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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12,423 | General methanogens: mcrA mlas-mod – mcrA-rev | 1 | dx.doi.org/10.17504/protocols.io.eq2lyk1qvx9k/v1 | https://www.protocols.io/view/general-methanogens-mcra-mlas-mod-mcra-rev-qdfds3n | Eva Petrova, Roey Angel | TITLE: General methanogens: mcrA mlas-mod – mcrA-rev
AUTHORS: Eva Petrova, Roey Angel
[DESCRIPTION]
Amplification of the marker gene methyl coenzyme M reductase alpha subunit (mcrA) using the general primers mlas-mod – mcrA-rev
mlas-mod GGY GGT GTM GGD TTC ACM CAR TA Angel et al. (2011), Plos One
mcrA-rev ... | ["[PCR mixture]", "[PCR program] 1. 94◦C – 5′\n2. x 5 {\n a. 60◦C – 1°C - 45''\n b. 72◦C – 30''\n c. 94◦C – 30'\n }\n 3. x 29 {\n a. 55◦C – 45''\n b. 72◦C – 30''\n c. 94◦C – 30''\n }\n \n4. 55◦C – 45''\n5. 72°C - 10'"] |
84,063 | Nanodrop Lite (Shared Equipment Lab) | 4 | null | https://www.protocols.click/view/nanodrop-lite-shared-equipment-lab-cwb7xarn | Nimalka M Weerasuriya | TITLE: Nanodrop Lite (Shared Equipment Lab)
AUTHORS: Nimalka M Weerasuriya
[DESCRIPTION]
How to use the Nanodrop Lite.
[BEFORE_START]
It is best to use a precision pipettor (0-2 μl) with precision tips to ensure that sufficient sample (1-2 μl) is delivered. Lower precision pipettors (0-10 μl and larger) are not as go... | ["[Basic Operation] Open arm or push any button to wake instrument.\nUsing the bottle of deionized water, slightly wet a Kimwipe and clean the lower and upper pedestal (metal prongs).", "[Nucleic Acid Measurements] Select the appropriate application from the Home screen (DNA or RNA). For DNA measurements, select either... |
92,920 | Microbiome DNA Enrichment for Fecal -seq using the the NEBNext Microbiome DNA Enrichment Kit manual (New England Biolabs cat. #E2612S) | 1 | dx.doi.org/10.17504/protocols.io.kqdg3xn21g25/v1 | https://www.protocols.io/view/microbiome-dna-enrichment-for-fecal-seq-using-the-c6yyzfxw | jbonnevie | TITLE: Microbiome DNA Enrichment for Fecal -seq using the the NEBNext Microbiome DNA Enrichment Kit manual (New England Biolabs cat. #E2612S)
AUTHORS: jbonnevie
[DESCRIPTION]
This protocol is taken from the Scientific Report "Methylation-based enrichment facilitates low-cost, noninvasive genomic scale sequencing of po... | ["[Before Beginning] Extract and prepare DNA samples\n\nWhile any fecal DNA (fDNA) extraction method should in principle be compatible with the MBD enrichment, methods that maximize the recovery of host DNA are preferable. Bead-beating methods that increase total DNA yield from feces, for example, should be avoided bec... |
101,850 | Zebrafish larvae dissociation for FACs sorting cells expressing fluorescent proteins | 4 | null | https://www.protocols.io/view/zebrafish-larvae-dissociation-for-facs-sorting-cel-dfp23mqe | Abigail Elliot, Yi Feng | TITLE: Zebrafish larvae dissociation for FACs sorting cells expressing fluorescent proteins
AUTHORS: Abigail Elliot, Yi Feng
[DESCRIPTION]
Large number of transgenic lines with cell/tissue specific expressing of fluorescent proteins are available in the zebrafish field. These tools provide an opportunity for isolating... | ["[Embryo Dissociation] Collect anaesthetised larvae in 2ml Eppendorf 5 min", "[Embryo Dissociation] Remove water and replace with 2ml Dissociation Solution with plastic pipette 5 min", "[Embryo Dissociation] Transfer larvae and solution to well of 12-well plate with plastic pipette. 2 min", "[Embryo Dissociation] Incu... |
50,676 | Tranexamic acid for the prevention of postpartum hemorrhage in women undergoing cesarean delivery: an updated meta-analysis | 1 | dx.doi.org/10.17504/protocols.io.bvqun5ww | https://www.protocols.io/view/tranexamic-acid-for-the-prevention-of-postpartum-h-bvqun5ww | Ioannis Bellos | TITLE: Tranexamic acid for the prevention of postpartum hemorrhage in women undergoing cesarean delivery: an updated meta-analysis
AUTHORS: Ioannis Bellos
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Postpartum hemorrhage represents a major complication of cesarean delivery, leading to significan... | ["Background Postpartum hemorrhage represents a major complication of cesarean delivery, leading to significant rates of maternal morbidity and mortality. Blood loss often necessitates resuscitation with red-cell transfusion, exposing patients at risk of hemolytic, anaphylactoid and infectious complications. To this en... |
18,994 | Glossopharyngeal Nerve Chronic Recording In Anesthetized Rat | 1 | dx.doi.org/10.17504/protocols.io.wssfeee | https://www.protocols.io/view/glossopharyngeal-nerve-chronic-recording-in-anesth-wssfeee | Grant Mccallum, Nathan Kostick, Joseph Marmerstein, Yang Zheng, Dominique Durand | TITLE: Glossopharyngeal Nerve Chronic Recording In Anesthetized Rat
AUTHORS: Grant Mccallum, Nathan Kostick, Joseph Marmerstein, Yang Zheng, Dominique Durand
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">We propose to develop a neural interface based on carbon nanotube (CNT) yarns with a size sim... | ["Hypoxia Challenge- Rats will be lightly sedated with either Isoflurane or Ketamine/Xylazine. Impeadance will be taken via the port. Neural recordings will be taken next. We will expose the rat to 10% O, 90%N (1L/min flow rate) until the oxygen saturation rate is reduced to 70%. This takes about 30 seconds. We al... |
50,825 | TH DAB staining | 1 | dx.doi.org/10.17504/protocols.io.j8nlk4yw1g5r/v1 | https://www.protocols.io/view/th-dab-staining-bvvhn636 | Pranay Srivastava, Waijiao Cai, Xiqun Chen | TITLE: TH DAB staining
AUTHORS: Pranay Srivastava, Waijiao Cai, Xiqun Chen
[DESCRIPTION]
This protocol details the stating procedure for TH DAB staining.
[STEPS]
SECTION: TH DAB staining
1. Wash a full set of sections (6-8 sections) in a well in PBS, 5 min × 3.
SECTION: TH DAB staining
2. Incubate sections in 1% H2O... | ["[TH DAB staining] Wash a full set of sections (6-8 sections) in a well in PBS, 5 min × 3.", "[TH DAB staining] Incubate sections in 1% H2O2 (1 mL 30% H2O2 in 29 mL TBST), 30 min at Room temperature.", "[TH DAB staining] Wash sections in TBST 5 min × 3.", "[TH DAB staining] Block sections in 5% NGS/TBST, 60 min at Roo... |
null | null | null | dx.doi.org/10.17504/protocols.io.iwgcfbw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This is the procedure used to cluster MAGs for the <em>Tara Oceans</em> dataset assembled by Benjamin Tully and Elaina Graham</p>
[BEFORE_START]
<p>Before starting be sure you have downloaded Binsanity. Please see the <a href="https://github.com/edgraham/BinSanity" target="_... | [] |
67,489 | SAMOSA-Tag - combining in-situ adenine methyltransferase footprinting with transposase-mediated single-molecule sequencing | 4 | dx.doi.org/10.17504/protocols.io.3byl4bob2vo5/v1 | https://www.protocols.io/view/samosa-tag-combining-in-situ-adenine-methyltransfe-cd59s896 | Scott Nanda, Ke Wu, Siva Kasinathan, vijay.ramani | TITLE: SAMOSA-Tag - combining in-situ adenine methyltransferase footprinting with transposase-mediated single-molecule sequencing
AUTHORS: Scott Nanda, Ke Wu, Siva Kasinathan, vijay.ramani
[DESCRIPTION]
Here we describe a protocol for SAMOSA-Tag: Tagmentation-assisted Single-molecule Adenine Methylated Oligonucleoso... | ["[Reagent Setup] Nuclear Lysis Buffer (prepared on ice): \n \n\nBuffer M (prepared on ice):\n \n\nNuclei Storage Buffer (prepared on ice):\n \n\n5x TD Premix (prepared at RT):\n \n\n\nSMRT-Tn5 adaptor assembly:\nwe recommend following the \"Annealing SMRT-Tag adaptors\" and \"Assembling SMRT-Tn5 transposomes (Tn5 load... |
55,630 | Immunofluorescent staining of formalin-fixed OCT-embedded human lung tissue | 1 | dx.doi.org/10.17504/protocols.io.b2jnqcme | https://www.protocols.io/view/immunofluorescent-staining-of-formalin-fixed-oct-e-b2jnqcme | Justinn Barr, Jamie Verheyden, Xin Sun | TITLE: Immunofluorescent staining of formalin-fixed OCT-embedded human lung tissue
AUTHORS: Justinn Barr, Jamie Verheyden, Xin Sun
[DESCRIPTION]
This protocol describes steps for immunofluorescent staining of formalin-fixed paraffin-embedded human lung tissue.
