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 |
|---|---|---|---|---|---|---|---|
26,648 | Compare estimates of people living 1, 5 and 10km from the coast in Pacific Island Countries and Territories | null | dx.doi.org/10.17504/protocols.io.59yg97w | null | Phil Bright, Neil L. Andrew, Luis de la Rua, Shwu Jiau Teoh, Mathew Vickers | TITLE: Compare estimates of people living 1, 5 and 10km from the coast in Pacific Island Countries and Territories
AUTHORS: Phil Bright, Neil L. Andrew, Luis de la Rua, Shwu Jiau Teoh, Mathew Vickers
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Compare estimates of the numbers of people living wi... | ["CREATE 1, 5 AND 10 KM COASTAL BUFFERS.Two main types of population datasets were used for the spatial analysis(in step 2):Census Population Data - analysed using three different methods depending on the data availability.Global population grids: SEDAC-CIESIN Gridded Population of the World v4 and the Oak Ridge Nation... |
63,612 | Expression and purification ATG13, ATG101 and FOLDON-ATG9A Proteins from HEK293GnTi Cells | 4 | null | https://www.protocols.io/view/expression-and-purification-atg13-atg101-and-foldo-cac4sayw | Adam Yokom | TITLE: Expression and purification ATG13, ATG101 and FOLDON-ATG9A Proteins from HEK293GnTi Cells
AUTHORS: Adam Yokom
[DESCRIPTION]
Expression and purification from HEK cells of ATG13, ATG101 and FOLDON-ATG9A proteins
[STEPS]
SECTION: Expression
1. Transfect HEK GNTI cells at concentration of 2 × 106 cells/ml
SE... | ["[Expression] Transfect HEK GNTI cells at concentration of 2 × 106 cells/ml", "[Purification] Resuspended pellet in lysis buffer (25 mM HEPES pH 7.5, 200 mM NaCl, 2 mM MgCl2, 1 mM TCEP, 5 mM EDTA, 10% Glycerol) with 1% Triton X-100 and protease inhibitor cocktail (Thermo Scientific, Waltham, MA)", "[Expression] Dilute... |
79,010 | Efeito do uso de antidepressivos na redução de escores de depressão em mulheres com câncer de mama em tratamento com quimioterápicos antineoplásicos: Revisão Sistemática e metanálise | 1 | dx.doi.org/10.17504/protocols.io.6qpvr4y6ogmk/v1 | https://www.protocols.io/view/efeito-do-uso-de-antidepressivos-na-redu-o-de-esco-creav3ae | brunosilva | TITLE: Efeito do uso de antidepressivos na redução de escores de depressão em mulheres com câncer de mama em tratamento com quimioterápicos antineoplásicos: Revisão Sistemática e metanálise
AUTHORS: brunosilva
[DESCRIPTION]
PRotocol for a sytematic review
[STEPS]
SECTION: Title
1. Effect of the use of antidepressants... | ["[Title] Effect of the use of antidepressants on the reduction of depression scores in women with breast cancer undergoing treatment with antineoplastic chemotherapy: Systematic Review and meta-analysis", "[Original title] Efeito do uso de antidepressivos na redução de escores de depressão em mulheres com câncer de ma... |
63,685 | Standard Operating Procedure for Solid Phase Adsorption Toxin Testing (SPATT) Assemblage and Extraction of HAB Toxins v2 | 3 | dx.doi.org/10.17504/protocols.io.dm6gpb255lzp/v1 | https://www.protocols.io/view/standard-operating-procedure-for-solid-phase-adsor-cafdsbi6 | Kendra Negrey, Meredith Howard, Jayme Smith, Raphael Kudela, David Caron | TITLE: Standard Operating Procedure for Solid Phase Adsorption Toxin Testing (SPATT) Assemblage and Extraction of HAB Toxins v2
AUTHORS: Kendra Negrey, Meredith Howard, Jayme Smith, Raphael Kudela, David Caron
[DESCRIPTION]
SPATT has been developed and tested for a variety of resins (see review by Kudela, 2017). These... | [] |
52,499 | Mary Berry CBD Gummies {UK} Reviews : (Scam Or Legit) | 1 | dx.doi.org/10.17504/protocols.io.bxhtpj6n | https://www.protocols.io/view/mary-berry-cbd-gummies-uk-reviews-scam-or-legit-bxhtpj6n | health | TITLE: Mary Berry CBD Gummies {UK} Reviews : (Scam Or Legit)
AUTHORS: health
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><a href="https://www.healthpills24x7.com/order-green-cbd-gummies" style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;">==> Get Mary Berry CBD Gum... | ["Prodect Name : Mary Berry CBD Gummies(Official Website) : Click Here To Order Now Mary Berry CBD GummiesMary Berry CBD Gummies UK Overview: Every individual these days is resisted with a variety of significant problems, several of which are really damaging and also must not be forgotten. CBD oils as well as variou... |
39,246 | Cold Spring Harbor - Intraductal Injection | 4 | dx.doi.org/10.17504/protocols.io.bijnkcme | https://www.protocols.io/view/cold-spring-harbor-intraductal-injection-bijnkcme | David Tuveson | TITLE: Cold Spring Harbor - Intraductal Injection
AUTHORS: David Tuveson
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">from Xiao et al., Nat Prot 2014, modified by KM. </div></div>
[STEPS]
?. [Anesthesia and Preparation]
Anesthetize mice with 2.5–3% (wt/vol) isoflurane by inhalation.
The inhalat... | ["[Anesthesia and Preparation]\nAnesthetize mice with 2.5–3% (wt/vol) isoflurane by inhalation.\nThe inhalation should be closely adjusted, according to the breathing and heart rate of the mice during surgery. A typical infusion surgery takes 15-20 min. Unnecessary delays in the surgery should be avoided. (use Nair to ... |
64,134 | Virion quantification by flow cytometry, without fixation or freezing | 4 | dx.doi.org/10.17504/protocols.io.6qpvr6q93vmk/v1 | https://www.protocols.io/view/virion-quantification-by-flow-cytometry-without-fi-cavese3e | Eva JP Lievens | TITLE: Virion quantification by flow cytometry, without fixation or freezing
AUTHORS: Eva JP Lievens
[DESCRIPTION]
This protocol uses flow cytometry to measure the concentration of virions in a sample, and was based on Brussaard (2004) and Wen et al. (2004). This protocol works without fixing or snap-freezing the samp... | ["[Preparation] Defrost 100X SYBR Green aliquot (keep in the dark).", "[Preparation] Turn on dry bath, set to 80°C. Put the ‘6x1.5ml’ heat blocks in the dry bath as well (on top of the 96-well heat block), so that they heat to 80°C too.", "[Preparation] Calculate volumes of TE buffer and 100X SYBR Green to use. Use an ... |
95,542 | Liquid-liquid extraction of 3,3'-dichlorobiphenyl (PCB11) and its hydroxylated metabolites from animal tissues | 1 | dx.doi.org/10.17504/protocols.io.36wgq3w8xlk5/v1 | https://www.protocols.io/view/liquid-liquid-extraction-of-3-3-39-dichlorobipheny-c9iwz4fe | Xueshu Li, Nicole M. Breese, Hansjoachim Lehmler | TITLE: Liquid-liquid extraction of 3,3'-dichlorobiphenyl (PCB11) and its hydroxylated metabolites from animal tissues
AUTHORS: Xueshu Li, Nicole M. Breese, Hansjoachim Lehmler
[DESCRIPTION]
This protocol describes a method to extract PCB11 (3,3'-dichlorobiphenyl) and its monohydoxylated metabolites from mouse tiss... | ["[Tissue homogenization] Place tissues (liver 100-200 mg, brain 200 mg, adipose 50-80 mg) in tube-A. Record weight on the working sheet.\n\nNote: Wash scalpel, forceps, and spatula between samples with water, acetone, and hexane subsequently.", "[Addition of Analytical Standards] Spike all tube-A samples (MB, TB, tiss... |
60,411 | Wastewater QC workflow in GalaxyTrakr (SSQuAWK3) | 1 | dx.doi.org/10.17504/protocols.io.kxygxzk5dv8j/v5 | https://www.protocols.io/view/wastewater-qc-workflow-in-galaxytrakr-ssquawk3-b683rhyn | Jasmine Amirzadegan, Tunc Kayikcioglu, hugh.rand , Ruth Timme, Maria Balkey | TITLE: Wastewater QC workflow in GalaxyTrakr (SSQuAWK3)
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 SSQuAWK3: 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... |
null | null | null | dx.doi.org/10.17504/protocols.io.d9j94m | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Concentrating Viruses via PEG precipitation
[STEPS] | [] |
89,456 | Nuclei Isolation for HMBA FACS | 4 | dx.doi.org/10.17504/protocols.io.kxygx35ywg8j/v1 | https://www.protocols.io/view/nuclei-isolation-for-hmba-facs-c3kqykvw | Lakme Caceres | TITLE: Nuclei Isolation for HMBA FACS
AUTHORS: Lakme Caceres
[DESCRIPTION]
This protocol is for purifying nuclei for downstream 10X sequencing.
[GUIDELINES]
Keep tissue/nuclei on ice as much as possible.
[STEPS]
SECTION: Prepare Fresh Solutions
4. Make 3 mL Homogenization Buffer by adding 2.892 mL Nuclear Isolation ... | ["[Prepare Fresh Solutions] Make 3 mL Homogenization Buffer by adding 2.892 mL Nuclear Isolation Media to a 5 mL eppendorf. Then add 60 uL protease inhibitor, 30 μL 10% Triton X-100, 15 uL RNase inhibitor, and 3 μL 100 mM DTT.", "[Prepare Stock Solutions] Make 50 mL Nuclear Isolation Media by filling a 100 mL bottle wi... |
63,511 | Nested VP1 PCR and Nanopore Sequencing from Stool and ES Samples v1.2 | 1 | dx.doi.org/10.17504/protocols.io.81wgbpkmovpk/v3 | https://www.protocols.io/view/nested-vp1-pcr-and-nanopore-sequencing-from-stool-b99xr97n | Alex Shaw, Manasi Majumdar, Catherine Troman, Aine.OToole, c.ansley, Joyce Akello, Erika Bujaki, rachel.colquhoun, arshady, khurshida, alammu, Andrew Rambaut, Javier Martin, Nick Grassly | TITLE: Nested VP1 PCR and Nanopore Sequencing from Stool and ES Samples v1.2
AUTHORS: Alex Shaw, Manasi Majumdar, Catherine Troman, Aine.OToole, c.ansley, Joyce Akello, Erika Bujaki, rachel.colquhoun, arshady, khurshida, alammu, Andrew Rambaut, Javier Martin, Nick Grassly
[DESCRIPTION]
This protocol is updated from t... | ["[Nested PCR First Round (PanEV)] Nested PCR First Round (panEV primers):\nPrepare a Master mix using reaction volumes as detailed below, excluding forward primer and the RNA:\n\nForward Primer (5'NTR): [TGGCGGAACCGACTACTTTGGGTG] (Arita et al. 2015)\nReverse Primer (Cre): [TCAATACGGTGTTTGCTCTTGAACTG] (Arita et al.... |
93,364 | TruAI Neuromelanin Quantification | 4 | null | https://www.protocols.io/view/truai-neuromelanin-quantification-c7euzjew | Anastasia Filimontseva, YuHong Fu, Glenda Halliday | TITLE: TruAI Neuromelanin Quantification
AUTHORS: Anastasia Filimontseva, YuHong Fu, Glenda Halliday
[DESCRIPTION]
Quantification of area and optical density of intracellular neuromelanin with TruAI.
