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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48,881 | High Throughput RNA Extraction and PCR Inhibitor Removal of Settled Solids for Wastewater Surveillance of SARS-CoV-2 RNA | 1 | dx.doi.org/10.17504/protocols.io.btyrnpv6 | https://www.protocols.io/view/high-throughput-rna-extraction-and-pcr-inhibitor-r-btyrnpv6 | Aaron Topol, marlene.wolfe , Krista Wigginton, Bradley White, Alexandria Boehm | TITLE: High Throughput RNA Extraction and PCR Inhibitor Removal of Settled Solids for Wastewater Surveillance of SARS-CoV-2 RNA
AUTHORS: Aaron Topol, marlene.wolfe , Krista Wigginton, Bradley White, Alexandria Boehm
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This process instruction describes t... | ["[RNA Extraction with the Chemagic 360 Process Steps]\nUsing a wide orifice 1000 µL pipette tip, transfer per well of homogenized sample (prepared as specified in High Throughput pre-analytical processing of wastewater settled solids for SARS-CoV-2 RNA analyses) to each well of the Sample Plate as follows:\n300 µl", ... |
null | null | null | dx.doi.org/10.17504/protocols.io.dw77hm | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol is from: <br /><span class="cit-title">Jian Cao, <em>et. al. </em>(2014) <a href="http://www.genetics.org/content/197/1/175.full" target="_blank">Insight into Insulin Secretion from Transcriptome and Genetic Analysis of Insulin-Producing Cells of Drosophila</a><br ... | [] |
47,301 | Mouse Whole Cell Tissue Processing for 10x Genomics Platform | 1 | dx.doi.org/10.17504/protocols.io.bsfdnbi6 | https://www.protocols.io/view/mouse-whole-cell-tissue-processing-for-10x-genomic-bsfdnbi6 | Allen Institute for Brain Science | TITLE: Mouse Whole Cell Tissue Processing for 10x Genomics Platform
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes how to isolate tissue from various ROI’s of the mouse brain followed by preparation of a highly concentrated single c... | [] |
39,946 | Coral tissue and skeleton Trizol RNA extraction | 4 | dx.doi.org/10.17504/protocols.io.bi9ikh4e | https://www.protocols.io/view/coral-tissue-and-skeleton-trizol-rna-extraction-bi9ikh4e | Molly Moynihan | TITLE: Coral tissue and skeleton Trizol RNA extraction
AUTHORS: Molly Moynihan
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol was modified from the TRIzol protocol provided by Invitrogen. </div><div class = "text-block"><a href="https://assets.thermofisher.com/TFS-Assets/LSG/manuals/t... | ["[Set Up]\nCleaning and tips to avoid contamination:Clean UV hood and fume hood with bleach, ethanol, RNaseZap, and sterilize UV hood for 15 minutes.Clean all pipette tips with bleach, ethanol, RNaseZap. Keep UV hood and fume hood pipettes separate.Use reagents that are dedicated for RNA work. Prepare solutions and al... |
83,826 | Induced Pluripotent Stem Cell Reagents | 3 | dx.doi.org/10.17504/protocols.io.rm7vzxnorgx1/v1 | https://www.protocols.click/view/induced-pluripotent-stem-cell-reagents-cv4sw8we | Mallory Wright | TITLE: Induced Pluripotent Stem Cell Reagents
AUTHORS: Mallory Wright
[DESCRIPTION]
reagents used to maintain our IPSC
[STEPS] | [] |
77,245 | DAPI-Based Polyphosphate Estimation with Extraction Sufficiency Validation: A Method for Quantifying Polyphosphate from Microalgae Samples | 1 | dx.doi.org/10.17504/protocols.io.ewov1ox87lr2/v1 | https://www.protocols.io/view/dapi-based-polyphosphate-estimation-with-extractio-cpn5vmg6 | Ying-Yu Hu, Zoe V. Finkel | TITLE: DAPI-Based Polyphosphate Estimation with Extraction Sufficiency Validation: A Method for Quantifying Polyphosphate from Microalgae Samples
AUTHORS: Ying-Yu Hu, Zoe V. Finkel
[DESCRIPTION]
The utilization of DAPI-based fluorometric estimation for polyphosphate (polyP) analysis from microalgae has become increasi... | ["[Sample collection] Filter microalgae in liquid media onto GFF or PC filters, using gentle vacuum pressure (5 inches Hg).", "[Sample collection] Rinse sample with filtered artificial seawater (no nutrients)", "[Sample collection] Place sample filters in cryogenic vials", "[Sample collection] Filter blank media (witho... |
80,055 | Total nucleic acid extraction - NucleoMag® DNA/RNA Water Kit (MACHEREY-NAGEL Inc.) | 4 | dx.doi.org/10.17504/protocols.io.q26g7yjq9gwz/v1 | https://www.protocols.io/view/total-nucleic-acid-extraction-nucleomag-dna-rna-wa-csexwbfn | Adélaïde Roguet, Melissa Schussman | TITLE: Total nucleic acid extraction - NucleoMag® DNA/RNA Water Kit (MACHEREY-NAGEL Inc.)
AUTHORS: Adélaïde Roguet, Melissa Schussman
[DESCRIPTION]
Total nucleic acid extraction from wastewater using Maxwell(R) HT Environmental TNA Kit, custom (Promega)
[BEFORE_START]
1. Clean the working area and all equipment: wipe... | ["[Total nucleic acid extraction] For HA filter extraction, let the sample thaw on ice and go to step 2. \n\nFor BCoV/BRSV extraction (in duplicate), add 5 µL of BCoV/BRSV solution to the 2-mL tube containing 475 µL MWA1. Vortex for 15 seconds (speed 7 out of 10) and flash freeze the tube. Go to step 4.\n\nFor Direct e... |
null | null | null | dx.doi.org/10.17504/protocols.io.uj5euq6 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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?. | ["Feet evil to hold long he open knew an no. Apartments occasional boisterous as solicitude to introduced. Or fifteen covered we enjoyed demesne is in prepare. In stimulated my everything it literature. Greatly explain attempt perhaps in feeling he. House men taste bed not drawn joy. Through enquire however do equally ... |
101,197 | Immunostaining- Fluorescent | 0 | dx.doi.org/10.17504/protocols.io.j8nlk88y6l5r/v1 | https://www.protocols.io/view/immunostaining-fluorescent-de3m3gk6 | daniel.dautan daniel, Per Svenningsson | TITLE: Immunostaining- Fluorescent
AUTHORS: daniel.dautan daniel, Per Svenningsson
[DESCRIPTION]
Staining of mouse brain sections with immunofluroescent visualization.
[STEPS]
1. Wash freshly sectioned slices of tissue 2-3 times with 1X PBS to remove OCT.
2. Block with 5% Normal donkey/Goat serum in 0.3% TRITON X-10... | ["Wash freshly sectioned slices of tissue 2-3 times with 1X PBS to remove OCT.", "Block with 5% Normal donkey/Goat serum in 0.3% TRITON X-100 in 1X PBS for 60 min at Room temperature.", "Wash sections 5 times in 1X PBS.", "Following washes, transfer sections to a primary antibody solution containing a mix of primary an... |
55,387 | DAPI reconstitution and viability staining | 1 | null | https://www.protocols.io/view/dapi-reconstitution-and-viability-staining-b2b3qaqn | Emily Stephenson | TITLE: DAPI reconstitution and viability staining
AUTHORS: Emily Stephenson
[DESCRIPTION]
For the reconstitution of DAPI to make a stock solution and dilution for a working solution.
Details of viability staining volumes also provided.
[STEPS]
SECTION: Reconstitution
1. Add 2ml of water to the 10mg vial of DAPI to... | ["[Reconstitution] Add 2ml of water to the 10mg vial of DAPI to make a 14.3mM (5mg/mL) stock solution. Vortexing may be required if the powder does not dissolve with pipetting. \n\n(Note: DAPI will not dissolve in PBS)\n\nAdd a label with the date of reconstitution and store this stock solution at 4 degrees C for 6 mon... |
89,369 | Quantification of Proteins and Genes Associated with Endothelial Cell Function after Different Shear Stress Intensities in vitro | 1 | dx.doi.org/10.17504/protocols.io.ewov1q34kgr2/v1 | https://www.protocols.io/view/quantification-of-proteins-and-genes-associated-wi-c3hzyj76 | Daniel Conde, Mario Garcia, Manuel Gomez, Alvaro Gurovich | TITLE: Quantification of Proteins and Genes Associated with Endothelial Cell Function after Different Shear Stress Intensities in vitro
AUTHORS: Daniel Conde, Mario Garcia, Manuel Gomez, Alvaro Gurovich
[DESCRIPTION]
This protocol describes the steps necessary to culture human umbilical vein endothelial cells (HUVEC),... | ["[Huvec Cell Seeding] Notes: This step aims to increase the number of HUVEC in a T-75 flask before seeding them in an Ibidi µ-Slide I Luer with a channel height of 0.2 mm. The following procedures must be performed inside a biosafety cabinet with HEPA-filtered laminar flow. To avoid contamination inside the biosafety ... |
48,878 | Purification of α-synuclein from E. coli | 4 | dx.doi.org/10.17504/protocols.io.btynnpve | https://www.protocols.io/view/purification-of-synuclein-from-e-coli-btynnpve | Felix Kraus, vtrinkaus , Ruben Fernandez Busnadiego | TITLE: Purification of α-synuclein from E. coli
AUTHORS: Felix Kraus, vtrinkaus , Ruben Fernandez Busnadiego
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol details methods for the purification of α-synuclein from E. coli – adapted from Volpicelly-Daley, Nat Protoc 2014.</div></div>
[... | ["[Purification of α-synuclein from E. coli]\nTransform plasmid pT7-7 α-synuclein (α-syn, WT or A53T mutant) into BL21(DE3) cells (Agilent).\npT7-7 plasmids contain an Ampicillin (Amp) resistance. We thank Hilal Lashuel for depositing the plasmids on Addgene (Addgene, #105727 and #36046).", "[Purification of α-synuclei... |
41,821 | Cellex qCoV Protocol | 4 | dx.doi.org/10.17504/protocols.io.bk35kyq6 | https://www.protocols.io/view/cellex-qcov-protocol-bk35kyq6 | X James Li, Kwok Min Hui, Don A Gabriel | TITLE: Cellex qCoV Protocol
AUTHORS: X James Li, Kwok Min Hui, Don A Gabriel
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Cellex’s qCOV assay is a viral enzyme activity assay, which detects the activity of coronaviral protease 3CL (chymotrypsin-like protease) in 15 minutes with sensitivity equiv... | ["[Sample Collection]\nPrep for Sample Collection: Prefill 0.25 mL of sample buffer to a sample extraction vial. Place the vial in a test tube rack.", "[Sample Collection]\nSample Collection: Use a throat swab to collect a throat swab specimen, making sure that epithelial cells are collected from the oropharynx. Inse... |
34,798 | Counting Microalgae Culture Density | null | dx.doi.org/10.17504/protocols.io.bd8ni9ve | https://www.protocols.io/view/counting-microalgae-culture-density-bd8ni9ve | Jakub Nedbal | TITLE: Counting Microalgae Culture Density
AUTHORS: Jakub Nedbal
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Counting culture cell density offers a reliable way of consistend seeding density for freshly inoculated cultures and allows tracking the growth of the cultures. Cell densiry counting, as... | ["[Loading Microalgae into the Hemocytometer]\nWipe down the sterile laminar flow cabinet with 70 % denatured ethanol solution.Prepare the hemocytometer, P20 pipette and pipette tips in the sterile cabinet.", "[Loading Microalgae into the Hemocytometer]\nMark down the temperature on the shaker.", "[Loading Microalgae... |
36,717 | High-throughput SARS-CoV-2 and host genome sequencing - alignment protocol | 1 | null | https://www.protocols.io/view/high-throughput-sars-cov-2-and-host-genome-sequenc-bf4mjqu6 | Christopher Hughes | TITLE: High-throughput SARS-CoV-2 and host genome sequencing - alignment protocol
AUTHORS: Christopher Hughes
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is designed to perform alignment on low-coverage (0.5x - 3x) whole-genome human sequences from Illumina MiSeq and NovaSeq platf... | ["[Alignment]\nThe pipeline is broken into two steps: alignment and recalibration. First, alignment is performed using the alignment.sh script:", "[Recalibration]\nAfter each lane for the sample has been aligned, the .bams are merged, duplicates are marked and base recalibration is performed using recalibration.sh:", "... |
25,184 | Detection of the rearrangement of exons 9-12 of the BRCA1 gene with the use of multiplex PCR | null | dx.doi.org/10.17504/protocols.io.4t8gwrw | null | Veronica Fragoso, Velazquez-Aragon JA, Alvarez-Gomez RM. | TITLE: Detection of the rearrangement of exons 9-12 of the BRCA1 gene with the use of multiplex PCR
AUTHORS: Veronica Fragoso, Velazquez-Aragon JA, Alvarez-Gomez RM.
