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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19,293 | Instructions for recreating elPrep 4.0.0 WGS benchmarks | null | dx.doi.org/10.17504/protocols.io.w35fgq6 | null | Charlotte Herzeel | TITLE: Instructions for recreating elPrep 4.0.0 WGS benchmarks
AUTHORS: Charlotte Herzeel
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Instructions for recreating the elPrep4.0.0 WGS benchmarks used in the following paper:</div><div class = "text-block">Herzeel C, Costanza P, Decap D, Fostier J, ... | ["Configuration1.1 Hardware1.2 Software\nThese instructions have been tested with elPrep v.4.0.0. The following assumes that everything is performed from a working directory WORKDIR.\n* 2x18-core Intel Xeon processor E5-2699v3 Haswell @ 2.3GHz* 256 GB RAM* 2x400 GB SSD\n* Ubuntu 14.04.5 LTS* elPrep 4.0.0", "Installatio... |
78,871 | Kraus et al., 2022 FBXO7 /Park15 | 2 | dx.doi.org/10.17504/protocols.io.kxygx99pwg8j/v2 | https://www.protocols.io/view/kraus-et-al-2022-fbxo7-park15-cq9xvz7n | Felix Kraus | TITLE: Kraus et al., 2022 FBXO7 /Park15
AUTHORS: Felix Kraus
[DESCRIPTION]
The protein kinase PINK1 and ubiquitin ligase Parkin promote removal of damaged mitochondria via a feed-forward mechanism involving ubiquitin (Ub) phosphorylation, Parkin activation, and ubiquitylation of mitochondrial outer membrane proteins... | [] |
92,655 | Spinal manipulations for migraine | 1 | dx.doi.org/10.17504/protocols.io.q26g7pne9gwz/v1 | https://www.protocols.io/view/spinal-manipulations-for-migraine-c6qpzdvn | Paul Posadzki, Edzard Ernst | TITLE: Spinal manipulations for migraine
AUTHORS: Paul Posadzki, Edzard Ernst
[DESCRIPTION]
Several new randomized trials evaluating the effectiveness and safety of spinal manipulative therapies (SMT) have been published since our previous systematic review (SR). Therefore, we aim at updating the evidence base for the... | ["Spinal manipulations for migraine: a protocol for an updated systematic review and meta-analysis of randomized clinical trials", "[Protocol]"] |
103,899 | Effect of OT-Bridge System Versus Multiunit Abutment on the Passive Fit and Stresses Induced by CAD/CAM Fabricated All-on-Four Screw-Retained Prostheses (In Vitro Study) | 0 | dx.doi.org/10.17504/protocols.io.14egn6e4zl5d/v1 | https://www.protocols.io/view/effect-of-ot-bridge-system-versus-multiunit-abutme-dhp335qn | Abdelrahman Hazem, Shaimaa Lotfy Mohamed, Sara Ibrahim Soliman Mohamed | TITLE: Effect of OT-Bridge System Versus Multiunit Abutment on the Passive Fit and Stresses Induced by CAD/CAM Fabricated All-on-Four Screw-Retained Prostheses (In Vitro Study)
AUTHORS: Abdelrahman Hazem, Shaimaa Lotfy Mohamed, Sara Ibrahim Soliman Mohamed
[DESCRIPTION]
The hazardous effect of stresses
induced by lack... | ["[Abstract] The hazardous effect of stresses\ninduced by lack of passivity in screw-retained prostheses necessitates the\nselection of a suitable intermediate component between the implant fixture and\nthe prosthetic framework. Thus, this study aims to evaluate passivity and\nstresses induced by CAD/CAM screw-retained... |
22,493 | The Illumina libraries preparation for the Scapharca broughtonii | null | dx.doi.org/10.17504/protocols.io.z75f9q6 | null | Chang-Ming Bai | TITLE: The Illumina libraries preparation for the Scapharca broughtonii
AUTHORS: Chang-Ming Bai
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol is used to detail the process of Illumina libraries preparation for the</span><span style = "font-style:italic;"> Scapharca broughtonii<... | ["The extracted DNA was sheared into fragments about 350 bp in size using a Bioruptor Pico Sonication System (Diagenode, Seraing, Belgium), and verified by agarose gel electrophoresis.\nThe sizes of the main fragments should between 200 bp and 500 bp.", "Fragments with size > 300 bp were purified using VAHTSTM DNA Clea... |
