome sequence data | 5 | dx.doi.org/10.17504/protocols.io.brz8m79w | https://www.protocols.io/view/a-bioinformatics-pipeline-for-processing-and-analy-brz8m79w | Ayam Gupta, Shalin Rajagopal, Sonal Gupta, Ashwani Kumar Mishra, Prashanth Suravajhala | TITLE: A bioinformatics pipeline for processing and analysis of whole transcriptome sequence data
AUTHORS: Ayam Gupta, Shalin Rajagopal, Sonal Gupta, Ashwani Kumar Mishra, Prashanth Suravajhala
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Recent advances in next generation sequencing (NGS) techno... | [] |
37,025 | Cell migration assay or Transwell assay | null | dx.doi.org/10.17504/protocols.io.bgd9js96 | https://www.protocols.io/view/cell-migration-assay-or-transwell-assay-bgd9js96 | Marzia Ognibene | TITLE: Cell migration assay or Transwell assay
AUTHORS: Marzia Ognibene
[STEPS]
?.
?. Cells are washed in cold PBS, detached with 5mM EDTA, centrifuged at 1200 g for 7 min and resuspended in serum-free medium.
?. Transwell chambers (Corning Costar) are prepared filling with 600 μl of complete medium the lower chamber... | ["Cells are washed in cold PBS, detached with 5mM EDTA, centrifuged at 1200 g for 7 min and resuspended in serum-free medium.", "Transwell chambers (Corning Costar) are prepared filling with 600 μl of complete medium the lower chamber.", "The desired amount of cells is plated in 100 μl of serum-free medium in the upper... |
24,358 | IHC on fixed frozen cryo sections | null | dx.doi.org/10.17504/protocols.io.32egqbe | null | Grace Burgin, Inbal Benhar | TITLE: IHC on fixed frozen cryo sections
AUTHORS: Grace Burgin, Inbal Benhar
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. 30-60 min Protein Block 5% Normal Horse (or Donkey) Serum in PBS + 0.3% Triton-X
?. Overnight (~18-22hrs) Primaries at 4C in PBS + 0.3% Triton-X
?. Wash 2x5 min w/ PBS
?. 2hr Seconda... | ["30-60 min Protein Block 5% Normal Horse (or Donkey) Serum in PBS + 0.3% Triton-X", "Overnight (~18-22hrs) Primaries at 4C in PBS + 0.3% Triton-X", "Wash 2x5 min w/ PBS", "2hr Secondaries at room temp in PBS + 0.3% Triton-X", "Wash 2x5 min w/ PBS", "Coverslip"] |
52,999 | Structure-from-motion multi-view photogrammetry applied to linear-scan sediment cores images | 1 | null | https://www.protocols.io/view/structure-from-motion-multi-view-photogrammetry-ap-bxzfpp3n | Kevin Jacq, William Rapuc, Claire Blanchet, Estelle Ployon, Cecile Pignol, Didier Coquin, Bernard Fanget | TITLE: Structure-from-motion multi-view photogrammetry applied to linear-scan sediment cores images
AUTHORS: Kevin Jacq, William Rapuc, Claire Blanchet, Estelle Ployon, Cecile Pignol, Didier Coquin, Bernard Fanget
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Image acquisition is the first step to... | ["[General description of the acquisition bench]", "[General description of the acquisition bench]", "[Camera acquisition parameters and calibration]\nIt is important that the parameters related to the camera (shutter speed, aperture, etc.) are fixed throughout the acquisition. The autofocus must also be disabled.", "[... |
62,245 | Keto Start ACV Gummies:|Reviews Safe Money|Weight Loss Reviews|Price|Gummies and Official Store| | 3 | dx.doi.org/10.17504/protocols.io.ewov1n5y7gr2/v1 | https://www.protocols.io/view/keto-start-acv-gummies-reviews-safe-money-weight-l-b82drya6 | garrick | TITLE: Keto Start ACV Gummies:|Reviews Safe Money|Weight Loss Reviews|Price|Gummies and Official Store|
AUTHORS: garrick
[DESCRIPTION]
"Keto Start ACV Gummies
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.ejdbci6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol outlines the analysis used to plot MEGAN taxonomic assignments. Based on the methods from the following publication:<br /><br />Hannigan, Geoffrey D., et al. "The Human Skin Double-Stranded DNA Virome: Topographical and Temporal Diversity, Genetic Enrichment, and D... | [] |
45,710 | Coronavirus Lateral Flow Assay (LFA) sample preparation protocol v2 | 4 | dx.doi.org/10.17504/protocols.io.bqvnmw5e | https://www.protocols.io/view/coronavirus-lateral-flow-assay-lfa-sample-preparat-bqvnmw5e | peijun he | TITLE: Coronavirus Lateral Flow Assay (LFA) sample preparation protocol v2
AUTHORS: peijun he
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Coronavirus Lateral Flow Assay (LFA) sample preparation protocol</div></div>
[STEPS]
?. For each clinical sample to be processed, label 1 screwcap tube with ... | ["For each clinical sample to be processed, label 1 screwcap tube with the patient’s ID. Make aliquots of Lysis buffer in each tube.Lysis buffer: in 1x PBS\n300 µl\n[Triton X - 100]", "Take out the swabs out of the freezer immediately before the analysis. Leave to thaw at RT for and insert into the respective screw... |
59,632 | Workflow for human placental bulk ATACseq | 4 | dx.doi.org/10.17504/protocols.io.kxygxzyo4v8j/v1 | https://www.protocols.io/view/workflow-for-human-placental-bulk-atacseq-b6gqrbvw | Scott Lindsay-Hewett, Valentina Stanley, Mana Parast, Louise Laurent | TITLE: Workflow for human placental bulk ATACseq
AUTHORS: Scott Lindsay-Hewett, Valentina Stanley, Mana Parast, Louise Laurent
[DESCRIPTION]
Described here is the workflow used by the Female Reproductive Tissue Mapping Center at UCSD to generate bulk ATACseq data from human placenta.
[STEPS]
SECTION: Tissue prep... | ["[Tissue preparation] As soon as possible after Cesarean section or vaginal delivery, prepare tissue according to the following protocol:\n\n\nHuman Placenta Tissue Collection and Preservation Methods - UCSD Female Reproductive TMC\n\n\nFor this protocol, use tissue that has been snap-frozen.", "[Nuclei isolation] Iso... |
null | null | null | dx.doi.org/10.17504/protocols.io.na2dage | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Polyol dehydrogenases are enzymes that convert polyalcohols into sugars, using NAD<sup>+</sup> as hydrogen acceptor. Sorbitol, mannitol or other polyalcohols can be used as substrates and NADH is produced. In this assay, proteins are first separated by native polyacrylamide g... | [] |
22,575 | Euplotes crassus transfection using FuGene HD Transfection Reagent as vehicle (provisional) | null | dx.doi.org/10.17504/protocols.io.2apgadn | null | RACHELE CESARONI, Rachele Cesaroni | TITLE: Euplotes crassus transfection using FuGene HD Transfection Reagent as vehicle (provisional)
AUTHORS: RACHELE CESARONI, Rachele Cesaroni
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. Collect 4 x 104 well-fed Euplotes crassus cells (we used E.coli as the only food source) by centrifugation at 400 rc... | ["Collect 4 x 104 well-fed Euplotes crassus cells (we used E.coli as the only food source) by centrifugation at 400 rcf for 3 minutes.", "Wash the cells twice with artificial sea water (see attachment for the recipe) and once with 500 mM sorbitol, 0.5 mM Tris-HCl, pH 7.0 (400 rcf for 3 minutes each time). Then resuspen... |
null | null | null | dx.doi.org/10.17504/protocols.io.qh6dt9e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>A protocol for diatom DNA extraction used in the Limnological Institute SB RAS for freshwater diatoms.</p>
<p> </p>
[STEPS]
?.
?.