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:left"><span>In this protocol we developed a... | ["[PCR mix to detection of the rearragement of exons 9-12 of BRCA1 gene]\nNote: This mix is to one reaction, you must consider how many reactions will be done. Add ultrapure water to microtube of each mix (two mixes). Mix one ; Mix two\n14.1 µl\n14.9 µl", "[PCR mix to detection of the rearragement of exons 9-12 of BRC... |
28,128 | DNA Extraction from Modern Dental Calculus | 1 | dx.doi.org/10.17504/protocols.io.7p8hmrw | https://www.protocols.io/view/dna-extraction-from-modern-dental-calculus-7p8hmrw | Franziska Aron | TITLE: DNA Extraction from Modern Dental Calculus
AUTHORS: Franziska Aron
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol for DNA extraction from modern dental calculus samples for Illumina sequencing. This protocol uses the Qiagen PowerSoil DNA extraction kit. </div></div>
[STEPS]
?. [Sam... | ["[Sample Preparation]\nWeigh out to of the calculus and transfer it into a 2ml-Eppendorf Safe-Lock DNA LoBind-Tube (use special accuracy scales)\n3 mg\n5 mg", "[Lysis]\nCrush the calculus with a sterile metal pestle within the tube.", "[Lysis]\nAdd EDTA and Proteinase K ( )\n250 µl\n12.5 µl\n[/ml]", "[Lysis]\nL... |
61,821 | Expression and purification protocol of GST-mCh-FYVE | 1 | dx.doi.org/10.17504/protocols.io.ewov1n39pgr2/v1 | https://www.protocols.io/view/expression-and-purification-protocol-of-gst-mch-fy-b8k5ruy6 | Liv Jensen, Chunmei Chang | TITLE: Expression and purification protocol of GST-mCh-FYVE
AUTHORS: Liv Jensen, Chunmei Chang
[DESCRIPTION]
This protocol details the expression and purification of GST-mCherry-FYVE.
[STEPS]
SECTION: Protein expression
1. Transform the E.Coli BL21DE3 cells with plasmid encoding for GST-mCh-FYVE and plate them on ... | ["[Protein expression] Transform the E.Coli BL21DE3 cells with plasmid encoding for GST-mCh-FYVE and plate them on Amp plate.", "[Protein expression] Carry out protein expression in 1 L medium, induce with 200 micromolar (µM) IPTG (isopropyl- -d-thiogalactopyranoside) to an OD600 of 0.8 and grow at 18 °C .", "[Protei... |
72,995 | Roadmap to the study of gene and protein phylogeny and evolution - a practical guide | 5 | dx.doi.org/10.17504/protocols.io.36wgq77e3vk5/v4 | https://www.protocols.io/view/roadmap-to-the-study-of-gene-and-protein-phylogeny-cjibukan | florian.jacques, Paulina Bolivar, Kristian Pietras, Emma Hammarlund | TITLE: Roadmap to the study of gene and protein phylogeny and evolution - a practical guide
AUTHORS: florian.jacques, Paulina Bolivar, Kristian Pietras, Emma Hammarlund
[DESCRIPTION]
Developments in sequencing technologies and the sequencing of an ever-increasing number of genomes have revolutionisedstudies into biodi... | ["[Introduction] We provide a protocol for non-bioinformatic users to reconstruct the phylogeny and evolutionary history of genes or proteins. \n\nWe present a compilation of DNA and protein databases, as well as bioinformatic tools for molecular phylogenetic reconstruction, and a wide range of studies on molecular evo... |
63,911 | Squeeze” enrichment of intact cells (eukaryotic and prokaryotic) from marine sponge tissues prior to routine DNA extraction | 4 | null | https://www.protocols.io/view/squeeze-enrichment-of-intact-cells-eukaryotic-and-canfsdbn | Joe Lopez | TITLE: Squeeze” enrichment of intact cells (eukaryotic and prokaryotic) from marine sponge tissues prior to routine DNA extraction
AUTHORS: Joe Lopez
[DESCRIPTION]
A “Squeeze” method to enrich for intact cells (eukaryotic and prokaryotic) prior to DNA Extraction from marine sponge tissues
Most marine demosponge sp... | ["With sterile scalpel and forceps cut a piece of sponge mesohyl (tissue) approximately 1 - 2 cm3 place in a sterile petri dish. This can also be done on small fresh or frozen sponge pieces. If frozen, do not let sponge thaw completely but only enough to slice, since cell lysis may begin during thaw.", "Soak sponge se... |
null | null | null | dx.doi.org/10.17504/protocols.io.gg2btye | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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80,104 | Immunohistochemistry (IHC) Whole-Mount Antibody Staining | 4 | dx.doi.org/10.17504/protocols.io.5jyl8jzn8g2w/v1 | https://www.protocols.io/view/immunohistochemistry-ihc-whole-mount-antibody-stai-csggwbtw | Talia Pittman | TITLE: Immunohistochemistry (IHC) Whole-Mount Antibody Staining
AUTHORS: Talia Pittman
[DESCRIPTION]
Immunohistochemistry (IHC) Whole-Mount Antibody Staining protocol @FishFloorUCL
[STEPS]
SECTION: Introduction
1. Protocol based on Jenny Regan's GFP protocol, modified by Tom Hawkins thomas.hawkins@ucl.ac.uk
SECTION:... | ["[Introduction] Protocol based on Jenny Regan's GFP protocol, modified by Tom Hawkins thomas.hawkins@ucl.ac.uk", "[Fix and dehydrate] Depending on the antigen, you should either fix in PFA or TCA. Always start with PFA (option 1). TCA (option2) can be better for older embryos >36hrs\n\nEither:\n\n(Option 1) Fix in PFA... |
51,811 | snmCAT_V1 | 1 | dx.doi.org/10.17504/protocols.io.bwubpesn | https://www.protocols.io/view/snmcat-v1-bwubpesn | Bang-An Wang, Chongyuan Luo, Joseph Ecker | TITLE: snmCAT_V1
AUTHORS: Bang-An Wang, Chongyuan Luo, Joseph Ecker
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">To comprehensively assess the molecular phenotypes of single cells in tissues, we devised single-nucleus methylCytosine, Chromatin accessibility and Transcriptome sequencing (snmCAT-s... | ["[Background]\nThis protocol is based on the originial protocol named as snmC2T-seq from the BioRxiv paper (ChongyuanLuo, et al. BioRxiv 2019) https://www.biorxiv.org/content/10.1101/2019.12.11.873398v1 and SMART-seq3 (Hagemann-Jensen, et al.Nat Biotechnol 2020, https://www.protocols.io/view/smart-seq3-protocol-bcq4i... |
49,493 | SPOT system protocol | 4 | dx.doi.org/10.17504/protocols.io.bujvnun6 | https://www.protocols.io/view/spot-system-protocol-bujvnun6 | Guanhua Xun, Huimin Zhao, stlane2 | TITLE: SPOT system protocol
AUTHORS: Guanhua Xun, Huimin Zhao, stlane2
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The need for rapid, accurate, and scalable testing systems for COVID-19 diagnosis is clear and urgent. Here we report a rapid </span><span style = ":UNDERLINE;">S</span><span... | ["Using the first provided microcap, collect a saliva sample into capillary 1, containing QuickExtract DNA Extraction Solution (Lucigen). Insert the capillary into the SPOT device and press the \"Start\" button to run the 5-minute pretreatment.\n95 °C", "After pretreatment, remove capillary 1 from the SPOT device and ... |
68,707 | Immunofluorescence imaging of cells expressing GolgiTAG (TMEM115-3HA) or HA-tagged non-Golgi annotated proteins | 1 | dx.doi.org/10.17504/protocols.io.q26g74qpkgwz/v1 | https://www.protocols.io/view/immunofluorescence-imaging-of-cells-expressing-gol-cfcbtisn | Rotimi Fasimoye, Dario R Alessi | TITLE: Immunofluorescence imaging of cells expressing GolgiTAG (TMEM115-3HA) or HA-tagged non-Golgi annotated proteins
AUTHORS: Rotimi Fasimoye, Dario R Alessi
[DESCRIPTION]
Immunofluorescent (IF) microscopy is a powerful tool used in cellular and molecular biology to monitor the subcellular localisation of proteins. ... | ["[Seeding cells for immunofluorescence microscopy] Coat coverslips (sterilised in 100% ethanol prior to use) with poly-L-lysine by immersing the coverslips in poly-L-lysine solution for 60 min.", "[Seeding cells for immunofluorescence microscopy] Rinse the coated coverslips in media and place in a 6-well plate(one cov... |
95,826 | An end-to-end workflow to study newly synthesized mRNA following rapid protein depletion in Saccharomyces cerevisiae | 4 | dx.doi.org/10.17504/protocols.io.n2bvj3dj5lk5/v2 | https://www.protocols.io/view/an-end-to-end-workflow-to-study-newly-synthesized-c9tsz6ne | John B. Ridenour, Rafal Donczew | TITLE: An end-to-end workflow to study newly synthesized mRNA following rapid protein depletion in Saccharomyces cerevisiae
AUTHORS: John B. Ridenour, Rafal Donczew
[DESCRIPTION]
In this protocol, we describe an end-to-end workflow for rapidly degrading a target protein using the AID system and quantifying newly synth... | ["[Yeast growth] Streak appropriate S. cerevisiae strain on YPD agar. Incubate culture at 30°C for 2-3 days.", "[Yeast growth] Transfer an individual colony to 5 ml of YPD. Incubate culture at 30°C with shaking at 220 rpm overnight.", "[Yeast growth] Dilute overnight culture to an OD600 of 0.2 in 40 ml of YPD. Incubate... |
28,754 | Lesion Size | null | dx.doi.org/10.17504/protocols.io.8bshsne | null | Cleo B. | TITLE: Lesion Size
AUTHORS: Cleo B.