94,641 | Scoping Review: Malaria risk stratification and incidence mapping | 1 | dx.doi.org/10.17504/protocols.io.3byl4qn9zvo5/v1 | https://www.protocols.io/view/scoping-review-malaria-risk-stratification-and-inc-c8nrzvd6 | Jessica Craig, Donal Bisanzio, Richard Reithinger | TITLE: Scoping Review: Malaria risk stratification and incidence mapping
AUTHORS: Jessica Craig, Donal Bisanzio, Richard Reithinger
[DESCRIPTION]
Context: As countries continue to make progress against
malaria at national level, transmission of malaria and, hence, risk becomes increasingly
heterogeneous. To maximize a... | ["[Rationale] Malaria is an acute febrile illness caused by a parasitic\ninfection transmitted by Anopheles mosquitoes. Human malaria is caused by five\ndifferent Plasmodium parasites, with P. falciparum being the predominant\nspecies in sub-Saharan Africa (SSA) [1]. Malaria burden has a marked spatial\nheterogeneity w... |
84,080 | DNA/RNA extraction from fresh-frozen tissue, AllPrep DNA/RNA/miRNA Universal Kit | 4 | null | https://www.protocols.click/view/dna-rna-extraction-from-fresh-frozen-tissue-allpre-cwcqxavw | Annika Fendler | TITLE: DNA/RNA extraction from fresh-frozen tissue, AllPrep DNA/RNA/miRNA Universal Kit
AUTHORS: Annika Fendler
[DESCRIPTION]
Protocol for combined RNA and DNA extraction from fresh-frozen tissue using the AllPrep DNA/RNA/miRNA Universal Kit.
[BEFORE_START]
Preparations:
FRN buffer: Add 42 ml Isoprop to new bottle
RP... | ["[Tissue preparation] This protocol is for \nOptional: Weigh tissue", "[Tissue preparation] Transfer tissue in 350 µL 600 µL RLT + ß-ME in 2 ml DNA LoBind tube.\n\nMake sure that the tissue does not defrost.", "[Tissue preparation] Add a 5mm bead to each tube and lyse tissue in TissueLyser for 2 min @ 20 Hz", "[T... |
27,385 | FTÅ200 Interfacial Tension Measurement | 1 | null | https://www.protocols.io/view/ft-200-interfacial-tension-measurement-6yzhfx6 | Kenneth Schackart | TITLE: FTÅ200 Interfacial Tension Measurement
AUTHORS: Kenneth Schackart
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">How to use the First Ten Ångstrom (FTÅ) 200 for measuring interfacial tension of aqueous solution. Some aspects of this protocol are specific to use in Yoon Biosensors Lab at The ... | ["[Mount Syringe]\nTwist needle onto glass syringe until tight, but not excessively tight.\nUse caution when grabbing needle. Avoid touching the tips of needles to prevent contamination.", "[Mount Syringe]\nMount syringe by sliding through the hole on the syringe mount, bringing the two halves of the white syringe clam... |
81,800 | Preparação para ir ao campo | 1 | dx.doi.org/10.17504/protocols.io.dm6gpjz31gzp/v3 | https://www.protocols.io/view/prepara-o-para-ir-ao-campo-ct5gwq3w | Alicia Rafaelly Vilefort Sales, Daniel Vartanian, Maria Augusta Medeiros Andrade | TITLE: Preparação para ir ao campo
AUTHORS: Alicia Rafaelly Vilefort Sales, Daniel Vartanian, Maria Augusta Medeiros Andrade
[DESCRIPTION]
Este protocolo foi desenhado para o processo de coleta de dados do projeto de pesquisa Sono e Gravidez. Consulte a aba Guidelines para visualizar o fluxograma do processo como um t... | ["[Agenda] Consulte a agenda do projeto e verifique a quantidade de gestantes a serem recrutadas em seu turno.", "[Agenda] Verifique os horários e o trajeto que você terá que fazer para que você chegue com ao menos 30 minutos de antecedência do horário de sua primeira consulta na Casa de Parto.", "[Actígrafos] Separe u... |