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.nkndcve | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol was used to determine when to collect sex biased samples for RNA extraction and establish expression profile throughout mealybug development.</p>
<p> </p>
<p>Sex ratio throughout oviposition was established first in Planococcus citri (Ross et al., 2010). We used... | [] |
18,765 | Maintenance of Undifferentiated hiPSC Cultures and Differentiation to Cardiomyocytes on Glass Surfaces | 1 | dx.doi.org/10.17504/protocols.io.wjmfck6 | https://www.protocols.io/view/maintenance-of-undifferentiated-hipsc-cultures-and-wjmfck6 | Angelique Nelson, Stephanie Dinh, Kaytlyn Gerbin, Melissa Hendershott, Caroline Hookway, Ruwanthi Gunawardane | TITLE: Maintenance of Undifferentiated hiPSC Cultures and Differentiation to Cardiomyocytes on Glass Surfaces
AUTHORS: Angelique Nelson, Stephanie Dinh, Kaytlyn Gerbin, Melissa Hendershott, Caroline Hookway, Ruwanthi Gunawardane
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "fon... | ["[Medium and vessel preparation ]\nPrepare fresh mTeSR1 medium for passaging hiPSCs:a. Thaw 5X supplement at, or at. Do not thaw 5X supplement at 37˚C.b. Combine 5X supplement with 400mL mTeSR1 and 5mL Pen/Strep.c. Sterile filter medium with a 0.22µM medium filter before first use.\n[for 4-6 hours]\n[overnight]", "[Me... |
21,731 | Immunoprecipitation assay | null | dx.doi.org/10.17504/protocols.io.zgbf3sn | null | Ning Zhang , Peng Gao | TITLE: Immunoprecipitation assay
AUTHORS: Ning Zhang , Peng Gao
[STEPS]
?. To harvest cells in nondenaturing conditions, remove media and rinse cells with ice cold 1×PBS
?. Remove PBS and add 0.5 ml ice cold cell lysis buffer to each plate(10cm) and incubate on ice for 5 min
?. native protein: Scrape cells off the pla... | ["To harvest cells in nondenaturing conditions, remove media and rinse cells with ice cold 1×PBS", "Remove PBS and add 0.5 ml ice cold cell lysis buffer to each plate(10cm) and incubate on ice for 5 min", "native protein: Scrape cells off the plate and transfer to microcentrifuge tubes. Keep on ice. Sonicate on ice 3 t... |
50,344 | Access to Source Data/Documents (Part 10 of Safety and Efficacy of Imatinib for Preserving Beta-Cell Function in New-onset Type 1 Diabetes Mellitus) | 1 | dx.doi.org/10.17504/protocols.io.bvegn3bw | https://www.protocols.io/view/access-to-source-data-documents-part-10-of-safety-bvegn3bw | Stephen.Gitelman , Jeffrey A. Bluestone | TITLE: Access to Source Data/Documents (Part 10 of Safety and Efficacy of Imatinib for Preserving Beta-Cell Function in New-onset Type 1 Diabetes Mellitus)
AUTHORS: Stephen.Gitelman , Jeffrey A. Bluestone
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is Part 10 of "Safety and Efficacy of Imat... | [] |
87,194 | Gewebesammlung Frischgewebe Nephrektomie | 1 | null | https://www.protocols.io/view/gewebesammlung-frischgewebe-nephrektomie-czd2x28e | Annika Fendler | TITLE: Gewebesammlung Frischgewebe Nephrektomie
AUTHORS: Annika Fendler
[DESCRIPTION]
Dieses Protokoll beschreibt die Schritte für die Sammlung von Frischgewebe, Gefriergewebe (Fresh-frozen), und Blut von Patienten mit Nierenzellkarzinom nach Nephrektomie.
Verwandte Dokumente:
Protokoll zur Blutaufarbeitung
[BEF... | ["[Gewebesammlung im Schnellschnitt] Nach Rückmeldung des Schnellschnitts geht eine Person zur Gewebeentnahme. \nTüte Niere und Stickstoffbehälter mitnehmen.\nArbeitsanleitung (siehe Abbildung) beachten.", "[Gewebesammlung im Schnellschnitt]", "[Gewebesammlung im Schnellschnitt] 3x 15 ml Falcons mit 10,2 ml Transportm... |
null | null | null | dx.doi.org/10.17504/protocols.io.e3jbgkn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><strong>Product description and procedure summary</strong>:</p>
<p>Target cells are either selected or depleted by incubating your sample with the biotin anti-human CD14 antibody (clone 63D3) followed by incubation with magnetic Streptavidin Nanobeads. The magnetically labele... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.g6nbzde | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><em>The following transformation protocol is designed for the insertion of linear DNA constructs into the nuclear genome of Skeletonema marinoi by non-homologous recombination.</em></p>
[STEPS]
?.
?.
?.
?.
?.
?.
?. | [] |
105,965 | Publishing Generic Organ Scaffold as a SPARC Dataset | 0 | dx.doi.org/10.17504/protocols.io.6qpvr8q72lmk/v3 | https://www.protocols.io/view/publishing-generic-organ-scaffold-as-a-sparc-datas-djqm4mu6 | Mabelle Lin, Hugh Sorby | TITLE: Publishing Generic Organ Scaffold as a SPARC Dataset
AUTHORS: Mabelle Lin, Hugh Sorby
[DESCRIPTION]
In this protocol, we will demonstrate how to prepare a generic organ scaffold for publication as a SPARC dataset using the Scaffold mapping tools. This protocol will ensure that a generic organ scaffold is made a... | ["Use the latest official version of the Scaffold mapping tools to generate your organ scaffold. Do not use a developer installation to generate a scaffold.", "Use the standard generic organ scaffold workflow to generate organ scaffold files. The workflow is installed by default with the mapping tools MAP Client instal... |
85,238 | Treatment of DNA with cisplatin | 4 | null | https://www.protocols.io/view/treatment-of-dna-with-cisplatin-cxgwxjxe | Martin O Pollard | TITLE: Treatment of DNA with cisplatin
AUTHORS: Martin O Pollard
[DESCRIPTION]
A protocol for treating Promega Human DNA with Cisplatin.
[GUIDELINES]
Dispose of excess cisplatin safely according to guidance received in SDS.
[STEPS]
SECTION: Treatment of DNA with Cisplatin
3. Pipette 8.811 µL of from stock tube at ... | ["[Treatment of DNA with Cisplatin] Pipette 8.811 µL of from stock tube at 227 µg/ml to a 1.8 mL Eppendorf tube to achieve 2 µg of DNA.", "[Treatment of DNA with Cisplatin] Add 7.27 µL of diluted cisplatin at 0.83 micromolar (µM) to the tube", "[Treatment of DNA with Cisplatin] Incubate for 960 min in the dark at 37 ... |
64,029 | BTI mobile plant phenotyping system: Image analysis protocol | 1 | dx.doi.org/10.17504/protocols.io.8epv59oz4g1b/v1 | https://www.protocols.io/view/bti-mobile-plant-phenotyping-system-image-analysis-car5sd86 | Li'ang Yu, Magdalena M Julkowska | TITLE: BTI mobile plant phenotyping system: Image analysis protocol
AUTHORS: Li'ang Yu, Magdalena M Julkowska
[DESCRIPTION]
This protocol is a part of BTI mobile plant phenotyping system (https://github.com/Leon-Yu0320/BTI-Plant-phenotyping). In this part, we'll introduce using jupyter book as an interactive user-fri... | ["[Package installation] Installation of packages required for analyiss\n\nJupyter notebook and plantCV are reuqired for analysis. Please refer https://jupyter.org/ for installating jupyter notebook and refer https://plantcv.readthedocs.io/en/stable/ for installing jupyter notebook. \n\nIn particular, we developed the... |
20,824 | Preparation of human Red Blood Cells for confocal imaging | null | dx.doi.org/10.17504/protocols.io.yjyfupw | null | Marie Anne Balanant | TITLE: Preparation of human Red Blood Cells for confocal imaging
AUTHORS: Marie Anne Balanant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is used to label red blood cells (RBC) for confocal imaging. Fluorescent beads are used to calibrate voxel size on the confocal microscope. The ... | ["[Imaging chamber]\nIn the center of the chamber, add of 4µm calibration beads, and let the slide dry in the dark\n2 µl", "[Imaging chamber]\nPrepare imaging chamber by using double-sided tape as a spacer between two coverslips : cut a square within the tape such as to form a frame. Without removing the non-adhesive ... |
91,583 | DToL Tissue and Blood Sampling Standard Operating Procedure: Chordata: Vertebrata (general) | 1 | dx.doi.org/10.17504/protocols.io.n92ldmjool5b/v1 | https://www.protocols.io/view/dtol-tissue-and-blood-sampling-standard-operating-c5n7y5hn | Inez Januszczak, Nancy Holroyd | TITLE: DToL Tissue and Blood Sampling Standard Operating Procedure: Chordata: Vertebrata (general)
AUTHORS: Inez Januszczak, Nancy Holroyd
[DESCRIPTION]
This Standard Operating Procedure (SOP) contains guidance on how to sample tissue and blood from Vertebrata specimens submitted to the Darwin Tree of Life (DToL) proj... | [] |
59,002 | Wastewater QC workflow in GalaxyTrakr (SSQuAWK2) | 1 | dx.doi.org/10.17504/protocols.io.b5u2q6ye | https://www.protocols.io/view/wastewater-qc-workflow-in-galaxytrakr-ssquawk2-b5u2q6ye | Jasmine Amirzadegan, Tunc Kayikcioglu, hugh.rand , Ruth Timme, Maria Balkey | TITLE: Wastewater QC workflow in GalaxyTrakr (SSQuAWK2)
AUTHORS: Jasmine Amirzadegan, Tunc Kayikcioglu, hugh.rand , Ruth Timme, Maria Balkey
[DESCRIPTION]
PURPOSE:
Step-by-step instructions for checking sequence quality for SARS-CoV-2 wastewater samples using SSQuAWK2: SARS - CoV - 2 Sequence Quality Assuranc... | ["[Account set up] Create a GalaxyTrakr account here: https://account.galaxytrakr.org/Account/Register", "[Account set up] Log into your GalaxyTrakr account: https://galaxytrakr.org", "[Create a new history] Create a new history. \n\nWe recommend creating a new history for each new MiSeq sequence set with details and d... |
28,157 | Priming and loading a MinION flowcell | null | dx.doi.org/10.17504/protocols.io.7q5hmy6 | null | Josh Quick | TITLE: Priming and loading a MinION flowcell
AUTHORS: Josh Quick
[STEPS]
?. Thaw the following reagents at room temperature before placing on ice: Sequencing buffer (SQB)Loading beads (LB)Flush buffer (FLB)Flush tether (FLT)
?. Add FLT to the FLB tube and mix well by vortexing.