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Measuring the lesion size in </span><span style = "font-style:italic;">Brassica oleracea</span><span> after infection with </span><span style = "font-style:italic;">Xanthomonas campestris </span><span>pv. camp... | ["Measure the lesion size on the leaf from the site of infection until the end of the yellow discoloration using a calliper."] |
null | null | null | dx.doi.org/10.17504/protocols.io.ekvbcw6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol is specifically designed for high throughput applications of Stellaris in 96 well glass bottom plates.</p>
[BEFORE_START]
<p align="LEFT">Reagents and Equipment</p>
<p align="LEFT">Reagents and Consumables:</p>
<p align="LEFT">a) TE buffer (10 mM Tris-HCl, 1 mM... | [] |
107,340 | RSVAB WGS and GF protocols | 1 | dx.doi.org/10.17504/protocols.io.kqdg3xbzqg25/v4 | https://www.protocols.io/view/rsvab-wgs-and-gf-protocols-dk3k4ykw | Maria Iglesias | TITLE: RSVAB WGS and GF protocols
AUTHORS: Maria Iglesias
[DESCRIPTION]
This SOP describes the procedure for generating cDNA from RSV viral nucleic acid extracts and subsequently producing amplicons tiling the viral genome using. We propose two systems for genomic characterization of RSV. First, a novel RSV amplicon-b... | ["[dsCDNA generation:] During this step three master mixes will be prepared: MMI, MMII and MMIII.\nMaterials: Kit Superscript III First Strand (Invitrogen)\n 100% DMSO\n RNAseH (Invitrogen)\n Klenow fragment 3' ->5' exo (New England Biolab... |
null | null | null | dx.doi.org/10.17504/protocols.io.jgwcjxe | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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21,611 | Vandy - Vertical Sleeve Gastrectomy in Mice | null | dx.doi.org/10.17504/protocols.io.zcjf2un | null | Teri Stevenson, Vance L. Albaugh | TITLE: Vandy - Vertical Sleeve Gastrectomy in Mice
AUTHORS: Teri Stevenson, Vance L. Albaugh
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">This is the protocol for the vertical sleeve gastrectomy in the mouse. This p... | ["Preoperative Care1. All animals must be singly-housed, given Ensure 12 hours before surgery and have all bedding removed. 2. Preoperative pain medications should be administered: a. Ketoprofen (5 mg/kg) b. Saline is given at the end of surgery and a second dose is given 24 hours later. 3. Ensure adequacy of a... |
30,468 | Small Drone Photos - Open Vegetation Protocol | null | dx.doi.org/10.17504/protocols.io.9zch72w | null | Sabine St-Jean, Etienne Laliberté | TITLE: Small Drone Photos - Open Vegetation Protocol
AUTHORS: Sabine St-Jean, Etienne Laliberté
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Here we describe the standardised protocol used by the </span><a href="http://www.caboscience.org/" style = "text-decoration:underline;color:blue;curs... | ["[Picture-Taking]\nFly the small drone to take photos of the plots and subplots.", "[Photo Import]\nImport the photos.", "[Picture-Taking]\nTurn on the drone and the controller. Connect the controller to your phone and open the DJI Go 4 App. Press Go Fly. Adjust the settings to Speed = 1:1000 and Iso = 400. If it is v... |
59,029 | TSS, TXS, SDS Serial Extraction | 4 | dx.doi.org/10.17504/protocols.io.b5vvq666 | https://www.protocols.io/view/tss-txs-sds-serial-extraction-b5vvq666 | Haley Geertsma | TITLE: TSS, TXS, SDS Serial Extraction
AUTHORS: Haley Geertsma
[DESCRIPTION]
This protocol is used to serially extract protein from mouse brain tissue in increasingly stringent buffers.
[STEPS]
1. Weigh brain sample and add 3X volume of TSS buffer + 1X protease inhibitor.
TSS Buffer: 140mM NaCl + 5mM Tris-HCl in H2... | ["Weigh brain sample and add 3X volume of TSS buffer + 1X protease inhibitor.\nTSS Buffer: 140mM NaCl + 5mM Tris-HCl in H2O", "Homogenize in a dounce homogenizer then transfer to a clean tube.", "Centrifuge at 21130g for 30 minutes at 4oC then save the supernatant as 'TSS fraction'.", "Resuspend the pellet in the same ... |
8,763 | Basketball game- two tables in a row | null | dx.doi.org/10.17504/protocols.io.ks3cwgn | null | Darja Darja | TITLE: Basketball game- two tables in a row
AUTHORS: Darja Darja
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Abstract:</span><span> Between May and June 1993, Slovenia competed in the qualifiers for the </span><a style = "text-decoration:underline;color:blue;cur... | ["[Slovene team]\nSlovene teamSlovenia did not reach the knockout stages of the competition until 2005, where the team, coached by Aleš Pipan, reached the quarter-finals for the first time.In 2009, Slovenia reached the semi-finals for the first time after eliminating Croatia in the quarter-finals with a 67–65 victory. ... |
62,741 | Orthogonal experiment of research on coordinated control method of indoor multiple pollutants | 1 | dx.doi.org/10.17504/protocols.io.3byl4bxpjvo5/v1 | https://www.protocols.io/view/orthogonal-experiment-of-research-on-coordinated-c-b9hvr366 | Yan Zhang, Wei Yu | TITLE: Orthogonal experiment of research on coordinated control method of indoor multiple pollutants
AUTHORS: Yan Zhang, Wei Yu
[DESCRIPTION]
Indoor air pollution in office buildings is complex and serious. This research is targeted at three types of air pollutants: CO2, VOCs, and PM2.5. In order to seek the optimal ... | ["Turn on the air conditioning. Turn on all the temperature, humidity, and indoor air quality sensors. Close the doors and windows. Start the experiment.", "Create the indoor air pollution sources artificially until the CO2, VOCs, and PM2.5 in the breathing zone have exceeded the values set for each condition, and then... |
null | null | null | dx.doi.org/10.17504/protocols.io.girbud6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div class="page" title="Page 1">
<div class="section">
<div class="layoutArea">
<div class="column">Estimate a protein concentration in a solution using the Bradford protein assay</div>
</div>
</div>
</div>
[STEPS]
?.
