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 |
|---|---|---|---|---|---|---|---|
94,844 | Barcoded and targeted cDNA library preparation for Oxford Nanopore Technologies sequencing | 4 | dx.doi.org/10.17504/protocols.io.kqdg3xzwzg25/v1 | https://www.protocols.io/view/barcoded-and-targeted-cdna-library-preparation-for-c8u4zwyw | Rosemary A Bamford, Szi Kay Leung, Aaron Jeffries, Jonathan Mill | TITLE: Barcoded and targeted cDNA library preparation for Oxford Nanopore Technologies sequencing
AUTHORS: Rosemary A Bamford, Szi Kay Leung, Aaron Jeffries, Jonathan Mill
[DESCRIPTION]
The NEBNext Single Cell/Low Input cDNA Synthesis & Amplification Module (NEB) was adapted for the purpose of adding Oxford Nanopore ... | ["[Bespoke barcoding of cDNA] Primer annealing for first strand synthesis\nPrepare in a PCR tube on ice. A reaction mix of up to 7 µL of total RNA (75 ng ) is added to 1 µL 2 millimolar (mM) TSO-ONT primer, 1 µL 10 millimolar (mM) dNTPs (NEB) and made up to 9 µL with nuclease-free H2O. Gently invert a few times ... |
77,594 | Single-cell dissociation of Drosophila melanogaster pupal tarsi | 4 | dx.doi.org/10.17504/protocols.io.x54v9dzbmg3e/v2 | https://www.protocols.click/view/single-cell-dissociation-of-drosophila-melanogaste-cpz2vp8e | Ben R. Hopkins, Olga Barmina, Artyom Kopp | TITLE: Single-cell dissociation of Drosophila melanogaster pupal tarsi
AUTHORS: Ben R. Hopkins, Olga Barmina, Artyom Kopp
[DESCRIPTION]
This protocol outlines a step-by-step guide to generating single-cell suspensions of Drosophila melanogaster pupal tarsi for use in 10x single-cell transcriptome profiling. This proto... | ["[Collecting, sexing, and ageing pupae] Collect white prepupae. Individuals should meet the P1 aging criteria laid out by Bainbridge and Bownes (1981): the pupae should be white or cream coloured, have stopped moving completely, and display everted anterior spiracles.", "Fold a kimwipe in half and then in half again a... |
null | null | null | dx.doi.org/10.17504/protocols.io.qxzdxp6 | null | null | TITLE: No Title
AUTHORS:
[BEFORE_START]
<p>Before starting, make 10X sterile Daigo solution in artificial seawater (ASW):</p>
<p>Dissolve 2.56 g Daigo powder in 1L ASW and filter sterilize through a 0.22 µm filter.</p>
[GUIDELINES]
<p> </p>
<p> </p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
53,511 | Western blot protocol for detecting ATP10B in mouse/rat brain | 1 | dx.doi.org/10.17504/protocols.io.byhfpt3n | https://www.protocols.io/view/western-blot-protocol-for-detecting-atp10b-in-mous-byhfpt3n | María Sanchiz Calvo, eduard.bentea , Veerle Baekelandt | TITLE: Western blot protocol for detecting ATP10B in mouse/rat brain
AUTHORS: María Sanchiz Calvo, eduard.bentea , Veerle Baekelandt
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol for detection of ATP10B in rat and mouse brain tissue by Western blotting</div></div>
[STEPS]
?. [Day 1]
Prep... | ["[Day 1]\nPrepare samples for Western blotting : proteins in of volume (adjust with milliQ water) of 6X SDS buffer + 10% of β-mercaptoethanol\n30 µg\n12 µl\n2.4 µl", "[Day 1]\nBoil the samples for at\n98 °C", "[Day 1]\nLoad samples, together with of mass marker (PageRuler™ Plus Prestained Protein Ladder) on a 3-8% ... |
49,640 | Measurement of dissolved black carbon in water via benzenepolycarboxylic acid (BPCA) oxidation and quantification using aqueous, inorganic, high-performance liquid chromatography | 6 | dx.doi.org/10.17504/protocols.io.buqgnvtw | https://www.protocols.io/view/measurement-of-dissolved-black-carbon-in-water-via-buqgnvtw | Riley Barton, Sasha Wagner | TITLE: Measurement of dissolved black carbon in water via benzenepolycarboxylic acid (BPCA) oxidation and quantification using aqueous, inorganic, high-performance liquid chromatography
AUTHORS: Riley Barton, Sasha Wagner
[DESCRIPTION]
Dissolved black carbon (DBC) is the condensed aromatic portion of dissolved organ... | ["[Solid Phase Extraction: Prepare and condition cartridges] The solid phase extraction (SPE) cartridges used in this protocol (Agilent Bond Elut PPL cartridge, 1g, 6 mL) is packed with a styrene-divinylbenzene polymer resin that recovers high proportions of dissolved organic matter (DOM) on a per-carbon basis. The res... |
19,548 | Enterovirus (EV) D68 real-time RT-PCR (EV-D68-TM2018) | null | dx.doi.org/10.17504/protocols.io.xb4fiqw | null | Ian Mackay, Judy Northill | TITLE: Enterovirus (EV) D68 real-time RT-PCR (EV-D68-TM2018)
AUTHORS: Ian Mackay, Judy Northill
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol aims to amplify enterovirus (EV) D68 viruses but not other viruses.</div><div class = "text-block">This protocol is modified from a previously... | ["[Oligonucleotide sequences]\nAB1NameSequence 5'-3'2EV-D68-For1TGTTYCCACGGTTGAAAAYAA3EV-D68-For2TTCCCACGGTTGAAARNYRAC4EV-D68-RevCAAGCTACACACGGGTTAGT5EV-D68-FAM-TM2018FAM - CCGTTAWCCGCTATAGTACTTCGAGAAACC - BHQ1MODIFICATIONS TO THE PUBLISHED ASSAY:Two modified forward primers, targeting the same region as the original a... |
null | null | null | dx.doi.org/10.17504/protocols.io.etibeke | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
<strong>Materials:</strong><br /><br />1.) host and viral DNAs<br />2.) 1X TE buffer (10 mM Tris, pH 8.0, 1 mM EDTA)<br />3.) 1 M NaOH<br />4.) 1 M Acetic acid<br />5.) nylon membrane, cut to 12.3 X16 cm (2 sheets)<br />6.) Whatman 3MM filter paper, cut 12.3X16 cm (2 sheets)<br /... | [] |
31,983 | Quantitative (q)PCR and Differential Expression Analysis | null | dx.doi.org/10.17504/protocols.io.bbgpijvn | null | Jeffrey Lewis, Amanda Scholes | TITLE: Quantitative (q)PCR and Differential Expression Analysis
AUTHORS: Jeffrey Lewis, Amanda Scholes
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>A generalizable protocol for measuring relative changes in gene expression via qPCR (cDNA synthesis, qPCR primer optimization, and qPCR analysi... | ["[qPCR Primer Design]\n1. Primer Design\nWe use Primer3 to design primers: http://biotools.umassmed.edu/bioapps/primer3_www.cgiPrimers are designed to have a Tm as close to 58°C as possible. This helps to ensure that primer annealing will be similar for all reactions. Primers should amplify a product of ~100 - 200 bp.... |
null | null | null | dx.doi.org/10.17504/protocols.io.rced2te | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Stains zebrafish larvae with Sudan Black B, which marks neutrophil granules.</p>
[BEFORE_START]
<p>You will need a rocker/nutator/rotator at 4ºC and at RT.</p>
<p> </p>
<p>Make both 1x and 10x stocks of PBS from powder packets, in water.</p>
<p>Make 70% Ethanol solution.</p>... | [] |
24,821 | Diagnostic Restriction Digest | null | dx.doi.org/10.17504/protocols.io.4gvgtw6 | null | Addgene The Nonprofit Plasmid Repository | TITLE: Diagnostic Restriction Digest
AUTHORS: Addgene The Nonprofit Plasmid Repository
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol is for running a diagnostic restriction digest. To see the full abstract and other resources, visit the </span><a href="https://www.addgene.org/p... | ["[Verifying Total Plasmid Size -OR- Insert and Backbone Size]\nThe simplest form of diagnostic digest is one in which you just want to verify that the plasmid that you have is the expected size, or that it is composed of a backbone and insert of expected sizes. This is frequently done after performing either PCR - or ... |
39,906 | SOLUTION -07 - RPMI/FBS 1% | 3 | dx.doi.org/10.17504/protocols.io.bi8akhse | https://www.protocols.io/view/solution-07-rpmi-fbs-1-bi8akhse | Marco Cosentino, Elisa Storelli, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Marco Ferrari, Franca Marino | TITLE: SOLUTION -07 - RPMI/FBS 1%
AUTHORS: Marco Cosentino, Elisa Storelli, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Marco Ferrari, Franca Marino
[STEPS] | [] |
65,598 | Natural killer cell depletion in vivo (mouse) | 4 | dx.doi.org/10.17504/protocols.io.rm7vzyezxlx1/v1 | https://www.protocols.io/view/natural-killer-cell-depletion-in-vivo-mouse-cca6sshe | Goran Tomic | TITLE: Natural killer cell depletion in vivo (mouse)
AUTHORS: Goran Tomic
[DESCRIPTION]
This protocol describes a validated procedure for antibody depletion of natural killer cells in mice (C57Bl/6J and 129SvEv strains), combined with the injection of cancer cells i.v. It is based on combining a few references and te... | ["Mice will receive an i.p. injection of the antibody in 200 µl PBS (Day 1) e.g. Monday", "Mice will receive an i.p. injection of the antibody in 200 µl PBS (Day 4) e.g. Thursday", "Mice will receive tail vein injection of the cell suspension in 100 µl PBS (Day 5) e.g. Friday", "Mice will receive an i.p. injection of t... |
55,577 | Genotyping Arabidopsis T-DNA lines | 1 | dx.doi.org/10.17504/protocols.io.b2hzqb76 | https://www.protocols.io/view/genotyping-arabidopsis-t-dna-lines-b2hzqb76 | Lynn Doran, Steven J Burgess | TITLE: Genotyping Arabidopsis T-DNA lines
AUTHORS: Lynn Doran, Steven J Burgess
[DESCRIPTION]
This protocol is used for genotyping Arabidopsis seedlings to test for the presence of a transfer DNA (T-DNA) insertion. By using two primer sets it is possible to determine whether a seedling is homozygous, heterozygous o... | ["[Prepare primer working solution] Re-suspend lyophilized primers in dH2O to a stock concentration of 100 mM. Note: primer sequences can be obtained from SALK T-DNA express if you have the T-DNA accession number (http://signal.salk.edu/tdnaprimers.2.html)", "[Prepare primer working solution] Create a 10 mM working sol... |
107,187 | Populating metadata templates for NCBI submissions using PulseNet 2.0 | 1 | dx.doi.org/10.17504/protocols.io.3byl4qn4ovo5/v2 | https://www.protocols.io/view/populating-metadata-templates-for-ncbi-submissions-dkwt4xen | Ruth Timme, Maria Balkey, Tina Lusk Pfefer, Candace Hope Bias | TITLE: Populating metadata templates for NCBI submissions using PulseNet 2.0
AUTHORS: Ruth Timme, Maria Balkey, Tina Lusk Pfefer, Candace Hope Bias
[DESCRIPTION]
PURPOSE: to define the standard operating procedure for collecting isolate metadata using PulseNet 2.0 for submission of food/environmental isolates to NCBI... | ["Metadata SampleSheet preparation \n\nPopulate the metadata spreadsheet form before uploading your sequencing run or linking NCBI sequencing records within PulseNet 2.0. \n\nPlease download the following metadata template, Guidance is included in the first tab. \n\n \n\nOnce you have filled out the template, import m... |
null | null | null | dx.doi.org/10.17504/protocols.io.mjgc4jw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Dicentric Chromosomes Assay</p>
[STEPS]
?.