30 µl
?. If required place a new MinIO... | ["Thaw the following reagents at room temperature before placing on ice: Sequencing buffer (SQB)Loading beads (LB)Flush buffer (FLB)Flush tether (FLT)", "Add FLT to the FLB tube and mix well by vortexing.\n30 µl", "If required place a new MinION flowcell onto the MinION by flipping open the lip and pushing one end of... |
42,236 | Study of MAIT Cell Activation in Viral Infections In Vivo | 2 | dx.doi.org/10.17504/protocols.io.bmg4k3yw | https://www.protocols.io/view/study-of-mait-cell-activation-in-viral-infections-bmg4k3yw | Timothy S C Hinks, Bonnie van Wilgenburg, Huimeng Wang, Liyen Loh, Marios Koutsakos, Katherine Kedzierska, Alexandra J. Corbett, Zhenjun Chen | TITLE: Study of MAIT Cell Activation in Viral Infections In Vivo
AUTHORS: Timothy S C Hinks, Bonnie van Wilgenburg, Huimeng Wang, Liyen Loh, Marios Koutsakos, Katherine Kedzierska, Alexandra J. Corbett, Zhenjun Chen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">MAIT cells are abundant, highly evol... | [] |
93,056 | Nigrostriatal organotypic cultures to study neuromelanin accumulation in dopaminergic circuits | 4 | dx.doi.org/10.17504/protocols.io.kxygx381wg8j/v1 | https://www.protocols.io/view/nigrostriatal-organotypic-cultures-to-study-neurom-c648zgzw | Mario Fernandez-Ballester, Federico N. Soria | TITLE: Nigrostriatal organotypic cultures to study neuromelanin accumulation in dopaminergic circuits
AUTHORS: Mario Fernandez-Ballester, Federico N. Soria
[DESCRIPTION]
In this protocol we describe the preparation and maintenance of rat organotypic cultures from parasagittal brain slices. We use a 13º slicing angle a... | ["[Culture preparation] Prepare a 6-well culture plate with Millipore 0.4 µm culture inserts (see Materials) placed on top of 1 mL of Pro-dopaminergic organotypic medium (see Materials) per well. Incubate it at 37 °C and 5% CO2 to warm up.", "[Culture preparation] Prepare a p100 petri dish with 25 mL of Hank’s Balanced... |
91,375 | Assembly: Chronic recoverable Neuropixels in mice | 1 | dx.doi.org/10.17504/protocols.io.eq2lynnewvx9/v8 | https://www.protocols.io/view/assembly-chronic-recoverable-neuropixels-in-mice-c5gpy3vn | Emily A Aery Jones | TITLE: Assembly: Chronic recoverable Neuropixels in mice
AUTHORS: Emily A Aery Jones
[DESCRIPTION]
This protocol collection explains how to build a low-cost, lightweight system to implant 1 Neuropixels 1.0 probe or 2 Neuropixels 2.0 probes into mice, record during freely moving behavior, then recover the probes for fu... | ["[3D print components] Single 1.0 probe: Build a print file for the following pieces per mouse: 1 each of body piece, back and front flex cable holders, and dome, plus 2 wings. \n\nDual 2.0 probes: Build a print file for the following pieces per mouse: 1 each of left body, right body, flex holder 1, flex holder 2 wit... |
19,250 | Technological advancements in image processing and analysis for label-free investigations of bone marrow stromal cell behavior | null | dx.doi.org/10.17504/protocols.io.w2sfgee | null | Deena Rennerfeldt, Pristinavae Manning, Joana S. Raminhos, Krystyn J. Van Vliet | TITLE: Technological advancements in image processing and analysis for label-free investigations of bone marrow stromal cell behavior
AUTHORS: Deena Rennerfeldt, Pristinavae Manning, Joana S. Raminhos, Krystyn J. Van Vliet
[STEPS]
?. | [] |
32,559 | Incidence and etiology of chronic pulmonary infections in patients with idiopathic pulmonary fibrosis | null | dx.doi.org/10.17504/protocols.io.bb2piqdn | null | Kyuto Odashima, Naho Kagiyama, Tetsu Kanauchi, Takashi Ishiguro, Noboru Takayanagi | TITLE: Incidence and etiology of chronic pulmonary infections in patients with idiopathic pulmonary fibrosis
AUTHORS: Kyuto Odashima, Naho Kagiyama, Tetsu Kanauchi, Takashi Ishiguro, Noboru Takayanagi
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:left"><s... | [] |
36,451 | Crossposting test 2 | null | dx.doi.org/10.17504/protocols.io.bfubjnsn | https://www.protocols.io/view/crossposting-test-2-bfubjnsn | Maxim Fisher, Monica Hassan | TITLE: Crossposting test 2
AUTHORS: Maxim Fisher, Monica Hassan
[STEPS] | [] |
85,976 | Chromogenic in situ hybridisation | 4 | null | https://www.protocols.io/view/chromogenic-in-situ-hybridisation-cx7yxrpw | 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... |
56,579 | Protocol for harvesting and dissociating mouse brain neurons for single cell RNA Sequencing on the 10X Genomics platform | 4 | dx.doi.org/10.17504/protocols.io.q26g74by3gwz/v1 | https://www.protocols.io/view/protocol-for-harvesting-and-dissociating-mouse-bra-b3hbqj2n | Viktor Feketa, Elena O. Gracheva | TITLE: Protocol for harvesting and dissociating mouse brain neurons for single cell RNA Sequencing on the 10X Genomics platform
AUTHORS: Viktor Feketa, Elena O. Gracheva
[DESCRIPTION]
Single-cell RNA sequencing has emerged as a powerful method to characterize gene expression on a single cell level. Producing useful ... | ["[Part 1: Advance preparation of solutions] Prepare stock solutions of media supplements", "[Part 1: Advance preparation of solutions] Lactic acid: prepare 1 Molarity (M) (90 mg/mL) solution of lactic acid in nuclease-free water and aliquot in50 µL aliquots. Store at -20 °C.", "[Part 1: Advance preparation of solutio... |
56,967 | Nuclear extraction from endometrial tumors for single nuclei sequencing | 1 | dx.doi.org/10.17504/protocols.io.b3vfqn3n | https://www.protocols.io/view/nuclear-extraction-from-endometrial-tumors-for-sin-b3vfqn3n | gracefoley | TITLE: Nuclear extraction from endometrial tumors for single nuclei sequencing
AUTHORS: gracefoley
[DESCRIPTION]
Modified from: Slyper, M. et al. A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors. Nat. Med. 2020 26526, 792–802 (2020).