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?. | [] |
85,582 | A First Experimental Protocol on Creative Engagement and Meaning Creation in Interactive Experiences for Cultural Heritage | 1 | dx.doi.org/10.17504/protocols.io.6qpvr367bvmk/v1 | https://www.protocols.io/view/a-first-experimental-protocol-on-creative-engageme-cxtnxnme | Manuele Veggi, sofia.pescarin | TITLE: A First Experimental Protocol on Creative Engagement and Meaning Creation in Interactive Experiences for Cultural Heritage
AUTHORS: Manuele Veggi, sofia.pescarin
[DESCRIPTION]
The following document contains the descriptive material for the testing protocol of the "caring prototype" MyTISSE, an interactive use... | ["[Preparatory Activities] Preparation of the material:\nTablet interface (XRF scan and two palettes)\nInformed Consent form\nOutline of the analysis of the painting\nDigital survey (with QR code to access it)", "[Creative Engagement] Participants are given a tablet and an interactive pen", "[Creative Engagement] Instr... |
31,412 | General Transfection | null | dx.doi.org/10.17504/protocols.io.bawuifew | null | Addgene the Nonprofit Plasmid Repository | TITLE: General Transfection
AUTHORS: Addgene the Nonprofit Plasmid Repository
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol is for general transfection. To see the full abstract and additional resources, visit the </span><a href="https://www.addgene.org/protocols/transfection/"... | ["[Seeding cells]\nSeed 293T packaging cells at 3.8x106 cells per plate in DMEM complete in 10 cm tissue culture plates.", "[Seeding cells]\nIncubate the cells at , 5% CO2 for ~.\n37 °C", "[Transfection]\nGently aspirate media, add fresh DMEM complete containing cloroquine diphosphate and incubate ~.\n10 ml\nFor of ... |
19,528 | Genotype imputation workflow v3.0 | null | dx.doi.org/10.17504/protocols.io.xbgfijw | null | Kalle Pärn, Marita A. Isokallio, Javier Nunez Fontarnau, Aarno Palotie, Samuli Ripatti, Priit Palta | TITLE: Genotype imputation workflow v3.0
AUTHORS: Kalle Pärn, Marita A. Isokallio, Javier Nunez Fontarnau, Aarno Palotie, Samuli Ripatti, Priit Palta
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. [Requirements and preparatory steps]
The actual imputation protocol begins at step 2. All consecutive steps (... | ["[Requirements and preparatory steps]\nThe actual imputation protocol begins at step 2. All consecutive steps (commands given in 'cmd COMMAND' sections) must be run to ensure high-quality results. For a 'quick and dirty' genotype imputation 'run', you can jump straight to Steps 9-10 and only run these (assuming you al... |
20,572 | Tracking bleach synchronized worms | null | dx.doi.org/10.17504/protocols.io.yb4fsqw | null | Priota Islam | TITLE: Tracking bleach synchronized worms
AUTHORS: Priota Islam
[STEPS]
?. [Preparing Imaging plates]
Prepare and pour low peptone NGM onto 35mm imaging plates Put them in the cold room for at least 2 days before use Seed imaging plates with 50ul of freshly made 1:10 solution (OP50:M9 solution) the day before recordi... | ["[Preparing Imaging plates]\nPrepare and pour low peptone NGM onto 35mm imaging plates Put them in the cold room for at least 2 days before use Seed imaging plates with 50ul of freshly made 1:10 solution (OP50:M9 solution) the day before recording Leave on bench to dry with lid on overnight", "[Preparing worms]\nChu... |
59,927 | Parallel DNA+RNA extraction from freshwater samples using the Quick-DNA/RNA Microprep Plus Kit and Zymo-Spin II-µHRC Filters (Zymo Research) | 4 | dx.doi.org/10.17504/protocols.io.14egn79bpv5d/v1 | https://www.protocols.io/view/parallel-dna-rna-extraction-from-freshwater-sample-b6rxrd7n | Christopher A Hempel | TITLE: Parallel DNA+RNA extraction from freshwater samples using the Quick-DNA/RNA Microprep Plus Kit and Zymo-Spin II-µHRC Filters (Zymo Research)
AUTHORS: Christopher A Hempel
[DESCRIPTION]
Parallel DNA+RNA extraction from freshwater samples using the Quick-DNA/RNA Microprep Plus Kit and Zymo-Spin II-µHRC Filters (Z... | ["[Procedure] Centrifuge bead tubes for 1 min at 13,000 xg and room temperature", "[Procedure] Transfer as much of the supernatant as possible into 2 mL tubes (ideally don’t transfer any beads)", "[Procedure] Add 1 volume of DNA/RNA Lysis Buffer to samples and vortex Note: because we transferred all the supernatant fr... |
65,203 | Silver Stain Gel for IP-TDMS Development | 1 | null | https://www.protocols.io/view/silver-stain-gel-for-ip-tdms-development-cbwtspen | Lauren Adams | TITLE: Silver Stain Gel for IP-TDMS Development
AUTHORS: Lauren Adams
[DESCRIPTION]
Silver stain gels can be used to examine total protein in a given sample. This method is less sensitive than western blotting, but typically more sensitive than Coomassie blue staining.
[STEPS]
1. Take aliquots from IP fractions and... | ["Take aliquots from IP fractions and add sample loading buffer to a final concentration of 1X. Boil samples in hot plate at 95ºC for 5-10 min. Briefly, centrifuge samples to ensure sample entire sample is towards bottom of the tube.", "Open gel and place into gel box. Add 1 x MES running buffer, ensuring that there ar... |
73,971 | UPitt TriState SenNet TMC Human lung single cell suspension (test run) | 4 | dx.doi.org/10.17504/protocols.io.eq2ly768plx9/v1 | https://www.protocols.io/view/upitt-tristate-sennet-tmc-human-lung-single-cell-s-ckgtutwn | Marta Bueno, Lanping Guo, koenigshoffm, Oliver Eickelberg | TITLE: UPitt TriState SenNet TMC Human lung single cell suspension (test run)
AUTHORS: Marta Bueno, Lanping Guo, koenigshoffm, Oliver Eickelberg
[DESCRIPTION]
Human lung tissue dissociation protocol to produce single cell suspension that can be used for different purposes. Optimal incubation times to obtain cell suspe... | ["[Before you start] Same-day preparation:", "[Before you start] Base media\n 500 mL DMEM + 5 mL anti/anti (100x)", "[Before you start] Digestion media (10 mL per digestion -> scale accordingly)\n\nI. Modified base media with Final DNAseI 100 µLper 10 mL (final 0.1mg/ml)\n\nII. Then add corresponding proteases:\n ... |
63,862 | Microbial Drug Discovery | 4 | dx.doi.org/10.17504/protocols.io.e6nvwk2rwvmk/v1 | https://www.protocols.io/view/microbial-drug-discovery-cakwscxe | contact.microbialtec | TITLE: Microbial Drug Discovery
AUTHORS: contact.microbialtec
[DESCRIPTION]
Drugs of natural origin have been classified as (i) original natural products, (ii) products derived or chemically synthesized from natural products or (iii) synthetic products based on natural product structures. Microbes have made a phenom... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.dy37ym | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Using DGGE, similar-sized PCR products that differ in nucleotide composition (sequence) can be separated in denaturing gradient gels. Denaturing gradient gels are created using acrylamide (structural material) solutions that contain different amounts of denaturants (urea and for... | [] |
36,444 | Statistical Code Summary for "Predicting the 10-Year Risk of Death from Other Causes in Men with Localized Prostate Cancer Using Patient-reported Factors: Development of a Tool" | 1 | dx.doi.org/10.17504/protocols.io.bft4jnqw | https://www.protocols.io/view/statistical-code-summary-for-34-predicting-the-10-bft4jnqw | Daniel Frendl | TITLE: Statistical Code Summary for "Predicting the 10-Year Risk of Death from Other Causes in Men with Localized Prostate Cancer Using Patient-reported Factors: Development of a Tool"
AUTHORS: Daniel Frendl
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This text document summarizes the steps used... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.mfxc3pn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>With the booming development of evacuation simulation software, developing an extensive database in indoor scenarios for evacuation models is imperative. In this paper, we conduct a qualitative and quantitative analysis on the collected videotapes and aim to provide a complet... | [] |
54,693 | SP3 protocol for proteomic analysis of tendon cryosections | 1 | null | https://www.protocols.io/view/sp3-protocol-for-proteomic-analysis-of-tendon-cryo-bzndp5a6 | Stefania Wunderli, Jess Snedeker, The Tendon Seed Network | TITLE: SP3 protocol for proteomic analysis of tendon cryosections
AUTHORS: Stefania Wunderli, Jess Snedeker, The Tendon Seed Network
[DESCRIPTION]
This protocol details the preparation of cryosection samples and laser capture microdissection (LCM) samples collected with a MMI Laser-Microdissection device for MS/MS a... | ["[Preparing cryosection samples] Fill a 200 µL PCR tube with 100 µL 100% EtOH.", "[Preparing cryosection samples] Wetten the dry tissue section on the glass slide with ca. 50 µL 100% EtOH.", "[Preparing cryosection samples] Use a 1.2x40mm needle (18Gx1.5) to gently scrape off the tissue section", "[Preparing cryosecti... |
29,221 | Structuralization and Incubation | null | dx.doi.org/10.17504/protocols.io.8sdhwa6 | null | Laura Armero H, Claudia Troncone Clemente | TITLE: Structuralization and Incubation
AUTHORS: Laura Armero H, Claudia Troncone Clemente
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The interaction between an aptamer and his target depends on the tertiary structure of the aptamer, to attempt to always have the same structure for all the roun... | ["Strcucturslization", "[Day 1 ]\nStrcuturalization", "[Day 1 ]\nAdd 10 μL of 100 uM ssDNA library to 190 ul of binding buffer. Incubate it at 95 °C for 10 min. After that, transfer immediately to ice-bath to prevent rehybridization ofthe single-stranded DNA library. If the transfer is poor performed, you can reheat ag... |
55,811 | CIDC_S16_NMR_Celegans_Extraction_Protocol | 1 | dx.doi.org/10.17504/protocols.io.b2rbqd2n | https://www.protocols.io/view/cidc-s16-nmr-celegans-extraction-protocol-b2rbqd2n | Brianna M Garcia, Amanda Shaver, Goncalo Gouveia | TITLE: CIDC_S16_NMR_Celegans_Extraction_Protocol
AUTHORS: Brianna M Garcia, Amanda Shaver, Goncalo Gouveia
[DESCRIPTION]
A sample preparation protocol for lyophilized C. elegans samples to be analyzed by NMR spectroscopy
[STEPS]
SECTION: Homogenization
1. Remove lyophilized C. elegans samples from -80 °C freezer
... | ["[Homogenization] Remove lyophilized C. elegans samples from -80 °C freezer", "[Homogenization] Add approximately 200 µL of Zirconia beads (BioSpec Cat. No. 11079110zx) to each sample.", "[Homogenization] Using a FastPrep-96™ instrument (MP Biomedicals) equipped with QuickFlex™ Sample Holder (or similar equipment)... |
74,963 | A human development-based protocol for the differentiation of human ESCs into midbrain dopaminergic neurons. | 4 | null | https://www.protocols.io/view/a-human-development-based-protocol-for-the-differe-cmftu3nn | Kaneyasu Nishimura, Emilia Síf Ásgrimsdottir, Shanzheng Yang, Ernest Arenas | TITLE: A human development-based protocol for the differentiation of human ESCs into midbrain dopaminergic neurons.