43,820 | Single-step generation of genetic reporter lines using CRISPR/Cas9 and transient antibiotic selection | 4 | null | https://www.protocols.io/view/single-step-generation-of-genetic-reporter-lines-u-bn2kmgcw | Carles Calatayud, William Serkin, Patrik Verstreken | TITLE: Single-step generation of genetic reporter lines using CRISPR/Cas9 and transient antibiotic selection
AUTHORS: Carles Calatayud, William Serkin, Patrik Verstreken
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The following protocol describes the generation of genetic reporters in hum... | ["[Preparing Cas9 mRNA and the gene-specific guide RNA through in vitro transcription (IVTR)]\nAmplify Cas9-T2A-mClover3 IVTR template from pIVTR(T7A)-Cas9-T2A-mClover3 using the following primers AB1Pre_T7_FwdACATTTCCCCGAAAAGTGCC2HBB_3UTR_150T_RvTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT... |
22,334 | Transfection of Crypthecodinium cohnii using labelled DNA | null | dx.doi.org/10.17504/protocols.io.z26f8he | null | José A. Fernández Robledo | TITLE: Transfection of Crypthecodinium cohnii using labelled DNA
AUTHORS: José A. Fernández Robledo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">José A. Fernández Robledo </div><div class = "text-block">Nastasia J. Freyria</div><div class = "text-block"> Bigelow Laboratory for Ocean Sciences</div... | ["[Reagents]\nLiquid mediumL1 + 10 gr/L glucose NPN (https://ncma.bigelow.org/ccmp316#.XLOpDZNKi2w)L1 medium with nitrogen limited (without yeast extract and glucose) to obtain cyst from C. cohnii swimming cellsPlatesPrepare Petri dishes containing L1 medium bacteriological agar (1.5%)Prepare PEG 8000 solution (0.4%) ... |
71,099 | SHInE - Simultaneous HCR, Immunohistochemistry, Nuclear staining and EdU | 4 | dx.doi.org/10.17504/protocols.io.5qpvobnyzl4o/v1 | https://www.protocols.io/view/shine-simultaneous-hcr-immunohistochemistry-nuclea-chn3t5gn | Aida Coric, Alexander W. Stockinger, Petra Schaffer, Dunja Rokvic, Kristin Tessmar-Raible, Florian Raible | TITLE: SHInE - Simultaneous HCR, Immunohistochemistry, Nuclear staining and EdU
AUTHORS: Aida Coric, Alexander W. Stockinger, Petra Schaffer, Dunja Rokvic, Kristin Tessmar-Raible, Florian Raible
[DESCRIPTION]
This protocol allows the multiplexed use of four different molecular labelling techniques in whole-mount Platy... | ["[Optional: EdU incubation] Optional: Chase out EdU with 3 millimolar (mM) thymidine for 60 min ; then replace thymidine solution with fresh ASW and incubate for desired chase length", "[Optional: EdU incubation] Incubate worms with 10 micromolar (µM) EdU in artificial sea water (ASW) (EdU aliquots in both DMSO and H... |
null | null | null | dx.doi.org/10.17504/protocols.io.pnpdmdn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><u>Goal:</u></p>
<p>This document aims to standardize the protocol for assaying the association of bacteria or fluorescent latex beads in eukaryotic cells by flow cytometry.</p>
<p> </p>
<p><u>General considerations:</u></p>
<p>- There are different models of flow cytometers,... | [] |
97,130 | Data-Independent Acquisition (DIA) Data Processing using Spectronaut/directDIA (Biognosys): Whole Proteome Analysis of Human Whole Lung Tissue | 0 | dx.doi.org/10.17504/protocols.io.261ge5p8og47/v1 | https://www.protocols.io/view/data-independent-acquisition-dia-data-processing-u-da4i2gue | Joanna Bons, J P Rose, M A Watson, B Schilling | TITLE: Data-Independent Acquisition (DIA) Data Processing using Spectronaut/directDIA (Biognosys): Whole Proteome Analysis of Human Whole Lung Tissue
AUTHORS: Joanna Bons, J P Rose, M A Watson, B Schilling
[DESCRIPTION]
Proteolytic peptide measurement of Human whole lung tissue using Liquid Chromatography-Tandem Mass ... | ["Search the DIA data with Spectronaut using the spectral library-free directDIA\nalgorithm against a Human UniProt-SwissProt proteome database (https://www.uniprot.org/proteomes), applying the settings described in Table 1."] |