[STEPS]
1. 2X5 min wash in Phosphate-buffered saline ... | ["2X5 min wash in Phosphate-buffered saline with Tween (PBSTW) in a slide holder on a flat rotator.", "Blocking:", "Mix up 5% serum (50 µL serum / 1 mL of PBSTW)", "Remove old PBSTW from the sample and add block.", "Cover with Hybrislip.", "Let sit in a humidified chamber at Room temperature for ≥ 1 hour.", "Primary a... |
28,906 | Feeding 6wp | 1 | dx.doi.org/10.17504/protocols.io.8gihtue | https://www.protocols.io/view/feeding-6wp-8gihtue | Andrea Argouarch | TITLE: Feeding 6wp
AUTHORS: Andrea Argouarch
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol for feeding dural cells after outgrowth from tissue in a 6 well plate. </div></div>
[STEPS]
?. [Observations]
Record observations Biopsy pieces should look dense and dark; it will not change morpho... | ["[Observations]\nRecord observations Biopsy pieces should look dense and dark; it will not change morphologyClean and straight edges on the tissue is best Outgrowth will vary between a few days to 2 weeks, depending on biopsyAfter a week, gently change media and then feed every 2-3 days o Be careful not to move... |
92,569 | ATAC-seq of primary human fibroblasts cultured on soft and stiff ECM | 4 | dx.doi.org/10.17504/protocols.io.ewov1q1kygr2/v1 | https://www.protocols.io/view/atac-seq-of-primary-human-fibroblasts-cultured-on-c6mzzc76 | Brian D. Cosgrove, Lexi Bounds, Carson Key Taylor, Alan L. Su, Anthony J. Rizzo, Alejandro Barrera, Andrea R Daniel, Gregory E. Crawford, Brenton D. Hoffman, Charles A. Gersbach | TITLE: ATAC-seq of primary human fibroblasts cultured on soft and stiff ECM
AUTHORS: Brian D. Cosgrove, Lexi Bounds, Carson Key Taylor, Alan L. Su, Anthony J. Rizzo, Alejandro Barrera, Andrea R Daniel, Gregory E. Crawford, Brenton D. Hoffman, Charles A. Gersbach
[DESCRIPTION]
This protocols describes methods for Omni ... | ["[Cell culture and soft hydrogel processing] Culture primary human neonatal fibroblasts (HFF cells, ATCC CRL-2097) in DMEM with 10% FBS, 1% AntiAnti, and 1% NEAA (Sigma) on tissue culture plastic (TCP).", "[Cell culture and soft hydrogel processing] Use polyacrylamide hydrogel 35 and 150 mm PetriSoft EasyCoat dishes (... |
10,594 | ActA purification protocol | null | dx.doi.org/10.17504/protocols.io.nkadcse | null | Sharifah Albraiki | TITLE: ActA purification protocol
AUTHORS: Sharifah Albraiki
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. [Day 1]
?.
?. [Day 2]
?. [Day 3]
?.
?.
?.
?.
?. [Day 3-5]
?. [Day 6]
?. [Day 7]
When I did the gel-filtration step I lost all my protein.
?.
?. [Buffers]
Lysis Buffer:20mM MOPS100mM KCl5mM Imi... | ["[Day 1]", "[Day 2]", "[Day 3]", "[Day 3-5]", "[Day 6]", "[Day 7]\nWhen I did the gel-filtration step I lost all my protein.", "[Buffers]\nLysis Buffer:20mM MOPS100mM KCl5mM Imidazole pH 7Wash Buffer:20mM MOPS100mM KCl20mM Imidazole pH 7Elution Buffer:20mM MOPS100mM KCl250mM Imidazole pH 7Storage Buffer:20... |
null | null | null | dx.doi.org/10.17504/protocols.io.einbcde | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol outlines the Bray-Curtis dissimilarity NMDS ordination and significance analysis of our manuscript. Here we will look at the clustering of the virome samples using our reference independent OTU table based on contig hits. We will compare skin environments (sebaceou... | [] |
99,789 | PCR amplification of the barcode region | 0 | dx.doi.org/10.17504/protocols.io.3byl49jjogo5/v1 | https://www.protocols.io/view/pcr-amplification-of-the-barcode-region-ddpm25k6 | Melinda Wheelock, Nicholas Popp, Raining Wang, Douglas Fowler | TITLE: PCR amplification of the barcode region
AUTHORS: Melinda Wheelock, Nicholas Popp, Raining Wang, Douglas Fowler
[DESCRIPTION]
This protocol details the gDNA amplification and plasmid DNA amplification.
[BEFORE_START]
Notes about PCR 1:
The first PCR in the gDNA amplification process is designed to both add ada... | ["[PCR 1: Adding adapters and/or crossing the recombination junction] For gDNA, set up 8 identical PCR reactions as follows:", "[PCR 1: Adding adapters and/or crossing the recombination junction] For plasmid DNA, set up 1 reaction as follows:", "[PCR 1: Adding adapters and/or crossing the recombination junction] Run 5 ... |
null | null | null | dx.doi.org/10.17504/protocols.io.c2yyfv | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Preparation of iron chloride resuspension buffer using disodium EDTA dihydrate and magnesium chloride in Tris buffer.
[GUIDELINES]
<strong><strong>Recipe as developed by Seth:<br /></strong></strong>
<table>
<tbody>
<tr>
<td><strong>Reagent (Formula Weight) </strong></td>... | [] |
58,690 | Very New York Behavioural Analysis Protocol v2.3 | 3 | dx.doi.org/10.17504/protocols.io.b5jaq4ie | https://www.protocols.io/view/very-new-york-behavioural-analysis-protocol-v2-3-b5jaq4ie | Gabriel Frazer-McKee, Bruno Courbon | TITLE: Very New York Behavioural Analysis Protocol v2.3
AUTHORS: Gabriel Frazer-McKee, Bruno Courbon
[DESCRIPTION]
This protocol contains descriptions of the constructional and semantico-pragmatic variables assessed while annotating the “very New York” dataset in our 2022 paper published in the journal Signifiances. ... | [] |
60,313 | Computer-Aided Drug Discovery | 1 | dx.doi.org/10.17504/protocols.io.dm6gpb918lzp/v1 | https://www.protocols.io/view/computer-aided-drug-discovery-b65zrg76 | BOC Sciences | TITLE: Computer-Aided Drug Discovery
AUTHORS: BOC Sciences
[DESCRIPTION]
Computer-aided drug design (CADD) is a widely used technology using computational tools and resources for the storage, management, analysis and modeling of compounds. It relies on digital repositories for the study of designing compounds with ph... | [] |
54,389 | SNARE-seq2 | 1 | dx.doi.org/10.17504/protocols.io.bzcvp2w6 | https://www.protocols.io/view/snare-seq2-bzcvp2w6 | Nongluk Plongthongkum, Dinh H Diep, Song Chen, Blue Lake, Kun Zhang | TITLE: SNARE-seq2
AUTHORS: Nongluk Plongthongkum, Dinh H Diep, Song Chen, Blue Lake, Kun Zhang
[DESCRIPTION]
To study the heterogeneity of complex tissues by joint profiling of gene expression and its regulation, we require an accurate and high-throughput method. Here we described improved high-throughput combinato... | ["[Reagent setup] 40% (wt/vol) PEG 6000. Weigh 16.0 g of PEG 6000 in 50 mL tube. Add nuclease-free water and bring the total volume to 40 mL. Rotate the tube at room temperature until PEG 6000 completely dissolved. Spin down the tube at 200 g for 2 min, at room temperature to remove the tiny bubble. CRITICAL: 40% (wt/v... |
27,843 | Bodo saltans Cassette for tagging EF1alpha gene__IG BsTub | null | dx.doi.org/10.17504/protocols.io.7fbhjin | null | Fatma Gomaa, Zhou Zhuha, Roberto Docampo, Virginia Edgcomb | TITLE: Bodo saltans Cassette for tagging EF1alpha gene__IG BsTub
AUTHORS: Fatma Gomaa, Zhou Zhuha, Roberto Docampo, Virginia Edgcomb
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. | [] |
50,051 | Purification of recombinant Synechocystis KaiA3-His6 with PureProteome Nickel Magnetic Beads | 4 | dx.doi.org/10.17504/protocols.io.bu5bny2n | https://www.protocols.io/view/purification-of-recombinant-synechocystis-kaia3-hi-bu5bny2n | Christin Köbler, Nicolas Schmelling, Alice Pawlowski, Philipp Spät, Nina Scheurer, Lutz Berwanger, Ilka Axmann, Annegret Wilde | TITLE: Purification of recombinant Synechocystis KaiA3-His6 with PureProteome Nickel Magnetic Beads
AUTHORS: Christin Köbler, Nicolas Schmelling, Alice Pawlowski, Philipp Spät, Nina Scheurer, Lutz Berwanger, Ilka Axmann, Annegret Wilde
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol c... | ["[Heterologous protein expression in E. coli]\nTransformationtransform the plasmid pET22sll0485 _his6 (for expression of the KaiA3-His6 fusion protein) into E. coli Tuner(DE3) cells by either using chemical competent cells or by using the TSS transformation method (dx.doi.org/10.17504/protocols.io.gtabwie) and plate o... |
107,508 | BIT595_Ligation Sequencing Kit_Individual Project_Birchler De Allende | 0 | null | https://www.protocols.io/view/bit595-ligation-sequencing-kit-individual-project-dk8u4zww | Ian Birchler De Allende | TITLE: BIT595_Ligation Sequencing Kit_Individual Project_Birchler De Allende
AUTHORS: Ian Birchler De Allende
[DESCRIPTION]
The Oxford Nanopore Ligation Sequencing Kit is a versatile tool for generating long-read sequencing data across a wide range of organisms. This protocol outlines the general steps for library pre... | ["[Intro and Overview] Before you begin, you must \n1. Extract DNA using kit of your choice, check for quality using Tapestation and Qubit\n2. Check kit has all equipment and reagents. Also check for any reagents required that do not come in the Ligation Sequencing Kit\n3. Check that you flow cell has the correct num... |
88,039 | Buck Institute Morphology H & E staining protocol | 1 | dx.doi.org/10.17504/protocols.io.36wgq3n2ylk5/v2 | https://www.protocols.io/view/buck-institute-morphology-h-amp-e-staining-protoco-cz8fx9tn | sbreslin | TITLE: Buck Institute Morphology H & E staining protocol
AUTHORS: sbreslin
[DESCRIPTION]
Histological Stain for FFPE slides
RESULTS: Nuclei-blue; Cytoplasm, red blood cells and connective tissue-shades of pink
[BEFORE_START]
Slides can be placed in 60 C oven prior to deparaffinization.
[STEPS]
SECTION: Hemato... | ["[Hematoxylin and Eosin Staining] Deparaffinization and rehydration: 2 x xylene 7 min, 100% ethanol 4 min, 95% 4 min, 80% 4 min, 70% 4 min, bring to water.", "[Hematoxylin and Eosin Staining] Hematoxylin staining for 30 seconds - 4 min. using filtered dye (usually 2 mins) - Modified Mayes’s Hematoxylin HXMMHPT StatLab... |
62,603 | Limitless Glucose 1 (Scam Pills Or Legit) Full Detailed Review! | 3 | dx.doi.org/10.17504/protocols.io.14egn7ermv5d/v1 | https://www.protocols.io/view/limitless-glucose-1-scam-pills-or-legit-full-detai-b9djr24n | Limitless Glucose | TITLE: Limitless Glucose 1 (Scam Pills Or Legit) Full Detailed Review!