A optimized protocol for nuclear extraction fr... | ["Place frozen tissue in a well of a 6 well plate containing 1 mL of cold NST disassociation buffer.", "Chop tissue using a scalpel until mostly homogenized", "Incubate solution on ice for 5 minutes", "Filter the homogenized solution through a 40 uM falcon cell strainer into a 50 mL falcon tube", "Use an additional 1 m... |
null | null | null | dx.doi.org/10.17504/protocols.io.ex6bfre | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol describes how to wash QCM-D sensors before usage and how to modify their surface using a composition of symmetric (poly)ethylene glycol (PEG) thiols consisting of 99% dS-PEG and 1% dS-PEG-biotin.
[BEFORE_START]
<br /><br /><br /><br /><br /><br /><br /><br /><br /... | [] |
63,926 | Via Keto Capsules FR Reviews, Side Effects, Ingredients 2022 | 1 | dx.doi.org/10.17504/protocols.io.rm7vzy2w2lx1/v1 | https://www.protocols.io/view/via-keto-capsules-fr-reviews-side-effects-ingredie-canwsdfe | viaketocapsulesreviews | TITLE: Via Keto Capsules FR Reviews, Side Effects, Ingredients 2022
AUTHORS: viaketocapsulesreviews
[DESCRIPTION]
Via Keto Capsules FR Reviews, Side Effects, Ingredients 2022
[STEPS]
1. Via Keto Capsules FR Reviews, Side Effects, Ingredients 2022
Via Keto Capsules- In moment's world, everyone is trapped in the vic... | ["Via Keto Capsules FR Reviews, Side Effects, Ingredients 2022\nVia Keto Capsules- In moment's world, everyone is trapped in the vicious cycle of life where they don't get time for their particular life. Everyone is busy working hard to earn a good living and they tend to forget that the body is the biggest asset of th... |
59,544 | Nuclei isolation from snap-frozen human placental tissue for bulk ATACseq | 1 | dx.doi.org/10.17504/protocols.io.kqdg3p2kel25/v1 | https://www.protocols.io/view/nuclei-isolation-from-snap-frozen-human-placental-b6dyra7w | Scott Lindsay-Hewett | TITLE: Nuclei isolation from snap-frozen human placental tissue for bulk ATACseq
AUTHORS: Scott Lindsay-Hewett
[DESCRIPTION]
This protocol describes the isolation of nuclei from snap-frozen human placental tissue for bulk ATACseq. It is a modified version of a protocol (SCBL Protocols - 10x Multiome Nuclei Isolation... | ["[Preparation] Pre-chill microfuge to 4 °C.", "[Preparation] Prepare bucket of ice, and chill metal plate (allows for a flat surface to place Petri dish on top of - to keep tissue cool while cutting).", "[Preparation] Thaw 110 µL aliquot of 100 millimolar (mM) and place on ice.", "[Make fresh buffers] Prepare 1 mL as ... |
101,022 | Library Bottlenecking Protocols | 0 | dx.doi.org/10.17504/protocols.io.x54v9227pl3e/v1 | https://www.protocols.io/view/library-bottlenecking-protocols-dev63e9e | David Ross | TITLE: Library Bottlenecking Protocols
AUTHORS: David Ross
[DESCRIPTION]
Protocol for bottlenecking a variant library for downstream use in the Pooled, Growth-Based Assay pipeline using either a positive-displacement flow cytometer or basic microbial culture equipment.
[STEPS]
SECTION: Create the first overnight cul... | ["[Create the first overnight culture] Dilute a full 1 mL vial of the library glycerol stock into 50 mL of media in a 250 mL baffled flask.", "[Prepare all flasks and tubes] One new 250-mL baffled flask with 50 mL media. \nThis is the final flask", "[Prepare all flasks and tubes] Six 15 mL snap-cap culture tubes, each ... |
93,742 | Concentration and nucleic acid extraction of viruses from wastewater primary sludge | 4 | dx.doi.org/10.17504/protocols.io.36wgq3k1xlk5/v1 | https://www.protocols.io/view/concentration-and-nucleic-acid-extraction-of-virus-c7snznde | Ari N Machtinger, Olivia S Hershey, William J Bradshaw, Emily H Soice, Daniel P Rice, Michael R McLaren | TITLE: Concentration and nucleic acid extraction of viruses from wastewater primary sludge
AUTHORS: Ari N Machtinger, Olivia S Hershey, William J Bradshaw, Emily H Soice, Daniel P Rice, Michael R McLaren
[DESCRIPTION]
This protocol details our workflow for performing concentration and total nucleic acid extraction fro... | ["[Reagent Preparation] Prepare a 1 % volume Tween 20 stock solution. For a 500 mL stock, combine 5 mL of Tween 20 with 495 mL of 1X PBS. Filter sterilize with a 0.22 um vacuum filtration unit.", "[Part 1: Sludge Handling, Dissociation, Centrifugation, Filtration] Transfer sludge sample (within secondary container) fro... |
28,193 | Protocol for Exonuclease III (NEB #M0206) | 1 | null | https://www.protocols.io/view/protocol-for-exonuclease-iii-neb-m0206-7r9hm96 | New England Biolabs | TITLE: Protocol for Exonuclease III (NEB #M0206)
AUTHORS: New England Biolabs
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Exonuclease III efficiently degrades nicked and linear dsDNA (with blunt or 5' overhangs) from 3' to 5' direction, leaving supercoiled dsDNA intact.*</div><div class = "text-... | ["Set-up the reaction as follows: AB1COMPONENTS50 μl REACTION2 DNA up to 5 μg3 NEBuffer 1 (10x) 5 μl (1X)4 Exonuclease III 0.5 μl (50 units)5 Nuclease-free H2O up to 50 μl\nAB1COMPONENTS50 μl REACTION2 DNA up to 5 μg3 NEBuffer 1 (10x) 5 μl (1X)4&nbs... |
57,183 | Studying yawning behavior in preterm neonates before and after feeding | 1 | dx.doi.org/10.17504/protocols.io.b337qqrn | https://www.protocols.io/view/studying-yawning-behavior-in-preterm-neonates-befo-b337qqrn | Damiano Menin, Marco Dondi | TITLE: Studying yawning behavior in preterm neonates before and after feeding
AUTHORS: Damiano Menin, Marco Dondi
[DESCRIPTION]
This protocol can be used to study yawning behavior in preterm neonates hospitalized in NICUs.