AUTHORS: Kaneyasu Nishimura, Emilia Síf Ásgrimsdottir, Shanzheng Yang, Ernest Arenas
[DESCRIPTION]
Protocol for the differentiation of human embryonic stem cells into midbrain dopaminergic neurons. This ... | ["[Maintenance of hESCs cells] Prior to the start of differentiation, hESCs are cultured in NutriStem® XF media on LN521 (1 ug/cm2) coated plates. Once the cells reach approximately 70-90% confluency, cells are passaged at a seeding density of 20.000 cells/cm2 with ROCK inhibitor (10 uM Y-27632), only during the first ... |
77,679 | Splenocyte Preparation for Immune Reconstitution (Humanisation) | 4 | dx.doi.org/10.17504/protocols.io.q26g7y6e9gwz/v1 | https://www.protocols.io/view/splenocyte-preparation-for-immune-reconstitution-h-cp4pvqvn | Sandra Petrus-Reurer, Kourosh Saeb-Parsy | TITLE: Splenocyte Preparation for Immune Reconstitution (Humanisation)
AUTHORS: Sandra Petrus-Reurer, Kourosh Saeb-Parsy
[DESCRIPTION]
This protocol guides through the steps required to humanise mice with human splenocytes
[STEPS]
1. Thaw vial (approx. 50x106 cells/vial) in water bath 37C for 2-3min (leave crystal)
... | ["Thaw vial (approx. 50x106 cells/vial) in water bath 37C for 2-3min (leave crystal)", "Add cells into 10mL/vial of warm 50% RPMI media + 50% FBS", "Centrifuge 7min at 300g", "Combine all vials in 10mL RPMI media + 10% FBS", "Centrifuge 7min at 300g", "Resuspend all vials in 10mL RPMI media + 10% FBS + add DNAse-I (typ... |
47,410 | Whole Blood, Plasma, and Buffy Coat Processing | 4 | dx.doi.org/10.17504/protocols.io.6qpvrdp8pgmk/v1 | https://www.protocols.io/view/whole-blood-plasma-and-buffy-coat-processing-bsisncee | Clemens Scherzer, Bradley Hyman, Charles Jennings | TITLE: Whole Blood, Plasma, and Buffy Coat Processing
AUTHORS: Clemens Scherzer, Bradley Hyman, Charles Jennings
[DESCRIPTION]
This protocol explains the Standard Operating Protocol for processing whole blood, plasma, and buffy coat.
[BEFORE_START]
Be sure to use only the low retention tubes and low retention tips fo... | ["[Whole Blood, Plasma, and Buffy Coat Processing] Before centrifuging the 10ml BD purple top tube, pipette 550 µL aliquots of whole blood into two Eppendorf tubes labeled “WB-01 and WB-02.”", "[Whole Blood, Plasma, and Buffy Coat Processing] Place the 10 ml BD purple top and the two 6 ml BD purple tops into the blue r... |
43,159 | Chromatin accessibility landscapes during onset of salmon maturation | 5 | dx.doi.org/10.17504/protocols.io.bndxma7n | https://www.protocols.io/view/chromatin-accessibility-landscapes-during-onset-of-bndxma7n | Amin Mohamed, Marina Naval-Sanchez, Moira Menzies, Bradley Evans, Harry King, Antonio Reverter, James Kijas | TITLE: Chromatin accessibility landscapes during onset of salmon maturation
AUTHORS: Amin Mohamed, Marina Naval-Sanchez, Moira Menzies, Bradley Evans, Harry King, Antonio Reverter, James Kijas
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Background:</div><div class = "text-block">Despite sexual d... | ["[Nuclei extraction, ATAC-seq library preparation and sequencing]\nATAC-seq libraries were prepared from frozen tissues using the Omni-ATAC method with the following modifications.Frozen tissue (20 mg) was ground in liquid nitrogen using a mortar and pestle. The pulverized tissue was transferred to a pre-chilled 2 ml ... |
null | null | null | dx.doi.org/10.17504/protocols.io.vhge33w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Bounce PCR: optimisation free PCR for synthetic biology cloning applications.
Synthetic biology projects require the cloning of multiple DNA components, and increasingly this is done though in-vitro gene synthesis. This remains an expensive alternative to traditional cloning by... | ["[Initial denaturation] {\"blocks\":[{\"key\":\"79r6\",\"text\":\" for \",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[],\"entityRanges\":[{\"offset\":0,\"length\":1,\"key\":0},{\"offset\":6,\"length\":1,\"key\":1}],\"data\":[]},{\"key\":\"35ehh\",\"text\":\"\",\"type\":\"unstyled\",\"depth\":0,\"inlineS... |
72,077 | Biogenic silica measurement from diatom | 6 | null | https://www.protocols.io/view/biogenic-silica-measurement-from-diatom-cimmuc46 | Ying-Yu Hu, Nuwanthi Samarasinghe, Zoe V. Finkel | TITLE: Biogenic silica measurement from diatom
AUTHORS: Ying-Yu Hu, Nuwanthi Samarasinghe, Zoe V. Finkel
[DESCRIPTION]
Here we describe the measurement of biogenic silica from diatoms. Biogenic silica is digested by wet-alkaline method, using 2 M sodium carbonate to hydrate and depolymerize amorphous silica and yield... | ["[Sample collection] Estimation:\nLow limit of detection of this assay is ~3 uM silicate per sample in the molybdate assay, equivalent to about 1 ug PON per filter.", "[Sample collection] Filter micro algae in liquid media onto polycarbonate filters, using gentle vacuum pressure (130 mmHg)", "[Sample collection] Rinse... |
28,012 | Colony PCR (Protocol for Thermo Scientific™ Phire™ Hot Start II DNA Polymerase) | null | dx.doi.org/10.17504/protocols.io.7kkhkuw | null | Alba Balletbó | TITLE: Colony PCR (Protocol for Thermo Scientific™ Phire™ Hot Start II DNA Polymerase)
AUTHORS: Alba Balletbó
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Thermo Scientific™ Phire™ Hot Start II DNA Polymerase is a novel DNA polymerase designed for use in all routine and high throughput PCR applic... | ["Add all components in a 250 μL tube making up to a 20 or 50 μl reaction.'Pro-tip': Carefully mix and centrifuge all tubes before opening to ensure homogeneity and improve recovery. When using Phire Hot Start II PCR Master Mix, it is not necessary to perform the PCR setup on ice. 'Note': Due to the unique nature of Ph... |
58,099 | Collection of GBS samples at 35-37 weeks of gestation and isolation | 4 | dx.doi.org/10.17504/protocols.io.b4ytqxwn | https://www.protocols.io/view/collection-of-gbs-samples-at-35-37-weeks-of-gestat-b4ytqxwn | lydiariver | TITLE: Collection of GBS samples at 35-37 weeks of gestation and isolation
AUTHORS: lydiariver
[DESCRIPTION]
Pregnant women's recto-vaginal samples were collected to identify Streptococcus
agalactiae (Group B Streptococci, GBS).
[STEPS]
1. Remove each swab from the packaging and insert the swab 2 cm into the vagina... | ["Remove each swab from the packaging and insert the swab 2 cm into the vagina, followed by the rectum, inserting the swab 1 cm through the anal sphincter. Three swabs were collected for each patient.", "The First swab was inoculated on Todd-Hewitt broth supplemented with gentamicin 8 μg/ml and nalidixic acid 15 μg/ml ... |
81,617 | AAV viral DNA and whole RNA recovery for AAV pool experiments in rhesus macaque | 4 | dx.doi.org/10.17504/protocols.io.3byl4jo68lo5/v1 | https://www.protocols.io/view/aav-viral-dna-and-whole-rna-recovery-for-aav-pool-ctxrwpm6 | Miguel Chuapoco | TITLE: AAV viral DNA and whole RNA recovery for AAV pool experiments in rhesus macaque
AUTHORS: Miguel Chuapoco
[DESCRIPTION]
This protocol outlines procedures to extract viral DNA and whole RNA from rhesus macaque tissue that had been treated with AAV in vivo
[STEPS]
SECTION: DNA/RNA extraction
1. Add 100 mg (brain ... | ["[DNA/RNA extraction] Add 100 mg (brain or liver) and 1 mL to bead homogenizer tubes. Use prefilled tubes with 1.5 mm Zirconium beads or 2.8 mm stainless steel beads.", "[DNA/RNA extraction] Homogenize tissue in using the following settings: \nSpeed: 5.0 m/s \nTime: 30 seconds \nPause: 1 minute\nCycles: 2\n\nIncubat... |
null | null | null | dx.doi.org/10.17504/protocols.io.k2kcycw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This version is based on a recipe (see<a href="https://www.protocols.io/view/human-parechovirus-a-real-time-rt-pcr-nix-assay-20-krpcv5n" target="_blank"> forked version</a>) my team and I used this assay between 2008-2015; we dubbed it the 'Nix assay'. It targets the 5'UTR an... | [] |
72,719 | Goga Lab RT-qPCR protocol: QuantStudio6 | 4 | null | https://www.protocols.io/view/goga-lab-rt-qpcr-protocol-quantstudio6-ci9puh5n | Jeremy.williams | TITLE: Goga Lab RT-qPCR protocol: QuantStudio6
AUTHORS: Jeremy.williams
[DESCRIPTION]
Guidelines for preparing RT-qPCR samples for QuantStudio 6 located in HSW7 lab space.
[BEFORE_START]
*Thaw on ice (leave time!) and keep all reagents on ice through preparation. Prepare the plate on ice.