30,640 | Visual attentional tasks | null | dx.doi.org/10.17504/protocols.io.96qh9dw | null | Chiara Valeria Marinelli, Pierluigi Zoccolotti, Cristina Romani | TITLE: Visual attentional tasks
AUTHORS: Chiara Valeria Marinelli, Pierluigi Zoccolotti, Cristina Romani
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The tasks examined a) visuo-spatial memory; b) visuo-attentional capacity; and c) serial visual-attention.</div></div>
[STEPS] | [] |
21,129 | Preparation of human Red Blood Cells for Scanning Electron Microscopy imaging | null | dx.doi.org/10.17504/protocols.io.yvhfw36 | null | Marie Anne Balanant | TITLE: Preparation of human Red Blood Cells for Scanning Electron Microscopy imaging
AUTHORS: Marie Anne Balanant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">SEM imaging can be used to quantify RBC shape. RBCs are sampled from fresh blood samples or from packed RBC units during storage. RBCs are... | ["[Coverslip preparation]\nPrepare glass coverslips by incubating them in poly-D-lysine solution in PBS for at RT\n10 Volume Percent", "[Coverslip preparation]\nRinse twice with milliQ water", "[Coverslip preparation]\nDry and keep at until use", "[RBC fixation with glutaraldehyde]\nWash of RBC in PBS ()\n100 µl\n... |
null | null | null | dx.doi.org/10.17504/protocols.io.shheb36 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol refers to a study having the aim to identify and test at field artificial structures suitable as collectors for common cuttlefish Sepia officinalis eggs in wild condition.</p>
<p>During the same study, three different protocols were tested and compared. This one... | [] |
50,155 | Sample collection and DNA purification from virus-enriched tangential flow filtration retentates | 1 | null | https://www.protocols.io/view/sample-collection-and-dna-purification-from-virus-bu8jnzun | Paul Den Uyl, Ed Delong | TITLE: Sample collection and DNA purification from virus-enriched tangential flow filtration retentates
AUTHORS: Paul Den Uyl, Ed Delong
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">To collect and concentrate viral particles, seawater samples were collected and prefiltered to remove bacterioplan... | ["[Pre-Cleaning]\nRecirculate 0.1N Sodium Hydroxide at feed speed for .\nCentrifuge: 330 33", "[Pre-Cleaning]\nFlush with MilliQ.\n30 L", "[Pre-Cleaning]\nDrain the system (see sample recovery).", "[Concentrating]\nFill retentate reservoir.", "[Concentrating]\nAttach retentate reservoir.", "[Concentrating]\nConnect f... |
21,008 | Environmental DNA (eDNA) extraction with modified Qiagen DNeasy Blood & Tissue kit | null | dx.doi.org/10.17504/protocols.io.yrqfv5w | null | Collin Closek, Hilary Starks, Elizabeth Andruszkiewicz, Alexandria Boehm | TITLE: Environmental DNA (eDNA) extraction with modified Qiagen DNeasy Blood & Tissue kit
AUTHORS: Collin Closek, Hilary Starks, Elizabeth Andruszkiewicz, Alexandria Boehm
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Nucleic acids extraction from the filters using the Qiagen DNeasy Blood and Tiss... | ["[Preparation]\nNucleic acids were extracted from the filters using the Qiagen DNeasy Blood and Tissue Kit with some modifications to the manufacturer’s protocol.", "[Preparation]\nPrior to extraction, 0.5 mm and 0.1 mm glass beads (BioSpec Products) transferred to glass beaker, covered with tin foil, and ashed at 500... |
106,332 | Pollen germination on wheat stigmas | 0 | dx.doi.org/10.17504/protocols.io.kxygxy42ol8j/v1 | https://www.protocols.io/view/pollen-germination-on-wheat-stigmas-dj344qqw | Marina Millán Blánquez | TITLE: Pollen germination on wheat stigmas
AUTHORS: Marina Millán Blánquez
[DESCRIPTION]
Aniline blue staining of pollen tube growth on the wheat stigma and through the style 4 h and 30 min after pollination.