[STEPS]
SECTION: Loading training label function in TruAI software
1. Open scanned images with Olympus VS200 Desktop ... | ["[Loading training label function in TruAI software] Open scanned images with Olympus VS200 Desktop (EVIDENT Technology GmbH, ver. 4.1.1 build 29408).", "[Loading training label function in TruAI software] Under the ‘Detect’ window, select ‘Training Labels’.", "[Creating NM foreground training label class] Create a ne... |
83,006 | EXPRESSION AND PURIFICATION OF HUMAN NEMO (GST-GFP-NEMO) | 1 | dx.doi.org/10.17504/protocols.io.261gedpojv47/v1 | https://www.protocols.io/view/expression-and-purification-of-human-nemo-gst-gfp-cva6w2he | Elisabeth Holzer | TITLE: EXPRESSION AND PURIFICATION OF HUMAN NEMO (GST-GFP-NEMO)
AUTHORS: Elisabeth Holzer
[DESCRIPTION]
This protocol describes how to express and purify human NEMO (IKK-γ) tagged N-terminally with GST and EGFP. The expression is performed with E. coli Rosetta pLysS cells. The protein is purified via a GST batch purif... | ["[Expression] Grow E. coli Rosetta (DE3) pLysS cells in 2 L LB medium at 37 °C until achieving an OD600 nm of 0.4.", "[Expression] Reduce temperature to 18 °C and continue growth to OD600 nm of 0.8.", "[Expression] Induce protein expression with 250 micromolar (µM) IPTG and continue growth for ~960 min at 18 °C", "[Ex... |
null | null | null | dx.doi.org/10.17504/protocols.io.i66chhe | null | null | TITLE: No Title
AUTHORS:
[BEFORE_START]
<p>Prepare appropriate stock-solutions of peptide according to the concentration added in the first well of the microtiter plate. </p>
[GUIDELINES]
<p>Be careful not to contaminate neighbouring wells/rows with the peptide added. If the peptides are highly potent it is a good i... | [] |
40,083 | Metabolite Extraction | 3 | dx.doi.org/10.17504/protocols.io.bjdtki6n | https://www.protocols.io/view/metabolite-extraction-bjdtki6n | avinash.kale | TITLE: Metabolite Extraction
AUTHORS: avinash.kale
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.dsi6cd | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
The following protocol is used to construct shotgun libraries from RNA virus assemblages. This method is designed to detect all RNA viruses, regardless of their genome orientation, and therefore provides a broader assessment of RNA virus diversity compared to the single-gene–bas... | [] |
81,607 | Immunohistochemistry of tissue sections from formalin-fixed paraffin embedded (FFPE) samples | 4 | dx.doi.org/10.17504/protocols.io.n2bvj86mngk5/v1 | https://www.protocols.io/view/immunohistochemistry-of-tissue-sections-from-forma-ctxfwpjn | Terri Li, Can Gong | TITLE: Immunohistochemistry of tissue sections from formalin-fixed paraffin embedded (FFPE) samples
AUTHORS: Terri Li, Can Gong
[DESCRIPTION]
H&E staining and immunohistochemistry of tissue sections from formalin-fixed paraffin embedded (FFPE) murine tissue samples were performed by the University of Chicago Human Tis... | ["Biotinylated anti-mouse Tn IgM antibody (clone 5F4) and WE scFv staining", "Tissue sections were deparaffinized and rehydrated through xylenes and serial dilutions of ethanol to deionized water.", "Tissue sections were incubated in antigen retrieval buffer (DAKO S2367) and heated in a steamer at over 97'C for 20 minu... |
90,507 | Extraction of brain tissue with fluorogold-labelled neurons for transmission electron-microscopy imaging | 1 | null | https://www.protocols.io/view/extraction-of-brain-tissue-with-fluorogold-labelle-c4mjyu4n | enrico.zampese | TITLE: Extraction of brain tissue with fluorogold-labelled neurons for transmission electron-microscopy imaging
AUTHORS: enrico.zampese
[DESCRIPTION]
Protocol for injection of Fluorogold particles for retrograde labelling or neurons, perfusion, fixation, and tissue extraction for Transmission Electron Microscopy obser... | ["[Stereotactic injection of fluorogold particles in the brain] Prepare the fluorogold working solution by dissolving fluorogold powder in the appropriate volume of sterile NaCl 0.9% saline. Recommended working concentration: 1% fluorogold", "[Stereotactic injection of fluorogold particles in the brain] Prepare a clean... |
93,053 | Rat organotypic cultures for AAV-mediated vital labeling of the extracellular matrix | 4 | dx.doi.org/10.17504/protocols.io.e6nvwdnzzlmk/v2 | https://www.protocols.io/view/rat-organotypic-cultures-for-aav-mediated-vital-la-c645zgy6 | Federico N. Soria, Mario Fernandez-Ballester | TITLE: Rat organotypic cultures for AAV-mediated vital labeling of the extracellular matrix
AUTHORS: Federico N. Soria, Mario Fernandez-Ballester
[DESCRIPTION]
In this protocol we describe the preparation and maintenance of rat organotypic cultures (cortico-striatal) for AAV-infection and imaging of the extracellular ... | ["[Culture preparation] Prepare a 6-well culture plate with Millipore 0.4 µm culture inserts placed on top of 1 mL of organotypic medium (see Materials) per well. Incubate it at 37 °C and 5% CO2 to warm up.", "[Culture preparation] Prepare a p100 and p60 petri dishes with 25 mL and 5 mL, respectively, of and keep the... |
25,319 | RNA Isolation from Plant Tissue Protocol 8: CTAB/Acid Phenol/Silica Membrane Method | null | dx.doi.org/10.17504/protocols.io.4yfgxtn | null | null | TITLE: RNA Isolation from Plant Tissue Protocol 8: CTAB/Acid Phenol/Silica Membrane Method
AUTHORS:
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Implemented by: Michael Deyholos</div><div class = "text-block">This protocol combines elements of standard CTAB, acid phenol, and silica-membrane prot... | ["Grind tissue to a powder in liquid nitrogen.", "Add– of ground, frozen tissue to of pre-heated extraction buffer in a 2 ml microcentrifuge tube.\n400 mg\n600 mg\n1.4 ml", "Vortex the tube until the tissue is mixed with the buffer.\nTo facilitate mixing, you may have to invert the tube on the vortex, and/or heat it b... |
null | null | null | dx.doi.org/10.17504/protocols.io.dfr3m5 | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
<strong>Primers:</strong><br /><br />926F: AAA CTY AAA KGA ATT GAC GG<br />1492R: TAC GGY TAC CTT GTT ACG ACT T<br />OR<br />GM3: AGA GTT TGA TCM TGG C These primers are for almost full-length 16s (8F/1492R)<br />GM4: TAC CTT GTT ACG ACT T<br /><br /><strong>... | [] |
21,106 | UC Davis - Mouse Gross Necropsy with Histology | null | dx.doi.org/10.17504/protocols.io.yusfwwe | null | Stephen M. Griffey | TITLE: UC Davis - Mouse Gross Necropsy with Histology
AUTHORS: Stephen M. Griffey
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span></div><div class = "text-block">
Gross necropsy with documentation of changes present. Collection and histologic processi... | ["Procedure: Gross necropsy with tissue collection1.1 All animals submitted to CPL for necropsy, are assigned a CPL accession number. Note: Make sure to match the animal’s ID number and the CPL accession number. Someanimal ID may be in the form of ear notch or toe snip.1.2 Prior to starting, record the CPL accession nu... |
76,339 | Phylogenesis of Small Ruminant Lentiviruses: a systematic review protocol | 1 | dx.doi.org/10.17504/protocols.io.n2bvj8zzwgk5/v1 | https://www.protocols.io/view/phylogenesis-of-small-ruminant-lentiviruses-a-syst-cnstveen | Silvia Pavone, Paola Gobbi, Massimiliano Orso, Monica Giammarioli | TITLE: Phylogenesis of Small Ruminant Lentiviruses: a systematic review protocol
AUTHORS: Silvia Pavone, Paola Gobbi, Massimiliano Orso, Monica Giammarioli
[DESCRIPTION]
Small ruminant lentiviruses (SRLV) include the closely related Visna-Maedi virus (VMV) and caprine arthritis encephalitis virus (CAEV), which infect ... | ["[INTRODUCTION] Rationale\nSmall ruminant lentiviruses (SRLVs) are members of the Retroviridae family and Lentivirus genus comprising the closely related Visna-Maedi virus (VMV) and caprine arthritis encephalitis virus (CAEV), which infect sheep and goats.1 These viruses cause huge economic losses in the small ruminan... |
31,918 | CMU Libraries Love Data Week 2020 - Valentine's Day Dessert Recipes | null | dx.doi.org/10.17504/protocols.io.bbenijde | null | Hannah Gunderman, Angelina Spotts, Emma Slayton | TITLE: CMU Libraries Love Data Week 2020 - Valentine's Day Dessert Recipes
AUTHORS: Hannah Gunderman, Angelina Spotts, Emma Slayton
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">At CMU Libraries, each year we celebrate Love Data Week (LDW) with events, workshops, speakers, and activities to he... | [] |
101,647 | Nuclei Isolation from Frozen Tissue or Frozen hPCLS | 0 | dx.doi.org/10.17504/protocols.io.eq2lyw6ewvx9/v1 | https://www.protocols.io/view/nuclei-isolation-from-frozen-tissue-or-frozen-hpcl-dfhp3j5n | Heidi Monroe, Nayra Cardenes, Melanie Königshoff, koenigshoffm, Robert Lafyatis | TITLE: Nuclei Isolation from Frozen Tissue or Frozen hPCLS
AUTHORS: Heidi Monroe, Nayra Cardenes, Melanie Königshoff, koenigshoffm, Robert Lafyatis
[DESCRIPTION]
This protocol follows the "Chromium Nuclei Isolation Kit" guidelines for the process for isolating Nuclei from frozen tissues and/or PCLS (Precision-Cut Lung... | ["[Nuclei Isolation] Add lysis buffer (200 µL) & dissociate with pestle until homogeneous while on ice.", "[Nuclei Isolation] Transfer frozen tissue (∼50 mg; use 2 slices if isolating from PCLS) to pre-chilled Sample Dissociation Tube (2000564) and place on wet ice.", "[Nuclei Isolation] Add lysis buffer (300 µL) and p... |
16,157 | Morphometry of Ophiothrix (Echinodermata: Ophiuroidea) | null | dx.doi.org/10.17504/protocols.io.tz5ep86 | null | Renata Alitto, Pablo Damian Borges Guilherme, Michela Borges, Letícia de Oliveira Dias, Helena Serrano | TITLE: Morphometry of Ophiothrix (Echinodermata: Ophiuroidea)
AUTHORS: Renata Alitto, Pablo Damian Borges Guilherme, Michela Borges, Letícia de Oliveira Dias, Helena Serrano
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Morphometry of </span><span style = "font-style:italic;">Ophiothrix </sp... | ["[Measurements]\nMeasurements were taken using an ocular micrometer and through the AxioVision VS program 40.4.8.20 (Carl Zeiss Microscopy, Germany) attached to a ZEISS Discovery V20 stereomicroscope for specimens less than 10 mm disc diameter and with a digital Mitutoyo CD-6 CS caliper for the larger specimens.", "[C... |
56,800 | DNA Extraction and Purification from Soil | 4 | dx.doi.org/10.17504/protocols.io.bp2l61npzvqe/v1 | https://www.protocols.io/view/dna-extraction-and-purification-from-soil-b3p8qmrw | Justingdbyrne , James JN Kitson | TITLE: DNA Extraction and Purification from Soil
AUTHORS: Justingdbyrne , James JN Kitson
[DESCRIPTION]
Affordable DNA extraction and purification from soil samples at scale.