AUTHORS: Limitless Glucose
[DESCRIPTION]
MUST CHECK: *Special Discounted Pricing Available For The First 50 Customers Only! (ORDER Limitless Glucose 1)
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.vcme2u6 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
SECTION: Plasmid preparation
?.
SECTION: In vivo mRNA synthesis
?.
SECTION: Transfection by electroporation
?.
SECTION: GFP observation
?. | ["[Plasmid preparation] {\"blocks\":[{\"key\":\"7iqmu\",\"text\":\"We created the plasmid vector (T7-SL-eGFP) that the egfp gene with a 5\\u2032 UTR of the P. marinus TPT2 gene and a 3\\u2032 UTR of the P. marinus MOE gene was inserted in pSP72 (Promega). The 5\\u2032 UTR contains the spliced leader sequence (ACCGTAGCC... |
28,984 | High Dose STZ Induction Protocol | null | dx.doi.org/10.17504/protocols.io.8iyhufw | null | Frank Brosius | TITLE: High Dose STZ Induction Protocol
AUTHORS: Frank Brosius
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block"><span>This protocol is used by DiaComp members to induce diabetes in a number of the animal models develope... | ["Prepare the buffers and solutions as described below. Please note that the STZ- Na-Citrate solution should be prepared immediately prior to injection so as to avoid degradation of the STZ.", "Mice should be fasted prior to injection; four hours is usually sufficient.", "Place one mouse in the Isoflurane drop jar, acc... |
45,241 | GenSwab Complete Protocol Collection | 2 | dx.doi.org/10.17504/protocols.io.bqezmtf6 | https://www.protocols.io/view/genswab-complete-protocol-collection-bqezmtf6 | huiyi.chen , Sid Roy | TITLE: GenSwab Complete Protocol Collection
AUTHORS: huiyi.chen , Sid Roy
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.cg4tyv | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?. | [] |
86,885 | Can light be used to treat obesity and diabetes? | 4 | dx.doi.org/10.17504/protocols.io.j8nlkooj1v5r/v2 | https://www.protocols.io/view/can-light-be-used-to-treat-obesity-and-diabetes-cy4dxys6 | Rédoane Daoudi | TITLE: Can light be used to treat obesity and diabetes?
AUTHORS: Rédoane Daoudi
[DESCRIPTION]
This document is highly theoretical lab method paper. It may be used to perform thermogenesis from several cells in a living organism instead of only brown adipocytes. We perform thermogenesis from white adipocytes. The purpo... | ["[Introduction] This document is highly theoretical lab method paper. It may be used to perform thermogenesis from several cells in a living organism instead of only brown adipocytes. We perform thermogenesis from white adipocytes. The purpose is to uptake the blood glucose and lipids to produce heat and subsequent we... |
41,208 | Wet lab SOP of the deep-sea sponge microbiome project | 1 | dx.doi.org/10.17504/protocols.io.kxygxer1kv8j/v1 | https://www.protocols.io/view/wet-lab-sop-of-the-deep-sea-sponge-microbiome-proj-bkgyktxw | Kathrin Busch, Andrea Hethke, Ina Clefsen, Ute Hentschel | TITLE: Wet lab SOP of the deep-sea sponge microbiome project
AUTHORS: Kathrin Busch, Andrea Hethke, Ina Clefsen, Ute Hentschel
[DESCRIPTION]
This protocol describes the wet lab standard operating procedures (SOPs) established for the Deep-sea Sponge Microbiome Project. It includes the field work procedures, as well a... | ["[Field work] The deep-sea sponge microbiome project dataset has been collected during 21 ship expeditions.\nFor these cruises we established the following standard operating procedures:\n\nA) Metadata collection:\n\nGather as much metadata as possible\nFill in this metadata table for all samples (and add anything els... |
45,495 | Analysis of De Novo Synthesized Proteins | 1 | dx.doi.org/10.17504/protocols.io.bqnxmvfn | https://www.protocols.io/view/analysis-of-de-novo-synthesized-proteins-bqnxmvfn | Anne Zemella, Theresa Richter, Lena Thoring, Stefan Kubick | TITLE: Analysis of De Novo Synthesized Proteins
AUTHORS: Anne Zemella, Theresa Richter, Lena Thoring, Stefan Kubick
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">This is part 3.4 of the "A Combined Cell-Free Protein Synthesis and Fluorescence-Based Approach to Inv... | ["[3.4.1 TCA Precipitation and Scintillation Counting]\nAfter the reaction is completed collect 2 × . Centrifuge the remaining mix at and collect 2 × . Resuspend the microsomal fraction in an equal volume of PBS in comparison to the volume of the translation mixture. Collect 2 × .\n[translation mixture]\nCentrifuge: 1... |
50,530 | Deep cleaning COPAS | 1 | dx.doi.org/10.17504/protocols.io.bvkan4se | https://www.protocols.io/view/deep-cleaning-copas-bvkan4se | Saul Moore | TITLE: Deep cleaning COPAS
AUTHORS: Saul Moore
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">To prevent gradual build-up of slime-mould and other contaminants in the COPAS tubing (particularly in the tubing from the sheath), that cause blockages in the flow cell and also lead to erroneous Extinct... | ["[Pre-sorting clean]\nFollow COPAS Protocol up to end of ‘Pre-sorting clean’ (steps 1-19):\n{\"blocks\":[{\"key\":\"66sl\",\"text\":\"Protocol for dispensing adult worms using the COPAS 500 flowpilot\",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[],\"entityRanges\":[],\"data\":[]}],\"entityMap\":[]}", "[DE... |
51,994 | The Podiatrists in Australia: Investigating Graduate Employment (PAIGE) Study | 3 | dx.doi.org/10.17504/protocols.io.bwz2pf8e | https://www.protocols.io/view/the-podiatrists-in-australia-investigating-graduat-bwz2pf8e | Cylie Williams, Anna Couch | TITLE: The Podiatrists in Australia: Investigating Graduate Employment (PAIGE) Study
AUTHORS: Cylie Williams, Anna Couch
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:left">The Podiatrists in Australia: Investigating Graduate Employment (PAIGE) study pro... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.saxeafn | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | ["{\"blocks\":[{\"key\":\"7vn1t\",\"text\":\"Download Illumina-based sequencing data from NCBI.\",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[],\"entityRanges\":[],\"data\":[]},{\"key\":\"7oelg\",\"text\":\" \",\"type\":\"atomic\",\"depth\":0,\"inlineStyleRanges\":[],\"entityRanges\":[{\"offset\":0,\"lengt... |
94,193 | Sholl analysis | 4 | dx.doi.org/10.17504/protocols.io.ewov1qw5kgr2/v1 | https://www.protocols.io/view/sholl-analysis-c78rzrv6 | mariangela.massarocenere | TITLE: Sholl analysis
AUTHORS: mariangela.massarocenere
[DESCRIPTION]
Protocol for Sholl analysis by Neurolucida software
[STEPS]
SECTION: cell body and branching tracing
1. Select the center for the analysis and the structures or markers to be compared
SECTION: cell body and branching tracing
1.1. Select one cell ... | ["[cell body and branching tracing] Select the center for the analysis and the structures or markers to be compared", "[cell body and branching tracing] Select one cell body that you want to use as the center for the analysis", "[cell body and branching tracing] Select one or more process/group of processes, puncta, an... |
91,579 | Serial Alberta Stroke Program Early CT Score to Predict Stroke-Associated Pneumonia after Thrombolysis in Patients with Acute Ischemic Stroke | 1 | dx.doi.org/10.17504/protocols.io.q26g7p6qkgwz/v1 | https://www.protocols.io/view/serial-alberta-stroke-program-early-ct-score-to-pr-c5n3y5gn | Sarawut Krongsut, Atiwat Soontornpun, Niyada Anusasnee | TITLE: Serial Alberta Stroke Program Early CT Score to Predict Stroke-Associated Pneumonia after Thrombolysis in Patients with Acute Ischemic Stroke
AUTHORS: Sarawut Krongsut, Atiwat Soontornpun, Niyada Anusasnee
[DESCRIPTION]
Objectives: To investigate the performance of serial Alberta Stroke Program Early CT Score (... | ["Serial Alberta Stroke\nProgram Early CT Score to Predict Stroke-Associated Pneumonia after Thrombolysis\nin Patients with Acute Ischemic Stroke"] |
53,038 | Cost-effectiveness and cost-utility evaluation of the individual vs. group transdiagnostic psychological treatment for emotional disorders in Primary Care (PsicAP-Costs) | 1 | dx.doi.org/10.17504/protocols.io.bx2npqde | https://www.protocols.io/view/cost-effectiveness-and-cost-utility-evaluation-of-bx2npqde | Angel Aguilera-Martin, Mario Gálvez-Lara, Fátima Cuadrado, Eliana Moreno, Francisco García-Torres, José F. Venceslá, Jorge Corpas, Francisco J. Jurado-González, Roger Muñoz-Navarro, César González-Blanch, Paloma Ruiz-Rodríguez, Sara Barrio-Martínez, Maider Prieto-Vila, María Carpallo-González, Antonio Cano-Vindel,... | TITLE: Cost-effectiveness and cost-utility evaluation of the individual vs. group transdiagnostic psychological treatment for emotional disorders in Primary Care (PsicAP-Costs)
AUTHORS: Angel Aguilera-Martin, Mario Gálvez-Lara, Fátima Cuadrado, Eliana Moreno, Francisco García-Torres, José F. Venceslá, Jorge Corpas, Fr... | ["[RECRUITMENT AND FIRST ASSESSMENT] The recruitment will be accomplished in three different primary care settings of the province of Cordoba: the \"Carlos Castilla del Pino\" Health Centre, the \"Levante Sur Dr. Manuel Barragán Solís\" Health Centre, and the Community Mental Health Unit of Montilla. General practition... |
50,829 | Microscale Thermophoresis determination of Rab29 binding to LRRK2 Armadillo Domain | 1 | dx.doi.org/10.17504/protocols.io.bvvmn646 | https://www.protocols.io/view/microscale-thermophoresis-determination-of-rab29-b-bvvmn646 | Edmundo G. Vides, Suzanne Pfeffer | TITLE: Microscale Thermophoresis determination of Rab29 binding to LRRK2 Armadillo Domain
AUTHORS: Edmundo G. Vides, Suzanne Pfeffer
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Several labs have shown that Rab29 GTPase can recruit LRRK2 to the surface of the Golgi complex. We describe here a met... | ["[Buffer exchange Proteins]\nUsing either Nanotemper “A-Column” provided in labeling kit or (our preference) Zeba Spin column 7MWCO. Twist off bottom of column and loosen cap.\n0.5 mL", "[Buffer exchange Proteins]\nPrespin column: Centrifuge at for to remove storage solution.\n4 °C\nCentrifuge: 1500 34", "[Buffer e... |
93,202 | Immunohistology | 1 | dx.doi.org/10.17504/protocols.io.rm7vzxed5gx1/v1 | https://www.protocols.io/view/immunohistology-c69szh6e | Mai-Anh Vu, mwhowe | TITLE: Immunohistology
AUTHORS: Mai-Anh Vu, mwhowe
[DESCRIPTION]
We have developed a new micro-fiber array approach capable of chronically measuring and optogenetically manipulating local dynamics across over 100 targeted locations simultaneously in head-fixed and freely moving mice, enabling investigation of cell-typ... | ["[Removing Lugol's contrast agent from tissue] In preparation for immunohistology, Lugol’s solution was removed from brain tissue after CT imaging by soaking the implanted brains in a solution of 5% sodium thiosulfate (STS, Carolina) in 1% PBS for 4-6 days (Hopkins et al., 2015).", "[Removing Lugol's contras... |
86,207 | Preparation of soluble and insoluble mitochondrial protein fractions for immunoblotting | 1 | dx.doi.org/10.17504/protocols.io.q26g7py9qgwz/v1 | https://www.protocols.io/view/preparation-of-soluble-and-insoluble-mitochondrial-cye7xthn | Louise Uoselis | TITLE: Preparation of soluble and insoluble mitochondrial protein fractions for immunoblotting
AUTHORS: Louise Uoselis
[DESCRIPTION]
Preparation of soluble and insoluble mitochondrial protein fractions from HeLa cells for immunoblotting.