?.
?.
?.
?.
?.
?. | [] |
54,647 | Protocol for ABC Immunohistochemistry and Quantifying Nerves | 4 | dx.doi.org/10.17504/protocols.io.eq2lypoymlx9/v1 | https://www.protocols.io/view/protocol-for-abc-immunohistochemistry-and-quantify-bzkxp4xn | Donald Hoover | TITLE: Protocol for ABC Immunohistochemistry and Quantifying Nerves
AUTHORS: Donald Hoover
[DESCRIPTION]
Cardiac tissue samples were obtained from human donors and sent to East Tennessee State University for processing. At ETSU, the tissue was dissected, sectioned with a cryostat, and stained for neuronal markers usin... | ["[Immunostaining Day 1] Using the PAP Pen, carefully draw a water barrier circle around the tissue sections on the slide — allow this circle to dry for several seconds or up to approximately one minute.", "[Immunostaining Day 1] Rinse slides by placing them into a Coplin jar filled with PBS (pH 7.3 - 7.4): 4 x 5 min e... |
null | null | null | dx.doi.org/10.17504/protocols.io.g7nbzme | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div class="page" title="Page 4">
<div class="layoutArea">
<div class="column">
<p>Infrared fluorescence detection with Odyssey Family Imaging Systems provides a quantitative two-color detection method for Western blots.</p>
<p> </p>
<p>This protocol is designed to help you achi... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.t4ceqsw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Sterilization and post-hatch care of gnotobiotic Periplaneta americana, as adapted from Doll et. al. (see below)
Doll J, Trexler P, Reynolds L, Bernard G. 1963. The use of peracetic acid to obtain germfree invertebrate eggs for gnotobiotic studies. Am Midl Nat 69:231-239
[STEP... | ["[Collect oothecae egg cases) from colony] Pulling egg cases directly off females' abdomens ensures the eggs have not been sitting in the litter a long time.\nThis also typically results in \"cleaner\" oothecae, with less excrement on the outside", "[Physically clean any visible/major excrement off of the outside of t... |
71,097 | MagAttract + Metapolyzyme metagenomic gDNA extraction from skin swabs | 4 | dx.doi.org/10.17504/protocols.io.q26g7yr19gwz/v2 | https://www.protocols.io/view/magattract-metapolyzyme-metagenomic-gdna-extractio-chnzt5f6 | Natalie Ring | TITLE: MagAttract + Metapolyzyme metagenomic gDNA extraction from skin swabs
AUTHORS: Natalie Ring
[DESCRIPTION]
A protocol for the metagenomic extraction of bacterial DNA from skin swab samples (optimised using canine swabs), for use in a rapid diagnostics pipeline. At the end of the protocol, the DNA is cleaned up a... | ["[Extended pre-lysis spin down] Bathe swab tip in 3 ml PBS in the swab tube for 10 minutes, with occasional vortexing. Remove swab from tube, squeezing the sides as you do.\n\n3 mL \n10 min", "[Extended pre-lysis spin down] Pellet 2x 1.5 ml aliquots of cell-PBS solution in 1.5 ml tubes by centrifuging at maximum speed... |
40,076 | In-silico analysis | 3 | dx.doi.org/10.17504/protocols.io.bjdkki4w | https://www.protocols.io/view/in-silico-analysis-bjdkki4w | avinash.kale | TITLE: In-silico analysis
AUTHORS: avinash.kale
[STEPS] | [] |
32,307 | Protocol Temephos Bioassay | 1 | dx.doi.org/10.17504/protocols.io.bbstinen | https://www.protocols.io/view/protocol-temephos-bioassay-bbstinen | Lara Ferrero Gomez | TITLE: Protocol Temephos Bioassay
AUTHORS: Lara Ferrero Gomez
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Performing bioassays to assess the larval susceptibility to Temephos</div></div>
[STEPS] | [] |
63,905 | Oprah Winfrey ACV Gummies Shark Tank: Where To Buy It? | 1 | dx.doi.org/10.17504/protocols.io.8epv59my5g1b/v1 | https://www.protocols.io/view/oprah-winfrey-acv-gummies-shark-tank-where-to-buy-cam9sc96 | Shark Tank | TITLE: Oprah Winfrey ACV Gummies Shark Tank: Where To Buy It?
AUTHORS: Shark Tank
[DESCRIPTION]
Oprah Winfrey ACV Gummies Shark Tank: Where To Buy It?
[STEPS]
SECTION: Oprah Winfrey ACV Gummies Shark Tank: Where To Buy It? Oprah Winfrey Keto – The Supplement for a Spare Shape and Slim Body! There's a superb p... | ["[Oprah Winfrey ACV Gummies Shark Tank: Where To Buy It? Oprah Winfrey Keto – The Supplement for a Spare Shape and Slim Body! There's a superb product out then in the request that we all know by the name that goes as the Oprah Winfrey Keto. This blog is a complete in- depth analysis of this outstanding as well ... |
24,048 | Production of magnetic GFP affinity beads using a Camelid anti-GFP nanobody | null | dx.doi.org/10.17504/protocols.io.3qqgmvw | null | Nichanok Auevechanichkul, Ruth Lintermann, Lennart Wirthmueller | TITLE: Production of magnetic GFP affinity beads using a Camelid anti-GFP nanobody
AUTHORS: Nichanok Auevechanichkul, Ruth Lintermann, Lennart Wirthmueller
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Our protocol for production of 'home-made' magnetic GFP affinity beads using a Camelid anti-GFP... | [] |
19,677 | Lysogeny Broth (1L) | null | dx.doi.org/10.17504/protocols.io.xf5fjq6 | null | Brian Smith, baltrus@email.arizona.edu micro.tucson | TITLE: Lysogeny Broth (1L)
AUTHORS: Brian Smith, baltrus@email.arizona.edu micro.tucson
[STEPS]
?. [Fill container aproximately 750mL of H2O]
Add stir bar and set to mix
?. [Add ingredients]
[Bacto Tryptone]
[Bacto Yeast Extract]
[NaCl]
?. [Bring volume to 1L by adding H2O]
Allow to mix again with stir bar.