This protocol outlines an affordable DNA extraction and purification technique to be used with soil samples processed at scale. In the materi... | ["[Sample Lysis] Add 2g of 1.0mm to 1.4mm diameter acid-washed garnet beads to a 5ml Eppendorf screw-cap tube", "[Sample Lysis] Add 2200μL of Lysis Solution 1 and vortex briefly.", "[Sample Lysis] Add 0.25g of sample to the tube, and shake briefly by hand to mix the contents.", "[Sample Lysis] Place in Geno/Grinder 201... |
71,103 | Preparation of bacterial cell lysate for SDS-PAGE (2022 iGEM) | 4 | dx.doi.org/10.17504/protocols.io.14egn2zwyg5d/v1 | https://www.protocols.io/view/preparation-of-bacterial-cell-lysate-for-sds-page-chn7t5hn | Team Fudan iGEM | TITLE: Preparation of bacterial cell lysate for SDS-PAGE (2022 iGEM)
AUTHORS: Team Fudan iGEM
[DESCRIPTION]
Preparation of bacterial cell lysate for SDS-PAGE
[STEPS]
SECTION: Preparation of bacterial cell lysate for SDS-PAGE
1. Grow the cells overnight, to an OD600 above 1. If IPTG induction needed, at it around OD60... | ["[Preparation of bacterial cell lysate for SDS-PAGE] Grow the cells overnight, to an OD600 above 1. If IPTG induction needed, at it around OD600 0.2-0.3 (keep IPTG stock solution at -20 freezer).", "[Preparation of bacterial cell lysate for SDS-PAGE] Take one 1 ml of OD600 = 1 from each sample. Correct the sample volu... |
61,969 | Protocol for Bulk Water Enrichment for the Isolation of Salmonella from Surface Water | 4 | dx.doi.org/10.17504/protocols.io.ewov1n3xygr2/v1 | https://www.protocols.io/view/protocol-for-bulk-water-enrichment-for-the-isolati-b8rrrv56 | Autumn L Kraft, Manan Sharma, Jonathan G Frye, James E Wells, Abasiofiok Mark Ibekwe, NARMS EWG | TITLE: Protocol for Bulk Water Enrichment for the Isolation of Salmonella from Surface Water
AUTHORS: Autumn L Kraft, Manan Sharma, Jonathan G Frye, James E Wells, Abasiofiok Mark Ibekwe, NARMS EWG
[DESCRIPTION]
This protocol details the bulk water enrichment for the isolation of Salmonella from surface water.
... | ["[Protocol] Take 1 of the water sample bottles (containing 1 L of surface water) and carefully transfer water into a sterile 2 L Pyrex bottle.", "[Protocol] If needed, add control strain to water sample by gently tipping vial over the opening. Close bottle tightly and thoroughly mix sample.", "[Protocol] Aseptically m... |
62,624 | Lifestyle Keto Gummies: Reviews, exposed 2022, 100% natural diet, does it work and is it trusted? | 4 | dx.doi.org/10.17504/protocols.io.bp2l61redvqe/v1 | https://www.protocols.io/view/lifestyle-keto-gummies-reviews-exposed-2022-100-na-b9d8r29w | Lifestyle Keto | TITLE: Lifestyle Keto Gummies: Reviews, exposed 2022, 100% natural diet, does it work and is it trusted?
AUTHORS: Lifestyle Keto
[DESCRIPTION]
Lifestyle Keto Gummies
[STEPS]
1. Official Website - Click Here for Lifestyle Keto Gummies
Availability Of Lifestyle Keto Gummies - Online On Website
ain Benefits - Burn F... | ["Official Website - Click Here for Lifestyle Keto Gummies\n\n\nAvailability Of Lifestyle Keto Gummies - Online On Website\n\nain Benefits - Burn Fat Without Any Side Effect\n\nOfficial Website - Click Here for Lifestyle Keto Gummies\n\nAvailability Of Lifestyle Keto Gummies - Online On Website\n\n\nMain Benefits - Bur... |
15,257 | ASW+NO3 medium | null | dx.doi.org/10.17504/protocols.io.s5zeg76 | null | Roscoff Culture Collection | TITLE: ASW+NO3 medium
AUTHORS: Roscoff Culture Collection
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Medium used for cyanobacteria based on artificial seawater (ASW)</div></div>
[STEPS]
?. Dissolve 25 g of NaCl in MilliQ waterTo this solution, add : Quantity
Compound
Stock Sol... | ["Dissolve 25 g of NaCl in MilliQ waterTo this solution, add : Quantity\n \n Compound\n \n Stock Solution\n Concentration in medium (in mM)\n mLstock\n /LASW\n g/LASW\n 10\n 0,75\n Sodium nitrate (NaNO3)\n 75 g/L\n 8.8\n 10\n 2\n Magnesium chloride hexahydrate (MgCl26H2O)\n 200 ... |
null | null | null | dx.doi.org/10.17504/protocols.io.mfsc3ne | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This short protocol describes how to maintain your fly stocks as single generation, age-matched populations. The method described encourages a health fly population, firstly, as individuals mate and oviposit during an optimal age when females are highly fecund and secondly, b... | [] |
48,615 | Protocol for Bioinformatics and Network Analysis of Microarray Data from Mixture Cell Type | 5 | dx.doi.org/10.17504/protocols.io.btqfnmtn | https://www.protocols.io/view/protocol-for-bioinformatics-and-network-analysis-o-btqfnmtn | Evan Maestri, Vladimir Kuznetsov | TITLE: Protocol for Bioinformatics and Network Analysis of Microarray Data from Mixture Cell Type
AUTHORS: Evan Maestri, Vladimir Kuznetsov
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This approach was utilized for microarray-based gene expression profiling of duodenum mucosa in mice to conduct ... | ["[Differential Gene Expression Analysis of Microarray Data]\nThe steps in this protocol assume a standard protocol for differential gene expression analysis has been previously followed for microarray or RNA-seq data. The goal is to highlight methodology for gaining biological insight into key networks and pathways ex... |
26,241 | GENOTYPING OF iPSCS WITH GENE INSERTIONS (Support Protocol 1) | null | dx.doi.org/10.17504/protocols.io.5u9g6z6 | null | Michael S. Fernandopulle, Ryan Prestil, Christopher Grunseich, Chao Wang, Li Gan, Michael E. Ward | TITLE: GENOTYPING OF iPSCS WITH GENE INSERTIONS (Support Protocol 1)
AUTHORS: Michael S. Fernandopulle, Ryan Prestil, Christopher Grunseich, Chao Wang, Li Gan, Michael E. Ward
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol will use genomic DNA isolated from the purified iPSC clones wi... | ["Set up PCR reaction (also see Kramer & Coen, 2001). For each 10 μl reaction, use the primer pairs recommended in Reagents and Solutions for the given safe-harbor site and donor construct chosen: Primer 1 Primer 2 purified genomic DNA from iPSC clone H2O 2 × PCR Master Mix.\n1 µl\n1 µl\n1 µl\n2 µl\n5 µl", "Run PCR rea... |
78,675 | Fast-n-Easy Plasmid Mini-Prep Kit (cellco) | 4 | null | https://www.protocols.io/view/fast-n-easy-plasmid-mini-prep-kit-cellco-cq3tvynn | Guilherme Barbosa | TITLE: Fast-n-Easy Plasmid Mini-Prep Kit (cellco)
AUTHORS: Guilherme Barbosa
[DESCRIPTION]
Description:
Fast-n-Easy Plasmid Mini-Prep Kit is designed for isolation of
high-purity plasmid or cosmid DNA from bacterial cells for
subsequent amplification, sequencing, restriction digests or
transformations. The 2-step alka... | ["[Mini-prep] Harvest the 1 ~ 3 mL of bacterial cell culture by 10000 rpm, 5 min. \nDiscard the supernatant media. \nResuspend of cell pellet with remained media by vigorously vortexing or pipetting. \nAdd 300 µLof Buffer S1. (Buffer S1 is Cell lysis buffer). \nInverting the tube immediately 2 ~ 3 times. \nDo Not Vorte... |
50,994 | Modifications to the "HTAPP_TST- Nuclei isolation from frozen tissue V.2" Protocol | 3 | null | https://www.protocols.io/view/modifications-to-the-34-htapp-tst-nuclei-isolation-bv2sn8ee | Xian Adiconis | TITLE: Modifications to the "HTAPP_TST- Nuclei isolation from frozen tissue V.2" Protocol
AUTHORS: Xian Adiconis
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">A few modifications </div></div>
[STEPS] | [] |
23,173 | UC Davis - Glugagon | null | dx.doi.org/10.17504/protocols.io.2vdge26 | null | Peter Havel | TITLE: UC Davis - Glugagon
AUTHORS: Peter Havel
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">Glucagon is a 29 amino acid polypeptide processed from proglucagon in pancreatic alpha cells. In intestinal L-cells proglu... | ["Prepare enzyme conjugate 1X solution and wash buffer 1X solution.", "Prepare sufficient microplate wells to accommodate Calibrators, controls and samples in duplicate.", "Pipette 10 µL each of Calibrators, controls and samples into appropriate wells.", "Add 50 µL enzyme conjugate 1X solution to each well and attach t... |
23,989 | Make LB agar plates to grown bacteria without antibiotic selection. | null | dx.doi.org/10.17504/protocols.io.3nvgme6 | null | Cancer Research UK / Wellcome Gurdon Institute media kitchen | TITLE: Make LB agar plates to grown bacteria without antibiotic selection.