[STEPS]
SECTION: Exclusion criteria
1. Exclusion criteria: Gestational Age ≥ 37 weeks; Congeni... | ["[Exclusion criteria] Exclusion criteria: Gestational Age ≥ 37 weeks; Congenital anomalies, heart or metabolic disorders, fetal infections, clear teratogenic factors, Apgar at five minutes < 6 and grade III or IV hemorrhages.", "[Procedure] Neonates for whom consent was obtained from parents should be observed two tim... |
26,697 | Plate Pouring | null | dx.doi.org/10.17504/protocols.io.6bhhaj6 | null | Priota Islam | TITLE: Plate Pouring
AUTHORS: Priota Islam
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">C. elegans is maintained in the laboratory on Nematode Growth Medium (NGM) agar which has been aseptically poured into petri plates. Smaller plates (35 mm diameter) are useful for mating or when using expensiv... | ["[Preparation of the Hood]\nSterilize the hood with EthanolCount the number of plates to be poured and stack them inside the hood (A stack of 10 or 5 depending on convenience), See Figure 1. Volumes to be poured for different sized plates are: Large plates 90mm: 35 mL – possible with 8mm tubing ... |
94,201 | PROTOCOL for “Systemic inflammation triggers long-lasting neuroinflammation and accelerates neurodegeneration in a rat model of Parkinson’s disease overexpressing human α-synuclein” | 2 | dx.doi.org/10.17504/protocols.io.j8nlkoj65v5r/v1 | https://www.protocols.io/view/protocol-for-systemic-inflammation-triggers-long-l-c78zzrx6 | mariangela.massarocenere, Valerio Chiurchiù, Nicola Biagio Mercuri | TITLE: PROTOCOL for “Systemic inflammation triggers long-lasting neuroinflammation and accelerates neurodegeneration in a rat model of Parkinson’s disease overexpressing human α-synuclein”
AUTHORS: mariangela.massarocenere, Valerio Chiurchiù, Nicola Biagio Mercuri
[DESCRIPTION]
Methodological collection for characteri... | [] |
73,399 | Quantitation of Eight Anticoagulant Rodenticides in Liver | 6 | dx.doi.org/10.17504/protocols.io.14egn26w6g5d/v1 | https://www.protocols.io/view/quantitation-of-eight-anticoagulant-rodenticides-i-cjwxupfn | megan.romano | TITLE: Quantitation of Eight Anticoagulant Rodenticides in Liver
AUTHORS: megan.romano
[DESCRIPTION]
Target analytes comprised two chemical classes: hydroxycoumarins (warfarin, coumachlor, dicoumarol, bromadiolone, brodifacoum, and difethialone) and indanediones (diphacinone and chlorophacinone).Liver extracts were cl... | ["[Prepare Solutions] 10 % (v/v) Methanol in Acetonitrile: Dilute 25 mL methanol to 250 mL with acetonitrile.", "[Prepare Solutions] Primary Stock Solutions – 1000 ug/mL: For each anticoagulant rodenticide, dissolve 5.0 mg standard reference material in 5 mL of the appropriate solvent (see Table 1), using a 5-mL volume... |
103,347 | Immunohistochemistry for anti-GFP | 0 | dx.doi.org/10.17504/protocols.io.eq2lywe8pvx9/v1 | https://www.protocols.io/view/immunohistochemistry-for-anti-gfp-dg6t3zen | Lauren C. Faget, Thomas Hnasko | TITLE: Immunohistochemistry for anti-GFP
AUTHORS: Lauren C. Faget, Thomas Hnasko
[DESCRIPTION]
Hnasko lab protocol for anti-GFP immunohistochemistry
[STEPS]
SECTION: Protocol:
1. Day 1
SECTION: Protocol:
1.1. Wash with 1X PBS (Phosphate Buffered Saline, 10X solution, Fisher bioreagents, BP399-1) pH 7.4 5 min
SE... | ["[Protocol:] Day 1", "[Protocol:] Wash with 1X PBS (Phosphate Buffered Saline, 10X solution, Fisher bioreagents, BP399-1) pH 7.4 5 min", "[Protocol:] Wash with 1X PBS containing 0.2% Triton X-100 (Sigma-Aldrich, X100-1L) (PBS-T). 5 min", "[Protocol:] Blocking step with appropriate normal serum (use serum from the sou... |
26,998 | Zona pellucida removal using Acid Tyrode solution and snap freezing | null | dx.doi.org/10.17504/protocols.io.6kwhcxe | null | Elizabeth Jannaman, Peter J. Hansen | TITLE: Zona pellucida removal using Acid Tyrode solution and snap freezing
AUTHORS: Elizabeth Jannaman, Peter J. Hansen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">A simple protocol to remove the zona pellucida from bovine embryos. This is a necessary step before freezing embryos for analysis o... | [] |
37,912 | UABMC - PDX Dissection Protocol | 4 | null | https://www.protocols.io/view/uabmc-pdx-dissection-protocol-bg9yjz7w | Christopher Willey | TITLE: UABMC - PDX Dissection Protocol
AUTHORS: Christopher Willey
[STEPS]
?. [TUMOR HARVEST]
Select 1 to 2 mice that have tumors that measure no more than 8-10mm in greatest diameter, are not ulcerated and appear to have grown in a consistent fashion.
This must be done aseptically using sterile surgical techniques
?.... | ["[TUMOR HARVEST]\nSelect 1 to 2 mice that have tumors that measure no more than 8-10mm in greatest diameter, are not ulcerated and appear to have grown in a consistent fashion.\nThis must be done aseptically using sterile surgical techniques", "[TUMOR HARVEST]\nEuthanize one mouse at a time with CO2 asphyxiation in de... |
34,635 | Mask Building Idea | null | dx.doi.org/10.17504/protocols.io.bd3ji8kn | null | Erica Wells | TITLE: Mask Building Idea
AUTHORS: Erica Wells
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Our limited findings</span><span>: This “DIY folding mask” tries to replicate some of the benefits of a n95 mask. It has been saccharin tested by several nurses and an NP.... | ["Make your pattern. Cut out your first set and use them for tracing. No need for perfection. The felt is around 9 x 12 inches. It's not wildly important that the measurements are exact. It's the shapes really. As long as it fits your face.", "Glue bottom to front. Match up curved edges.", "Glue top to front so that it... |
24,356 | Poly-d lysine coating slides | null | dx.doi.org/10.17504/protocols.io.32cgqaw | null | Grace Burgin | TITLE: Poly-d lysine coating slides
AUTHORS: Grace Burgin
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">coating standard blank slides with poly-d lysine to increase adhesion of tissue </div></div>
[STEPS]
?. Make .3mg/ml in 0.1M borate buffer [ → add 16.67 ml 0.1M borate to 5mg bottle of poly-D l... | ["Make .3mg/ml in 0.1M borate buffer [ → add 16.67 ml 0.1M borate to 5mg bottle of poly-D lysine lyophylized powder]", "coat the slides once by dipping", "Dry", "Rinse twice with dH20", "Dry"] |
70,189 | DNA extraction | 1 | null | https://www.protocols.io/view/dna-extraction-cgsmtwc6 | lilyli | TITLE: DNA extraction
AUTHORS: lilyli
[DESCRIPTION]
A protocol for DNA extraction
[STEPS]
1. Grind samples
2. add solution | ["Grind samples", "add solution"] |
106,654 | Expression and purification of bacterial proteins (via N-terminal His-tag) | 0 | dx.doi.org/10.17504/protocols.io.261ge514yg47/v1 | https://www.protocols.io/view/expression-and-purification-of-bacterial-proteins-dkd64s9e | Verena Dederer, Sebastian Mathea, Stefan Knapp | TITLE: Expression and purification of bacterial proteins (via N-terminal His-tag)
AUTHORS: Verena Dederer, Sebastian Mathea, Stefan Knapp
[DESCRIPTION]
Recombinant protein production in bacteria provides an efficient system for obtaining high yields in a short time and at low cost. Although not every protein is suita... | ["[Plamid Transformation into E.coli Rosetta cells] Thaw 10 µL E.coli Rosetta cells gently on ice", "[Large Scale Protein Expression (4L)] Next morning, dilute grown overnight culture 10 mL into 1000 mL terrific broth expression medium containing the appropriate antibiotic", "[Large Scale Protein Expression (4L)] From ... |
106,284 | NEBNext® Poly(A) mRNA Magnetic Isolation Module NEB #E7490S/L (Standard Protocol) | 0 | dx.doi.org/10.17504/protocols.io.yxmvmeb55g3p/v1 | https://www.protocols.io/view/nebnext-poly-a-mrna-magnetic-isolation-module-neb-dj2k4qcw | Isabel Gautreau | TITLE: NEBNext® Poly(A) mRNA Magnetic Isolation Module NEB #E7490S/L (Standard Protocol)
AUTHORS: Isabel Gautreau
[DESCRIPTION]
The NEBNext Poly(A) mRNA Magnetic Isolation Module is designed to isolate intact poly(A)+ RNA from previously isolated total RNA. The technology is based on the coupling of Oligo d(T)25 to 1 ... | ["[Starting Material: 1–5 μg* of DNA-free total RNA (Standard Protocol)] Dilute the total RNA with nuclease-free water to a final volume of 50 µL in a nuclease-free 0.2 ml PCR tube and keep on ice.", "[Starting Material: 1–5 μg* of DNA-free total RNA (Standard Protocol)] To wash the NEBNext Oligo d(T)25 Beads, add the ... |
24,618 | Bacterial Media Preparation | null | dx.doi.org/10.17504/protocols.io.4aigsce | null | Andrew Crowley | TITLE: Bacterial Media Preparation
AUTHORS: Andrew Crowley
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol for the preparation of bacterial culture and recovery media, with options for several types of antibiotics.</div><div class = "text-block">Default scale - 1 L</div></div>
[STEPS]
?. A... | ["Add powdered LB ( ) to deionized water ( )\n25 g\n1 L\nn.b.Particulates may remain after addition, but these will dissolve during the autoclave cycle", "Autoclave using liquid cycle", "Allow media to cool to\n50 °C", "Select antibiotic from the list below:", "Add kanamycin and mix thoroughly\n50 mg", "Add ampicilli... |
56,060 | Cleanbox UV-C sterilization chamber | 1 | null | https://www.protocols.io/view/cleanbox-uv-c-sterilization-chamber-b2y4qfyw | Ryan Straight | TITLE: Cleanbox UV-C sterilization chamber
AUTHORS: Ryan Straight
[DESCRIPTION]
Using the Cleanbox CX2 UV-C sterilization chamber.