?. [Autcla... | ["[Fill container aproximately 750mL of H2O]\nAdd stir bar and set to mix", "[Add ingredients]\n[Bacto Tryptone]\n[Bacto Yeast Extract]\n[NaCl]", "[Bring volume to 1L by adding H2O]\nAllow to mix again with stir bar.", "[Autclave]\nAdd agar to container to be autclavedThen add media\n15 g", "[Autclave]\nAutclave at 121... |
70,871 | In vitro transcription of guide RNAs and 5'-triphosphate removal | 1 | dx.doi.org/10.17504/protocols.io.n2bvjyp5vk5w/v14 | https://www.protocols.io/view/in-vitro-transcription-of-guide-rnas-and-5-39-trip-chfxt3pn | Mark Dewitt, Julia Wong, Beeke Wienert, Moritz F Schlapansky, Eric Aird | TITLE: In vitro transcription of guide RNAs and 5'-triphosphate removal
AUTHORS: Mark Dewitt, Julia Wong, Beeke Wienert, Moritz F Schlapansky, Eric Aird
[DESCRIPTION]
sgRNA template assembly, in vitro T7 transcription, and sgRNA column cleanup to remove 5'-triphosphate groups
[GUIDELINES]
The primers used are: o... | ["[Design sgRNA and order PCR oligos] Add the desired protospacer sequence to the T7FwdVarV2 oligo and order the oligo from your favorite oligonucleotide supplier. There are many programs available for protospacer design that attempt to optimize on- and/or off-target activity. Which program is most useful depends upon ... |
95,481 | Histological processing of octocoral tissue | 4 | dx.doi.org/10.17504/protocols.io.81wgbx38nlpk/v1 | https://www.protocols.io/view/histological-processing-of-octocoral-tissue-c9gzz3x6 | Maria Rakka, Gala G Edery, Marina Carreiro-Silva | TITLE: Histological processing of octocoral tissue
AUTHORS: Maria Rakka, Gala G Edery, Marina Carreiro-Silva
[DESCRIPTION]
In recent years, there has been a significant focus on coral habitats, encompassing both shallow and deep ecosystems. Historically, most studies concentrated on scleractinian corals, however cont... | ["[Fixation] Use 10% seawater formalin to fix the samples", "[Dissection] Using a scalpel and forceps, make an incision parallel to the coral axis. Carefully separate the tissue from the axis by using the forceps, and remove the axis completely.", "[Decalcification] Place tissue in eppendorfs (or other plastic/glass vi... |
93,737 | Gewebesammlung Frischgewebe Nephrektomie | 1 | null | https://www.protocols.io/view/gewebesammlung-frischgewebe-nephrektomie-c7shznb6 | Annika Fendler, Bettina Ergün | TITLE: Gewebesammlung Frischgewebe Nephrektomie
AUTHORS: Annika Fendler, Bettina Ergün
[DESCRIPTION]
Dieses Protokoll beschreibt die Schritte für die Sammlung von Frischgewebe, Gefriergewebe (Fresh-frozen), und Blut von Patienten mit Nierenzellkarzinom nach Nephrektomie.
Verwandte Dokumente:
Protokoll zur Blutaufa... | ["[Gewebesammlung im Schnellschnitt] Nach Rückmeldung des Schnellschnitts geht eine Person zur Gewebeentnahme. \nTüte Niere und Stickstoffbehälter mitnehmen.\nArbeitsanleitung (siehe Abbildung) beachten.", "[Gewebesammlung im Schnellschnitt]", "[Gewebesammlung im Schnellschnitt] 3x 15 ml Falcons mit 10,2 ml Transportm... |
null | null | null | dx.doi.org/10.17504/protocols.io.fjwbkpe | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The printed instructions accompanying each Foldscope kit are very detailed and easy to follow. Even easier is <a href="https://www.youtube.com/watch?v=wJtJJixMncA" target="_blank">this</a> excellent 14-minute video tutorial for the assembly. </p>
<p> </p>
<p>I didn't know abo... | [] |
66,943 | DNA extraction (BOMB) | 4 | null | https://www.protocols.io/view/dna-extraction-bomb-cdk7s4zn | Tsu-Chun Hung, Yin-Tse Huang | TITLE: DNA extraction (BOMB)
AUTHORS: Tsu-Chun Hung, Yin-Tse Huang
[DESCRIPTION]
DNA extraction (BOMB)
[STEPS]
SECTION: Sample Collection
1. Add 200 µL of 1mm beads to 2ml enppendorf tube
SECTION: Sample Collection
2. Add200 µL of 0.5mm beads to 2ml enppendorf tube
SECTION: Sample Collection
3. Add 225 µL of TE... | ["[Sample Collection] Add 200 µL of 1mm beads to 2ml enppendorf tube", "[Sample Collection] Add200 µL of 0.5mm beads to 2ml enppendorf tube", "[Sample Collection] Add 225 µL of TE buffer to 2ml enppendorf tube", "[Sample Collection] Add 375 µL of lysis buffer to 2ml enppendorf tube", "[Sample Collection] Add 267 µL of ... |
79,924 | Open, non-comparative, clinical investigation to evaluate the performance and safety of the medical device H42 (collagen paste for filling) in repairing periodontal pockets due to periodontitis. | 1 | dx.doi.org/10.17504/protocols.io.4r3l27rzxg1y/v2 | https://www.protocols.io/view/open-non-comparative-clinical-investigation-to-eva-csauwaew | franco.barattini | TITLE: Open, non-comparative, clinical investigation to evaluate the performance and safety of the medical device H42 (collagen paste for filling) in repairing periodontal pockets due to periodontitis.
AUTHORS: franco.barattini
[DESCRIPTION]
Research protocol to evaluate safety and overall performance of a collagen p... | ["[Open, non-comparative, clinical investigation to evaluate the performance and safety of the medical device H42 (collagen paste for filling) in repairing periodontal pockets due to periodontitis.] Open, non-comparative, clinical investigation to evaluate the performance and safety of the medical device H42 (collagen ... |
null | null | null | dx.doi.org/10.17504/protocols.io.dp95r5 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Northeastern's method for plasmid extraction and purification. From Thermo Scientific's GeneJET Plasmid Miniprep Kit
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.cjrum5 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This is the protocol for a large-scale Protein Expression Using BL21(DE3) Competent E. coli cells(C2527).
[BEFORE_START]
Determine the optimal time/temperature for the protein expression in a small scale trial.
[GUIDELINES]
<strong>BL21(DE3) Genotype:</strong><br />fhuA2 ... | [] |
81,626 | B-4 BLOOD TESTING | 4 | dx.doi.org/10.17504/protocols.io.rm7vzbze8vx1/v1 | https://www.protocols.io/view/b-4-blood-testing-ctx2wpqe | REDI-NET Consortium | TITLE: B-4 BLOOD TESTING
AUTHORS: REDI-NET Consortium
[DESCRIPTION]
This protocol details standard operating procedure for blood testing.
[BEFORE_START]
BEFORE START
Check the DNA and RNA concentrations in each sample of total nucleic acid (TNA) extraction.
If the concentrations are detectable, choose the sequencin... | ["[gDNA PREPARATION] When the RNA concentration of the sample is lower than the detectable range of the Qubit High Sensitivity Assay (<0.01 ng/µl), the sample is subjected to gDNA sequencing. The cDNA synthesis can be skipped.", "[gDNA PREPARATION] When the DNA concentration >10 ng/µl, calculate the required volume of ... |
null | null | null | dx.doi.org/10.17504/protocols.io.kvycw7w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Paraffin sections of formalin-fixed human pancreas and isolated human islets were treated with 0.05% pronase for antigen retrieval, blocked with 2% bovine serum albumin (BSA; Sigma)/phosphate buffered saline (PBS), incubated overnight (4°C) with 10E4 (anti-HS) mAb (1/10; US B... | [] |
76,744 | Setting up Zotero and Google Drive for syncing reference libraries (PC) | 1 | null | https://www.protocols.io/view/setting-up-zotero-and-google-drive-for-syncing-ref-cn7gvhjw | Carie M. Frantz | TITLE: Setting up Zotero and Google Drive for syncing reference libraries (PC)
AUTHORS: Carie M. Frantz
[DESCRIPTION]
This protocol is useful if you wish to sync a LARGE reference library across multiple computers. It uses Zotero, which has built-in free syncing for up to 300 MB of files (roughly 50-100 papers). For l... | ["[Set up Google Drive syncing] Install Drive for desktop on both computers", "[Install and set up Zotero on Computer 1] Install Zotero desktop\n\nDefault installation settings are fine.", "[Install and set up Zotero on Computer 2] Repeat the steps above for your second computer\n\nIf you do not have a prior (e.g., Men... |
65,948 | RNAlater recipe | 4 | dx.doi.org/10.17504/protocols.io.bp2l61w35vqe/v1 | https://www.protocols.io/view/rnalater-recipe-ccm4su8w | Yin-Tse Huang | TITLE: RNAlater recipe
AUTHORS: Yin-Tse Huang
[DESCRIPTION]
RNAlater recipe
[STEPS]
SECTION: Before you start
1. Submerge all your equipment and glassware in 1% bleach to get rid of nuclease
SECTION: Reagents
None. 0.5M Disodium dihydrate EDTA
SECTION: Reagents
None.
SECTION: Before you start
None. Autoclave ... | ["[Before you start] Submerge all your equipment and glassware in 1% bleach to get rid of nuclease", "[Reagents] 0.5M Disodium dihydrate EDTA", "[Reagents]", "[Before you start] Autoclave to deactivate DEPC", "[Before you start] Keep the DEPC treated water at 4 °C", "[Reagents] DEPC treated water\n1. Add 1 mL DEPC in 1... |
80,491 | Forage and Range Research Laboratory Nursery and Plant Measurement Standard Operating Procedures (SOP) and Protocols | 1 | null | https://www.protocols.io/view/forage-and-range-research-laboratory-nursery-and-p-csujweun | blair.waldron, B Shaun Bushman, Alexander J Hernandez, Kevin B Jensen, Thomas A Jones, Steven R Larson, Thomas A Monaco, Michael D Peel, Matthew D Robbins, Joseph G. Robins, Richard R-C Wang | TITLE: Forage and Range Research Laboratory Nursery and Plant Measurement Standard Operating Procedures (SOP) and Protocols
AUTHORS: blair.waldron, B Shaun Bushman, Alexander J Hernandez, Kevin B Jensen, Thomas A Jones, Steven R Larson, Thomas A Monaco, Michael D Peel, Matthew D Robbins, Joseph G. Robins, Richard R-C W... | ["[Breeding Nursery and Plant Trait Measurements] Forage Mass", "[Breeding Nursery and Plant Trait Measurements] Using a sickle bar or flail forage harvester, cut forage plots to an 8-cm stubble height. On research sites unsuitable for the harvester, hand harvest the forage from at least three random 1-m2 quadrats thro... |
45,040 | Mollusk pedal mucus effects on epilithic biofilms | 4 | null | https://www.protocols.io/view/mollusk-pedal-mucus-effects-on-epilithic-biofilms-bp8qmrvw | Clara Maria Arboleda-Baena, Claudia Pareja , Isadora Pla, Ramiro Logares, Rodrigo De La Iglesia, Sergio A. Navarrete | TITLE: Mollusk pedal mucus effects on epilithic biofilms
AUTHORS: Clara Maria Arboleda-Baena, Claudia Pareja , Isadora Pla, Ramiro Logares, Rodrigo De La Iglesia, Sergio A. Navarrete
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. We cultured epilithic biofilms on cover glass slides inside a Polycarbonate ... | ["We cultured epilithic biofilms on cover glass slides inside a Polycarbonate cell culture plate of 6-Wells, for one week in K medium (Keller et al. 1987).", "We collected, during nocturnal low tides, animals of each mollusk species from wave-exposed platforms and brought them to the laboratory in coolers and then pla... |
47,529 | Bulk DNA Extraction (Ding Lab) | 4 | dx.doi.org/10.17504/protocols.io.bsnhndb6 | https://www.protocols.io/view/bulk-dna-extraction-ding-lab-bsnhndb6 | Reyka Jayasinghe, Li Ding, Feng Chen, Satok | TITLE: Bulk DNA Extraction (Ding Lab)
AUTHORS: Reyka Jayasinghe, Li Ding, Feng Chen, Satok
[DESCRIPTION]
Bulk DNA Extraction
[STEPS]
1. Cut tissue (~5 mg) and place in a 1.5 mL microcentrifuge tube. Add 180 µL Buffer ATL and 20 µL proteinase K, mix by vortexing and incubate at 56°C until completely lysed (1–3 h).