[GUIDELINES]
*start with ... | ["Dilute stock IDT primers to 100uM", "Mix your forward and reverse primer pairs together, to a final dilution of 10uM forward and 10uM reverse. For example, add 10uL each of forward and reverse primers to 80uL PCR-quality DI for 100uL final volume.", "Mix *total reagent volumes required* (see excel spreadsheet, green)... |
39,606 | SOLUTION- 09 - Trypan Blue solution | 3 | dx.doi.org/10.17504/protocols.io.biwwkffe | https://www.protocols.io/view/solution-09-trypan-blue-solution-biwwkffe | Marco Cosentino, Elisa Storelli, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Marco Ferrari, Franca Marino | TITLE: SOLUTION- 09 - Trypan Blue solution
AUTHORS: Marco Cosentino, Elisa Storelli, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Marco Ferrari, Franca Marino
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This recepe is used in the following protocols:</div><div class = "text-block"><s... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.hmxb47n | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?. | [] |
21,513 | Insect Vision 1.0.1 | null | dx.doi.org/10.17504/protocols.io.y9hfz36 | null | Evripidis Gkanias, Benjamin Risse, Michael Mangan, Barbara Webb | TITLE: Insect Vision 1.0.1
AUTHORS: Evripidis Gkanias, Benjamin Risse, Michael Mangan, Barbara Webb
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><h2>InsectVision</h2></div><div class = "text-block">Computer Vision Toolbox for Insect Vision</div><div class = "text-block"><h2>Version 1.0.1</h2></di... | [] |
59,827 | Differentiation of iPSCs with the hNIL construct into motor neurons protocol | 1 | dx.doi.org/10.17504/protocols.io.14egn76kqv5d/v1 | https://www.protocols.io/view/differentiation-of-ipscs-with-the-hnil-construct-i-b6ntrden | Maria Sckaff, Kenneth Wu, Hana Ghanim, Aradhana Sachdev, Gokul N Ramadoss, Carissa M. Feliciano, Luke M. Judge, Bruce Conklin, Claire D Clelland | TITLE: Differentiation of iPSCs with the hNIL construct into motor neurons protocol
AUTHORS: Maria Sckaff, Kenneth Wu, Hana Ghanim, Aradhana Sachdev, Gokul N Ramadoss, Carissa M. Feliciano, Luke M. Judge, Bruce Conklin, Claire D Clelland
[DESCRIPTION]
This protocol describes the differentiation of induced pluripot... | ["[Maintenance and Preparation of the iPSCs for the hNIL differentiation into motor neurons: Maintaining iPSCs] Culture iPSCs for at least 2-3 passages after initial hNIL transfection or from frozen stocks before starting a motor neuron differentiation.", "[Maintenance and Preparation of the iPSCs for the hNIL differen... |
41,792 | SPOT2 protocol | 4 | dx.doi.org/10.17504/protocols.io.bk28kyhw | https://www.protocols.io/view/spot2-protocol-bk28kyhw | Huimin Zhao, stlane2 , Guanhua Xun | TITLE: SPOT2 protocol
AUTHORS: Huimin Zhao, stlane2 , Guanhua Xun
[STEPS]
?. Label test kit bag with patient's name and a unique sample number for the test run. Provide a 20 uL microcap and PCR tube and have patient collect a saliva sample and place it into then seal the PCR tube. Label PCR tube with sample number m... | ["Label test kit bag with patient's name and a unique sample number for the test run. Provide a 20 uL microcap and PCR tube and have patient collect a saliva sample and place it into then seal the PCR tube. Label PCR tube with sample number matching the test kit bag.", "Place PCR tubes into floating rack and insert i... |
69,397 | Isolation of PBMCs From Whole Blood | 4 | dx.doi.org/10.17504/protocols.io.j8nlkwbm6l5r/v1 | https://www.protocols.io/view/isolation-of-pbmcs-from-whole-blood-cfzvtp66 | Gerardo Ongari | TITLE: Isolation of PBMCs From Whole Blood
AUTHORS: Gerardo Ongari
[DESCRIPTION]
This protocol details methods for the isolation of peripheral blood mononuclear cells (PBMCs) from Whole Blood
[BEFORE_START]
Pre-procedure: Ensure all reagents are at room temperature (15 - 25°C). The procedure must be carried out under... | ["[Step 1: Plasma Isolation] Collect 36 mL whole blood into EDTA tubes", "[Step 1: Plasma Isolation] Centrifuge the blood samples at 1000 x g, 20 min, 25 Room temperature", "[Step 1: Plasma Isolation] Carefully remove collection tubes from centrifuge; plasma is the top layer above the rest of the whole blood layer", "[... |
59,000 | NCBI submission protocol for SARS-CoV-2 wastewater data: SRA, BioSample, and BioProject | 1 | dx.doi.org/10.17504/protocols.io.b5uyq6xw | https://www.protocols.io/view/ncbi-submission-protocol-for-sars-cov-2-wastewater-b5uyq6xw | Ruth Timme, Maria Balkey | TITLE: NCBI submission protocol for SARS-CoV-2 wastewater data: SRA, BioSample, and BioProject
AUTHORS: Ruth Timme, Maria Balkey
[DESCRIPTION]
PURPOSE:
This method was developed at the FDA’s Center for Food Safety and Applied Nutrition for GenomeTrakr’s pandemic response project, monitoring SARS-CoV-2 variants in ... | ["["Ingredients" to have in place before starting your submissions] Set up a new NCBI submission environment for your lab\n1.1: Create an NCBI user account\n1.2: Set up an NCBI submission user group for your lab\n1.4: Bookmark the link to your Submission Portal\n1.5. Identify or establish new BioProjects (det... |
47,964 | Probiotic research protocol | 1 | dx.doi.org/10.17504/protocols.io.bs34ngqw | https://www.protocols.io/view/probiotic-research-protocol-bs34ngqw | Mohammad Abdus Salam | TITLE: Probiotic research protocol
AUTHORS: Mohammad Abdus Salam
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Gut probiotic improves growth and health of </span><span style = "font-style:italic;">B. gonionotus</span><span> fishes</span></div></div>
[STEPS]
?. [Euthanasia methods]
Pure clo... | ["[Euthanasia methods]\nPure clove oil was first dissolved in ethyl alcohol in 1:9 ratio (clove oil: ethyl alcohol)", "[Euthanasia methods]\nThis solution then diluted in water in order to obtain concentrations of 0.05 mL (50 mg), and 0.20 mL (200 mg) of clove oil per 500 mL of water", "[Euthanasia methods]\nFor hemato... |
90,934 | SEQUENCING Protocol Template | 1 | null | https://www.protocols.io/view/sequencing-protocol-template-c42wyyfe | Kathleen Pitz, Raissa.meyer | TITLE: SEQUENCING Protocol Template
AUTHORS: Kathleen Pitz, Raissa.meyer
[DESCRIPTION]
A protocol template created through the BeBOP project for sequencing.
[STEPS]
SECTION: MIOP: Minimum Information about an Omics Protocol
1.
MIOP Term
Value
methodology category
project
purpose
analyses
geograp... | ["[MIOP: Minimum Information about an Omics Protocol] MIOP Term\nValue\n \nmethodology category\n\n \nproject\n\n \npurpose\n\n \nanalyses\n\n \ngeographic location\n\n \nbroad-scale environmental context\n\n \nlocal environmental context\n\n \nenvironmental medium\n\n \ntarget\n\n \ncreator\n\n \nmaterials required\... |
94,630 | Brain SeqStain Protocol | 4 | dx.doi.org/10.17504/protocols.io.261gedmdyv47/v1 | https://www.protocols.io/view/brain-seqstain-protocol-c8nezvbe | Ishwarya Venkatesh, Ameera M Shaw, Sowmya Gurusamy Kamaraj, Anirudh Vattikota, Mohamed A Youssef, Xiaobo Li, Disha Varma, Bryan A. Killinger, Ashley Harms, Jeffrey H. Kordower, Vineet Gupta | TITLE: Brain SeqStain Protocol
AUTHORS: Ishwarya Venkatesh, Ameera M Shaw, Sowmya Gurusamy Kamaraj, Anirudh Vattikota, Mohamed A Youssef, Xiaobo Li, Disha Varma, Bryan A. Killinger, Ashley Harms, Jeffrey H. Kordower, Vineet Gupta
[DESCRIPTION]
Multiplex immunofluorescence imaging allows detection of multiple molecular... | ["[BRAIN SEQSTAIN PROTOCOL] Schematic Representation of Brain SeqStain Protocol:", "[Step 2. Crosslinking step using an optimized shortened SHIELD protocol (Short SHIELD)] Obtain necessary components such as ice, distilled water, SHIELD buffer, SHIELD epoxy, and conical falcon centrifuge tubes.", "[Step 2. Crosslinking... |
9,638 | Karyotype on fixed mealybug tissue | 1 | dx.doi.org/10.17504/protocols.io.mnec5be | https://www.protocols.io/view/karyotype-on-fixed-mealybug-tissue-mnec5be | Isabelle Vea, Stevie Bain | TITLE: Karyotype on fixed mealybug tissue
AUTHORS: Isabelle Vea, Stevie Bain
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. Males testes: Fix material in Bradley Carnoy (4:3:1 chloroform: ethanol: acetic acid) and keep at 4 degree celcius overnight (can keep up to 7 days for male testes)Embryos: no need... | ["Males testes: Fix material in Bradley Carnoy (4:3:1 chloroform: ethanol: acetic acid) and keep at 4 degree celcius overnight (can keep up to 7 days for male testes)Embryos: no need to fix", "Males testes: Dissect the tissue in 45% acetic acid (add 20ul of 45% acetic acid on a slide coverslip, pipet out the males a... |
24,796 | Field Collecting Protocol for Vascular Plants. Denver Botanic Gardens. Kathryn Kalmbach Herbarium of Vascular Plants | null | dx.doi.org/10.17504/protocols.io.4f4gtqw | null | Christina Alba, Melissa Islam | TITLE: Field Collecting Protocol for Vascular Plants. Denver Botanic Gardens. Kathryn Kalmbach Herbarium of Vascular Plants
AUTHORS: Christina Alba, Melissa Islam
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Floristic surveys and plant collections represent baseline data critical to understanding... | [] |
102,388 | In Vitro αS PFF Treatment | 0 | dx.doi.org/10.17504/protocols.io.5qpvoko4bl4o/v1 | https://www.protocols.io/view/in-vitro-s-pff-treatment-df8u3rww | Scott Vermilyea | TITLE: In Vitro αS PFF Treatment
AUTHORS: Scott Vermilyea
[DESCRIPTION]
This collection of protocol details the uptake and clearance of αS PFF Treatment.