[STEPS]
1. Ensure the Cleanbox is powered on. (Green light in front will be lit.)
2. Insert the item to be sterilized into the Cleanbox. For headsets, hang using the headstrap from the... | ["Ensure the Cleanbox is powered on. (Green light in front will be lit.)", "Insert the item to be sterilized into the Cleanbox. For headsets, hang using the headstrap from the platform inside the chamber, so the lens portion is hanging down. If the equipment you're cleaning is wired, run the wires through the small hol... |
30,852 | Quantitative analysis method of mRNA expression using dual RNA in situ hybridization by comparison with housekeeping genes | null | dx.doi.org/10.17504/protocols.io.badcia2w | null | Byung Joon Seung | TITLE: Quantitative analysis method of mRNA expression using dual RNA in situ hybridization by comparison with housekeeping genes
AUTHORS: Byung Joon Seung
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">In retrospective formalin-fixed paraffin-embedded (FFPE) samples, RNA quality of FFPE tissues sh... | ["[RNA-ISH original image]\nRNA-ISH images were acquired at ×400 magnification.", "[Counting the blue dots]\nThe original images were converted using Fiji program [1].[1] Schindelin J, Arganda-Carreras I, Frise E, Kaynig V, Longair M, Pietzsch T, et al. Fiji: an open-source platform for biological-image analysis. Nat M... |
102,306 | Crystallisation protocol for SARS-CoV-2 nsp3 macrodomain in P1 21 1 | 1 | dx.doi.org/10.17504/protocols.io.261ge5ej7g47/v1 | https://www.protocols.io/view/crystallisation-protocol-for-sars-cov-2-nsp3-macro-df6a3rae | Jasmin Aschenbrenner, Peter Marples, Lizbé Koekemoer, Charlie Tomlinson, Daren Fearon | TITLE: Crystallisation protocol for SARS-CoV-2 nsp3 macrodomain in P1 21 1
AUTHORS: Jasmin Aschenbrenner, Peter Marples, Lizbé Koekemoer, Charlie Tomlinson, Daren Fearon
[DESCRIPTION]
The COVID-19 pandemic has demonstrated the need for novel therapeutic interventions and improved pandemic preparedness strategies again... | ["[Crystallization experiment] Protein and buffer requirements:\n115.2 µL21.6 mg/mL \n2.88 mL \n28.8 µL seeds, dilution 1:2", "[Crystallization experiment] Dispense 30 µL into SwissCI 3 lens plate reservoir wells using a 100 µl multi-channel pipette.\nDispense 400 nL21.6 mg/mL to each lens using the SPT mosquito.... |
43,469 | UCSC_Genome_Browser_and_BLAST_protocol | 5 | null | https://www.protocols.io/view/ucsc-genome-browser-and-blast-protocol-bnpmmdk6 | , | TITLE: UCSC_Genome_Browser_and_BLAST_protocol
AUTHORS: ,
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">In this lab, students will work through BLAST and the UCSC Genome browser to find and analyze information about their genes of interest. </div></div>
[STEPS]
?. [Setup: UCSC Genome Browser]
G... | ["[Setup: UCSC Genome Browser]\nGenome BrowserThe browser offers a variety of interfaces that can be used to explore reference genomic data including the current reference human genome (Hg38), reference RNA expression databases, and SARS-CoV-2 reference genomes and phylogenies.Goals + Motivation: Molecular biology, gen... |
25,798 | Long-read DNA preparation for metagenomic samples | null | dx.doi.org/10.17504/protocols.io.5feg3je | null | Christian Brandt | TITLE: Long-read DNA preparation for metagenomic samples
AUTHORS: Christian Brandt
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">General:</span></div><div class = "text-block">This is an DNA isolation protocol adapted to the properties of sludge samples from bioga... | ["[Sample pre preparation]\nAdd 1 ml of homogenic sludge/substrate via 10 ml syringe (without needle) to a 2 ml tube\n[sludge/substrate]", "[Sample pre preparation]\nCentrifuge for 5 min at 20,000g and remove supernatant", "[Cell Lysis]\nTransfer sample to lysing matrix E tube and add 778 µl sodium phosphate buffer\n[s... |
47,509 | Polymer-brush-bilayers-under-stationary-shear-motion-at-linear-response-regime | 1 | dx.doi.org/10.17504/protocols.io.bsmvnc66 | https://www.protocols.io/view/polymer-brush-bilayers-under-stationary-shear-moti-bsmvnc66 | Mike Edwards | TITLE: Polymer-brush-bilayers-under-stationary-shear-motion-at-linear-response-regime
AUTHORS: Mike Edwards
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Statistical mechanics is employed to tackle the problem of polymer brush bilayers under stationary shear motion. The article addresses, s... | [] |
79,039 | HV-CTAB-PCI DNA Extraction Protocol | 1 | dx.doi.org/10.17504/protocols.io.n2bvj818ngk5/v1 | https://www.protocols.io/view/hv-ctab-pci-dna-extraction-protocol-cre7v3hn | Vicky Ooi, Lee McMichael, Margaret E. Hunter, Aristide Takoukam Kamla, Janet M. Lanyon | TITLE: HV-CTAB-PCI DNA Extraction Protocol
AUTHORS: Vicky Ooi, Lee McMichael, Margaret E. Hunter, Aristide Takoukam Kamla, Janet M. Lanyon
[DESCRIPTION]
Non-invasively collected faecal samples are an alternative source of DNA to tissue samples, that may be used in genetic studies of wildlife when direct sampling of an... | ["[Disinfection of working bench] Clean the working bench with TriGene disinfectant.", "[Faecal Sampling and Processing] Scrape 1 g of faecal material from the outer surface of a faeces and put it into a 15 mL centrifuge tube. \n\n1 g", "[Faecal Sampling and Processing] Transfer the faecal material into a mortar and gr... |
76,363 | Preparation and transformation of chemically hyper-competent Escherichia coli | 4 | null | https://www.protocols.io/view/preparation-and-transformation-of-chemically-hyper-cntjvekn | Andreas Sagen | TITLE: Preparation and transformation of chemically hyper-competent Escherichia coli
AUTHORS: Andreas Sagen
[DESCRIPTION]
Based on a protocol produced by Liu, et al.