2. ... | ["Cut tissue (~5 mg) and place in a 1.5 mL microcentrifuge tube. Add 180 µL Buffer ATL and 20 µL proteinase K, mix by vortexing and incubate at 56°C until completely lysed (1–3 h).", "Add 2 µL RNase (100 mg/ml) and incubate for 30 min. at 37°C", "Add 200 µL Buffer AL. Vortex for 15 sec.", "Incubate at 70°C for 10 min. ... |
86,065 | FM1-43 endocytic uptake assay in HIPSC derived neurons | 4 | dx.doi.org/10.17504/protocols.io.3byl4qj52vo5/v1 | https://www.protocols.io/view/fm1-43-endocytic-uptake-assay-in-hipsc-derived-neu-cyarxsd6 | Sakthi Kumar | TITLE: FM1-43 endocytic uptake assay in HIPSC derived neurons
AUTHORS: Sakthi Kumar
[DESCRIPTION]
FM1-43 is a lipophilic styryl dye, nontoxic to the cells, virtually nonfluorescent in aqueous media. The dye will become fluorescent once it binds to the plasma membrane. In neurons that are actively releasing neurotransm... | ["[Reagents needed:] FM1-43 dye (Thermo fisher scientific, catalog no: T3163).\nThis dye is available in both live and fixable versions. Also, available in different colors like FM4-64", "[Mature neurons- hipsc derived Dopaminergic, Cortical or GABAergic neurons:] mDA, CTX or GABAergic neuron progenitors were plated in... |
null | null | null | dx.doi.org/10.17504/protocols.io.kwdcxa6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Intracavernous pressure (ICP) measurement is a well-established technique for assessing the erectile function, which was performed by cannulating either crus or shaft of the penis. But yet, as far as we know, no consensus has reached on the ES parameters of frequency and volt... | [] |
94,545 | Laptop setup and piranhaGUI install | 5 | null | https://www.protocols.io/view/laptop-setup-and-piranhagui-install-c8jrzum6 | Aine.OToole | TITLE: Laptop setup and piranhaGUI install
AUTHORS: Aine.OToole
[DESCRIPTION]
This protocol provides step-by-step guidance on installing piranhaGUI and its dependency Docker Desktop.
[STEPS]
SECTION: Install piranha through piranhaGUI
7. PiranhaGUI can be installed on a Windows, MacOSX or Linux machine.
To install... | ["[Install piranha through piranhaGUI] PiranhaGUI can be installed on a Windows, MacOSX or Linux machine. \nTo install piranhaGUI, navigate to piranhaGUI GitHub on a web browser. You should see a page similar to the one below, which shows the latest releases of piranha GUI, along with some installation instructions.", ... |
78,418 | Characterization of human immune cell subpopulations in cerebrospinal fluid using mass cytometry. | 5 | dx.doi.org/10.17504/protocols.io.36wgqjp4ovk5/v1 | https://www.protocols.io/view/characterization-of-human-immune-cell-subpopulatio-cqtsvwne | Gerardina Gallaccio, Meng Wang, Stephan Schlickeiser, Desiree Kunkel, chotima.boettcher, Camila Fernández-Zapata | TITLE: Characterization of human immune cell subpopulations in cerebrospinal fluid using mass cytometry.
AUTHORS: Gerardina Gallaccio, Meng Wang, Stephan Schlickeiser, Desiree Kunkel, chotima.boettcher, Camila Fernández-Zapata
[DESCRIPTION]
Phenotypic and compositional changes of immune cells in cerebrospinal fluid (... | ["[Sample collection and storage] Prepare the anchor sample. \n\nAn anchor sample is peripheral blood mononuclear cells (PBMCs) used as internal reference across different measurements/batches to facilitate the signal normalization8.\nHowever, cell types other than PBMCs can also be used as an anchor sample but they sh... |
50,879 | OMS Atlas OCT Spatial Mapping | 1 | dx.doi.org/10.17504/protocols.io.bvw7n7hn | https://www.protocols.io/view/oms-atlas-oct-spatial-mapping-bvw7n7hn | Brett Johnson, Danielle Galipeau, Todd Camp, George Thomas | TITLE: OMS Atlas OCT Spatial Mapping
AUTHORS: Brett Johnson, Danielle Galipeau, Todd Camp, George Thomas
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the procedure by which the OMS Atlas serially sections an OCT block, prepares the resulting slides and samples, and then di... | ["[Preparation]\nVerify the identity of the OCT block to be cut against written request for sectioning.", "[Preparation]\nRemove OCT block from freezer and acclimate to cryostat ( ) for minimum of .\n-80 °C\n-20 °C", "[Preparation]\nLabel all slides and cryotubes with a unique BEMS ID and Part#, corresponding to the w... |
62,967 | Botanical Farms CBD Gummies - Reviews, Side Effects, Benefits, Price & Ingredients! | 3 | dx.doi.org/10.17504/protocols.io.4r3l2oyqpv1y/v1 | https://www.protocols.io/view/botanical-farms-cbd-gummies-reviews-side-effects-b-b9qxr5xn | Botanical Farms CBD Gummies | TITLE: Botanical Farms CBD Gummies - Reviews, Side Effects, Benefits, Price & Ingredients!
AUTHORS: Botanical Farms CBD Gummies
[DESCRIPTION]
Botanical Farms CBD Gummies
[STEPS] | [] |
35,633 | PhotoId-Whale: blue whale dorsal fin classification for mobile devices | 1 | dx.doi.org/10.17504/protocols.io.be2rjgd6 | https://www.protocols.io/view/photoid-whale-blue-whale-dorsal-fin-classification-be2rjgd6 | Rosa I Ramos-Arredondo, Blanca E, Diane Gendron, J. Francisco Gallegos-Funes, Dante Mújica-Vargas, J.B. Rosas-Fernández | TITLE: PhotoId-Whale: blue whale dorsal fin classification for mobile devices
AUTHORS: Rosa I Ramos-Arredondo, Blanca E, Diane Gendron, J. Francisco Gallegos-Funes, Dante Mújica-Vargas, J.B. Rosas-Fernández
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Photoidentification is a method used by biolo... | ["[Image to be classified]\nObtain the image to be classified. The image is obtained from the database or acquired in the field. CICIMAR-IPN researchers.", "[Image Pre-Processing]\nThis stage is divided into two substages, which are described belowi)\tROI selection: by means of a graphical interface, the initial point ... |
49,171 | MIBI staining | 1 | dx.doi.org/10.17504/protocols.io.bt9tnr6n | https://www.protocols.io/view/mibi-staining-bt9tnr6n | Marc Bosse, Sean Bendall, Mike Angelo | TITLE: MIBI staining
AUTHORS: Marc Bosse, Sean Bendall, Mike Angelo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is the standard FFPE tissue staining procedure recommended for Multiplex Ion Beam Imaging Time of Flight instrument (MIBI_TOF) developed in the Sean C. Bendall and Michae... | ["[Slide for MIBI]\nFFPE or frozen sections should be deposited on special conductive slides for MIBIIt is recommended to use freshly cut tissue sections. Otherwise tissue section slides should be stored properly using different state of the art methods (vacuum chamber, nitrogen chamber or vacuum sealed bags)", "[Slid... |
25,813 | SELECTION AND ENRICHMENT OF TRANSGENIC CELL POPULATIONS (Basic Protocol 3) | null | dx.doi.org/10.17504/protocols.io.5fvg3n6 | null | Michael S. Fernandopulle, Ryan Prestil, Christopher Grunseich, Chao Wang, Li Gan, Michael E. Ward | TITLE: SELECTION AND ENRICHMENT OF TRANSGENIC CELL POPULATIONS (Basic Protocol 3)
AUTHORS: Michael S. Fernandopulle, Ryan Prestil, Christopher Grunseich, Chao Wang, Li Gan, Michael E. Ward
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>While lipid-mediated transient transfection and expressio... | ["[Cell Preparation]\nCulture cells after transfection and expand to at least one full 6-well plate or one 10 cm dish by EDTA split (see Basic Protocol 1).\nPost-transfection recovery and expansion should take about 1 week; this enables the degradation / dilution of transient plasmids and permits expansion of edited ce... |
null | null | null | dx.doi.org/10.17504/protocols.io.iykcfuw | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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null | null | null | dx.doi.org/10.17504/protocols.io.d7r9m5 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
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46,867 | Actinobacteria collection, enrichment and isolation | 4 | dx.doi.org/10.17504/protocols.io.brztm76n | https://www.protocols.io/view/actinobacteria-collection-enrichment-and-isolation-brztm76n | Rene Flores Clavo, Cristian Daniel Asmat Ortega, Nataly Ruiz Quinones | TITLE: Actinobacteria collection, enrichment and isolation
AUTHORS: Rene Flores Clavo, Cristian Daniel Asmat Ortega, Nataly Ruiz Quinones
[STEPS]
?. [Collection]
Collect samples aseptically in 600 ml screw-capped glass jar.