[STEPS]
1.
Thaw mitochondrial stocks on ice, and take two aliquots of 15 µg o... | ["Thaw mitochondrial stocks on ice, and take two aliquots of 15 µg of mitochondria each for each sample (one aliquot will be the ‘total’ sample fraction, and one aliquot will represent the ‘fractionation’ sample).", "Centrifuge samples at 10000 rcf for 10 min at 4 °C, and carefully aspirate the supernatant.", "Add 15 µ... |
42,235 | Viral Plaque Assay | 4 | dx.doi.org/10.17504/protocols.io.bmg3k3yn | https://www.protocols.io/view/viral-plaque-assay-bmg3k3yn | Timothy S C Hinks, Bonnie van Wilgenburg, Huimeng Wang, Liyen Loh, Marios Koutsakos, Katherine Kedzierska, Alexandra J. Corbett, Zhenjun Chen | TITLE: Viral Plaque Assay
AUTHORS: Timothy S C Hinks, Bonnie van Wilgenburg, Huimeng Wang, Liyen Loh, Marios Koutsakos, Katherine Kedzierska, Alexandra J. Corbett, Zhenjun Chen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is part 3.6 of the "Study of MAIT Cell Activation in Viral Infections ... | ["[Passaging MDCK cells:]\nWarm up MDCK cell media, trypsin–versene, and PBS at .\n37 °C", "[Passaging MDCK cells:]\nCheck the confluency of MDCK cells, aspirate the medium, add , aspirate the medium, and repeat wash.\n[PBS]", "[Passaging MDCK cells:]\nDiscard PBS, add 2–3 mL of trypsin–versene (stored ) to MDCK monola... |
96,165 | KASP genotyping | 4 | dx.doi.org/10.17504/protocols.io.kqdg39qr7g25/v2 | https://www.protocols.io/view/kasp-genotyping-c96dz9a6 | Francois Kroll, FishFloorUCL | TITLE: KASP genotyping
AUTHORS: Francois Kroll, FishFloorUCL
[DESCRIPTION]
KASP is a genotyping assay which you can use to differentiate wild types vs heterozygous vs homozygous larvae/finclips. It is well suited to genotype a SNP or a small CRISPR-generated indel. Once you confirmed it is working well, the assay is p... | ["[Design the KASP primers] Eirinn Mackay, a Fish Floor alumnus (Wilson lab), created an online tool to create the KASP primer. This circumvents using the company's service, which charges ~ 60£ for a simple mix of three PCR primers.\n\nGo to\nhttps://kasp.eirinn.org/\n\nWe are assuming here that you already sequenced y... |
null | null | null | dx.doi.org/10.17504/protocols.io.fthbnj6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The Sequence Read Archive (SRA) is a database for biological sequence data and is maintained by the National Center for Biotechnology Information (NCBI). Sequence files can be obtained by using the SRA Toolkit. This protocol provides the steps necessary to use the SRA toolkit... | [] |
36,882 | Subcellular fractionation of suspension Chinese Hamster Ovary (CHO) cells | 1 | dx.doi.org/10.17504/protocols.io.bf9sjr6e | https://www.protocols.io/view/subcellular-fractionation-of-suspension-chinese-ha-bf9sjr6e | Saumel Perez Rodriguez, María De Jesús Ramírez-Lira, Tune Wulff, Bjørn Gunnar Voldbor, Octavio T Ramírez, Mauricio A Trujillo-Roldán, Norma A Valdez-Cruz | TITLE: Subcellular fractionation of suspension Chinese Hamster Ovary (CHO) cells
AUTHORS: Saumel Perez Rodriguez, María De Jesús Ramírez-Lira, Tune Wulff, Bjørn Gunnar Voldbor, Octavio T Ramírez, Mauricio A Trujillo-Roldán, Norma A Valdez-Cruz
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">S... | ["[Cell disruption]\nQuantify cell concentration and viability during cell culture to reach 300-700 millions of viable cells, with a viability higher than 90%.", "[Cell disruption]\nCentrifuge cells at , in conical tubes.\nCentrifuge: 185 34, 5 min, 4 10\n50 mL", "[Cell disruption]\nDiscard supernatant gently to avoid... |
71,750 | Schistosoma mansoni cercariae sexing | 4 | null | https://www.protocols.io/view/schistosoma-mansoni-cercariae-sexing-cibeuaje | Sarah K Buddenborg | TITLE: Schistosoma mansoni cercariae sexing
AUTHORS: Sarah K Buddenborg
[DESCRIPTION]
This DNA extraction method for Schistosoma mansoni cercariae is based on the HOTSHOT method https://health.uconn.edu/mouse-genome-modification/protocols/hotshot-method-of-dna-preparation/. DNA isolation is followed by PCR amplificati... | ["[Cercariae Collection] While holding with wide-tip featherweight forceps, rinse patent Biomphalaria glabrata snails, individually, with MilliQ water", "[Cercariae Collection] Place rinsed snails into individual wells of 6- or 12-well plates", "[Cercariae Collection] Add 3-4ml of MilliQ water to each well", "[Cercari... |
null | null | null | dx.doi.org/10.17504/protocols.io.s25egg6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Preparation of Zymos<em>eptoria tritici </em>isolates for extraction of chromosomes via pulsed-field electrophoresis</p>
<p> </p>
<p>Pat Martinez 1990 (Bruce McDonald lab) (Simplified from Cooley, et al, Curr. Genet. 13:383-389.)</p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?... | [] |
63,845 | Working Reverse Primer Plate(s) | 4 | null | https://www.protocols.io/view/working-reverse-primer-plate-s-cakdscs6 | Allyson Hirsch, George Testo | TITLE: Working Reverse Primer Plate(s)
AUTHORS: Allyson Hirsch, George Testo
[DESCRIPTION]
Stock primers should not be directly used in a PCR because they are concentrated. Working from one tube is a bad idea, and thus it only takes a small amount of contamination to render your primers ineffective. For this reason, ... | ["[Preparing PCR Hood] Decontaminate a PCR hood with DNA Away and Ethanol.", "[Preparing PCR Hood] Place materials inside of the PCR Hood (refer to materials section).", "[Preparing PCR Hood] Turn on the UV setting for at least 30 min.", "[Preparing Skirted Plates] Temporary seal 6 96-well skirted plates and label each... |
35,622 | Core Protocol for Serial Imaging of Fluorescently-Labeled Mouse Brain on the TissueCyte 1000 System | null | dx.doi.org/10.17504/protocols.io.be2ejgbe | null | Allen Institute for Brain Science | TITLE: Core Protocol for Serial Imaging of Fluorescently-Labeled Mouse Brain on the TissueCyte 1000 System
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the instructions for setup and scanning of fluorescently-labeled tissue sectio... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.pijdkcn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Here is a general tutoral on how to begin annotating proteins with Hidden Markov Models. A small test set of HMMs is provided in the Git repo downloaded in the first step. </p>
[STEPS]
?.
?.
?.
?.
?.
?.
?. | [] |
34,447 | BD FACS Aria II Shutdown | null | dx.doi.org/10.17504/protocols.io.bdvpi65n | null | Allen Institute for Brain Science | TITLE: BD FACS Aria II Shutdown
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol provides step by step instructions for shutting down the BD FACS Aria II and cleaning it of potentially hazardous materials.</div><div class = "text-block"><span s... | [] |
44,209 | What is the prevalence of joint contractures in a long-term care population: a systematic review and meta-analysis | 1 | dx.doi.org/10.17504/protocols.io.bpermjd6 | https://www.protocols.io/view/what-is-the-prevalence-of-joint-contractures-in-a-bpermjd6 | H Prentice | TITLE: What is the prevalence of joint contractures in a long-term care population: a systematic review and meta-analysis
AUTHORS: H Prentice
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Background</span></div><div class = "text-block">Joint contractures, a disor... | ["IntroductionJoint contractures, a disorder that can loosely be defined as a reduction in range of movement around a joint(1, 2), are frequently cited as a complication of immobility in older people(3, 4)and are associated with pain(5)and a general reduction in quality of life(6).Past reviews and studies show high var... |
96,800 | Systematic Literature Review | 0 | null | https://www.protocols.io/view/systematic-literature-review-dar82d9w | Leonardo Rocha, Rodrigo Clemente Thom de Souza, Alan Cesar | TITLE: Systematic Literature Review
AUTHORS: Leonardo Rocha, Rodrigo Clemente Thom de Souza, Alan Cesar
[DESCRIPTION]
This systematic review investigates the use of artificial intelligence (AI) algorithms in locating facilities for humanitarian causes, focusing on issues related to the mobility of refugees and statele... | ["[Context] Human mobility is one of the most intriguing phenomena of the present days. The movement of people around the world has increased in recent years. This has placed groups around the globe in adverse situations. Known as refugees and stateless persons, these are individuals who find themselves forced for some... |
80,444 | ARIAS: An AR-based interactive advertising system | 3 | dx.doi.org/10.17504/protocols.io.e6nvwjyq2lmk/v2 | https://www.protocols.io/view/arias-an-ar-based-interactive-advertising-system-css4wegw | wantchoosejoy | TITLE: ARIAS: An AR-based interactive advertising system
AUTHORS: wantchoosejoy
[DESCRIPTION]
ARIAS is an AR-based advertising system, it can be manipulated by gestures interactively.