AUTHORS: Cancer Research UK / Wellcome Gurdon Institute media kitchen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Make LB agar plates to grown bacteria without antibiotic selection.</div></div>
[STEPS]
?.
?. ABC1Ingredi... | ["ABC1IngredientsQuantity2LB Agar 1L3Petri dishes90mm304 140mm10\nABC1IngredientsQuantity2LB Agar 1L3Petri dishes90mm304 140mm10", "A1Melt LB Agar in autoclave (media melt cycle).2Allow the medium to cool to ~60oC in the water bath. Mix on a magnetic stirrer (to prevent air\n bubbles). Transfer to the laminar fl... |
87,161 | Collecting, freezing and shipping frozen post mortem skeletal muscle for single nuclear and spatial RNAseq | 4 | dx.doi.org/10.17504/protocols.io.dm6gp3zz1vzp/v1 | https://www.protocols.io/view/collecting-freezing-and-shipping-frozen-post-morte-czczx2x6 | Prech Uapinyoying | TITLE: Collecting, freezing and shipping frozen post mortem skeletal muscle for single nuclear and spatial RNAseq
AUTHORS: Prech Uapinyoying
[DESCRIPTION]
Collecting and freezing skeletal muscle tissue from a clinical site for experimentation at a remote location can be a
logistical challenge. This protocol provides ... | ["[Prior to freezing] Collect the human muscle autopsy samples, keeping them moist in transplant solution or saline, weigh and divide the muscle into 250mg pieces or less beforehand.", "[Freezing the muscle samples] Prepare several items and reagents and place on laboratory bench", "[Freezing the muscle samples] Fill a... |
55,936 | DiMeLo-seq: Directed Methylation with Long-read sequencing | 4 | dx.doi.org/10.17504/protocols.io.b2u8qezw | https://www.protocols.io/view/dimelo-seq-directed-methylation-with-long-read-seq-b2u8qezw | Nicolas Altemose, Annie Maslan, Owen Smith, Kousik Sundararajan, Rachel Brown, Aaron Straight, Aaron Streets | TITLE: DiMeLo-seq: Directed Methylation with Long-read sequencing
AUTHORS: Nicolas Altemose, Annie Maslan, Owen Smith, Kousik Sundararajan, Rachel Brown, Aaron Straight, Aaron Streets
[DESCRIPTION]
Directed Methylation and Long-read sequencing (DiMeLo-seq) is a powerful method to map protein-DNA interactions a... | ["[Introduction] This protocol is part of the broader Directed Methylation and Long-read sequencing (DiMeLo-seq) method. DiMeLo-seq targets a protein A-Hia5 methyltransferase fusion protein (pA-Hia5) to a protein of interest (using an antibody). Hia5 methylates adenines in the vicinity of the protein, the DNA is extrac... |
43,135 | Protocol 2: LAMP | 5 | null | https://www.protocols.io/view/protocol-2-lamp-bnc7mazn | TITLE: Protocol 2: LAMP
AUTHORS:
[STEPS]
?. Get FASTA sequenceYou’ll need to look up the gene for the sequence you are trying to amplify and download the FASTA file for it.
?. Go to Primer ExplorerYou will need to go to the Primer Explorer webpage, http://primerexplorer.jp/lampv5e/index.html, in order to upload your... | ["Get FASTA sequenceYou’ll need to look up the gene for the sequence you are trying to amplify and download the FASTA file for it.", "Go to Primer ExplorerYou will need to go to the Primer Explorer webpage, http://primerexplorer.jp/lampv5e/index.html, in order to upload your FASTA file.", "Select which primers to choos... | |
null | null | null | dx.doi.org/10.17504/protocols.io.pcrdiv6 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
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?. | [] |
46,002 | Exploration of rehabilitation through the use of virtual reality interventions for patients with upper limb conditions: protocol for scoping review. | 1 | dx.doi.org/10.17504/protocols.io.bq6smzee | https://www.protocols.io/view/exploration-of-rehabilitation-through-the-use-of-v-bq6smzee | Stefanie Andrew, Carol Clark, Sheppard Z.A., Evans M., Hutt J., Crook T. B. | TITLE: Exploration of rehabilitation through the use of virtual reality interventions for patients with upper limb conditions: protocol for scoping review.
AUTHORS: Stefanie Andrew, Carol Clark, Sheppard Z.A., Evans M., Hutt J., Crook T. B.
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span st... | ["[Steps]\nProtocol and registration: The protocol for this scoping review is publicly available from protocols.io.", "[Steps]\nEligibility criteria: All study types including controlled, validation, evaluation, observational studies, conference proceedings and abstracts will be included, published between 2010 – 202... |
57,153 | Synchronized C. elegans culture on NGM plates for FACS isolation of intestine cells | 4 | null | https://www.protocols.io/view/synchronized-c-elegans-culture-on-ngm-plates-for-f-b329qqh6 | Robert TP Williams, Erin Osborne Nishimura | TITLE: Synchronized C. elegans culture on NGM plates for FACS isolation of intestine cells
AUTHORS: Robert TP Williams, Erin Osborne Nishimura
[DESCRIPTION]
This protocol details the steps necessary to scale-up and synchronize C. elegans cultures for FACS isolation of intestine cells. The protocol utilizes agar-based ... | ["[Grow mixed stage cultures of cell sorting strain] Identify a 60 mm petri plate culture of the sorting strain that has recently exhausted the E. coli lawn", "[Expand mixed stage cultures of cell sorting strain] Harvest the the mixed stage worm population from the 5 plates by washing each plate with ~10 ml of M9", "[S... |
55,321 | Analysis of Islet Function by Glucagon Enzyme-linked Immunosorbent Assay (ELISA) | 4 | dx.doi.org/10.17504/protocols.io.bz9zp976 | https://www.protocols.io/view/analysis-of-islet-function-by-glucagon-enzyme-link-bz9zp976 | IIDP-HIPP | TITLE: Analysis of Islet Function by Glucagon Enzyme-linked Immunosorbent Assay (ELISA)
AUTHORS: IIDP-HIPP
[DESCRIPTION]
This Standard Operating Procedure (SOP) is based on the Vanderbilt University Medical Center Human Islet Phenotyping Program (HIPP) Islet Functional Analysis. This SOP provides the HIPP procedure... | ["[Procedures] Preparation of Samples, Standards, and internal Quality Controls", "[Procedures] Thaw archived samples intended for analysis in room temperature water. Once thawed, invert capped samples ten times to thoroughly mix.", "[Procedures] Bring the Glucagon Standard to room temperature. Keep remaining kit compo... |
20,770 | UC Davis - Echocardiography | null | dx.doi.org/10.17504/protocols.io.yiafuae | null | Anil Singapuri | TITLE: UC Davis - Echocardiography
AUTHORS: Anil Singapuri
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span><span style = "font-weight:bold;"> </span></div><div class = "text-block">Cardiac hypertrophy is one of the most common causes of heart failure.... | ["The animals’ chest will be shaved and then be placed in a supine position on a warmed (37°C) towel covered surgical table.", "The mice are restrained in a 50 ml conical tube with an opening for the nose and chest, a standard procedure for imaging mice for this kind of study.", "The imaging generally lasts for only 2-... |
85,724 | Mod3D Live Cell Chambers and holders 3D printing and Assembly | 1 | dx.doi.org/10.17504/protocols.io.n92ldz587v5b/v2 | https://www.protocols.io/view/mod3d-live-cell-chambers-and-holders-3d-printing-a-cxx4xpqw | and Ray Truant | TITLE: Mod3D Live Cell Chambers and holders 3D printing and Assembly
AUTHORS: and Ray Truant
[DESCRIPTION]
Live-cell microscopy imaging typically involves the use of high-quality glass-bottom chambers that allow cell culture, gaseous buffer exchange and optical properties suitable for microscopy applications. However,... | ["For FDM prints of holders, print at 20% grid infill with a layer height of 0.16 mm on either a Creality Ender 3 or a CR10 printer (Creality, Shenzhen, China) or similar FDM printer. Poly lactic acid (PLA) or Polyethylene terephthalate glycol (PETG) 1.75mm filament should be used. Acrylonitrile butadiene styrene (ABS)... |
20,248 | Bovine satellite cell Pax7 ICC | null | dx.doi.org/10.17504/protocols.io.xzyfp7w | null | Andrew Stout, Natalie Rubio | TITLE: Bovine satellite cell Pax7 ICC
AUTHORS: Andrew Stout, Natalie Rubio
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Staining primary bovine satellite cells for Pax7, a common marker of satellite cells and myogenic potential. Protocol developed for </span><a style = "text-decoration:unde... | ["[Fixation and Permeabilization (1 hour)]\nAspirate media from cells", "[Fixation and Permeabilization (1 hour)]\nadd cold 4% PFA to cells (enough to cover cells or scaffolds)", "[Fixation and Permeabilization (1 hour)]\nIncubate at room temperature for 30 minutes", "[Fixation and Permeabilization (1 hour)]\nWash 3x w... |
65,218 | Use of cholera toxin subunit B to label neural projections to major pelvic ganglia | 1 | dx.doi.org/10.17504/protocols.io.36wgq71jovk5/v1 | https://www.protocols.io/view/use-of-cholera-toxin-subunit-b-to-label-neural-pro-cbxaspie | Janet R Keast, Peregrine B Osborne, Nicole Wiedmann, John-Paul Fuller-Jackson | TITLE: Use of cholera toxin subunit B to label neural projections to major pelvic ganglia
AUTHORS: Janet R Keast, Peregrine B Osborne, Nicole Wiedmann, John-Paul Fuller-Jackson
[DESCRIPTION]
This protocol is used to visualise preganglionic neurons in the spinal cord innervating pelvic visceral organs (e.g., the lower ... | ["[Preparation for surgery] Prepare cholera toxin subunit B solutions: low salt formulation with 0.05% Evans Blue.", "[Preparation for surgery] Anesthetise animal (2.5% isoflurane in oxygen, or as required for maintenance)", "[Preparation for surgery] Apply eye lubricant and place animal on heated pad.", "[Preparation ... |
12,439 | Ethanol precipitation of small DNA fragments | 1 | dx.doi.org/10.17504/protocols.io.n2bvj7jnvk5w/v1 | https://www.protocols.io/view/ethanol-precipitation-of-small-dna-fragments-qdxds7n | Eva Petrova, Roey Angel | TITLE: Ethanol precipitation of small DNA fragments
AUTHORS: Eva Petrova, Roey Angel
[DESCRIPTION]
This protocol is for a simple ethanol precipitation of small fragments and/or small amounts of DNA. Note that this protocol simply concentrates your sample and removes enough salts/enzymes for ligation to be successful. ... | ["Transfer the sample to 1.5 mL eppendorf tube.", "Adjust the salt conc. of the sample to 0.3M sodium acetate and 0.01M MgCl2.\n0.3 21\n0.01 21", "Add 1 µl of Pellet Paint NF.\n1 1", "Add 1 µl of non labeled genomic DNA e.g. from E.coli (this acts as a carrier and increases precipitation yield).\n1 1", "Add 2 volumes c... |
null | null | null | dx.doi.org/10.17504/protocols.io.ehfbb3n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
PCPipe is a protein-clustering tool. The input is a set of ORFs and a FASTA file with already clustered ORFs. <br /><br />The process entails:<br />
<ul>
<li>Use <a href="http://weizhongli-lab.org/cd-hit/" target="_blank">cd-hit-2d</a> to compare the input peptides to previousl... | [] |
82,008 | Anti-Borrelia ELISA (IgG) | 4 | dx.doi.org/10.17504/protocols.io.kxygx9j7kg8j/v1 | https://www.protocols.io/view/anti-borrelia-elisa-igg-cubywspw | Апельсинка Малиновая, bayaraa | TITLE: Anti-Borrelia ELISA (IgG)
AUTHORS: Апельсинка Малиновая, bayaraa
[DESCRIPTION]
Enzyme-linked immunosorbent assays (ELISAs) were performed to detect Borrelia spp.