?. [Collection]
Pack the flasks in cool boxes with ice bags and transport them to the laborator... | ["[Collection]\nCollect samples aseptically in 600 ml screw-capped glass jar.", "[Collection]\nPack the flasks in cool boxes with ice bags and transport them to the laboratory", "[Collection]\nIdentify each sample by writing a code, sampling date, depth, sample color, pH, and sample location", "[Enrichment and pre-trea... |
100,443 | Non-destructive microplastic isolation from water and sediment samples | 0 | dx.doi.org/10.17504/protocols.io.4r3l2q264l1y/v1 | https://www.protocols.io/view/non-destructive-microplastic-isolation-from-water-deb33aqn | Jonas Stadfeld, Sneha Suresh, Srijak Bhatnagar | TITLE: Non-destructive microplastic isolation from water and sediment samples
AUTHORS: Jonas Stadfeld, Sneha Suresh, Srijak Bhatnagar
[DESCRIPTION]
Microplastics in aquatic ecosystems serve as unique habitats for diverse microbial communities, collectively referred to as the plastisphere. Investigating these microbes ... | ["[Microplastic Isolation - Water] NOTE: Use only metal and glass equipment. Tubing should be silicone.", "[Microplastic Isolation - Water] Filter at least 40L of water through a 20µm Cellulose filter (47 mm).\n\nNote: Depending upon the murkiness, the filter may clog before 40L is filtered. In that case, multiple filt... |
48,735 | Human Lung Digestion: Deriving a single cell suspension | 4 | null | https://www.protocols.io/view/human-lung-digestion-deriving-a-single-cell-suspen-btt7nnrn | Morrisey Lab | TITLE: Human Lung Digestion: Deriving a single cell suspension
AUTHORS: Morrisey Lab
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Human Lung Digestion: Deriving a single cell suspension </span></div></div>
[STEPS] | [] |
48,141 | Monitoring fly feeding behavior and timing by beetle luciferase reporters | 1 | dx.doi.org/10.17504/protocols.io.bs9mnh46 | https://www.protocols.io/view/monitoring-fly-feeding-behavior-and-timing-by-beet-bs9mnh46 | Misha Koksharov | TITLE: Monitoring fly feeding behavior and timing by beetle luciferase reporters
AUTHORS: Misha Koksharov
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Feeding behavior of flies carrying a beetle (e.g. firefly) luciferase gene can be conveniently monitored in real-time by measuring bioluminescence... | ["[Placing flies into 96-well plates]\nAnesthetize flies by cooling them on ice or by using a CO2 pad. The CO2 pads are the most common method used in fly labs while cooling is the simplest. \"In addition, it [cooling] is the only method which will not affect fly neurology, therefore behavior studies may begin after t... |
28,660 | RNA extraction with PGTX | null | dx.doi.org/10.17504/protocols.io.78uhrww | null | Lutz Berwanger | TITLE: RNA extraction with PGTX
AUTHORS: Lutz Berwanger
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is used for RNA extraction in cyanobacteria after Pinto et al. 2009.</div><div class = "text-block"><span style = "font-weight:bold;">Pinto, Fernando Lopes; Thapper, Anders; Sontheim... | ["Centrifuge for 3 minutes at 4˚C and 4.000 g.", "Resuspend the cell pellet in 1 ml of PGTX. Freeze in liquid nitrogen and store at -20 ˚C.\nWear goggles, a lab coat and gloves when dealing with PGTX and liquid nitrogen.", "Incubate for 5 min at 95 °C, shaking at 250 rpm in Thermomixer (Eppendorf)", "Rapidly chill 5 mi... |
null | null | null | dx.doi.org/10.17504/protocols.io.k7yczpw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Proximity Ligation Protocol with Concurrent IF</p>
[STEPS] | [] |
58,739 | 96 well spin column TNA extraction from plants - CTAB method | 4 | dx.doi.org/10.17504/protocols.io.n2bvj685plk5/v1 | https://www.protocols.io/view/96-well-spin-column-tna-extraction-from-plants-cta-b5ktq4wn | James JN JN Kitson | TITLE: 96 well spin column TNA extraction from plants - CTAB method
AUTHORS: James JN JN Kitson
[DESCRIPTION]
This protocol is designed for extracting total nucleic acids (TNA) from plant material. In reality the drying step probably means that you won't isolate plant mRNA but viral RNA (and probably plant ribosomal R... | ["[Preparation of grinding tubes and buffer] Source steel beads (ball bearings) for tissue grinding (Tungsten beads are not usually necessary). We use hardened 3mm carbon steel or stainless steel bearings from simplybearings.co.uk. This protocol requires three beads per sample tube.", "[Initial homogenisation of plant ... |
57,047 | Intracellular cytokine detection based on flow cytometry in hemocytes from Galleria mellonella larvae | 4 | dx.doi.org/10.17504/protocols.io.b3xxqppn | https://www.protocols.io/view/intracellular-cytokine-detection-based-on-flow-cyt-b3xxqppn | Anna Katarzyna Wrońska, Agata Kaczmarek, Mieczysława Irena Boguś | TITLE: Intracellular cytokine detection based on flow cytometry in hemocytes from Galleria mellonella larvae
AUTHORS: Anna Katarzyna Wrońska, Agata Kaczmarek, Mieczysława Irena Boguś
[DESCRIPTION]
Invertebrates are becoming increasingly popular models for research on the immune system. The innate immunity possessed by... | ["[Sample preparation] Before bleeding, wash the larvae with distilled water (15 seconds) and then immerse briefly (5 seconds) in 70% (v/v) ethanol to sterilize their surfaces, thus reducing the chance of contamination of hemolymph samples.", "[Sample preparation] Collect the hemolymph into sterile tube from the larvae... |
null | null | null | dx.doi.org/10.17504/protocols.io.mepc3dn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Quantitative measurements of both the copy number and spatial distribution of large fractions of the transcriptome in single-cells could revolutionize our understanding of a variety of cellular and tissue behaviors in both healthy and diseased states. Single-molecule Fluoresc... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.tfeejje | null | null | TITLE: No Title
AUTHORS:
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.ssdeea6 | null | null | TITLE: No Title
AUTHORS:
[BEFORE_START]
<p>Clean the work area with 70% alcohol. Use all filters and autoclaved tips. Refrigerate your centrifuge to 4C.</p>
[STEPS]
?.
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null | null | null | dx.doi.org/10.17504/protocols.io.ib6care | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Please contact Dr. Steven Wilhelm (wilhelm@utk.edu) for additional information regarding this protocol.</p>
<p> </p>
<p>Modified from <span style="font-family: 'Segoe UI', sans-serif; font-size: small;">Schwyn, B. & Neilands, J. B. Universal chemical assay for the detecti... | [] |
71,297 | Transfection of Atlantic salmon primary hepatocytes | 4 | dx.doi.org/10.17504/protocols.io.j8nlkw4p1l5r/v1 | https://www.protocols.io/view/transfection-of-atlantic-salmon-primary-hepatocyte-chu9t6z6 | Alex K. Datsomor, Ragnhild Wilberg, Jacob S. Torgersen, Simen R. Sandve, Thomas N Harvey | TITLE: Transfection of Atlantic salmon primary hepatocytes
AUTHORS: Alex K. Datsomor, Ragnhild Wilberg, Jacob S. Torgersen, Simen R. Sandve, Thomas N Harvey
[DESCRIPTION]
This protocol is for isolation and transfection of primary hepatocytes from Atlantic salmon. We have confirmed plasmid transfection efficiency of up... | ["[Prepare buffers and plates] Coat wells of the culture plate with 1x PEI.", "[Prepare buffers and plates] Dilute PEI stock 1:100 in 0.1 M borate buffer.", "[Prepare buffers and plates] Add sufficient volume to empty wells. Enough to cover the bottom of the well.", "[Prepare buffers and plates] Incubate for 60 min at ... |
null | null | null | dx.doi.org/10.17504/protocols.io.et2beqe | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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82,751 | immunofluorescent staining with anti-GFP and anti-CD63 antibodies | 4 | dx.doi.org/10.17504/protocols.io.14egn2pypg5d/v1 | https://www.protocols.click/view/immunofluorescent-staining-with-anti-gfp-and-anti-cu27wyhn | rosanne.wouters, Peter Vangheluwe | TITLE: immunofluorescent staining with anti-GFP and anti-CD63 antibodies
AUTHORS: rosanne.wouters, Peter Vangheluwe
[DESCRIPTION]
This protocol was used for immunofluorescent staining in fixed HeLa cells with anti-GFP and anti-CD63 antibodies, followed by confocal imaging.
[STEPS]
2. fix cells with 4% paraformaldehyd... | ["fix cells with 4% paraformaldehyde for 20 min at room temperature", "permeabilize cells with 0.1% Triton X-100 in PBS for 5 min", "block for 1 h with blocking buffer (PBS with 0.5% Tween20, 0.1% BSA, 0.2% FBS)", "incubate coverslips with primary antibodies for 2 h at room temperature\n(anti-CD63, exbio, 11-343-C100, ... |
null | null | null | dx.doi.org/10.17504/protocols.io.c7bzim | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
.