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.dyg7tv | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol is for extracting RNA from 25 mm filters and can be used with filters stored in RNAlater for preservation. This protocol has been tested with 0.22 μm pore size Durapore filters. Custom synthesized RNA transcript standards are added at the time of extraction and are... | [] |
44,517 | Intein-assisted Bisection Mapping (IBM) | 5 | dx.doi.org/10.17504/protocols.io.bpqdmms6 | https://www.protocols.io/view/intein-assisted-bisection-mapping-ibm-bpqdmms6 | Trevor Ho, Baojun Wang | TITLE: Intein-assisted Bisection Mapping (IBM)
AUTHORS: Trevor Ho, Baojun Wang
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Split inteins are powerful tools for seamless ligation of synthetic split proteins. Yet, their use remains limited because the already intricate split site identification pr... | ["[Introduction]\nIBM starts with a transposition reaction: a staging vector carries a 5’ and 3’ trimmed gene of interest (GOI) with the internal BsaI, BbsI and SapI sites removed. The staging plasmid is mixed in vitro with the MuA transposase and the mini-Mu transposon, which generates the initial insertion library. A... |
103,924 | ADE 2024 Day 1: Background and Fieldwork | 3 | null | https://www.protocols.io/view/ade-2024-day-1-background-and-fieldwork-dhqu35ww | Tom Little, Nathan Medd | TITLE: ADE 2024 Day 1: Background and Fieldwork
AUTHORS: Tom Little, Nathan Medd
[DESCRIPTION]
ADE 2024 description of work to be done on Day 1 of the practical work
[STEPS] | [] |
79,882 | Handling and Sampling Birds - ISL Peru | 1 | dx.doi.org/10.17504/protocols.io.6qpvr4zwpgmk/v1 | https://www.protocols.io/view/handling-and-sampling-birds-isl-peru-cr9iv94e | Jorge Luis Mendoza-Silva, Giancarlo Inga Diaz, Roberto Salazar, Cristian Tirapelle, Mrinalini Watsa, Gideon Erkenswick | TITLE: Handling and Sampling Birds - ISL Peru
AUTHORS: Jorge Luis Mendoza-Silva, Giancarlo Inga Diaz, Roberto Salazar, Cristian Tirapelle, Mrinalini Watsa, Gideon Erkenswick
[DESCRIPTION]
Program Timing:
Sample collection occurs annually during the rainforest dry season (June - August). Sample transport and analyses o... | ["[PREPARATORY PHASE] Day before capture\ninstall 4-12 nylon mist nets (6 - 12 x 2.7 m, 4 - 5 shelves, mesh size 15 - 20 mm) in selected areas. The number of mist nets used should reflect the size of the bird team and frequency of capture at that particular site. Nets are activated from sunrise until around 11:00.\npac... |
null | null | null | dx.doi.org/10.17504/protocols.io.qvfdw3n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol is used to clarity the process of RNA extraction for our Betta splendens genome.</p>
[STEPS]
?.
?.
?.
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?. | [] |
48,360 | Immunohistochemistry – Novolink Polymer Detection Systems | 1 | dx.doi.org/10.17504/protocols.io.yxmvmkwdog3p/v1 | https://www.protocols.io/view/immunohistochemistry-novolink-polymer-detection-sy-btggnjtw | Judi O'Shaughnessy, Dr Jenna Gregory | TITLE: Immunohistochemistry – Novolink Polymer Detection Systems
AUTHORS: Judi O'Shaughnessy, Dr Jenna Gregory
[DESCRIPTION]
Immunohistochemistry is a method used to detect specific antigens in tissue sections. It exploits the principal of antibodies binding to specific antigens (epitopes). Visualisation of the target... | ["[Before Starting] - Purpose:\nThe purpose of this SOP is to outline the correct procedures for performing Immunohistochemistry (IHC) using the Novolink Polymer Detection System kit. It is adapted from the Novolink Polymer Detection Systems instruction manual and is intended for the use by all staff, students, and use... |
81,794 | B2- BLOOD PROCESSING | 4 | dx.doi.org/10.17504/protocols.io.x54v9dqemg3e/v1 | https://www.protocols.io/view/b2-blood-processing-ct5awq2e | REDI-NET Consortium | TITLE: B2- BLOOD PROCESSING
AUTHORS: REDI-NET Consortium
[DESCRIPTION]
This protocol details blood processing.
[BEFORE_START]
BEFORE START
Pre-cool the Bullet Blender by adding dry ice into the cooling compartment and running the cooling program.
Clean the work surfaces with RNaseZap, then wipe the surfaces with ... | ["[1. WHOLE BLOOD AND BUFFY COAT LYSIS]", "[1. WHOLE BLOOD AND BUFFY COAT LYSIS] Add 200 µL sterile 1x PBS to a 200 µL whole blood or buffy coat sample.", "[1. WHOLE BLOOD AND BUFFY COAT LYSIS] Include a positive control for each batch of samples: transfer 37.5 µL ZymoBIOMICS Microbial Community Standard Material, 100 ... |
101,627 | Sample Preparation for Elemental Analysis of Auxenochlorella protothecoides (UTEX 250) Cells and Spent Media by Inductively Coupled Plasma Mass Spectrometry (ICP-MS/MS) and Total Organic Carbon (TOC). | 0 | dx.doi.org/10.17504/protocols.io.14egn69wml5d/v1 | https://www.protocols.io/view/sample-preparation-for-elemental-analysis-of-auxen-dfg33jyn | Dimitrios Camacho, Charles Perrino, Sabeeha Merchant | TITLE: Sample Preparation for Elemental Analysis of Auxenochlorella protothecoides (UTEX 250) Cells and Spent Media by Inductively Coupled Plasma Mass Spectrometry (ICP-MS/MS) and Total Organic Carbon (TOC).
AUTHORS: Dimitrios Camacho, Charles Perrino, Sabeeha Merchant
[DESCRIPTION]
This protocol describes a method fo... | ["[Procedure] Collect 1 × 108 - 3 × 108 cells at 17000 x g, 2 min, 22 °C in red screw cap 15 mL tubes using the JXN-26 centrifuge. Do not disturb the pellet. The pellet will partially adhere to the side of the tube at a 45-degree angle. \n\nIf cells are sticking to the side of the tube and not collecting to the bottom ... |
99,379 | Protocol for Facially Guided Digital Diagnosis in Orthodontics and Interdisciplinary Dentistry | 1 | dx.doi.org/10.17504/protocols.io.8epv5x9q6g1b/v3 | https://www.protocols.io/view/protocol-for-facially-guided-digital-diagnosis-in-ddat22en | Rupert HG Kelley, Álvaro Ferrando Cascales, Raúl Ferrando Cascales | TITLE: Protocol for Facially Guided Digital Diagnosis in Orthodontics and Interdisciplinary Dentistry
AUTHORS: Rupert HG Kelley, Álvaro Ferrando Cascales, Raúl Ferrando Cascales
[DESCRIPTION]
As the digital age of dentistry continues to flourish, it has never been more important to have protocols to guide dentists th... | ["[Treatment Planning] STEP 1 - Records: Natural head position pictures, occlusal scan and radiographic imaging", "[Treatment Planning] STEP 2 - Orientation and alignment of STL and DICOM files with photographs\n\nOnce all the records have been obtained, the digital scans (STLs) can be superimposed onto the NHP photogr... |
44,953 | Another test protocol | 1 | dx.doi.org/10.17504/protocols.io.bp5zmq76 | https://www.protocols.io/view/another-test-protocol-bp5zmq76 | Andrew Khramchenkov | TITLE: Another test protocol
AUTHORS: Andrew Khramchenkov
[STEPS]
?. Very test protocol, please ignore it | ["Very test protocol, please ignore it"] |
87,457 | DNA extraction and Nanopore library prep from 15-30 whole flies- V.3.2 | 1 | dx.doi.org/10.17504/protocols.io.81wgbxzb1lpk/v1 | https://www.protocols.io/view/dna-extraction-and-nanopore-library-prep-from-15-3-czm9x496 | Bernard Y Kim, Hannah Gellert | TITLE: DNA extraction and Nanopore library prep from 15-30 whole flies- V.3.2
AUTHORS: Bernard Y Kim, Hannah Gellert
[DESCRIPTION]
This protocol is optimized for rapid and cost-effective (about $150) genome assembly of Drosophila species from laboratory lines using ONT PromethION sequencers. Following this protocol, a... | ["[(Optional) Hydration of ethanol-fixed tissue] Place flies on a sheet of filter paper and briefly dab with a Kimwipe to remove excess ethanol, then transfer the flies to a 1.5 mL tube.", "[(Optional) Hydration of ethanol-fixed tissue] Add 1.0 mL Buffer STE to the tube with the flies.", "[(Optional) Hydration of ethan... |
106,626 | Whole cell protein extraction and Western blotting | 0 | dx.doi.org/10.17504/protocols.io.rm7vzje8rlx1/v1 | https://www.protocols.io/view/whole-cell-protein-extraction-and-western-blotting-dkda4s2e | Isabel Lam, Alain Ndayisaba, Vikram Khurana | TITLE: Whole cell protein extraction and Western blotting
AUTHORS: Isabel Lam, Alain Ndayisaba, Vikram Khurana
[DESCRIPTION]
Whole cell protein extraction and Western blotting
[STEPS] | [] |
72,963 | Untargeted metabolomics analysis for Golgi immunopurification (Golgi-IP) | 4 | dx.doi.org/10.17504/protocols.io.n2bvj83exgk5/v1 | https://www.protocols.io/view/untargeted-metabolomics-analysis-for-golgi-immunop-cjhbuj2n | Wentao Dong, Eshaan S Rawat, Monther Abu-Remaileh | TITLE: Untargeted metabolomics analysis for Golgi immunopurification (Golgi-IP)
AUTHORS: Wentao Dong, Eshaan S Rawat, Monther Abu-Remaileh
[DESCRIPTION]
The Golgi apparatus functions as a central hub in the cell that processes, packages, and distributes proteins. Despite its critical cellular function, there has been ... | ["[LC/MS metabolomics settings] Set an ID-X tribrid mass spectrometer (Thermo Fisher Scientific) with an electrospray ionization (ESI) probe, for initial polar metabolite profiling.\n\nPrepare a SeQuant® ZIC®-pHILIC 150 x 2.1 mm column (Millipore Sigma 1504600001) coupled with a 20 x 2.1 mm (Millipore Sigma 1504380001)... |
50,222 | 2021 Featured Protocols | 2 | null | https://www.protocols.io/view/2021-featured-protocols-bvann2de | protocols.io team | TITLE: 2021 Featured Protocols
AUTHORS: protocols.io team
[DESCRIPTION]
This is a growing collection that includes all protocols that were featured in 2021 on our welcome page and on social media (Twitter, Facebook).