[STEPS] | [] |
109,530 | Sinai SCENT TMC - Bronchoscopy Lung Collection | 0 | dx.doi.org/10.17504/protocols.io.bp2l628yrgqe/v2 | https://www.protocols.io/view/sinai-scent-tmc-bronchoscopy-lung-collection-dn725hqe | Monica Kraft, Santos Bermejo, Sojin Kim | TITLE: Sinai SCENT TMC - Bronchoscopy Lung Collection
AUTHORS: Monica Kraft, Santos Bermejo, Sojin Kim
[DESCRIPTION]
Cellular senescence is a stress-response, as well as a critical component of cell fate during development, repair, resilience, and normal aging. Deepening and broadening our investigations into cellula... | ["[Goal and Objective] This project aims to collect, handle, store, and allocate normal healthy lung tissues and biofluids for constructing cellular senescence maps according to the standards established by the Steering Committee of the SenNet consortium. It seeks to identify senescent cell differences across the body,... |
37,468 | SCoPE-MS | null | dx.doi.org/10.17504/protocols.io.bgt4jwqw | https://www.protocols.io/view/scope-ms-bgt4jwqw | Bogdan Budnik, Ezra Levy, Guillaume Harmange, Nikolai Slavov | TITLE: SCoPE-MS
AUTHORS: Bogdan Budnik, Ezra Levy, Guillaume Harmange, Nikolai Slavov
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Cellular heterogeneity is important to biological processes, including cancer and development. However, proteome heterogeneity is largely unexplored because of the li... | ["[Plate preperation]\nPut 1ul of HPLC grade water into each well of a plate using the Nanodrop or a multi-channel pipette.", "Conver up the plate and freeze until sorting.", "[Cell Prep]\nFor suspension cells simply place 1 to 2mL of cell culture in an Eppendorf tube and start step 8. For Adherent cells start at step ... |
63,932 | Repeatability of the XY positioning of motorized xy-tables of light microscopes | 1 | dx.doi.org/10.17504/protocols.io.kxygxz2rdv8j/v1 | https://www.protocols.io/view/repeatability-of-the-xy-positioning-of-motorized-x-can4sdgw | Mariana T Carvalho, Hans Fried, Stuart Jarvis, Claire A Mitchell, Roland Nitschke, Kees van der Oord, Arnd Rühl, Stanley Schwartz, Martin Spitaler, Roman Zantl, Arne Seitz | TITLE: Repeatability of the XY positioning of motorized xy-tables of light microscopes
AUTHORS: Mariana T Carvalho, Hans Fried, Stuart Jarvis, Claire A Mitchell, Roland Nitschke, Kees van der Oord, Arnd Rühl, Stanley Schwartz, Martin Spitaler, Roman Zantl, Arne Seitz
[DESCRIPTION]
The time it takes for the entire micr... | ["[Acquisition] When starting the acquisition software, first initialize (if applicable) the motorized stage platform in the XY direction.", "[Acquisition] Select a 10x or 20x dry lens and select the XYT acquisition mode of the system control software. Any drift control of the instrument itself must be disabled.", "Pos... |
39,711 | 603.3 & 604.5_URMC_HTC_Whole Lung and Lobe Processing | 4 | dx.doi.org/10.17504/protocols.io.biz7kf9n | https://www.protocols.io/view/603-3-amp-604-5-urmc-htc-whole-lung-and-lobe-proce-biz7kf9n | Gloria Pryhuber, Heidie Huyck | TITLE: 603.3 & 604.5_URMC_HTC_Whole Lung and Lobe Processing
AUTHORS: Gloria Pryhuber, Heidie Huyck
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:justify"><span style = "font-weight:bold;">Purpose and Scope of the Procedure</span></div><style>
.... | ["i.CT Scan\n\t\t\t\t\t\t\t .justify:after {\n\t\t\t\t\t\t\t content: \"\";\n\t\t\t\t\t\t\t display:inline-block;\n\t\t\t\t\t\t\t width: 100%;\n\t\t\t\t\t\t\t }\n\t\t\t\t\t\t\t ii.Separation of Lobes\n\t\t\t\t\t\t\t .justify:after {\n\t\t\t\t\t\t\t content: \"\";\n\t\t\t\t\t\t\t display:inline-bloc... |
99,912 | Mouse Cardiac Perfusion Fixation and Brain Collection | 1 | dx.doi.org/10.17504/protocols.io.8epv51bejl1b/v6 | https://www.protocols.io/view/mouse-cardiac-perfusion-fixation-and-brain-collect-ddtg26jw | Allen Institute for Brain Science | TITLE: Mouse Cardiac Perfusion Fixation and Brain Collection
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
This protocol describes the procedures for intracardiac perfusion fixation of postnatal mice, including anesthesia, exsanguination, fixation, brain removal and post-fixation storage.
Note: Research r... | [] |
67,892 | Noninvasive RNA-sequencing collection and processing | 2 | dx.doi.org/10.17504/protocols.io.kqdg3pjzzl25/v1 | https://www.protocols.io/view/noninvasive-rna-sequencing-collection-and-processi-ceiutcew | mem | TITLE: Noninvasive RNA-sequencing collection and processing
AUTHORS: mem
[DESCRIPTION]
This set of protocols accompanies the publication "Low cost, noninvasive RNA-sequencing to enable massive scaling of transcriptome studies" by Martorella et al.. Here you will find procedures for collecting noninvasive samples and p... | [] |
93,383 | UV decontamination of reagents/buffers | 3 | dx.doi.org/10.17504/protocols.io.n92ldmeyol5b/v1 | https://www.protocols.io/view/uv-decontamination-of-reagents-buffers-c7ffzjjn | Elena Essel, Matthias Meyer, Merlin Szymanski | TITLE: UV decontamination of reagents/buffers
AUTHORS: Elena Essel, Matthias Meyer, Merlin Szymanski
[DESCRIPTION]
Protocol for reducing DNA contamination of reagents and buffers used in the ancient DNA cleanroom by UV treatment.
Change log:
small formatting edits (20240111, EE)
small language edits for consistency (... | [] |
37,492 | Initiating and Performing in vivo experiments of anti-cancer treatments in mice (General) | 1 | dx.doi.org/10.17504/protocols.io.kqdg35n5pv25/v1 | https://www.protocols.io/view/initiating-and-performing-in-vivo-experiments-of-a-bguujwww | Randall J Kimple | TITLE: Initiating and Performing in vivo experiments of anti-cancer treatments in mice (General)
AUTHORS: Randall J Kimple
[DESCRIPTION]
This protocol describes our approach to setting up and designing experiments to study the effects of a cancer treatment in mice.
[STEPS]
SECTION: A. Design
1. What question(s) will ... | ["[A. Design] What question(s) will this experiment answer?\nBefore initiating a large experiment, consider performing a pilot study with fewer animals to prove/test concept. \nConsider working with a statistician using power and sample size calculations.\nDetermine:", "[A. Design] Species and strain of animal that wil... |
102,546 | E. coli recombineering (pSIJ8) | 0 | dx.doi.org/10.17504/protocols.io.x54v921e4l3e/v1 | https://www.protocols.io/view/e-coli-recombineering-psij8-dgds3s6e | is Sparrow | TITLE: E. coli recombineering (pSIJ8)
AUTHORS: is Sparrow
[DESCRIPTION]
This protocol is adapted from Jensen et al., 2015 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4672327/
for recombineering of gene deletions and posterior excision of antibiotic resistance cassettes using the plasmid pSIJ8
[STEPS]
SECTION: Creat... | ["[Create your deletion primers] Amplify a linear DNA fragment for recombineering through PCR. The primers must contain ~50 bp homology arms upstream of the priming sites which flank the region of the genome in to which you wish to introduce your DNA of interest, in addition to the priming sites below. \n\nPrimers shou... |
55,692 | High Throughput RNA Extraction and PCR Inhibitor Removal of Settled Solids for Wastewater Surveillance of SARS-CoV-2 RNA | 1 | dx.doi.org/10.17504/protocols.io.b2mkqc4w | https://www.protocols.io/view/high-throughput-rna-extraction-and-pcr-inhibitor-r-b2mkqc4w | Aaron Topol, marlene.wolfe , Krista Wigginton, Bradley White, Alexandria B B Boehm | TITLE: High Throughput RNA Extraction and PCR Inhibitor Removal of Settled Solids for Wastewater Surveillance of SARS-CoV-2 RNA
AUTHORS: Aaron Topol, marlene.wolfe , Krista Wigginton, Bradley White, Alexandria B B Boehm
[DESCRIPTION]
Please note that while this protocol is for TNA extraction using the Perkin Elmer... | ["[Preparation] If necessary, dissolve lyophilized Proteinase K in 11 mLof nuclease free water and resuspend Poly A following manufacturer directions.", "[Preparation] Label one 50 mL conical tube as Lysis buffer.", "[Preparation] Label a deep-well-plate as “Sample Plate”.", "[Preparation] If the Chemagic 360 has not b... |
97,031 | Reference Sequence Browser: An R application with a User-Friendly GUI to rapidly query sequence databases | 0 | dx.doi.org/10.17504/protocols.io.q26g71zxqgwz/v1 | https://www.protocols.io/view/reference-sequence-browser-an-r-application-with-a-dazf2f3n | Sriram Ramesh, Samuel Rapp, Jorge Tapias Gomez, Zia Truong, Dickson Chung, Benjamin Levine, Daniel Tapias-Gomez | TITLE: Reference Sequence Browser: An R application with a User-Friendly GUI to rapidly query sequence databases
AUTHORS: Sriram Ramesh, Samuel Rapp, Jorge Tapias Gomez, Zia Truong, Dickson Chung, Benjamin Levine, Daniel Tapias-Gomez
[DESCRIPTION]
Knowledge of which organisms have publicly available reference sequence... | ["[NCBI Tab] Welcome Tab: Using the navigation bar at the top, we can go to the NCBI section of the tool. Clicking on the NCBI button on the navigation bar will bring up the welcome tab of the NCBI database. There are several important things to pay attention to in this tab.", "[Welcome to the RSB] When you first start... |
null | null | null | dx.doi.org/10.17504/protocols.io.pdydi7w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>How to design primers for qPCR when testing the expression in different Arabidopsis accessions. A simple protocol - suggestions welcome. </p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.iygcftw | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
<p>1. Many factors can affect blood pressure (BP) measurements: first-time measurements, temperature, stress, noise and inappropriate handling.</p>
<p>2. Measure a minimum of 3 days and a maximum of 5 consecutive days.</p>
<p>3. Measure at the same time each day because BP varies... | [] |
75,296 | 18S rDNA amplification of Kudoa musculoliquefaciens in broadbill swordfish | 1 | null | https://www.protocols.io/view/18s-rdna-amplification-of-kudoa-musculoliquefacien-cmr8u59w | Jessica A Bolin | TITLE: 18S rDNA amplification of Kudoa musculoliquefaciens in broadbill swordfish
AUTHORS: Jessica A Bolin
[DESCRIPTION]
Protocol for extracting and purifying genomic DNA from Kudoa musculoliquefaciens infecting broadbill swordfish Xiphias gladius, harvested off Eastern Australia. Used in Bolin et al. 2021 Parasitol. ... | ["[Extraction and purification of genomic DNA] Cut ~15mg of swordfish muscle tissue into small pieces, and place in a microtube.", "[Extraction and purification of genomic DNA] Add 180µl of ATL buffer to the sample.", "[Extraction and purification of genomic DNA] Add 20µl of proteinase K and vortex for 10 sec.", "[Extr... |
91,117 | L-5 LEECH SHIPPING | 4 | dx.doi.org/10.17504/protocols.io.3byl4qdbrvo5/v1 | https://www.protocols.io/view/l-5-leech-shipping-c48myzu6 | REDI-NET Consortium | TITLE: L-5 LEECH SHIPPING
AUTHORS: REDI-NET Consortium
[DESCRIPTION]
This protocol describes leech shipping.