[STEPS]
?. | [] |
88,645 | Barcode Composition by Overlap-Extension PCR | 1 | null | https://www.protocols.io/view/barcode-composition-by-overlap-extension-pcr-c2tdyei6 | Mathew Chu | TITLE: Barcode Composition by Overlap-Extension PCR
AUTHORS: Mathew Chu
[DESCRIPTION]
Traditionally, DNA barcodes are synthesised as random oligonucleotides. However, this leads to uncertainty regarding the ground truth of barcode sequences in the experimental setting. Without reference sequences, it is impossible to ... | ["[Single Stranded DNA Pools for Combinatorial Assembly] ssDNA oligos for combinatorial assembly can be ordered as a pool (oPool). For a final barcode of n units, each with m diversity, order a set of m different barcode sequences for each unit:\n \nwhere unit i (1 ≤ i ≤ n) consists of m barcodes flanked by left (L) an... |
97,912 | The State of Research on LGBTQ+ Fertility: Trends, Gaps, and Future Directions | 0 | dx.doi.org/10.17504/protocols.io.yxmvme7dbg3p/v1 | https://www.protocols.io/view/the-state-of-research-on-lgbtq-fertility-trends-ga-dbuy2nxw | Demian Glujovsky, Julieta quaglia, Fiamma Belén Di Biase, Mariana Miguens, Romina Pesce, Belen Herrero, Agustín Ciapponi | TITLE: The State of Research on LGBTQ+ Fertility: Trends, Gaps, and Future Directions
AUTHORS: Demian Glujovsky, Julieta quaglia, Fiamma Belén Di Biase, Mariana Miguens, Romina Pesce, Belen Herrero, Agustín Ciapponi
[DESCRIPTION]
The hypothesis is that in the last decade the trend of published studies about reproducti... | ["[Background] Rationale and potential applied impact \nThe LGBTQ+ community has made significant progress in recent years in terms of visibility and awareness. This has probably contributed to an increase in the number of LGBTQ+ people who are seeking fertility treatments, gaining access to these types of treatments t... |
null | null | null | dx.doi.org/10.17504/protocols.io.ukgeutw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
The following protocol describes resuspension of lyophilized primers from (4) 96-Well plates shipped from Integrated DNA Technologies (IDT) at 3nmol per well using the epMotion 5075.
For information about ordering consult the Earth Micriobiome Projects website.
Barcoded primer... | ["[Prepare reagents] {\"blocks\":[{\"key\":\"9h1q2\",\"text\":\"In a sterile 30mL reservoir, add 11.725\\u00a0ml (required minimum volume) of PCR Clean Water to resuspend (4) 96-Well plates. \",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[],\"entityRanges\":[],\"data\":[]},{\"key\":\"4odgr\",\"text\":\" \",... |
72,557 | NARMS-KS-1-Autoclave Use | 4 | null | https://www.protocols.io/view/narms-ks-1-autoclave-use-ci4mugu6 | tdoerks | TITLE: NARMS-KS-1-Autoclave Use
AUTHORS: tdoerks
[DESCRIPTION]
Instructions on how to use autoclave in Mosier P209.
[STEPS]
SECTION: Waste
1. Make sure waste to be autoclaved is in a biohazard bag (no more than 3/4 full) and place in autoclavable container.
SECTION: Waste
2. Wrap 2 Steam Migrating Integrator Strips t... | ["[Waste] Make sure waste to be autoclaved is in a biohazard bag (no more than 3/4 full) and place in autoclavable container.", "[Waste] Wrap 2 Steam Migrating Integrator Strips together with autoclave tape and a piece of string and place in the middle of the bag of waste to be autoclaved with the piece of string hangi... |
40,094 | Lyophilized metal-antibody reconstitution | 4 | dx.doi.org/10.17504/protocols.io.bjd6ki9e | https://www.protocols.io/view/lyophilized-metal-antibody-reconstitution-bjd6ki9e | Marc Bosse, Mike Angelo, Sean Bendall | TITLE: Lyophilized metal-antibody reconstitution
AUTHORS: Marc Bosse, Mike Angelo, Sean Bendall
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the procedure to prepare the reconstitution buffer and the resuspension of metal-labeled antibody.</div></div>
[STEPS]
?. [Stock so... | ["[Stock solutions preparation]\nPrepare Tris (10 mM), sodium azide (0.02%)", "[Stock solutions preparation]\nAdd Tris 1M, pH 7.5 in tube\n500 µl\n50 mL", "[Stock solutions preparation]\nAdd sodium azide ()\n500 µl", "[Stock solutions preparation]\nComplete with 50 mL ultrapure water", "[Stock solutions preparation]\... |
97,346 | Protein Digestion with S-trap Spin Columns using Conditioned Concentrated Media | 4 | dx.doi.org/10.17504/protocols.io.x54v928eml3e/v1 | https://www.protocols.io/view/protein-digestion-with-s-trap-spin-columns-using-c-dbba2iie | Joanna Bons, J P Rose, M A Watson, B Schilling | TITLE: Protein Digestion with S-trap Spin Columns using Conditioned Concentrated Media
AUTHORS: Joanna Bons, J P Rose, M A Watson, B Schilling
[DESCRIPTION]
Trypsin digestion of isolated proteins using S-trap Spin columns in preparation for downstream proteomic profiling.
For trypsin digestion of proteins from condi... | ["In a 2-mL microcentrifuge tube add an appropriate proportion of volume from the concentrated condition media, 10% SDS for a final concentration of 4% SDS, 1M TEAB pH 8 solution for a final concentration of 50 mM TEAB, and HPLC-grade water if necessary to bring the volume up to a minimum of 50 µL.", "Add 250 mM DTT fo... |
57,083 | Test for blog post | 1 | dx.doi.org/10.17504/protocols.io.n92ldz9y7v5b/v1 | https://www.protocols.io/view/test-for-blog-post-b3y3qpyn | Emma Ganley | TITLE: Test for blog post
AUTHORS: Emma Ganley
[DESCRIPTION]
Just a test
[STEPS]
1.
2. | [] |
60,115 | Wastewater QC workflow in GalaxyTrakr (SSQuAWK3) | 1 | dx.doi.org/10.17504/protocols.io.kxygxzk5dv8j/v4 | https://www.protocols.io/view/wastewater-qc-workflow-in-galaxytrakr-ssquawk3-b6xtrfnn | 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... |
21,332 | Yale - HDL Cholesterol | null | dx.doi.org/10.17504/protocols.io.y3ufynw | null | John Stack, Gary Cline | TITLE: Yale - HDL Cholesterol
AUTHORS: John Stack, Gary Cline
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">Procedure used to determine the concentration of HDL cholesterol in blood, serum, and plasma. HDL Cholestero... | ["Calibrate Cobas for HDL analysis by running a lipid calibrator, HDL Direct Reagent Reagent 1 and HDL Direct Reagent 2.", "Sample handling as performed by the Cobas Mira Plus. a) Pipette 3µL of sample into cuvette. b) Add 180 µL of Direct Reagent 1. c) Add 60 µL of Direct Reagent 2. d) Mixture is incubated at 37ºC... |
39,615 | Open Source Microfluidic Scaffolds | 5 | dx.doi.org/10.17504/protocols.io.biw7kfhn | https://www.protocols.io/view/open-source-microfluidic-scaffolds-biw7kfhn | Harry Felton, Robert Hughes | TITLE: Open Source Microfluidic Scaffolds
AUTHORS: Harry Felton, Robert Hughes
[STEPS]
?. [Design]
User designs the required microfluid system from the sub-systems available.
?. [Generate Models]
Download, install and open Fusion 360.
NB: Although Fusion 360 works on iOS and Android devices the add-in will not and so ... | ["[Design]\nUser designs the required microfluid system from the sub-systems available.", "[Generate Models]\nDownload, install and open Fusion 360.\nNB: Although Fusion 360 works on iOS and Android devices the add-in will not and so a Windows or MacOS device should be used.", "[Generate Models]\nLoad the µ-fluid add-i... |
77,719 | In situ IRF4 detection in formalin-fixed, paraffin-embedded (FFPE) pig tissues | 4 | dx.doi.org/10.17504/protocols.io.4r3l27bdqg1y/v1 | https://www.protocols.io/view/in-situ-irf4-detection-in-formalin-fixed-paraffin-cp5xvq7n | Jayne E Wiarda, Crystal Loving | TITLE: In situ IRF4 detection in formalin-fixed, paraffin-embedded (FFPE) pig tissues
AUTHORS: Jayne E Wiarda, Crystal Loving
[DESCRIPTION]
An immunohistochemistry (IHC) staining protocol for in situ identification of porcine IRF4
[BEFORE_START]
Starting specimens:
Starting samples = FFPE tissues cut to 4 micron th... | ["[Baking] Before starting the assay: \nPreheat a dry oven to 60℃ \nLoad slides for assay into vertical slide rack\n\nBaking\nBake slides 20 min 60℃\n\nWhile slides bake:\nPrepare 0.05% PBS-T (can store at RT up to 1 month)", "[Deparaffinizing & Rehydrating] Immediately before deparaffinizing:\nAdd ~200 mL xylenes ... |
44,817 | Lab 6 Notebook | 3 | dx.doi.org/10.17504/protocols.io.bpzrmp56 | https://www.protocols.io/view/lab-6-notebook-bpzrmp56 | TITLE: Lab 6 Notebook
AUTHORS:
[STEPS] | [] | |
89,665 | Pole Test | 1 | dx.doi.org/10.17504/protocols.io.3byl4q362vo5/v1 | https://www.protocols.io/view/pole-test-c3s9ynh6 | Jhodi Webster | TITLE: Pole Test
AUTHORS: Jhodi Webster
[DESCRIPTION]
This protocol describes the pole test, a simple and rapid behavioral assay used to evaluate motor coordination, balance, and bradykinesia (slowness of movement) in mice and rats. The test involves placing an animal head-up at the top of a vertical textured pole and... | ["[Setup] Allow for one hour habituation period for mice in the testing room.", "[Setup] Place pole (approx 20.5in long, with rubber bands place at 1 inch intervals)", "[Setup] Have an extra empty cage handy", "[Training:] place mouse nose-down at the base of the pole and allow it to climb off onto the floor of the enc... |
101,203 | Cell counting | 0 | dx.doi.org/10.17504/protocols.io.14egn66rql5d/v1 | https://www.protocols.io/view/cell-counting-de3t3gnn | daniel.dautan daniel, Per Svenningsson | TITLE: Cell counting
AUTHORS: daniel.dautan daniel, Per Svenningsson
[DESCRIPTION]
Used for counting cells labeled with immunofluorescent markers in mouse brain sections. Sections should be stained, mounted, and imaged with high resolution (2048 x 2048 scanning).