(B. afzelii, B. garinii, and B. burgdorferi sensu stricto) using an Anti-Borrelia Plus VlsE ELISA
for IgG kit (Euroimmun AG, Aktiengesellschaft, Lübec... | ["[Procedure] Sample incubation:\n(1st step)\n\nTransfer 100 µl of the diluted serum samples. One serum sample per well. Incubate\nat room temperature (+18 0 C to +25 0 C) for 30 minutes.\n\nWashing: Aspirate off the liquid from each well and wash 3 times each with 450µl working-\nstrength universal buffer on a rocking... |
93,212 | Immunocytochemistry | 4 | dx.doi.org/10.17504/protocols.io.yxmvm3146l3p/v1 | https://www.protocols.io/view/immunocytochemistry-c694zh8w | Oriol Busquets, Hanqin Li, Khaja Mohieddin Syed, Riana Lo Bu, Frank Soldner, Dirk Hockemeyer | TITLE: Immunocytochemistry
AUTHORS: Oriol Busquets, Hanqin Li, Khaja Mohieddin Syed, Riana Lo Bu, Frank Soldner, Dirk Hockemeyer
[DESCRIPTION]
This protocol summarizes the steps to immunostain hPSCs or differentiated cultures.
Protocol Overview
A. Cell fixation
B. Immunocytochemistry
[STEPS]
SECTION: Cell fixation
1... | ["[Cell fixation] Remove the media and gently rinse the cells with 1X PBS. Remove PBS and add 4% PFA in PBS. Incubate the cells at Room temperature (RT) for 15 min to 20 minutes.", "[Cell fixation] After fixation, discard the PFA and wash cells with 1xPBS at Room temperature for 3 times 10 min each.", "[Cell fixation] ... |
108,963 | Combining NexteraXT and Native BK to Identify Gene Expression Differences in Staphylococcus aureus Strains | 0 | null | https://www.protocols.io/view/combining-nexteraxt-and-native-bk-to-identify-gene-dnnb5dan | Katelyn Roberts | TITLE: Combining NexteraXT and Native BK to Identify Gene Expression Differences in Staphylococcus aureus Strains
AUTHORS: Katelyn Roberts
[DESCRIPTION]
The purpose of these two protocols combined is to improve the accuracy of genome assembly and gene expression analysis, especially when investigating the mechanisms o... | ["[Lysis and Confirmation] Measure Optical Density at 600nm and record the value as a reference.", "[Lysis and Confirmation] Dilute lysostaphin to a final concentration of 100 µg/µL in nuclease-free water.", "[Lysis and Confirmation] Store the lysostaphin solution on ice until ready for use.", "[Lysis and Confirmation... |
98,226 | DART Infusion Protocol | 0 | dx.doi.org/10.17504/protocols.io.rm7vzj8orlx1/v1 | https://www.protocols.io/view/dart-infusion-protocol-db6s2ree | Sasha Burwell | TITLE: DART Infusion Protocol
AUTHORS: Sasha Burwell
[DESCRIPTION]
This protocol details how to perform a DART (drug acutely restricted by tethering) intracranial infusion.
[STEPS]
SECTION: Prepare the pump
1. Attach infusion tubing (sized to match your infusion cannula) to the one or two Hamilton syringes, depending... | ["[Prepare the pump] Attach infusion tubing (sized to match your infusion cannula) to the one or two Hamilton syringes, depending on whether you are doing a unilateral or bilateral infusion.", "[Prepare the pump] Soak internal cannula (fit to guide with .5mm projection) in 100% ethanol, then dry with an air can.", "[Pr... |
52,882 | Annotating PDF documents for the GeoArchive | 1 | null | https://www.protocols.io/view/annotating-pdf-documents-for-the-geoarchive-bxvspn6e | Sky Bristol | TITLE: Annotating PDF documents for the GeoArchive
AUTHORS: Sky Bristol
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol provides steps to catalog NI 43-101 Technical Reports within the Zotero reference management system and use PDF highlighting and annotation to identify specific citat... | ["[Setup Collection in Zotero]\nSetup a local collection for the reports/documents you want to start annotating in Zotero.\nWe have created a group library in Zotero that can be used for this work, or you may elect to work in a separate collection in your own library (\"My Library\" in the Zotero client). If you would ... |
null | null | null | dx.doi.org/10.17504/protocols.io.srwed7e | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
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77,383 | Preparation Of Bacteria For Optical Microscopy (DAPI) | 1 | dx.doi.org/10.17504/protocols.io.n92ldpjr8l5b/v1 | https://www.protocols.io/view/preparation-of-bacteria-for-optical-microscopy-dap-cptfvnjn | Alfonso Pérez Escudero, gabrielmadirolas, Alid Al-Asmar | TITLE: Preparation Of Bacteria For Optical Microscopy (DAPI)
AUTHORS: Alfonso Pérez Escudero, gabrielmadirolas, Alid Al-Asmar
[DESCRIPTION]
This protocol explains how to prepare bacterial samples for optical microscopy imaging, with a DAPI staining step.
[BEFORE_START]
In order to perform this protocol, you will ne... | ["[Bacteria preparation] Pick a colony with a sterile loop and transfer it to 5mL of LB medium, in a closed 50mL tube, on 300 rpm shaking, for 22-26 hours at room temperature (our room has a controlled temperature around 22.5°C).", "[Slide preparation] Melt Agarose 1% stock by putting it in an incubator around 60°C for... |
null | null | null | dx.doi.org/10.17504/protocols.io.e34bgqw | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
<p><strong>Kit Components</strong></p>
<p><br />• Capture Antibody Coated Plate* - 1 plate<br />• a-Synuclein Standard - (1) 25μg vial<br />• 5X Wash Buffer - 250mL<br />• 2X Reagent Diluent - 32mL<br />• Biotinylated Primary Antibody - 25μL<br />• Streptavidin-HRP - 25μL<br />• ... | [] |
20,107 | U Mass - Creatinine | null | dx.doi.org/10.17504/protocols.io.xvjfn4n | null | Jason Kim | TITLE: U Mass - Creatinine
AUTHORS: Jason Kim
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span><span style = "font-weight:bold;"> </span></div><div class = "text-block">
This experiment involves a spectrophotometric measurement using Roche Cobas Clinic... | ["Perform daily quality control assessment of instrumentation before analysis.", "Load each sample into a specialized micro-sample cup for the clinical chemistry analyzer.", "Select Creatinine test on display and run the analysis.", "Collect and analyze the data."] |
60,360 | Isolation and Culture of Mouse Cortical Astrocytes | 1 | dx.doi.org/10.17504/protocols.io.yxmvmn94og3p/v1 | https://www.protocols.io/view/isolation-and-culture-of-mouse-cortical-astrocytes-b67grhjw | Ashley V Kumar, Francesca Telese | TITLE: Isolation and Culture of Mouse Cortical Astrocytes
AUTHORS: Ashley V Kumar, Francesca Telese
[DESCRIPTION]
We provide a detailed protocol to isolate and culture primary astrocytes from the cortex of postnatal day 1 or 2 (P1/P2) mice.
[BEFORE_START]
Coating tissue culture plates
Coat desired number of T75 fla... | ["[Culture Plating and Maintenance] Move inside the biosafety cabinet. Spray 15 mL tubes with alcohol. Aspirate the HBSS-G + P/S, leaving as little of the dissection medium as possible without disturbing the tissue or exposing it to air.", "[Tissue Dissection] Use a 10 cm Petri dish with ice-cold HBSS-G+P/S to dissect ... |
82,662 | LC3 Lipidation assay for ATG3 Mutants | 1 | dx.doi.org/10.17504/protocols.io.e6nvwjxodlmk/v1 | https://www.protocols.click/view/lc3-lipidation-assay-for-atg3-mutants-cuyewxte | lmstrong | TITLE: LC3 Lipidation assay for ATG3 Mutants
AUTHORS: lmstrong
[DESCRIPTION]
LC3 lipidation assay on liposomes
[STEPS]
1. Mix 1 μM ATG3 WT or mutant, 1 μM ATG7, 500 nM WIPI2d, 1 μM ATG12–ATG5-ATG16L1, 5μM LC3B
and 0.5 mg/mL extruded liposomes in reaction buffer (25mM HEPES pH 7.4, 150 mM NaCl, 1 mM TCEP).