Liu, Chang, W., Pan, L., Liu, X., Su, L., Zhang, W., Li, Q., & Zheng, Y. (2018). An Improved Method of Preparing High Efficiency Transformation Escheric... | ["[Preparation of CRM transformation buffer] In a sterile flask, add 200 mL distilled water", "[Transformation] Quickly thaw a single reaction tube with 100 µL hyper-competent cells in CRM-DMSO", "[Preparation of CRM transformation buffer] Measure 2.5 mL (1 Molarity (M)) PIPES, 2.177 g Manganese(II) chloride tetrahydra... |
93,149 | High-throughput workflow for the genotypic characterization of transposon insertion library variants | 4 | dx.doi.org/10.17504/protocols.io.kqdg394jzg25/v2 | https://www.protocols.io/view/high-throughput-workflow-for-the-genotypic-charact-c675zhq6 | Lorea Alejaldre, Ana Mariya Anhel, Lewis Grozinger, Ángel Goñi-Moreno | TITLE: High-throughput workflow for the genotypic characterization of transposon insertion library variants
AUTHORS: Lorea Alejaldre, Ana Mariya Anhel, Lewis Grozinger, Ángel Goñi-Moreno
[DESCRIPTION]
This is a workflow for the genotypic characterization of transposon library variants. It has been developed using an o... | ["[Colony picking in selective media] Dispense 100 µL of selective media (M9-citrate for P. putida or Luria-Bertani plus 20 ng/µL nalidixic acid for DH5α E. coli) plus transposon cassette antiobiotic in a 96-well plate", "[Counter-selection and glycerol stocks pre-cultures] Inoculation of counter-selection plate in sel... |
28,406 | MojoSort™ Human Pan Monocyte Isolation Kit Protocol | null | dx.doi.org/10.17504/protocols.io.7ywhpxe | null | Sam Li | TITLE: MojoSort™ Human Pan Monocyte Isolation Kit 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>This kit is designed for the isolation of untouched pan monocytes from PBMC. Target cel... | ["[Platelet Removal Protocol]\nDilute blood with 2-4 times (volume/volume) 1X PBS.", "[Platelet Removal Protocol]\nCarefully layer diluted blood over 12.5mL of isolation medium in a 50mL tube.", "[Platelet Removal Protocol]\nCentrifuge at 400xg for 25 minutes at room temperature in a swinging-bucket rotor without the b... |
30,605 | Embedding and freezing fresh human tissue in OCT using isopentane | null | dx.doi.org/10.17504/protocols.io.95mh846 | null | Kenny Roberts, Liz Tuck | TITLE: Embedding and freezing fresh human tissue in OCT using isopentane
AUTHORS: Kenny Roberts, Liz Tuck
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">For many cutting-edge spatial transcriptomic analysis methods, it is essential to prepare and store tissue in a manner that preserves RNA integrit... | ["[Pre-embedding and freezing (fixed frozen only)]\nFor tissues that are to be fixed prior to freezing, transfer tissues to 10% neutral-buffered formalin (such as a CellStor Pot) and fix at 4°C or room temperature for between 2 and 36 hours, depending upon the tissue and application.", "[Pre-embedding and freezing (fix... |
null | null | null | dx.doi.org/10.17504/protocols.io.dbq2mv | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
<strong>YTSS</strong> <br /> per 500 ml<br />
<table>
<tbody>
<tr>
<td> </td>
<td><strong>1/2</strong></td>
<td><strong>1/10</strong></td>
</tr>
<tr>
<td>Trypton</td>
<td>1.25 g</td>
<td... | [] |
86,332 | Protocol to isolate and fix nuclei from flash frozen mouse liver for IGVF | 4 | null | https://www.protocols.io/view/protocol-to-isolate-and-fix-nuclei-from-flash-froz-cyi4xugw | Elisabeth Rebboah | TITLE: Protocol to isolate and fix nuclei from flash frozen mouse liver for IGVF
AUTHORS: Elisabeth Rebboah
[DESCRIPTION]
This protocol describes isolation of nuclei from 10 week old whole mouse livers from 8 founder strains (B6J, AJ, 129S1J, NZOJ, WSBJ, NODJ, PWKJ, and CASTJ), preparation of a single nucleus suspensi... | ["[Setup] Coat SHARE-seq nuclei prep tubes with BSA. Fill 8 1.5 ml tubes with 1.5 ml 1% BSA in H2O and incubate for 30 minutes. After incubation, aspirate BSA solution and dry for 30 minutes. Store at 4C.", "[Setup] Label tubes.", "[Setup] Pre-chill centrifuge to 4C.", "[Setup] Prepare ice buckets.", "[Setup] Prepare l... |
70,512 | Drosophila small RNA isolation | 1 | dx.doi.org/10.17504/protocols.io.yxmvm2xpog3p/v1 | https://www.protocols.io/view/drosophila-small-rna-isolation-cg4qtyvw | Rosalyn M. Fey, Eileen S. Chow, Barbara O. Gvakharia, Jaga Giebultowicz, David A. Hendrix | TITLE: Drosophila small RNA isolation
AUTHORS: Rosalyn M. Fey, Eileen S. Chow, Barbara O. Gvakharia, Jaga Giebultowicz, David A. Hendrix
[DESCRIPTION]
Drosophila small RNA sequencing samples are often overwhelmed by the abundant 30-nucleotide 2S rRNA fragment. Small RNA of interest can be isolated from total RNA witho... | ["[Reagents Needed] Cleaning:\nRNase Away spray\n3% hydrogen peroxide\n70% ethanol\n\nGel:\nnuclease-free (NF) water\nagar\nultrapure urea\n40% polyacrylamide (19:1 acrylamide:bis-acrylamide) (Bio-Rad #1610144)\nTEMED \n10% ammonium persulfate (APS)\n10X TBE buffer\nZymo small RNA ladder (17, 21, 25, 29 nt bands) (Zymo... |
36,681 | Personality disorder in an Early Intervention Psychosis cohort: Findings from the Social Epidemiology of Psychoses in East Anglia (SEPEA) study | 1 | dx.doi.org/10.17504/protocols.io.bf3hjqj6 | https://www.protocols.io/view/personality-disorder-in-an-early-intervention-psyc-bf3hjqj6 | Ka-young Ban, D Osborn, Y Hameed, S Pandey, J Perez, PB Jones, JB Kirkbride | TITLE: Personality disorder in an Early Intervention Psychosis cohort: Findings from the Social Epidemiology of Psychoses in East Anglia (SEPEA) study
AUTHORS: Ka-young Ban, D Osborn, Y Hameed, S Pandey, J Perez, PB Jones, JB Kirkbride
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Aim: Personality... | [] |
45,070 | Approximating silica uptake in diatoms using PDMPO and flow cytometry | 4 | dx.doi.org/10.17504/protocols.io.x54v9jpdqg3e/v1 | https://www.protocols.io/view/approximating-silica-uptake-in-diatoms-using-pdmpo-bp9nmr5e | Phoebe Argyle, Jana Hinners, Nathan G. Walworth, Sinead Collins, Naomi M. Levine, Martina A. Doblin | TITLE: Approximating silica uptake in diatoms using PDMPO and flow cytometry
AUTHORS: Phoebe Argyle, Jana Hinners, Nathan G. Walworth, Sinead Collins, Naomi M. Levine, Martina A. Doblin
[DESCRIPTION]
A protocol to quantify relative change in uptake of silica by diatoms using the proxy stain PDMPO.
This protocol is ba... | ["[Sample culture and fix for cell counts] Take a 200 µL aliquot of each experimental culture/well (if growing in well-plates) and transfer into a 96 well round-bottomed plate to count via flow cytometry (see step 6).", "[Initiate the assay] Transfer 2 500 µL aliquots of culture into a 48-well tissue culture plate. On... |
42,552 | Flow cytometry analysis of mouse islet cell expression of heparan sulfate (HS), heparan sulfate proteoglycans (HSPGs) and heparanase (HPSE) | 1 | dx.doi.org/10.17504/protocols.io.bmsyk6fw | https://www.protocols.io/view/flow-cytometry-analysis-of-mouse-islet-cell-expres-bmsyk6fw | Sarah Popp, Sarita Dhounchak, Charmaine Simeonovic | TITLE: Flow cytometry analysis of mouse islet cell expression of heparan sulfate (HS), heparan sulfate proteoglycans (HSPGs) and heparanase (HPSE)
AUTHORS: Sarah Popp, Sarita Dhounchak, Charmaine Simeonovic
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Isolated mouse islets were dispersed into si... | ["See Guidelines, “Before starting” .", "Transfer isolated mouse islets to a 15 ml tube and remove excess medium using a Pasteur pipette. Resuspend in ~10-15 ml PBS/3mM EDTA. Centrifuge at 249g.", "Resuspend the islets in PBS/3mM EDTA. Centrifuge at 249g then carefully remove the supernatant.", "Gently resuspend each p... |
89,222 | Bulk RNASeq Delivery | 5 | dx.doi.org/10.17504/protocols.io.rm7vzxx9rgx1/v3 | https://www.protocols.io/view/bulk-rnaseq-delivery-c3deyi3e | Tyler Stahl | TITLE: Bulk RNASeq Delivery
AUTHORS: Tyler Stahl
[DESCRIPTION]
This protocol will give an overview of the grc data delivery structure and results files
[STEPS]
SECTION: Analysis Overview
1. In brief, the RNASeq analysis follows pre-processing (quality control/filtering/trimming), alignment, post-processing, and dif... | ["[Analysis Overview] In brief, the RNASeq analysis follows pre-processing (quality control/filtering/trimming), alignment, post-processing, and differential expression analysis between sample groups with DESeq2. A detailed overview of the analysis can be found in the README.txt and methods.txt file. Also, please see ... |