Every week, we feature 3 new protocols that are particularly fantastic examples of reproducible and ... | [] |
74,985 | P4. PROCEDIMIENTO DE ADMISIÓN Y MATRICULACIÓN | 1 | dx.doi.org/10.17504/protocols.io.dm6gpjybdgzp/v1 | https://www.protocols.io/view/p4-procedimiento-de-admisi-n-y-matriculaci-n-cmghu3t6 | cgarcia | TITLE: P4. PROCEDIMIENTO DE ADMISIÓN Y MATRICULACIÓN
AUTHORS: cgarcia
[DESCRIPTION]
P4. PROCEDIMIENTO DE ADMISIÓN Y MATRICULACIÓN
[STEPS]
SECTION: P4. PROCEDIMIENTO DE ADMISIÓN Y MATRICULACIÓN
1. Admisión
La Comisión Académica de cada Programa trasladará a la EIDUCAM la resolución de las admisiones.
Secretaría de EI... | ["[P4. PROCEDIMIENTO DE ADMISIÓN Y MATRICULACIÓN] Admisión\n\nLa Comisión Académica de cada Programa trasladará a la EIDUCAM la resolución de las admisiones.\nSecretaría de EIDUCAM comunicará a los doctorandos su admisión o no en el programa, así como los nombres de su tutor y director/es. Esta secretaría también comun... |
96,945 | Protocol for Preparing Brain Samples for MUSIC | 0 | dx.doi.org/10.17504/protocols.io.x54v92e8ml3e/v2 | https://www.protocols.io/view/protocol-for-preparing-brain-samples-for-music-dawr2fd6 | Wenxin Zhao, Sheng Zhong | TITLE: Protocol for Preparing Brain Samples for MUSIC
AUTHORS: Wenxin Zhao, Sheng Zhong
[DESCRIPTION]
Here states the detailed procedure to prepare brain samples for MUSIC study.
[STEPS]
SECTION: Tissue pulverization and crosslinking
1. Cut a portion of post-mortem human brain frontal cortex sample collected from The... | ["[Tissue pulverization and crosslinking] Cut a portion of post-mortem human brain frontal cortex sample collected from The Brain and Body Donation Program (BBDP) at Banner Sun Health Research Institute on dry ice with heavy razor blades, and collect 50 mg of the sample in a 1.5 mL LoBind tube.", "[Nuclei isolation] Us... |
51,654 | WORKFLOW FOR THE NUCLEIC ACID BASED IDENTIFICATION OF INSECTS USING WHOLE GENOME AMPLIFICATION AND NANOPORE SEQUENCING - KAWA | 1 | dx.doi.org/10.17504/protocols.io.bwpepdje | https://www.protocols.io/view/workflow-for-the-nucleic-acid-based-identification-bwpepdje | Jürg E Frey, Beatrice Frey, Daniel Frei, Morgan Gueuning, Simon Blaser, Andreas Bühlmann | TITLE: WORKFLOW FOR THE NUCLEIC ACID BASED IDENTIFICATION OF INSECTS USING WHOLE GENOME AMPLIFICATION AND NANOPORE SEQUENCING - KAWA
AUTHORS: Jürg E Frey, Beatrice Frey, Daniel Frei, Morgan Gueuning, Simon Blaser, Andreas Bühlmann
[DESCRIPTION]
BACKGROUND
World-wide trade with plant material has dramatically inc... | ["[1 Sample preparation] All samples should be stored frozen at -20 °C or stored in 70 % (few days at Room temperature or at 4 °C in the refrigerator) until processed. Samples can be stored frozen indefinitely. Use sterile dissection equipment where appropriate. As we are mostly using crude DNA extracts with or withou... |
58,354 | ScenGen | 3 | null | https://www.protocols.io/view/scengen-b48sqzwe | Elena L. Peredo | TITLE: ScenGen
AUTHORS: Elena L. Peredo
[DESCRIPTION]
test1
[STEPS] | [] |
88,493 | Mid-lumbar (L3) epidural stimulation effects on bladder and external urethral sphincter in non-injured and chronically transected urethane-anesthetized rats | 1 | dx.doi.org/10.17504/protocols.io.bp2l6xdk5lqe/v2 | https://www.protocols.io/view/mid-lumbar-l3-epidural-stimulation-effects-on-blad-c2nmydc6 | Daniel Medina Aguinaga, Robert Hoey, Natasha L. Wilkins, Beatrice Ugiliweneza, Jason Fell, Susan J. Harkema, Charles H. Hubscher | TITLE: Mid-lumbar (L3) epidural stimulation effects on bladder and external urethral sphincter in non-injured and chronically transected urethane-anesthetized rats
AUTHORS: Daniel Medina Aguinaga, Robert Hoey, Natasha L. Wilkins, Beatrice Ugiliweneza, Jason Fell, Susan J. Harkema, Charles H. Hubscher
[DESCRIPTION]
Cur... | ["[Post-surgical care] After surgery, the rat's urinary bladder was manually emptied 3/day until voiding reflexively.", "[Terminal mapping - Electromyography and cystometrogram sensors surgical placement] The rat is placed on their ventrum throughout testing. The hindlimbs are taped down to the platform\nas the electri... |
64,589 | Dissection and immunohistochemistry of mouse lung | 1 | dx.doi.org/10.17504/protocols.io.3byl4b6kjvo5/v1 | https://www.protocols.io/view/dissection-and-immunohistochemistry-of-mouse-lung-cbbmsik6 | Seol-Hee Kim, Thomas Taylor-Clark | TITLE: Dissection and immunohistochemistry of mouse lung
AUTHORS: Seol-Hee Kim, Thomas Taylor-Clark
[DESCRIPTION]
Mice are euthanized, perfused with fixative for lung tissue collection. Mouse lung is cryosectioned and slices are stained for protein expression using immunohistochemistry. Expression of specific proteins... | ["[Tissue collection] §6 to 8 weeks old mice (male) were euthanized by CO2 inhalation.", "[Tissue collection] §Mice were transcardially perfused with phosphate buffered saline (PBS) to remove blood followed by 3.7% formaldehyde (PFA).", "[Tissue collection] §Larynx, Trachea and lung were collected.", "[Tissue collectio... |
91,986 | DAB staining protocol for subsequent stereological cell counting | 1 | dx.doi.org/10.17504/protocols.io.e6nvwdq47lmk/v1 | https://www.protocols.io/view/dab-staining-protocol-for-subsequent-stereological-c53sy8ne | Martin T. Henrich, Fanni F. Geibl | TITLE: DAB staining protocol for subsequent stereological cell counting
AUTHORS: Martin T. Henrich, Fanni F. Geibl
[DESCRIPTION]
This protocol describes the steps for performing a double chromogen staining using DAB and SK- 4700. Stained sections can subsequently be imaged and used for stereological cell quantificatio... | ["[DAB staining – Before the procedure:] Prepare 0.1 Molarity (M) PB (PB).", "[DAB Staining Procedure] Place brain sections ( - ) in 12-well-plates with netwell inserts (up to 6-10 sections per netwell insert, depending on the size of the sections).", "[DAB Staining Procedure] Quench sections for 15 min at Room tempera... |
26,403 | Quantitative analysis of methylation and hydroxymethylation using oXBS-qMSP | 1 | dx.doi.org/10.17504/protocols.io.52bg8an | https://www.protocols.io/view/quantitative-analysis-of-methylation-and-hydroxyme-52bg8an | Hector Hernandez-Vargas, Chloe Goldsmith | TITLE: Quantitative analysis of methylation and hydroxymethylation using oXBS-qMSP
AUTHORS: Hector Hernandez-Vargas, Chloe Goldsmith
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">There are several tools for investigating the methylation status of genomic DNA; many of these are expensive, do not al... | ["[Preparing Control DNA]\nFully methylated, fully hydroxymethylated and fully unmethylated stanandards (synthetic DNA controls)In addition to the fully methylated and unmethylated controls, it is also important to have a control for the oXBS conversion. For this, it is possible to use synthetic DNA controls in order t... |
51,482 | Chemiluminescence of coelenterazine catalyzed by cyclodextrins as a luminescence reference standard for luminometers | 4 | dx.doi.org/10.17504/protocols.io.bwh2pb8e | https://www.protocols.io/view/chemiluminescence-of-coelenterazine-catalyzed-by-c-bwh2pb8e | Misha Koksharov | TITLE: Chemiluminescence of coelenterazine catalyzed by cyclodextrins as a luminescence reference standard for luminometers
AUTHORS: Misha Koksharov
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Bioluminescence and chemiluminescence are widely used in sensitive detection methods in biomedical s... | ["Prepare for the experiment.", "Bring the reference assay solutions (with 10 mM β-CD and/or with 10 mM TMCD) to room temperature.", "Turn on the luminescence plate reader or luminometer, warm it up and make it ready for the measurements.", "Take out a small (20-40 μl) aliquot of 15 mM CTZ in propylene glycol from and... |
51,374 | Growing Soybean in the Greenhouse | 1 | dx.doi.org/10.17504/protocols.io.bwenpbde | https://www.protocols.io/view/growing-soybean-in-the-greenhouse-bwenpbde | Lynn Doran | TITLE: Growing Soybean in the Greenhouse
AUTHORS: Lynn Doran
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol for planting, germinating, and growing soybeans in the UIUC RIPE or ACES Plant Care Facility greenhouse. Has been verified on Petite Havana and Samson cultivars. </div></div>
[ST... | ["Fill classic 1000 pots to within a half inch of the brim with soil. Tamp the soil down firmly with your hands.", "Water the soil in thoroughly. The soybean soil mixes contain high levels of sand and drainage is slow. It may take several hours for the soil to be saturated and to drain any standing water.\nThe soil ... |
52,733 | Statistical analysis | 5 | dx.doi.org/10.17504/protocols.io.bxq5pmy6 | https://www.protocols.io/view/statistical-analysis-bxq5pmy6 | Chunmei Chang | TITLE: Statistical analysis
AUTHORS: Chunmei Chang
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Statistical analysis</div></div>
[STEPS]
?. Perform statistical analysis with GraphPad Prism 9.