[GUIDELINES]
OBJECTIVE
To outline steps for proper packaging and shipping of preserved leech samples from a REDI-NET Silver Lab to a REDI-NET Gold Lab.
SUMMARY/SCOPE
The overarching aim of the REDI-NET is t... | ["[SAMPLE PREPARATION] Primary holding sample holding containers must be leak-proof. Samples should be preserved in appropriate preservative, if applicable (REDI-NET Leech Storage SOP L-3 ). Ensure that the lids are tightly closed to prevent leaking of storage media while in transit.", "[SAMPLE PREPARATION] Pack vials ... |
23,996 | Biochemical Measures of Neuropathy - Aconitase | null | dx.doi.org/10.17504/protocols.io.3n4gmgw | null | Eva Feldman | TITLE: Biochemical Measures of Neuropathy - Aconitase
AUTHORS: Eva Feldman
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span></div><div class = "text-block">Oxidative stress is highly correlated with the metabolic changes caused by hyperglycemia. Increa... | ["[Sample Preparation — Tissue]\n1. Weigh tissue sample. 2. Mince tissue. 3. Homogenize at 1% (w/v) in ice cold 0.2mM sodium citrate for 15-20 seconds. (new protocol calls for sodium citrate in 50mM Tris-HCl, pH 7.4). 4. Centrifuge at 800 x g for 10 minutes at 4°C. 5. Remove 25µl supernatant for protein assay. 6. Remov... |
77,369 | Create a MongoDB Atlas cluster | 5 | dx.doi.org/10.17504/protocols.io.rm7vzb1r5vx1/v1 | https://www.protocols.io/view/create-a-mongodb-atlas-cluster-cpszvnf6 | Mateusz Jundzill, Riccardo Spott, Mara Lohde, Martin Hölzer, Adrian Viehweger, Christian Brandt | TITLE: Create a MongoDB Atlas cluster
AUTHORS: Mateusz Jundzill, Riccardo Spott, Mara Lohde, Martin Hölzer, Adrian Viehweger, Christian Brandt
[DESCRIPTION]
A step-by-step guide on setup process for MongoDB Atlas tailored for data administrators with limited IT knowledge.
[STEPS]
SECTION: MongoDB Atlas set up
1. Cr... | ["[MongoDB Atlas set up] Create an account on MongoDB website.", "[MongoDB Atlas set up] Create an organization. Select Create a new organization and name your organization with e.g. the name of the institute or the group responsible for data administration. In the Select Cloud Service window, choose MongoDB Atlas and ... |
46,169 | Fixation of Eyes at UAB | 1 | dx.doi.org/10.17504/protocols.io.brbzm2p6 | https://www.protocols.io/view/fixation-of-eyes-at-uab-brbzm2p6 | David Anderson, Jeffrey Messinger, Angela Kruse, Jamie Allen, Carrie Romer, Kevin Schey, Jeff Spraggins, Christine Curcio | TITLE: Fixation of Eyes at UAB
AUTHORS: David Anderson, Jeffrey Messinger, Angela Kruse, Jamie Allen, Carrie Romer, Kevin Schey, Jeff Spraggins, Christine Curcio
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The accession and fixation of whole human eye specimens at University... | ["Whole eyes arrive from deceased human donors via Advancing Sight Network (Birmingham AL; formerly the Alabama Eye Bank) ≤6 hours death-to-preservation.", "Fixation is performed on the globe with lens and iris in place by immersing in buffered 4% paraformaldehyde overnight.", "Initially the cornea is removed with a 2-... |
61,079 | Nuclei extraction for single-cell RNAseq from frozen tissue using Singulator™ 100 | 1 | null | https://www.protocols.io/view/nuclei-extraction-for-single-cell-rnaseq-from-froz-b7vxrn7n | Ignas Masilionis, Ojasvi Chaudhary, Ronan Chaligne, Linas Mazutis | TITLE: Nuclei extraction for single-cell RNAseq from frozen tissue using Singulator™ 100
AUTHORS: Ignas Masilionis, Ojasvi Chaudhary, Ronan Chaligne, Linas Mazutis
[DESCRIPTION]
This protocol describes nuclei extraction from snap frozen tissue (human or mouse) using Singulator, including washing nuclei suspension in ... | ["[Singulator] Add RNAse inhibitor (0.2-1.0 U/uL final depending on tissue type - Final volume ~ 3.5 mL for standard protocol, ~2.5 for low volume) and DTT (1M, final 1mM) directly into Nuclei Isolation Cartridge just before the run.\n\nTransfer tissue into the cooled Nuclei Isolation Cartridge and start Nuclei isolati... |
70,242 | Staphylococcus Aureus Sampling | 4 | dx.doi.org/10.17504/protocols.io.81wgb6pk1lpk/v8 | https://www.protocols.io/view/staphylococcus-aureus-sampling-cguatwse | 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... |
46,736 | HTAPP_Test protocol_Dissociation of primary neuroblastoma resection to a single-cell suspension for single-cell RNA-seq (using papain and ACK) | 1 | dx.doi.org/10.17504/protocols.io.brvqm65w | https://www.protocols.io/view/htapp-test-protocol-dissociation-of-primary-neurob-brvqm65w | Sara Napolitano, Jingyi Wu, Michal Slyper, Sébastien Vigneau, Asaf Rotem, Bruce Johnson, Orit Rozenblatt-Rosen, Aviv Regev | TITLE: HTAPP_Test protocol_Dissociation of primary neuroblastoma resection to a single-cell suspension for single-cell RNA-seq (using papain and ACK)
AUTHORS: Sara Napolitano, Jingyi Wu, Michal Slyper, Sébastien Vigneau, Asaf Rotem, Bruce Johnson, Orit Rozenblatt-Rosen, Aviv Regev
[DESCRIPTION]
<div class = "text-bloc... | ["[Tissue Description]\nReport sample processing information.\nSample ID:Date:Time Received:Media Used for Transportation:Person Processing:", "[Tissue Description]\nTransfer sample to a Petri dish with cold PBS kept on ice to better visualize its composition. Take a picture of the resection alongside a ruler and annot... |
107,592 | Western blotting of Syp-VAMP2 complex | 0 | dx.doi.org/10.17504/protocols.io.kqdg32doev25/v1 | https://www.protocols.io/view/western-blotting-of-syp-vamp2-complex-dmbg42jw | Caroline Brown, Snehasish Ghosh, Kallol Gupta | TITLE: Western blotting of Syp-VAMP2 complex
AUTHORS: Caroline Brown, Snehasish Ghosh, Kallol Gupta
[DESCRIPTION]
The intricate molecular environment of the native membrane profoundly influences every aspect of membrane protein (MP) biology. Despite this, the most prevalent method of studying MPs uses detergent-like m... | ["[Reagents needed for protocol] Acquire the following antibodies for the Western blotting protocol:", "[Reagents needed for protocol] Primary Antibody: rabbit Na/K ATPase (Abcam Cat# ab167390, 1:5000)", "[Reagents needed for protocol] Primary Antibody: Synaptophysin Rabbit mAb (ABClonal Cat#A19122, 1:5000)", "[Reagent... |
50,412 | Protocol for hippocampal neuronal cultures | 1 | dx.doi.org/10.17504/protocols.io.bvgkn3uw | https://www.protocols.io/view/protocol-for-hippocampal-neuronal-cultures-bvgkn3uw | Andrés Guillén-Samander, Pietro De Camilli | TITLE: Protocol for hippocampal neuronal cultures
AUTHORS: Andrés Guillén-Samander, Pietro De Camilli
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol details the procedure for preparation of neuronal cultures from mice hippocampi as it was performed in </span><a href="https://doi... | ["[Protocol for hippocampal neuronal cultures]\nCoat MatTek dishes with per dish of Poly-D-Lysine (Sigma) for at least to at .\n1 mL\n37 °C", "[Protocol for hippocampal neuronal cultures]\nWash dishes twice with culture grade water and let dry.", "[Protocol for hippocampal neuronal cultures]\nPrepare papain solutio... |
41,266 | Fabrication and characterization of a pixel pressure detector using 3-D printable materials or classical PCB materials | 1 | dx.doi.org/10.17504/protocols.io.bkiskuee | https://www.protocols.io/view/fabrication-and-characterization-of-a-pixel-pressu-bkiskuee | German Sanchez | TITLE: Fabrication and characterization of a pixel pressure detector using 3-D printable materials or classical PCB materials
AUTHORS: German Sanchez
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol presents the fabrication process for a piezoelectric ( 3D printed or PCB) pixel pressure... | ["[3D OR PCB PIXEL DETEXCTOR DESIGN]\nInto a 3D designer. In this case, inventor, generate an initial base of 38 mm * 38 mm with a thickness of 0.7 mm asshown:", "[3D OR PCB PIXEL DETEXCTOR DESIGN]\nCreate a different piece (the one that is expected to be printed in a conductive material), generating pixels of an area ... |
73,079 | Fly Model Protocols | 2 | dx.doi.org/10.17504/protocols.io.q26g7ypeqgwz/v1 | https://www.protocols.io/view/fly-model-protocols-cjkxukxn | Mel Feany | TITLE: Fly Model Protocols
AUTHORS: Mel Feany
[DESCRIPTION]
A collection of protocols describing experimental work with fly models.
[STEPS] | [] |
62,992 | Liberty CBD Gummy Bears [SHARK TANK] Shocking Scam Report! | 3 | dx.doi.org/10.17504/protocols.io.kqdg3pbq1l25/v1 | https://www.protocols.io/view/liberty-cbd-gummy-bears-shark-tank-shocking-scam-r-b9rqr55w | H Douglas Morris | TITLE: Liberty CBD Gummy Bears [SHARK TANK] Shocking Scam Report!
AUTHORS: H Douglas Morris
[DESCRIPTION]
This is the reason it is so important to include heart healthy foods in your diet.
[STEPS] | [] |
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