68,276 | Post-Surgical Dissection of Cervix | 4 | dx.doi.org/10.17504/protocols.io.5jyl89467v2w/v1 | https://www.protocols.io/view/post-surgical-dissection-of-cervix-cewutfew | Stephen Fisher, Marielena Grijalva, Rong Guo, sarahjoh, Hieu Nguyen, John Renz, Jean G Rosario, Steven Rudich, Brian Gregory, Junhyong Kim, Kate O'Neill | TITLE: Post-Surgical Dissection of Cervix
AUTHORS: Stephen Fisher, Marielena Grijalva, Rong Guo, sarahjoh, Hieu Nguyen, John Renz, Jean G Rosario, Steven Rudich, Brian Gregory, Junhyong Kim, Kate O'Neill
[DESCRIPTION]
This protocol describes dissection of the ectocervix and endocervix in preparation for 10X Visium, 10... | ["[Dissection of Ectocervix] Remove uterus from ice and dry the cervix.", "[Dissection of Endocervix] Remove uterus and remaining cervix from ice and dry.", "[Dissection of Ectocervix] Using a large grossing knife with a fresh blade, remove the most distal portion (1cm length) of the cervix which contains the ectocervi... |
84,180 | iNIL/iNIP transcription factor-induced motor neuron differentiation v2 (Mazzoni lab) | 4 | null | https://www.protocols.click/view/inil-inip-transcription-factor-induced-motor-neuro-cwfuxbnw | Dylan E. Iannitelli, Hoa (Emma) Nguyen, Albert Tan, Esteban O. Mazzoni | TITLE: iNIL/iNIP transcription factor-induced motor neuron differentiation v2 (Mazzoni lab)
AUTHORS: Dylan E. Iannitelli, Hoa (Emma) Nguyen, Albert Tan, Esteban O. Mazzoni
[BEFORE_START]
Preparing base human motor neuron media (hMNM)
1X Neurobasal Media 500mL
50X B27 ... | ["[Day 0] Aspirate media and gently wash iPSCs with 1X DPBS", "[Day 0] Harvest iNIL/iNIP iPSCs", "[Day 0] Count cells", "[Day 0] Seed directly into hMN media + Y-27632 (10 μM) + dox (3 μM) \nSeed at 8,000 cells/cm2 (Example: 600,000 cells/10cm dish)", "[Day 2] Aspirate all media", "[Day 2] Replenish with hMN media + Y-... |
64,415 | Condor CBD Gummies 2022 Price, Side Effects And More Details | 3 | dx.doi.org/10.17504/protocols.io.n2bvj6bw5lk5/v1 | https://www.protocols.io/view/condor-cbd-gummies-2022-price-side-effects-and-mor-ca57sg9n | fluxactive | TITLE: Condor CBD Gummies 2022 Price, Side Effects And More Details
AUTHORS: fluxactive
[DESCRIPTION]
Availability Of Condor CBD Gummies - Online On Website
[STEPS] | [] |
42,233 | Lung Homogenization | 4 | dx.doi.org/10.17504/protocols.io.bmgzk3x6 | https://www.protocols.io/view/lung-homogenization-bmgzk3x6 | Timothy S C Hinks, Bonnie van Wilgenburg, Huimeng Wang, Liyen Loh, Marios Koutsakos, Katherine Kedzierska, Alexandra J. Corbett, Zhenjun Chen | TITLE: Lung Homogenization
AUTHORS: Timothy S C Hinks, Bonnie van Wilgenburg, Huimeng Wang, Liyen Loh, Marios Koutsakos, Katherine Kedzierska, Alexandra J. Corbett, Zhenjun Chen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is part 3.4 of the "Study of MAIT Cell Activation in Viral Infections... | ["Collect the lungs into .\n[RPMI supplemented with penicillin/streptomycin]", "For homogenization, place the lung and the into 10 mL falcon tubes with lids (see Note 16).\n[media]", "Prepare 10 or 15 mL Falcon tubes with 2 × for cleaning the homogenization probe initially and 1 tube containing HBSS. For each group ... |
99,762 | Staining of Dissociated Lung Cells for Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE sequencing) | 0 | dx.doi.org/10.17504/protocols.io.e6nvw1jk7lmk/v1 | https://www.protocols.io/view/staining-of-dissociated-lung-cells-for-cellular-in-ddns25ee | Gautam Bandyopadhyay, Jeffrey Malik, Heidie Huyck, Ravi Misra, John_Ashton, Gloria S Pryhuber | TITLE: Staining of Dissociated Lung Cells for Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE sequencing)
AUTHORS: Gautam Bandyopadhyay, Jeffrey Malik, Heidie Huyck, Ravi Misra, John_Ashton, Gloria S Pryhuber
[DESCRIPTION]
This article describes step by step protocol for antibody-staining frozen l... | ["[Thawing of frozen dissociated human lung cells] Frozen cells were thawed in 37°C water bath and soon after the freezing medium melted cells were transferred into a 15 ml conical tube and the tubes were filled with staining buffer [1% BSA (w/v, Millipore) in DPBS (Biowhittaker)] to dilute the DMSO in freezing medium.... |
52,301 | SFGR Isolation from Clinical Diagnostic Material: Small volume inoculum | 4 | dx.doi.org/10.17504/protocols.io.bxbmpik6 | https://www.protocols.io/view/sfgr-isolation-from-clinical-diagnostic-material-s-bxbmpik6 | Marah Condit, Cecilia Kato | TITLE: SFGR Isolation from Clinical Diagnostic Material: Small volume inoculum
AUTHORS: Marah Condit, Cecilia Kato
[DESCRIPTION]
Rickettsiae are small obligate intracellular gram-negative bacteria that are grown in a Biological Safety Level 3 (BSL-3) laboratory setting.This protocol uses antibiotic-free medium, and th... | ["[Media Preparation] All reagents should be thawed, well mixed and not expired prior to use.Reagents should be stored at the appropriate temperatures recommended by the manufacturer.Prepared media expires 1 month after preparation date.", "[Media Preparation] Clean the BSC with 5% quaternary ammonium solution followed... |
59,623 | Test Protocol for Demo Purposes | 1 | null | https://www.protocols.io/view/test-protocol-for-demo-purposes-b6gfrbtn | Andrew McLaughlin | TITLE: Test Protocol for Demo Purposes
AUTHORS: Andrew McLaughlin
[DESCRIPTION]
This is a test protocol for demo purposes
[STEPS]
SECTION: Section 1
1. TEST
SECTION: Section 1
2. Test content here. | ["[Section 1] TEST", "[Section 1] Test content here."] |
95,907 | SCN Cyst Extraction from Greenhouse Cultures (crocks) | 0 | dx.doi.org/10.17504/protocols.io.q26g7pod8gwz/v1 | https://www.protocols.io/view/scn-cyst-extraction-from-greenhouse-cultures-crock-c9wbz7an | Casey A Schlenker | TITLE: SCN Cyst Extraction from Greenhouse Cultures (crocks)
AUTHORS: Casey A Schlenker
[DESCRIPTION]
SCN Cyst Extraction from Greenhouse Cultures (crocks)
[STEPS]
SECTION: Preparing Green House Cultures for Cyst Extraction
1. Put on gloves to protect hands before beginning preparation
SECTION: Preparing Green House ... | ["[Preparing Green House Cultures for Cyst Extraction] Put on gloves to protect hands before beginning preparation", "[Preparing Green House Cultures for Cyst Extraction] Using gardening shears, clip off all of the stems on the chosen soybean plant, leaving behind 1-2 inches of the stem. Place stems in the 3-gallon buc... |
13,978 | Effective early disease risk assessment with matrix factorization on a large-scale medical database | null | dx.doi.org/10.17504/protocols.io.rv2d68e | null | Chu-Yu Chin, Sun-Yuan Hsieh, Vincent S. Tseng | TITLE: Effective early disease risk assessment with matrix factorization on a large-scale medical database
AUTHORS: Chu-Yu Chin, Sun-Yuan Hsieh, Vincent S. Tseng
[DESCRIPTION]
<p>The early assessment of disease risk is an emerging topic in medical informatics. If diseases are detected at an early stage, prognosis can ... | ["[Install Prerequisite software and libraries]\nThis protocol requires:Matlab 2016aLibSVM version 3.22Each instruction can be verified on property websites.The following steps include: dataset preparation, executing NMF multiplicative update algorithm, paremeter settings for SVM and effectiveness evaluation on the SVM... |
30,711 | Sandwich ELISA Protocol | null | dx.doi.org/10.17504/protocols.io.98xh9xn | null | Sam Li | TITLE: Sandwich ELISA Protocol
AUTHORS: Sam Li
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. [Coat the Plate:]
Dilute unlabeled capture antibody to a final concentration of 0.5-8µg/ml in Coating Buffer (BioLegend, Cat. No. 421701) and transfer 100µl to each well of a high affinity, protein-binding ELISA ... | ["[Coat the Plate:]\nDilute unlabeled capture antibody to a final concentration of 0.5-8µg/ml in Coating Buffer (BioLegend, Cat. No. 421701) and transfer 100µl to each well of a high affinity, protein-binding ELISA plate (e.g., BioLegend Cat. No. 423501).", "[Coat the Plate:]\nSeal plate to prevent evaporation. Incubat... |
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