2. Incub... | ["Mix 1 μM ATG3 WT or mutant, 1 μM ATG7, 500 nM WIPI2d, 1 μM ATG12–ATG5-ATG16L1, 5μM LC3B \nand 0.5 mg/mL extruded liposomes in reaction buffer (25mM HEPES pH 7.4, 150 mM NaCl, 1 mM TCEP).", "Incubate at room temperature for 20 minutes.", "Quench with 4X LDS loading buffer. Boil samples for 10 minutes at 60ºC. Load an... |
null | null | null | dx.doi.org/10.17504/protocols.io.gtbbwin | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Isolation of plasmid DNA from E. coli using the alkaline lysis method modified from Birnboim <em>et al.</em>, 1979. </p>
<p>This protocol is suitable for fast, cheap recovery of large amounts of plasmid, e.g. for cloning purposes or restriction analysis. However, the purity o... | [] |
94,857 | Protocol 1* | 5 | dx.doi.org/10.17504/protocols.io.ewov1qbkygr2/v3 | https://www.protocols.io/view/protocol-1-c8vhzw36 | Mitt Coats | TITLE: Protocol 1*
AUTHORS: Mitt Coats
[DESCRIPTION]
A short abstract
[STEPS]
3.
SECTION: S2
4.
SECTION: S2
5.
SECTION: S2
6.
SECTION: S0
1.
SECTION: S1
2.
SECTION: S2
7. Done
SECTION: S2
8. Yolo | ["[S2]", "[S2]", "[S2]", "[S0]", "[S1]", "[S2] Done", "[S2] Yolo"] |
93,764 | Nuclei Isolation from human cortical tissue for enrichment of endothelial and microglial cells | 4 | dx.doi.org/10.17504/protocols.io.5qpvo344zv4o/v1 | https://www.protocols.io/view/nuclei-isolation-from-human-cortical-tissue-for-en-c7tczniw | Bruno A. Benitez | TITLE: Nuclei Isolation from human cortical tissue for enrichment of endothelial and microglial cells
AUTHORS: Bruno A. Benitez
[DESCRIPTION]
This protocol of nuclei Isolation from human cortical tissue is enriched for isolation of endothelial & microglial cells
[GUIDELINES]
Use standard BSL-2 precautions when workin... | ["Protocol:\nTurn on the ultracentrifuge, set it to 4oC and ensure that decelerations are set to no brake. Get the Beckman SW 60 Ti Rotor (Swinging Bucket) and from the cold room. Beckman centrifuge tubes Ref#=328874 for 4 mLs.\nKeep all the solutions and materials on wet ice. Prepare of rest of the working solutions. ... |
104,068 | Protocol for the production and storage of Diplodia sapinea pycnidiospores | 0 | dx.doi.org/10.17504/protocols.io.kqdg3271pv25/v1 | https://www.protocols.io/view/protocol-for-the-production-and-storage-of-diplodi-dhvc362w | Anne Geertje Oostlander, Laura Brodde, Miriam von Bargen, Rasmus Enderle, Marco Leiterholt, Dagmar Trautmann, Malin Elfstrand, Jan Stenlid, André Fleißner | TITLE: Protocol for the production and storage of Diplodia sapinea pycnidiospores
AUTHORS: Anne Geertje Oostlander, Laura Brodde, Miriam von Bargen, Rasmus Enderle, Marco Leiterholt, Dagmar Trautmann, Malin Elfstrand, Jan Stenlid, André Fleißner
[DESCRIPTION]
An efficient, standardized protocol for the production and ... | ["Inoculate a 5.5 cm Petri dish containing 10 to 15 ml of solid VMM with D. sapinea with an agar plug with mycelia from a preculture on VMM.", "Incubate the plate for 21 d at 26 to 29°C with constant light (cold daylight at an intensity of 5000 to 650 lux). Pycnidia will form on the surface of the culture and open to r... |
68,271 | Tissue Slice Preparation for Visium Analysis | 4 | dx.doi.org/10.17504/protocols.io.eq2lyno9qvx9/v1 | https://www.protocols.io/view/tissue-slice-preparation-for-visium-analysis-cewptfdn | Stephen Fisher, Marielena Grijalva, Rong Guo, sarahjoh, Hieu Nguyen, John Renz, Jean G Rosario, Steven Rudich, Brian Gregory, Junhyong Kim, Kate O'Neill | TITLE: Tissue Slice Preparation for Visium Analysis
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 the preparation of tissue slices for processing with the 10X Genomi... | ["Use a cryostate to acquire a tissue slice of approximately 10μm from the OCT tissue block.", "Mount on a standard slide and perform H&E staining for quality control and the selection of the region of interest (Kruse et al., 2021). \n\nTip: When mounting the slice, take particular care to note the orientation of the s... |
94,136 | Constant Potential Amperometry in vitro | 4 | dx.doi.org/10.17504/protocols.io.yxmvm34p9l3p/v1 | https://www.protocols.io/view/constant-potential-amperometry-in-vitro-c76yzrfw | mariangela.massarocenere | TITLE: Constant Potential Amperometry in vitro
AUTHORS: mariangela.massarocenere
[DESCRIPTION]
Protocol for Constant Potential Amperometry recordings in vitro of evoked dopamine release in the rat striatum
[STEPS]
SECTION: Slice preparation
1. Anesthetize the animal by isofluorane inhalation and decapitate the animal... | ["[Slice preparation] Anesthetize the animal by isofluorane inhalation and decapitate the animal.", "[Slice preparation] Revome quickly and carefully the brain from the skull, and slice the brain in 250–300 µm thick coronal slices containing the striatum by a vibratome immersed in cooled bubbled (95% O2, 5% CO2) ‘sucro... |
71,475 | Invertebrate bulk sample metabarcoding protocol collection | 2 | dx.doi.org/10.17504/protocols.io.j8nlkw4n6l5r/v3 | https://www.protocols.io/view/invertebrate-bulk-sample-metabarcoding-protocol-co-ch2tt8en | Dominik Buchner | TITLE: Invertebrate bulk sample metabarcoding protocol collection
AUTHORS: Dominik Buchner
[DESCRIPTION]
This is a collection of protocols currently used in the LeeseLab to perform invertebrate bulk sample metabarcoding. Feel free to contact us if any questions arise.
[STEPS] | [] |
70,243 | Staphylococcus Aureus Sampling | 4 | dx.doi.org/10.17504/protocols.io.81wgb6pk1lpk/v9 | https://www.protocols.io/view/staphylococcus-aureus-sampling-cgubtwsn | Mar Roca Cugat, Olga Sánchez | TITLE: Staphylococcus Aureus Sampling
AUTHORS: Mar Roca Cugat, Olga Sánchez
[DESCRIPTION]
This protocol is intended to study the affectation of Staphylococcus Aureus, including the MRSA, VISA and VRSA variants, even if it makes the test more difficult to perform. It outlines the basic protocol for a multi-subject stud... | ["[Preparation] Wash your hands with soap. Put on your lab coat, your mask, and your goggles or face shield. Make sure your mask is airtight and air cannot escape through the sides.", "[Preparation] Prepare the area where you are going to work. Disinfect the surfaces with the bleach solution.\nThe subjects should not b... |
82,525 | High Efficiency Yeast Library Transformation | 4 | dx.doi.org/10.17504/protocols.io.j8nlkw7o6l5r/v1 | https://www.protocols.click/view/high-efficiency-yeast-library-transformation-cut5wwq6 | Benedetta Bolognesi | TITLE: High Efficiency Yeast Library Transformation
AUTHORS: Benedetta Bolognesi
[DESCRIPTION]
This is a protocol to achieve high-efficiency (10^6 transformants/replicate) when transforming yeast cells with mutational libraries.
[GUIDELINES]
Always work in sterile conditions: flame or microbiological hood.
[STEPS]
... | ["[DAY -2] Restreak yeast strains to transform from glycerol stock", "[DAY 0 Pre - growth] For each biological replicate, put 1 individual yeast colony to grow in 3 mL YPDA in culture tubes (choose three colonies that are similar in size and not too big, not too little)", "[DAY 0 Pre - growth] Prepare all media (see Ma... |
51,389 | Protocol 2 - MRI data protocol | 5 | dx.doi.org/10.17504/protocols.io.bwe5pbg6 | https://www.protocols.io/view/protocol-2-mri-data-protocol-bwe5pbg6 | Sophie Adler, Mathilde Ripart, Meld Project, Konrad Wagstyl | TITLE: Protocol 2 - MRI data protocol
AUTHORS: Sophie Adler, Mathilde Ripart, Meld Project, Konrad Wagstyl
[DESCRIPTION]
The MELD Project is an international collaboration aiming to create open-access, robust and generalisable tools for FCD detection.
This MRI data protocol details
1) The MRI data required / des... | ["[Retrieval of MRI data] Prepare your data \n\nDownload the meld_focal_epilepsy_data folder from : https://figshare.com/s/763e50f4eb51a4f76f58\n\nKeep note of where you save this folder as it will be your data folder : <path_to_meld_focal_epilepsy_data_folder> \n\nYou will need to unzip the folder :\n\n \n\n\n\nAnonym... |
70,965 | Phosphorus Extraction - Bray Method | 1 | dx.doi.org/10.17504/protocols.io.3byl4jkbolo5/v1 | https://www.protocols.io/view/phosphorus-extraction-bray-method-chivt4e6 | maggie.bowman | TITLE: Phosphorus Extraction - Bray Method
AUTHORS: maggie.bowman
[DESCRIPTION]
The method estimates the relative bioavailability of inorganic ortho-phosphate (PO4-P) in soils with acid to neutral pH.