[STEPS]
1. Using 2-3 sections to encompass the brain r... | ["Using 2-3 sections to encompass the brain region of interest, acquire high resolution images (2048 x 2048) using tile scanning and z-stack acquisition.", "Import images into ImageJ.", "Apply maximum average projection and color adjust as needed, making sure to apply the same settings to all images.", "For each image,... |
60,038 | Screening whole proteome of Aedes aegypti and identification of potential targets for in-silico molecular and structural interaction studies against natural bioactives | 5 | dx.doi.org/10.17504/protocols.io.e6nvwkbj2vmk/v1 | https://www.protocols.io/view/screening-whole-proteome-of-aedes-aegypti-and-iden-b6vere3e | Anagha S Setlur, Chandrashekar K, Manas Sarkar, Vidya Niranjan | TITLE: Screening whole proteome of Aedes aegypti and identification of potential targets for in-silico molecular and structural interaction studies against natural bioactives
AUTHORS: Anagha S Setlur, Chandrashekar K, Manas Sarkar, Vidya Niranjan
[DESCRIPTION]
As a dangerous etiological agent for dengue, chik... | ["[IDENTIFICATION OF PROTEIN TARGETS] Reference proteome identification\n\nAedes aegypti is a yellow fever mosquito, that is also an etiological agent for dengue, chikungunya and zika. Hence, identification of the significant proteins in the organism’s reference proteome by a whole proteome screening is essential to us... |
72,274 | Selecting a Region of Interest for Hidden Markov Modeling using ebFRET | 1 | null | https://www.protocols.io/view/selecting-a-region-of-interest-for-hidden-markov-m-citsuene | Clark Fritsch | TITLE: Selecting a Region of Interest for Hidden Markov Modeling using ebFRET
AUTHORS: Clark Fritsch
[DESCRIPTION]
This protocol follows from the "Basic Analysis Protocol" and is the first step towards analyzing your data using Hidden Markov Modeling. In this protocol, you select traces containing features that you wi... | ["After generating a catalog of traces that you consider worthy of further analysis and saving these traces to your \"GoodOnes.txt\" file for a given directory (as described in the \"Basic Analysis Protocol\") you will have the opportunity to measure specific parameters in your traces by manually selecting regions of i... |
67,378 | Ready XL Male Enhancement Reviews Pills Side Effects | 1 | dx.doi.org/10.17504/protocols.io.261genmqwg47/v1 | https://www.protocols.io/view/ready-xl-male-enhancement-reviews-pills-side-effec-cd2ss8ee | Alpha State Male Enhancement | TITLE: Ready XL Male Enhancement Reviews Pills Side Effects
AUTHORS: Alpha State Male Enhancement
[DESCRIPTION]
Ready XL Male Enhancement Reviews Pills Side Effects
[STEPS]
SECTION: Ready XL Male Enhancement Reviews Pills Side Effects Ready Xl Male Enhancement- Women blame individualities for being occupied with co... | ["[Ready XL Male Enhancement Reviews Pills Side Effects Ready Xl Male Enhancement- Women blame individualities for being occupied with coitus. What a nationalist and disparaging comment! In any case, they are correct, so we should assume the stylish about them. Assuming that your abettor is womanish, she presumably ant... |
95,635 | Descending Platform | 4 | dx.doi.org/10.17504/protocols.io.14egn3ko6l5d/v2 | https://www.protocols.io/view/descending-platform-c9mtz46n | daniel.dautan daniel, Per Svenningsson | TITLE: Descending Platform
AUTHORS: daniel.dautan daniel, Per Svenningsson
[DESCRIPTION]
Behavioral test to assess motor function.
The test is using a custom made 45-degree grid path with a width of 5cm and a length of 45cm. The 15cm one side is oriented with a 45-degree angle. The grid is formed by metal mesh with a ... | ["Place the custom-made, metal mesh grid to have an angle of 45 degrees with the floor.", "At the end of the platform, place the animal cage to provide a safe target.", "Place a camera above the grid to record the entire procedure. Here we use the Logitech C920 webcam and windows camera software.", "Using the video, re... |
30,602 | Micro-CT imaging of iodine-stained rat stomach | 1 | dx.doi.org/10.17504/protocols.io.95ih84e | https://www.protocols.io/view/micro-ct-imaging-of-iodine-stained-rat-stomach-95ih84e | Deborah Jaffey, Terry Powley, Logan Chesney | TITLE: Micro-CT imaging of iodine-stained rat stomach
AUTHORS: Deborah Jaffey, Terry Powley, Logan Chesney
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes how to prepare a rat stomach for micro-CT imaging to enable a 3D description of the organ. Iodine is used to stain the ti... | ["[Training]\nSelect 4 rats within the preferred weight distribution. Each animal is trained to consume a quantity of palatable In the first 2 days, the animal is supplied with both regular rat chow and a half container of Dietgel (the Dietgel is put in a dish in the cage at 11AM) to accustom itself to the Dietgel. In... |
36,525 | Short protocol for mitochondrial CO1 gene analysis of shark | 1 | dx.doi.org/10.17504/protocols.io.bfwmjpc6 | https://www.protocols.io/view/short-protocol-for-mitochondrial-co1-gene-analysis-bfwmjpc6 | Sutanto Hadi, Noviar Andayani, Effin Muttaqin, Benaya M Simeon, Muhammad Ichsan, Beginer Subhan, Hawis Madduppa | TITLE: Short protocol for mitochondrial CO1 gene analysis of shark
AUTHORS: Sutanto Hadi, Noviar Andayani, Effin Muttaqin, Benaya M Simeon, Muhammad Ichsan, Beginer Subhan, Hawis Madduppa
[STEPS]
?. [Shark Tissue Sampling]
Shark Tissue Sampling
.justify:after {
content: "";
display:inlin... | ["[Shark Tissue Sampling]\nShark Tissue Sampling\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\tPrepare sampling tools and equipment: camera, ruler or scale band, gloves, scissors or cutter an... |
102,397 | Lysosomal activity DQ-Red BSA assay | 0 | dx.doi.org/10.17504/protocols.io.j8nlk8dp6l5r/v1 | https://www.protocols.io/view/lysosomal-activity-dq-red-bsa-assay-df853ry6 | Razaul Karim | TITLE: Lysosomal activity DQ-Red BSA assay
AUTHORS: Razaul Karim
[DESCRIPTION]
This protocol details the Lysosomal activity DQ-Red BSA assay.
[STEPS]
SECTION: Cell Culture/Treatments:
1. 0.5x10^4/ml of cells plated on coverslips.
SECTION: Cell Culture/Treatments:
2. PFF-488 treatment.
SECTION: Cell Culture/Treatments... | ["[Cell Culture/Treatments:] 0.5x10^4/ml of cells plated on coverslips.", "[Cell Culture/Treatments:] PFF-488 treatment.", "[Cell Culture/Treatments:] PBS/trypsin (0.01%) wash.", "[Cell Culture/Treatments:] DQ-BSA Red treatment: \n\n10 152790 min at 37 °C.", "[Cell Culture/Treatments:] Fix cells using 4% PFA.", "[Imagi... |
92,203 | Establishment of patient-derived enteroids/colonoids from endoscopic biopsies | 4 | dx.doi.org/10.17504/protocols.io.14egn3rxql5d/v1 | https://www.protocols.io/view/establishment-of-patient-derived-enteroids-colonoi-c6ajzacn | Tatiana Karakasheva | TITLE: Establishment of patient-derived enteroids/colonoids from endoscopic biopsies
AUTHORS: Tatiana Karakasheva
[DESCRIPTION]
This protocol describes the full procedure of generating an enteroid or colonoid culture from endoscopic biopsy (either freshly procured or recovered from cryopreservation), was developed for... | [] |
71,186 | Microscopy-based pUb-coverage measurements of mitochondria in iNeurons | 4 | dx.doi.org/10.17504/protocols.io.e6nvwj529lmk/v1 | https://www.protocols.io/view/microscopy-based-pub-coverage-measurements-of-mito-chrst56e | Felix Kraus | TITLE: Microscopy-based pUb-coverage measurements of mitochondria in iNeurons
AUTHORS: Felix Kraus
[DESCRIPTION]
Protocol for microscopy-based pUb-coverage measurements of mitochondria in iNeurons
[STEPS]
SECTION: Differentiation of iNeurons
22. Day 0: Treat AAVS1-TRE3G-NGN2 cells with Accutase and plate the dissocia... | ["[Differentiation of iNeurons] Day 0: Treat AAVS1-TRE3G-NGN2 cells with Accutase and plate the dissociated cells in matrigel-coated 6-well plates (2x105 cells/well) in ND1 Medium supplemented with Y27632 (10 μM). \nND1 Medium: \nDMEM/F12 \nN2 (100x) 1x \nBDNF 10 ng/ml \nNT3 10 n... |
98,503 | SenNet URMC 10X Genomics Single-Nucleus RNA-Sequencing for Transcriptomic Profiling | 1 | dx.doi.org/10.17504/protocols.io.14egn6zb6l5d/v1 | https://www.protocols.io/view/sennet-urmc-10x-genomics-single-nucleus-rna-sequen-dcff2tjn | Jeffrey Malik, blake, Gloria S Pryhuber | TITLE: SenNet URMC 10X Genomics Single-Nucleus RNA-Sequencing for Transcriptomic Profiling
AUTHORS: Jeffrey Malik, blake, Gloria S Pryhuber
[DESCRIPTION]
10X Genomics Single Cell 3' (v3.1) RNA sequencing is a microdroplet-based method that permits the effective capture and sequencing of the mRNA and pre-mRNA molecule... | ["[Isolate Nuclei] Resuspend nuclei in 100 µL to 1 mL of PBS + 0.1% RNase Inhibitor (volume depends on target concentration)", "[Isolate Nuclei] Perform manual trypan blue nuclear exclusion counts on a hemacytometer.", "[Isolate Nuclei] Check nuclei integrity by light microscope concurrent with manual trypan exclusion ... |
37,914 | UABMC - Stemness Determination Protocol | 4 | null | https://www.protocols.io/view/uabmc-stemness-determination-protocol-bg92jz8e | Christopher Willey | TITLE: UABMC - Stemness Determination Protocol
AUTHORS: Christopher Willey
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This procedure describes the assays for determining stem-ness in the PDMC models. </div><div class = "text-block">The phenotypic and marker-based assays that can and will be use... | ["[LIMITING DILUTION ASSAY]\nEnsure cultures are healthy with minimal percentages of dead cells", "[LIMITING DILUTION ASSAY]\nDissociate cells using Accutase as usual", "[LIMITING DILUTION ASSAY]\nWhile cells are dissociating, add stem cell media to inner wells (6x10) at 200uL per well and to well H2. Add water to the... |
55,703 | Isolation and RNA extraction from Marine Protist Single Cells for Transcriptomics (sc-RNAseq) | 1 | dx.doi.org/10.17504/protocols.io.x54v9mk3qg3e/v4 | https://www.protocols.io/view/isolation-and-rna-extraction-from-marine-protist-s-b2mxqc7n | Sarah Romac | TITLE: Isolation and RNA extraction from Marine Protist Single Cells for Transcriptomics (sc-RNAseq)
AUTHORS: Sarah Romac
[DESCRIPTION]
It is difficult to get clean RNA from uncultivated protists (phyto and zooplankton), as they have to be isolated by micromanipulation and very sensitive to exogenous contaminations.
H... | ["[1. Cell Isolation] Isolate individually protist cells (5-500µm in length) using a glass bent micropipette (or a micropipette adapted to the length of the microorganism) under a binocular microscope or an inverted microscope.", "[1. Cell Isolation] Wash each cell in three successive baths of 0.22µm-filtered and... |
53,259 | Female reproductive organs procurement | 4 | dx.doi.org/10.17504/protocols.io.bx9jpr4n | https://www.protocols.io/view/female-reproductive-organs-procurement-bx9jpr4n | kone | TITLE: Female reproductive organs procurement
AUTHORS: kone
[DESCRIPTION]
Description of procurement of non-pregnant female reproductive tract from deceased donor for HuBMAP.
[STEPS]
SECTION: Modification of donor procurement
1. During the typical aortic cannulation in a standard abdominal organ procurement, the in... | ["[Modification of donor procurement] During the typical aortic cannulation in a standard abdominal organ procurement, the inferior aorta distal to the cannulation site is ligated. This occurs usually at the level of the bifurcation of the aorta with the common iliac arteries. This ligation is necessary in order to p... |
null | null | null | dx.doi.org/10.17504/protocols.io.nyzdfx6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This is the protocol for the touchdown PCR assay</p>
[BEFORE_START]
<p>The assay has been optimized and validated for the Bio-rad C1000 Touch Thermocycler.</p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
103,409 | comments retest discarded | 0 | null | https://www.protocols.io/view/comments-retest-discarded-dg8r3zv6 | Maria Gulyakina | TITLE: comments retest discarded
AUTHORS: Maria Gulyakina
[DESCRIPTION]
qa
[STEPS]
1. test
2. comment
3. test 2
4. test 3 | ["test", "comment", "test 2", "test 3"] |
66,639 | Extracellular DNA extraction from lake sediments | 1 | null | https://www.protocols.io/view/extracellular-dna-extraction-from-lake-sediments-cdbps2mn | Charline Giguet-Covex, Pierre Taberlet, Francesco Gentile Ficetola | TITLE: Extracellular DNA extraction from lake sediments
AUTHORS: Charline Giguet-Covex, Pierre Taberlet, Francesco Gentile Ficetola
[DESCRIPTION]
Over the past decade, an increasing number of studies has used environmental DNA from lake sediments to trace past lake ecosystem and landscape changes, agricultural activ... | ["[exDNA extraction] Preparation of the SW2 buffer within the kit (NucleoSpin® Soil kit from Macherey-Nagel):\n\nThis step is only FOR the FIRST USE of this BUFFER\n\nAdd correct volume of ethanol to SW2 (e.g. for 250 prep kit, add 400 mLof ethanol to 100 mLSW2 concentrate).", "[exDNA extraction] Phosphate buffer prepa... |
28,884 | PCR Amplification of Desired Gene | null | dx.doi.org/10.17504/protocols.io.8fuhtnw | null | iGEM Dusseldorf | TITLE: PCR Amplification of Desired Gene
AUTHORS: iGEM Dusseldorf
[STEPS]
?. Pipette PCR components in the following order. Always set up at least two replicates.
?. ABCD1# Reactions[µl]Thermocycler ConditionsRounds2Water32.51. 98°C for 0:30 min3Green HF Buffer10.02. 98°C for 0:10 min5x4dNTPs (10 mM)1.03... | ["Pipette PCR components in the following order. Always set up at least two replicates.", "ABCD1# Reactions[µl]Thermocycler ConditionsRounds2Water32.51. 98°C for 0:30 min3Green HF Buffer10.02. 98°C for 0:10 min5x4dNTPs (10 mM)1.03. X°C for 0:20 min5F Primer (10 µM)2.54. 72°C for X min6R Pri... |
47,284 | Direct cDNA Sequencing (SQK-DCS109) | 4 | dx.doi.org/10.17504/protocols.io.yxmvmkpxng3p/v1 | https://www.protocols.io/view/direct-cdna-sequencing-sqk-dcs109-bseunbew | e.gustavsson | TITLE: Direct cDNA Sequencing (SQK-DCS109)
AUTHORS: e.gustavsson
[DESCRIPTION]
This protocol describes how to prepare direct cDNA Sequencing libraries for nanopore sequencing without using PCR.
[STEPS]
SECTION: Reverse transcription and strand-switching
1.
SECTION: Reverse transcription and strand-switching
2. Pr... | ["[Reverse transcription and strand-switching]", "[Reverse transcription and strand-switching] Prepare the RNA in Nuclease-free water.", "[Reverse transcription and strand-switching] Transfer 100 ng into a 1.5 ml Eppendorf DNA LoBind tube.", "[Reverse transcription and strand-switching] Adjust the volume to up to 7.5 µ... |
101,159 | Isolation and Characterization of Tissue and Cell-Derived Extracellular Vesicles and Non-Vesicular Extracellular Particles | 0 | dx.doi.org/10.17504/protocols.io.5jyl822k8l2w/v2 | https://www.protocols.io/view/isolation-and-characterization-of-tissue-and-cell-de2f3gbn | Marta Garcia Contreras, Emeli Chatterjee, Abhik Chakraborty, Michail Spanos, Kriti Bomb, Priyanka Gokulnath, Jeffery L. Franklin, Erika Duggan, John P. Nolan, Priyadarshini Pantham, Louise C. Laurent, Saumya Das | TITLE: Isolation and Characterization of Tissue and Cell-Derived Extracellular Vesicles and Non-Vesicular Extracellular Particles
AUTHORS: Marta Garcia Contreras, Emeli Chatterjee, Abhik Chakraborty, Michail Spanos, Kriti Bomb, Priyanka Gokulnath, Jeffery L. Franklin, Erika Duggan, John P. Nolan, Priyadarshini Pantham,... | ["[Processing of Conditioned Culture Media following Tissue and Cell Culture] Culture DiFi cells11 under the appropriate culture conditions as previously\npublished. BeWo cells were cultured as published earlier12,13 with the\nmodification of addition of 10% exosome-depleted FBS).", "[Processing of Conditioned Culture ... |
68,580 | Transforming Yeast (Instructor Protocol) | 4 | null | https://www.protocols.io/view/transforming-yeast-instructor-protocol-ce8cthsw | Brian Teague | TITLE: Transforming Yeast (Instructor Protocol)
AUTHORS: Brian Teague
[DESCRIPTION]
This is the instructor protocol for
The yeast transformation is adapted from Geitz and Schiestl:
[GUIDELINES]
We use dropout media components from Sunrise Science, but I'm sure media from other vendors is fine. Double-check,... | ["[Prepare 250 ml of 2xYPD media] Put 250 mL of deionized water in a 250 ml or 500 ml bottle, then add:\n10 g \n5 g", "[Prepare 250 ml of 2xYPD media] Autoclave at 121 °C for 30 min on a liquid cycle.", "[Prepare 250 ml of 2xYPD media] Cool, then using good sterile technique, add 25 mLof a 40 Mass / % volume solution... |
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