?. Analyze the data of bead-based binding assay by one-way ANOVA with Dunn’s multiple comparisons test... | ["Perform statistical analysis with GraphPad Prism 9.", "Analyze the data of bead-based binding assay by one-way ANOVA with Dunn’s multiple comparisons test.", "Analyze the data of ULK1 kinase activity assay by two-way ANOVA with Šídák's multiple comparisons test."] |
80,642 | Step by step protocol for the Laparoscopic examination of American alligators | 1 | dx.doi.org/10.17504/protocols.io.36wgqj8r5vk5/v1 | https://www.protocols.io/view/step-by-step-protocol-for-the-laparoscopic-examina-cszawf2e | Jaylene Flint, Mark Flint, Jeff Miller | TITLE: Step by step protocol for the Laparoscopic examination of American alligators
AUTHORS: Jaylene Flint, Mark Flint, Jeff Miller
[DESCRIPTION]
This protocol describes a minimally invasive surgical technique and approach to successfully examine the gonads of live American alligators as part of a reproductive examin... | ["[Surgical approach] Before any animal is examined using laparoscopy, it should be medically assessed to ensure it is fit and able to have a minimally invasive procedure conducted. Examination should include visual inspection of body condition score, activity level, and overt signs of illness or trauma.", "[Surgical a... |
41,893 | vBio Voice Analysis | 4 | null | https://www.protocols.io/view/vbio-voice-analysis-bk6dkza6 | David Levesque | TITLE: vBio Voice Analysis
AUTHORS: David Levesque
[STEPS]
?. [Demographic & Endpoints]
Study ProtocolAges Eligible for Study: 18 Years and older (Adult, Older Adult) Sexes Eligible for Study: Male FemaleAll Accepts Healthy Volunteers: YesNo Sampling Method: Non-Probability SampleSites: 60 hospitals, Africa, EU, Asia... | ["[Demographic & Endpoints]\nStudy ProtocolAges Eligible for Study: 18 Years and older (Adult, Older Adult) Sexes Eligible for Study: Male FemaleAll Accepts Healthy Volunteers: YesNo Sampling Method: Non-Probability SampleSites: 60 hospitals, Africa, EU, Asia, U.S.Study PopulationsPatients with positive COVID-19 PCR t... |
58,137 | DNA Extract wash from filter paper stored at room temperature | 1 | dx.doi.org/10.17504/protocols.io.b4zzqx76 | https://www.protocols.io/view/dna-extract-wash-from-filter-paper-stored-at-room-b4zzqx76 | Katie Izenour, Anwar Kalalah, Fayez Salib, Sarah Zohdy | TITLE: DNA Extract wash from filter paper stored at room temperature
AUTHORS: Katie Izenour, Anwar Kalalah, Fayez Salib, Sarah Zohdy
[DESCRIPTION]
Preservation of samples requiring cold-chain storage is an often unavoidable challenge especially when doing laboratory work outside the western world. Samples are a pr... | ["[Whole blood collection from animal] Using a sterile syringe and needle, collect 1-5 mL of whole blood from animal's forelimb. Immediately express the contents of the syringe into a new, clean EDTA tube and invert several times to mix.", "[Whole blood storage] IF EXTRACTING DNA ON THE SAME DAY AS BLOOD COLLECTION - ... |
28,043 | Use IPython to run bioconda tools in jupyter | null | dx.doi.org/10.17504/protocols.io.7mjhk4n | null | Alise J. Ponsero | TITLE: Use IPython to run bioconda tools in jupyter
AUTHORS: Alise J. Ponsero
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Learn how to run shell commands directly in your jupyter notebook using IPython</div></div>
[STEPS]
?. [installing vsearch ]
Open Anaconda Navigator and go to your environme... | ["[installing vsearch ]\nOpen Anaconda Navigator and go to your environment manager. Select the class environment and search for the vsearch package in the \"not installed\" packages list.Install vsearch in the environment. If you don't remember how to do this. Do not panic and go back to the Anaconda protocol (https:/... |
87,469 | DNA extraction and Nanopore library prep from single flies | 1 | dx.doi.org/10.17504/protocols.io.ewov1q967gr2/v1 | https://www.protocols.io/view/dna-extraction-and-nanopore-library-prep-from-sing-cznmx5c6 | Bernard Y Kim, Hannah Gellert | TITLE: DNA extraction and Nanopore library prep from single flies
AUTHORS: Bernard Y Kim, Hannah Gellert
[DESCRIPTION]
This protocol is optimized for rapid and cost-effective (about $150) genome assembly of Drosophila species from single flies using ONT PromethION sequencers. Following this protocol, a typical Drosoph... | ["[(Optional) Hydration of ethanol-fixed tissue] Place flies on a sheet of filter paper and briefly dab with a Kimwipe to remove excess ethanol, then transfer the flies to a 1.5 mL tube.", "[(Optional) Hydration of ethanol-fixed tissue] Add 300 µL Buffer STE to the tube with the flies.", "[(Optional) Hydration of ethan... |
83,945 | Electroporation of Cas9 protein into human pluripotent stem cells | 1 | dx.doi.org/10.17504/protocols.io.ewov1qykkgr2/v1 | https://www.protocols.io/view/electroporation-of-cas9-protein-into-human-pluripo-cv8hw9t6 | Jiuchun Zhang, Harper JW | TITLE: Electroporation of Cas9 protein into human pluripotent stem cells
AUTHORS: Jiuchun Zhang, Harper JW
[DESCRIPTION]
This protocol describes the electroporation of Cas9 protein into human pluripotent stem cells.
[BEFORE_START]
Use ThermoFisher Kit to directly electroporate ESCs with Cas9 protein and sgRNA.
Works ... | ["Add 10 µL to a sterile 1.5 ml tube. Add 6 µg. Then add 1.2 µg. Pipet up and down to mix. Let it sit at Room temperature for 10 min. This is enough for 2 transfections (== one 6 well).", "While waiting for the Cas9 to bind to sgRNA, individualize cells with Accutase. Neutralize Accutase with 5x volume E8 with Rock inh... |
86,732 | Analysis of products from deconstructed nylon-6 by UHPLC-MS/MS (dMRM) | 6 | dx.doi.org/10.17504/protocols.io.kxygx331dg8j/v1 | https://www.protocols.io/view/analysis-of-products-from-deconstructed-nylon-6-by-cyxkxxkw | Kelsey J. Ramirez, Morgan A Ingraham, Elizabeth L. Bell, Gregg T. Beckham | TITLE: Analysis of products from deconstructed nylon-6 by UHPLC-MS/MS (dMRM)
AUTHORS: Kelsey J. Ramirez, Morgan A Ingraham, Elizabeth L. Bell, Gregg T. Beckham
[DESCRIPTION]
An analysis method was developed for the quantitation of products produced by deconstruction of nylon-6 utilizing ultra-high performance liquid c... | ["[Preparation of Standards] By weight, create individual 2000 µg/mL stock solutions of all analytes listed below using ultrapure water (18.2MΩ⋅cm)(UPW) as a diluent, except for 6-aminohexanoic acid cyclic-dimer in which methanol is used: \nɛ-Caprolactam\n6-Aminohexanoic acid\n6-Aminohexanoic acid dimer (6-(6-aminohexa... |
31,725 | L-Type Ca2+ Current Protocol | 1 | dx.doi.org/10.17504/protocols.io.ba8mihu6 | https://www.protocols.io/view/l-type-ca2-current-protocol-ba8mihu6 | Robert Harvey, Shailesh Agarwal | TITLE: L-Type Ca2+ Current Protocol
AUTHORS: Robert Harvey, Shailesh Agarwal
[DESCRIPTION]
This protocol is for patch-clamp recordings of L-type Ca2+ current and slow delayed rectifier K+ current responses to norepinephrine and acetylcholine.
[STEPS]
1. Membrane currents were recorded from isolated rat venticular my... | ["Membrane currents were recorded from isolated rat venticular myocytes using the whole-cell configuration of the patch clamp technique.", "Isolated cells were placed in a perfusion chamber (Warner Instruments) on the stage of an inverted microscope (Olympus IX71) and bathed in a K+-free extracellular solution containi... |
70,897 | Plasmid transduction using competent cell | 4 | dx.doi.org/10.17504/protocols.io.j8nlkw4e5l5r/v1 | https://www.protocols.io/view/plasmid-transduction-using-competent-cell-chgrt3v6 | An.Huang | TITLE: Plasmid transduction using competent cell
AUTHORS: An.Huang
[DESCRIPTION]
Plasmid can be transduced into bacteria at competent state using heat shock. This protocol helps transduce plasmid into competent cells.