[STEPS]
1. Print the required labels needed for Bray extraction for each site, depth, and replicate.
2. Weigh out 2... | ["Print the required labels needed for Bray extraction for each site, depth, and replicate.", "Weigh out 2 gof soil into labeled 50 mL centrifuge tubes.", "Add 14 mL of Bray 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... |
null | null | null | dx.doi.org/10.17504/protocols.io.fewbjfe | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
<p>The following is a list of antibody concentrations for use with the protocol 'Immunohistochemistry - Drosophila Embryos'<br />Custom antibodies were provided by the published authors.<br /><br />DSHB Antibodies</p>
<table style="border-collapse: collapse; width: 853pt;" border... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.chnt5d | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?. | [] |
91,715 | Dual-target detection of Mpox virus | 1 | dx.doi.org/10.17504/protocols.io.n2bvj3b8plk5/v1 | https://www.protocols.io/view/dual-target-detection-of-mpox-virus-c5tby6in | Alan O'Dwyer, Tracy Lee, Michael Chan, Branco Cheung, Frankie Tsang, John Tyson, Kathleen Kolehmainen, Natalie Prystajecky, Agatha Jassem | TITLE: Dual-target detection of Mpox virus
AUTHORS: Alan O'Dwyer, Tracy Lee, Michael Chan, Branco Cheung, Frankie Tsang, John Tyson, Kathleen Kolehmainen, Natalie Prystajecky, Agatha Jassem
[DESCRIPTION]
This procedure provides instructions for detecting Mpox virus and human beta-globin using a laboratory developed fa... | ["[Prepare master mix] Prepare the master mix cocktail according to the following table. Invert mixture gently several times to mix and quickly spin down.", "[Mpox PCR] In a Biological Safety Cabinet, transfer 5µL of sample extract and controls to the optical plate in order:\nPatient Sample Extracts\nPositive and Negat... |
48,101 | Freeze Drier Vacuum Pump Oil Change Protocol | 1 | null | https://www.protocols.io/view/freeze-drier-vacuum-pump-oil-change-protocol-bs8dnhs6 | Josh Birlingmair | TITLE: Freeze Drier Vacuum Pump Oil Change Protocol
AUTHORS: Josh Birlingmair
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol for changing the oil of a Freeze Drier Vacuum</div></div>
[STEPS]
?. [Removing Pump from Freeze Drier]
Take fill plug out of top end of pump reservoir with Allen wr... | ["[Removing Pump from Freeze Drier]\nTake fill plug out of top end of pump reservoir with Allen wrench", "[Removing Pump from Freeze Drier]\nOpen Oil drain valve on back of pump and drain oil into small drain pans dumping as needed into gallon jug marked used oil.", "[Removing Pump from Freeze Drier]\nUnplug pump from ... |
18,478 | Epidural morphine combined with single-injection femoral nerve block for postoperative analgesia in patients after total knee arthroplasty: a randomized controlled trial | null | dx.doi.org/10.17504/protocols.io.wanfade | null | Zhao-Ting Meng, Fan Cui, Xue-Ying Li, Dong-Xin Wang | TITLE: Epidural morphine combined with single-injection femoral nerve block for postoperative analgesia in patients after total knee arthroplasty: a randomized controlled trial
AUTHORS: Zhao-Ting Meng, Fan Cui, Xue-Ying Li, Dong-Xin Wang
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Total knee art... | ["[Enrollment]\nPatients will be screened the day before surgery. And eligible patients will be enrolled for their consent in advance and written informed consent will be signed.", "[Randomization]\nThis is a randomized, double-blind, and placebo-controlled one-center trial. The random numbers were generated in a 1:1 r... |
48,176 | MojoSort™ Human CD56 Nanobeads Protocol | 4 | null | https://www.protocols.io/view/mojosort-human-cd56-nanobeads-protocol-btaqnidw | Ken Lau | TITLE: MojoSort™ Human CD56 Nanobeads Protocol
AUTHORS: Ken Lau
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">"MojoSort™ Human CD56 Nanobeads Protocol</span><span></span></div></div>
[STEPS]
?. Prepare cells from your tissue of interest or blood without lysing er... | ["Prepare cells from your tissue of interest or blood without lysing erythrocytes.", "In the final wash of your sample preparation, resuspend the cells in MojoSort™ Buffer by adding up to 4 mL in a 5 mL (12 x 75 mm) polypropylene tube.Note: Keep MojoSort™ Buffer on ice throughout the procedure.", "Filter the cells with... |
null | null | null | dx.doi.org/10.17504/protocols.io.rkkd4uw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Lentiviral vectors pseudotyped with influenza surface glycoproteins represent an alternative to wild type virus for serological assays. The influenza neuraminidase (NA) has the ability to bud and release new virions with or without the contribution of Haemagglutinin (HA). Inf... | [] |
103,529 | Perturb-FISHv3 | 4 | dx.doi.org/10.17504/protocols.io.6qpvr356bvmk/v1 | https://www.protocols.io/view/perturb-fishv3-dhch32t6 | loic binan, Sami Farhi, Brian Cleary | TITLE: Perturb-FISHv3
AUTHORS: loic binan, Sami Farhi, Brian Cleary
[DESCRIPTION]
This is the 07-21-2024 update version to this protocol protocol describes how the Sami Farhi lab, https://www.broadinstitute.org/bios/sami-farhi, carries out Perturb-FISH and was provided by Loïc Binan, https://sites.broadinstitute.org/o... | [] |
39,671 | SOLUTION- 12 – HBSS-HEPES for ROS measurement in PMN | 3 | dx.doi.org/10.17504/protocols.io.biyxkfxn | https://www.protocols.io/view/solution-12-hbss-hepes-for-ros-measurement-in-pmn-biyxkfxn | Marco Cosentino, Elisa Storelli, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Marco Ferrari, Franca Marino | TITLE: SOLUTION- 12 – HBSS-HEPES for ROS measurement in PMN
AUTHORS: Marco Cosentino, Elisa Storelli, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Marco Ferrari, Franca Marino
[STEPS] | [] |
102,587 | Crude Subcellular fractionation of FAM177A1-GFP expressing cells | 0 | dx.doi.org/10.17504/protocols.io.n2bvjn2ypgk5/v1 | https://www.protocols.io/view/crude-subcellular-fractionation-of-fam177a1-gfp-ex-dge33tgn | Berrak Ugur, Michael G. Hanna, Pietro De Camilli | TITLE: Crude Subcellular fractionation of FAM177A1-GFP expressing cells
AUTHORS: Berrak Ugur, Michael G. Hanna, Pietro De Camilli
[DESCRIPTION]
This protocol details the crude subcellular fractionation of FAM177A1-GFP expressing cells.
[STEPS]
SECTION: Crude Subcellular fractionation
1.
Culture and transfect HeLa... | ["[Crude Subcellular fractionation] Culture and transfect HeLa cells as described in dx.doi.org/10.17504/protocols.io.eq2lyp55mlx9/v1", "[Crude Subcellular fractionation] 1440 min-2880 min after transfection, wash cells in 6 well plates with PBS.", "[Crude Subcellular fractionation] Add 200 µL PBS (or fractionation buf... |
18,370 | Drug distribution imaging of rabbit whole-eye section by MALDI mass spectrometry | null | dx.doi.org/10.17504/protocols.io.v7ae9ie | null | Naoto Mori, Takaharu Mochizuki, Fumiyoshi Yamazaki, Shiro Takei, Hidetoshi Mano, Takeshi Matsugi, Mitsutoshi Setou | TITLE: Drug distribution imaging of rabbit whole-eye section by MALDI mass spectrometry
AUTHORS: Naoto Mori, Takaharu Mochizuki, Fumiyoshi Yamazaki, Shiro Takei, Hidetoshi Mano, Takeshi Matsugi, Mitsutoshi Setou
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Matrix-assisted laser desorption/ionizat... | ["[Enucleation of eyeball from rabbit]\nImmediately after euthanizing the animal, its eyeball is excised, washed in saline, and enucleated. Excess saline solution is absorbed by blotting with a paper towel.\nWash out ophthalmic solution by washing the eyeball in saline to prevent contamination.", "[Preparation of froze... |
60,136 | Modified NEBNext® VarSkip Short SARS-CoV-2 Library Prep Kit for Illumina Platforms - adapted for wastewater samples | 1 | dx.doi.org/10.17504/protocols.io.5jyl89n26v2w/v3 | https://www.protocols.io/view/modified-nebnext-varskip-short-sars-cov-2-library-b6ygrftw | Padmini Ramachandran, Tamara Walsky, Amanda Windsor, Maria Hoffmann, Chris Grim | TITLE: Modified NEBNext® VarSkip Short SARS-CoV-2 Library Prep Kit for Illumina Platforms - adapted for wastewater samples
AUTHORS: Padmini Ramachandran, Tamara Walsky, Amanda Windsor, Maria Hoffmann, Chris Grim
[DESCRIPTION]
PURPOSE:
This method was developed at the FDA’s Center for Food Safety and Applied Nu... | ["[cDNA Synthesis]", "[cDNA Synthesis] Gently mix and spin down the LunaScript RT SuperMix reagent. Prepare the cDNA synthesis reaction as described below:\n \n\nFor no template controls, mix the following components:", "[cDNA Synthesis] Flick the tubes or pipet up and down 10 times to mix followed by a quick spin.", "... |
39,264 | iSeq Bacterial WGS Protocol | 1 | dx.doi.org/10.17504/protocols.io.bij8kcrw | https://www.protocols.io/view/iseq-bacterial-wgs-protocol-bij8kcrw | Sarah Nemser, Laura Goodman, Renee Anerson, Melanie Prarat, Katherine Shiplett | TITLE: iSeq Bacterial WGS Protocol
AUTHORS: Sarah Nemser, Laura Goodman, Renee Anerson, Melanie Prarat, Katherine Shiplett
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Whole genome sequencing procedure using Qiagen spin columns for DNA extraction, Illumina DNA Prep (previously called Nextera Flex... | ["[Bacterial propagation and DNA extraction]\nFrozen isolates should be sub-cultured on Trypticase Soy + 5% Sheep Blood Agar plates (BAPs) or equivalent media. If the culture appears pure, pick an isolated colony, and streak it on a fresh BAP; incubate at 35°C overnight (24±2 hours) in aerobic conditions.", "[Bacterial... |
32,871 | Electroporation Protocol (C2986) | 1 | dx.doi.org/10.17504/protocols.io.bccfistn | https://www.protocols.io/view/electroporation-protocol-c2986-bccfistn | New England Biolabs | TITLE: Electroporation Protocol (C2986)
AUTHORS: New England Biolabs
[DESCRIPTION]
NEB Turbo Electrocompetent E. coli cells are suitable for high efficiency electroporation and rapid colony growth. These cells are ideal for DNA library constructions and all cloning purposes.