[STEPS]
2. When the cells are completely thawed, pipette 2 µL plasmid DNA solution into 100 µL compe... | ["When the cells are completely thawed, pipette 2 µL plasmid DNA solution into 100 µL competent cell.\nPut the cell in ice for 30 min", "Conduct heat shock on the competent cell by placing the cell in 42 °C water bath for 90 s.\nPut the cells back into ice for 2 min", "Take competent cell out from -80℃ fridge and thaw ... |
28,019 | Phage stock preparation | null | dx.doi.org/10.17504/protocols.io.7kthkwn | null | Marijn Ceelen | TITLE: Phage stock preparation
AUTHORS: Marijn Ceelen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">A protocol for phage lambda and phage T7 phage stock preparation</div></div>
[STEPS]
?. Grow E. coli bacterial host (for example LE392, DH10B or DH5alpha) in LB medium overnight at
37 °C
?. Prepare... | ["Grow E. coli bacterial host (for example LE392, DH10B or DH5alpha) in LB medium overnight at\n37 °C", "Prepare and autoclave CaCl2 and MgCl2", "Add of CaCl2 and of MgCl2 to of LB medium. Make aliquots of 10 mL and inoculate with 0.1 volumes of overnight bacterial host.\n50 µl\n50 µl\n50 ml", "Incubate with agita... |
88,695 | Light Sheet Fluorescence Microscopy of Human Kidney Using Active Clearing with the SHIELD Reagent | 4 | dx.doi.org/10.17504/protocols.io.eq2lyjxmqlx9/v1 | https://www.protocols.io/view/light-sheet-fluorescence-microscopy-of-human-kidne-c2uxyexn | Liam Mclaughlin, Bo Zhang, Amanda Knoten, Praveen Krishnamoorthy, Sanjay Jain | TITLE: Light Sheet Fluorescence Microscopy of Human Kidney Using Active Clearing with the SHIELD Reagent
AUTHORS: Liam Mclaughlin, Bo Zhang, Amanda Knoten, Praveen Krishnamoorthy, Sanjay Jain
[DESCRIPTION]
Light sheet fluorescence microscopy (LSFM) is a method to cover micro-mesoscale (µm-cm) areas of tissue while a... | ["[Tips] Tips:\n\n•\tActive clearing of SHIELD (Park et al., 2018; PMID: 30556815; PMCID: PMC6579717; DOI: 10.1038/nbt.4281) -infiltrated samples takes around seven days to complete.\n\n•\tThe first phase uses a polyepoxy matrix dubbed Stabilization under Harsh conditions via Intramolecular Epoxide Linkages to prevent ... |
45,027 | SARS-CoV-2 Whole Genome Sequencing on Illumina - Tiling PCR | 1 | null | https://www.protocols.io/view/sars-cov-2-whole-genome-sequencing-on-illumina-til-bp8bmrsn | Guerrino Macori, Seamus Fanning | TITLE: SARS-CoV-2 Whole Genome Sequencing on Illumina - Tiling PCR
AUTHORS: Guerrino Macori, Seamus Fanning
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This SOP describes the procedure for generating cDNA from SARS-CoV-2 viral nucleic acid extracts and subsequently obtaining, through the amplico... | ["[SARS-CoV-2 WvGS protocol - cDNA Preparation Reverse Transcription]\ncDNA/Reverse Transcription Section Date/Initials:_________________In this section, the nucleic acid extracted and used for the qPCR diagnostic test is used as starting material for the sequencing.", "[SARS-CoV-2 WvGS protocol - cDNA Preparati... |
null | null | null | dx.doi.org/10.17504/protocols.io.c5iy4d | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Modified from H. Ochman protocol: <em>Environ. Micro. 2009 Kunin, Engelbrekson Ochman & Hugenholt</em>z
[GUIDELINES]
<strong>Protocol Using Takara Hot Start EX Taq (cat. no RR006A)</strong><br /><br />
<table style="height: 250px; width: 250px;" width="416">
<tbody>
<tr>
<t... | [] |
27,156 | Preparation of PCR amplicons from edited cells for deep sequencing | null | dx.doi.org/10.17504/protocols.io.6ruhd6w | null | Mark DeWitt | TITLE: Preparation of PCR amplicons from edited cells for deep sequencing
AUTHORS: Mark DeWitt
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes how to extract and amplify DNA from genome-edited cells, and sequence the resulting amplicons using Illumina MiSeq NGS.</div></div>
... | ["[Prepare first PCR (genomic DNA PCR)]\nPrepare the following Master Mix using the initial PCR primers (annealing outside the HDR template region, see guidelines for design requirements), and the PrimeStar GXL polymerase kit from Clontech. Include a master mix-only control.Master mix (per reaction): 0.15 µL 100 µM... |
100,540 | Detection of avian Influenza Virus H5N1 with a Real time PCR kit | 0 | dx.doi.org/10.17504/protocols.io.5qpvok38bl4o/v1 | https://www.protocols.io/view/detection-of-avian-influenza-virus-h5n1-with-a-rea-dee43bgw | Sudhir Bhatia, Gudrun Baersch | TITLE: Detection of avian Influenza Virus H5N1 with a Real time PCR kit
AUTHORS: Sudhir Bhatia, Gudrun Baersch
[DESCRIPTION]
Avian Influenza virus H5N1 has caused a number of outbreaks in human beings in recent years. Recently it has caused outbreak in human and cows in USA. Therefore it is essential to detect the pre... | ["Thaw one tube each: A, B, Y, D1 and D2. After thaw, put the tubes at 4°C (as it is better). If the kit is not in use, store them at -20 ° C.", "Mark your microtubes with a sample number, +ve Control and –ve Control. Otherwise use a 96 well microwell plate instead of tubes.", "Add 7µl of Tube A to each tube.", "Add 1... |
48,755 | Multiplexed scNOMe-seq protocol based on isolated single nuclei | 1 | dx.doi.org/10.17504/protocols.io.btutnnwn | https://www.protocols.io/view/multiplexed-scnome-seq-protocol-based-on-isolated-btutnnwn | Sebastian Pott, Michael Wasney, Nadia Khan | TITLE: Multiplexed scNOMe-seq protocol based on isolated single nuclei
AUTHORS: Sebastian Pott, Michael Wasney, Nadia Khan
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">What follows is the protocol for performing single-cell Nucleosome Occupancy and Methylome sequencing on single nuclei (scNOMe-se... | ["[Nuclei Isolation and GpC Methylation]\nBefore commencing with nuclei isolation and GpC Methyltransferase step, prepare 384- or 96-well collection plates with digestion mix. This can be prepared the day before and kept at 4ºC. ABCD1ReagentReaction concentration (based on reaction volume)Volumes for 2 384-well plates... |
82,350 | MicroMPN: Software for Automating Most Probable Number Estimates from Laboratory Microplates | 5 | null | https://www.protocols.click/view/micrompn-software-for-automating-most-probable-num-cunnwvde | Adam R Rivers, Karla Franco Melendez | TITLE: MicroMPN: Software for Automating Most Probable Number Estimates from Laboratory Microplates
AUTHORS: Adam R Rivers, Karla Franco Melendez
[DESCRIPTION]
The most probable number assay is a commonly used method for estimating the concentration of viable microbes, such as bacteria and fungi (1, 2) present in envi... | ["[Example of Input file 1: namefile.csv] Example of CSV file with relative fluorescence units (RFU) data . In this example, a microplate contains 8 replicates by 11 10-fold serial dilutions. \n\nColumn names:\nplate_unique\nplate_well\nrfu", "[Example of Input file 2: namefile.toml] In this .toml file , each row (A... |
36,391 | Islet Culture and Preparation for Cold Shipping | 1 | dx.doi.org/10.17504/protocols.io.bfsfjnbn | https://www.protocols.io/view/islet-culture-and-preparation-for-cold-shipping-bfsfjnbn | Integrated Islet Distribution Program | TITLE: Islet Culture and Preparation for Cold Shipping
AUTHORS: Integrated Islet Distribution Program
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This SOP defines a standardized method for packaging and cold shipping of research quality islets to approved investigators of human isolated islet pr... | ["[Preparation of Supplies and Reagents]\nReceipt of Supplies:The majority of supplies should be stored in appropriate dry, temperature-controlled environments (room temperature 16°-28°C).The Prodo Labs PIM(R) should be stored, in the dark, between and upon receipt but is stable at room temperature.The Gemini AB se... |
44,863 | Operative Wound Care in Total Knee Artroplasty | 1 | dx.doi.org/10.17504/protocols.io.bp27mqhn | https://www.protocols.io/view/operative-wound-care-in-total-knee-artroplasty-bp27mqhn | Luisa Mululo, Fabricio Loures, Marcia Vanzillota, José Mauricio Moraes do Carmo, Marcelo Campos | TITLE: Operative Wound Care in Total Knee Artroplasty
AUTHORS: Luisa Mululo, Fabricio Loures, Marcia Vanzillota, José Mauricio Moraes do Carmo, Marcelo Campos
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Guidelines for surgical wound care for patients undergoing total knee arthroplasty surgery p... | [] |
90,238 | MTT assay | 1 | dx.doi.org/10.17504/protocols.io.e6nvwdoqwlmk/v1 | https://www.protocols.io/view/mtt-assay-c4c6ysze | Alexander Röntgen | TITLE: MTT assay
AUTHORS: Alexander Röntgen
[DESCRIPTION]
Protocol for MTT cytotoxicity assay on SH-SY5Y cells.
[STEPS]
SECTION: General
1. Culture human SH-SY5Y cells at 37 °C and 5% CO2
SECTION: Day 1
3. Count cells and seed 10000 cells/well
SECTION: Day 1
4. Incubate at 37 °C and 5% CO2 for 24 h
SECTION: Day 2
5. ... | ["[General] Culture human SH-SY5Y cells at 37 °C and 5% CO2", "[Day 1] Count cells and seed 10000 cells/well", "[Day 1] Incubate at 37 °C and 5% CO2 for 24 h", "[Day 2] Aspirate medium from cells", "[Day 2] Add in protein solutions", "[Day 2] Place back at 37 °C and 5% CO2 for 24 h", "[Day 3] Dilute MTT 1:10 in RPMI me... |
31,184 | Library Preparation of Bee 18S and 28S rRNA amplicons for High-Throughput Illumina Sequencing | null | dx.doi.org/10.17504/protocols.io.bapqidmw | null | Brian Darby, Russ Bryant, Abby Keller, Madison Jochim, Josephine Moe, Zoe Schreiner, Carrie Pratt, Ned H. Euliss Jr., Mia Park, Rebecca Simmons, Clint Otto | TITLE: Library Preparation of Bee 18S and 28S rRNA amplicons for High-Throughput Illumina Sequencing
AUTHORS: Brian Darby, Russ Bryant, Abby Keller, Madison Jochim, Josephine Moe, Zoe Schreiner, Carrie Pratt, Ned H. Euliss Jr., Mia Park, Rebecca Simmons, Clint Otto
[DESCRIPTION]
<div class = "text-blocks"><div class =... | ["[Sample preparation and gDNA extration]\nPlace one mesothoracic leg from each specimen (of a sample) into a 2.0 ml microcentrifuge tube, and repeat this with a new microcentrifuge tube for all samples that are to be separately barcoded.", "[First Round PCR Amplifcation]\nPrepare Master Mix 1 for each locus separately... |
28,433 | 2-step Polymerase Chain Reaction (PCR) | null | dx.doi.org/10.17504/protocols.io.7zrhp56 | null | Dana Mozaffari, Laura Kvedarauskaite | TITLE: 2-step Polymerase Chain Reaction (PCR)
AUTHORS: Dana Mozaffari, Laura Kvedarauskaite
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Polymerase Chain Reaction (PCR) is a method of making multiple copies of a DNA sequence, involving repeated reactions with a polymerase enzyme, which comes in d... | ["[Gene specific PCR]\nSet up the thermocycler programFor initial denaturation98°C for 2 minutesFor 35 cycles:98°C for 30 seconds for denaturation30 seconds for primers annealing at temperature depending on primers and polymerase72°C for 30 seconds per kb of DNA for elongationFinal extension:72°C for 7 minutes4°C on ho... |
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