[GUIDELINES]
Features
Electroporation T... | ["[Preparation] Prepare 17 mm x 100 mm round-bottom culture tubes (e.g. VWR #60818-667) at Room temperature.", "[Preparation] Place SOC recovery medium in a 37 °C water bath.", "[Preparation] Pre-warm selective plates at 37 °C for 60 min.", "[Electroporation] Place electroporation cuvettes (1 mm) and microcentrifuge tu... |
null | null | null | dx.doi.org/10.17504/protocols.io.re2d3ge | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol is for comparing two different samples at the transcript level, using long reads that are mapped to transcripts.</p>
<p> </p>
<p><strong>Input(s)</strong>: stranded fastq files (see steps 1-8 of <a href="https://dx.doi.org/10.17504/protocols.io.n8ddhs6" target="... | [] |
82,877 | Extraction and qPCR of Environmental Surveillance samples for the detection of Salmonella Typhi | 4 | dx.doi.org/10.17504/protocols.io.8epv5zrw4v1b/v3 | https://www.protocols.click/view/extraction-and-qpcr-of-environmental-surveillance-cu65wzg6 | Dilip Abraham, Nicola Elviss, Nicholas Feasey, Nick Grassly, Jacob John, Gagandeep Kang, John Scott Meschke, Venkata Raghava Mohan, Satheesh Nair, Jonathan Rigby, Rajan Srinivasan, Catherine Troman, Christopher Uzzell, Nicolette Zhou | TITLE: Extraction and qPCR of Environmental Surveillance samples for the detection of Salmonella Typhi
AUTHORS: Dilip Abraham, Nicola Elviss, Nicholas Feasey, Nick Grassly, Jacob John, Gagandeep Kang, John Scott Meschke, Venkata Raghava Mohan, Satheesh Nair, Jonathan Rigby, Rajan Srinivasan, Catherine Troman, Christoph... | ["[DNA Extraction] For extraction from Moore swabs, empty the contents of a PowerBead tube provided in the extraction kit into the PowerBead tube used for storing the filter.\n\nFor the pellet from membrane filtration, resuspend the pellet in 800µl CD1 from the first step of the DNA extraction protocol, then transfer t... |
71,452 | Drug feeding protocol | 4 | dx.doi.org/10.17504/protocols.io.5jyl8j9n9g2w/v1 | https://www.protocols.io/view/drug-feeding-protocol-chz4t78w | Mel Feany | TITLE: Drug feeding protocol
AUTHORS: Mel Feany
[DESCRIPTION]
This protocol covers the steps for drug feeding in fly models.
[STEPS]
1. Collect flies for feeding:
-Clear bottles the day before collecting
-Select appropriate genotype for feeding
2. Prepare drugs to be fed:
-Thaw drugs
-Add 3 mL water to each vial
-Add... | ["Collect flies for feeding:\n-Clear bottles the day before collecting\n-Select appropriate genotype for feeding", "Prepare drugs to be fed:\n-Thaw drugs\n-Add 3 mL water to each vial\n-Add appropriate number of ul drug to water, mix by swirling", "Make fly food in vials that contain water and drug:\n-Place the label t... |
null | null | null | dx.doi.org/10.17504/protocols.io.g2nbyde | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>We have developed a plaque assay for AaV with a modified protocol from Schroeder et. al 2002. </p>
<p> </p>
<p> </p>
<p><em>Protocol modified from</em>:</p>
<p> </p>
<p>Schroeder, D.C., et al.,<em> Coccolithovirus</em> (<em>Phycodnaviridae</em>): Characterisation of a new lar... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.cqevtd | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This is a protocol for a typical DNase I Reaction, using the M0303 RNase-free DNase I.
[STEPS]
?.
?.
?.
?.
?.
?. | [] |
95,698 | Nuclei Preparation from Frozen Tissue for 10X Multiome using Dounce Homogenization, Iodixanol Gradient Centrifugation, and FANS (v1.2, Jan 2024) | 0 | dx.doi.org/10.17504/protocols.io.rm7vzx435gx1/v1 | https://www.protocols.io/view/nuclei-preparation-from-frozen-tissue-for-10x-mult-c9psz5ne | ereisner | TITLE: Nuclei Preparation from Frozen Tissue for 10X Multiome using Dounce Homogenization, Iodixanol Gradient Centrifugation, and FANS (v1.2, Jan 2024)
AUTHORS: ereisner
[DESCRIPTION]
This protocol describes isolation of nuclei from frozen tissue using dounce homogenization, iodixanol gradient centrifugation, and FANS... | ["[Reagent Preparation] Prepare stock Diluent Buffer (1 mL) and 50% iodixanol (6 mL) at room temperature, if needed.", "[Reagent Preparation] on ice Prepare all other buffers fresh on ice.", "[Nuclei Preparation] Pre-chill a large, swing-bucket tabletop centrifuge to 4°C.", "[Nuclei Preparation] Retrieve a 1 mL dounce ... |
64,979 | 2022 featured protocols | 2 | dx.doi.org/10.17504/protocols.io.q26g74nk3gwz/v1 | https://www.protocols.io/view/2022-featured-protocols-cbptsmnn | Admin User | TITLE: 2022 featured protocols
AUTHORS: Admin User
[DESCRIPTION]
2022 featured protocols
[STEPS] | [] |
78,945 | CARD COUNT AND VIAL DEPLOYMENT/RETRIEVAL PROTOCOL | 4 | dx.doi.org/10.17504/protocols.io.ewov1oky2lr2/v1 | https://www.protocols.io/view/card-count-and-vial-deployment-retrieval-protocol-crb9v2r6 | Grace Sandel, Laura Barragan, Erica Garibay, Kiran Bengard, Ellis Gelt, Sage Moloney, Juliet Capriola, Kalani Alcala, clairewiegand, ame | TITLE: CARD COUNT AND VIAL DEPLOYMENT/RETRIEVAL PROTOCOL
AUTHORS: Grace Sandel, Laura Barragan, Erica Garibay, Kiran Bengard, Ellis Gelt, Sage Moloney, Juliet Capriola, Kalani Alcala, clairewiegand, ame
[DESCRIPTION]
Procedure to conduct "Crazy Yellow Ant Sampling on Tetiaroa"
This protocol provides instructions for p... | ["[Card Count Protocol] If needed, scrape the ground (at least a 10x10cm area) at the site so the card sits flat on the ground (i.e. if there are branches or leaf litter, scrape them away).", "[Card Count Protocol] Place the card down on the ground.", "[Card Count Protocol] For 30 seconds, count the number of yellow cr... |
89,301 | OSU TriState SenNet H&E staining of Formalin-Fixed, Paraffin-Embedded (FFPE) tissue sections | 1 | dx.doi.org/10.17504/protocols.io.j8nlkombxv5r/v1 | https://www.protocols.io/view/osu-tristate-sennet-h-amp-e-staining-of-formalin-f-c3fvyjn6 | Lorena Rosas, Ana L Mora, mauricio.rojas | TITLE: OSU TriState SenNet H&E staining of Formalin-Fixed, Paraffin-Embedded (FFPE) tissue sections
AUTHORS: Lorena Rosas, Ana L Mora, mauricio.rojas
[DESCRIPTION]
Hematoxylin and eosin (H&E) stains are essential for recognizing the different tissue types and morphologic changes that contribute to the diagnosis of... | ["[Staining Procedure] Prepare slides", "[Staining Procedure] Place the slides at 60 °C for 30 minutes.", "[Staining Procedure] The solutions are fill in square glass staining jars.", "[Staining Procedure] Place slides in glass staining racks.", "[Staining Procedure] Deparaffinization of tissue slides: Remove remaining... |
50,456 | Single-cell total RNA extraction from marine protists (e.g. Acantharia, Strombidium cf basimorphum, and Prymnesium parvum) | 4 | dx.doi.org/10.17504/protocols.io.bvhyn37w | https://www.protocols.io/view/single-cell-total-rna-extraction-from-marine-proti-bvhyn37w | Joost Mansour, Konstantinos Anestis, Fabrice Not, Uwe John | TITLE: Single-cell total RNA extraction from marine protists (e.g. Acantharia, Strombidium cf basimorphum, and Prymnesium parvum)
AUTHORS: Joost Mansour, Konstantinos Anestis, Fabrice Not, Uwe John
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:left">Man... | ["[Reagent and general preparations]\nSamples need to have been acquired in (from the ). See our sampling protocol here:dx.doi.org/10.17504/protocols.io.bqvrmw56\n100 µl", "[Reagent and general preparations]\nPrepare and label two RNase-free tubes per sample, one tube for the total RNA extract and one tube for an aliq... |
99,790 | Tissue culture- Purity sorting HEK293T LLP iCasp9 cells | 0 | dx.doi.org/10.17504/protocols.io.36wgqnjjxgk5/v1 | https://www.protocols.io/view/tissue-culture-purity-sorting-hek293t-llp-icasp9-c-ddpn25me | Raining Wang, Melinda Wheelock | TITLE: Tissue culture- Purity sorting HEK293T LLP iCasp9 cells
AUTHORS: Raining Wang, Melinda Wheelock
[DESCRIPTION]
This protocol covers the sorting of landing pad cells (HEK293T-LLP-iCasp9-blast) for purity prior to starting VAMPseq experiments. This avoids using cells which have undergone landing pad silencing, and... | ["[Preparation of cells] Remove media from flask by aspiration.", "[Preparation of cells] Wash flask with 10 mL DPBS. Remove DPBS by aspiration.", "[Preparation of cells] Add 3 mL trypsin to the culture flask. Place in a 37 °C incubator with 5% CO2 for 5 min.", "[Preparation of cells] Visualize trypsinized cells under ... |
103,644 | 3D fluorescence staining and imaging of low amount of organoids | 0 | dx.doi.org/10.17504/protocols.io.kqdg323m7v25/v1 | https://www.protocols.io/view/3d-fluorescence-staining-and-imaging-of-low-amount-dhf433qw | Ami G. Toulehohoun, Carolin Bouzin, Aurelie Daumerie, Luca Maccioni, Peter Stärkel | TITLE: 3D fluorescence staining and imaging of low amount of organoids
AUTHORS: Ami G. Toulehohoun, Carolin Bouzin, Aurelie Daumerie, Luca Maccioni, Peter Stärkel
[DESCRIPTION]
The emerging field of 3D organ modeling encounters several imaging issues in particular related to antigen retrieval and sample lost during st... | ["[Crypt isolation ○ Timing 3h] Collect duodenum biopsies in sterile PBS (without Ca2+ or Mg2+).", "[Crypt isolation ○ Timing 3h] Wash 3x2 min under mild rotation in PBS + antibiotics and antimycotic 100X (Invitrogen, 15240062, 1/200). (1/3)", "[Crypt isolation ○ Timing 3h] Incubate for 60 min in 2 millimolar (mM) EDTA... |
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