[STEPS]
SECTION: Hand pollination
1. Please refer to wheat-training.com for detailed explanations on how to ... | ["[Hand pollination] Please refer to wheat-training.com for detailed explanations on how to perform hand pollinations. Link to pdf: https://www.wheat-training.com/wp-content/uploads/Wheat_growth/pdfs/How-to-cross-wheat-pdf.pdf", "[Carpel dissection and fixation] Using a pair of tweezers, dissect carpels 4.5 h after pol... |
41,618 | Harmony Transfer Pipette Protocol | 4 | dx.doi.org/10.17504/protocols.io.bkvskw6e | https://www.protocols.io/view/harmony-transfer-pipette-protocol-bkvskw6e | Jack H Kotnik, Nuttada Panpradist, Ian Hull, Qin Wang, Mike Roller, Amy Oreskovic, Enos Kline, Daniel Leon, Barry Lutz, Robert Atkinson | TITLE: Harmony Transfer Pipette Protocol
AUTHORS: Jack H Kotnik, Nuttada Panpradist, Ian Hull, Qin Wang, Mike Roller, Amy Oreskovic, Enos Kline, Daniel Leon, Barry Lutz, Robert Atkinson
[STEPS]
?. [Intended Use]
The Harmony assay is used with the Harmony instrument for the detection of SARS-CoV-2 viral RNA in lower na... | ["[Intended Use]\nThe Harmony assay is used with the Harmony instrument for the detection of SARS-CoV-2 viral RNA in lower nares (nasal swab) specimens collected from individuals suspected of SARS-CoV-2 infection. The assay is intended for the qualitative detection of SARS-CoV-2 nucleic acid from direct specimens.The a... |
null | null | null | dx.doi.org/10.17504/protocols.io.mahc2b6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Efficiency of plaquing (EOP) assay for <em>C. jejuni </em>phages</p>
<p>Jessica Sacher (with help from Stephanie Guerra</p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
32,653 | Enzymatic disaggregation of human myometrium for 10X Single Cell RNA-seq | null | dx.doi.org/10.17504/protocols.io.bb5miq46 | null | Aymara Mas, Alba Machado-Lopez, Patricia Escorcia, Carlos Simón | TITLE: Enzymatic disaggregation of human myometrium for 10X Single Cell RNA-seq
AUTHORS: Aymara Mas, Alba Machado-Lopez, Patricia Escorcia, Carlos Simón
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol describes the procedure for dissociating myometrial samples, which is based in ... | ["[Tissue collection and transportation]\nUterine tissues should be transported in preservation solution (HypoThermosol® FRS) at from the surgery room to the lab.\n4 °C", "[Dissociation]\nRinse the sample with wash buffer, removing blood or mucus.", "[Remove red blood cells]\n[Optional] If after centrifugation there i... |
88,358 | 18S V9 PCR | 4 | null | https://www.protocols.io/view/18s-v9-pcr-c2ieycbe | Kathleen Pitz | TITLE: 18S V9 PCR
AUTHORS: Kathleen Pitz
[DESCRIPTION]
This protocol is aimed at amplifying the 18S rRNA hypervariable region 9 (18S V9) in eukaryotes with a focus on microbial eukaryotes. Amplicons generated using this protocol can then be sequenced using the Illumina platform. The primers (1391F, EukBr) utilized in ... | ["[Minimum Information about an Omics Protocol (MIOP)] MIOP Term\nValue\n \nmethodology category\n\n \nproject\n\n \npurpose\n\n \nanalyses\n\n \ngeographic location\n\n \nbroad-scale environmental context\n\n \nlocal environmental context\n\n \nenvironmental medium\n\n \ntarget\n18S gene\n \ncreator\n\n \nmaterials ... |
64,396 | True Ketogenics Keto Bundle: Weight Loss Pills [Pros & Cons]| Ingredients, Price and Warnings!! | 3 | dx.doi.org/10.17504/protocols.io.bp2l61y61vqe/v1 | https://www.protocols.io/view/true-ketogenics-keto-bundle-weight-loss-pills-pros-ca5ksg4w | shinelsom | TITLE: True Ketogenics Keto Bundle: Weight Loss Pills [Pros & Cons]| Ingredients, Price and Warnings!!
AUTHORS: shinelsom
[DESCRIPTION]
"True Ketogenics Keto Bundle
[STEPS] | [] |
36,798 | Human Neurosurgical Tissue Processing | null | dx.doi.org/10.17504/protocols.io.bf66jrhe | https://www.protocols.io/view/human-neurosurgical-tissue-processing-bf66jrhe | Allen Institute for Brain Science | TITLE: Human Neurosurgical Tissue Processing
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the procedure for receiving human surgical tissue, followed by trimming, mounting, embedding, and slicing under sterile conditions in order ... | [] |
93,070 | Culture of human epithelial cells (skin, cornea, thymus) on 3T3J2 feeder layer cells | 4 | dx.doi.org/10.17504/protocols.io.14egn31ezl5d/v2 | https://www.protocols.io/view/culture-of-human-epithelial-cells-skin-cornea-thym-c65nzg5e | Pierluigi Giuseppe Manti | TITLE: Culture of human epithelial cells (skin, cornea, thymus) on 3T3J2 feeder layer cells
AUTHORS: Pierluigi Giuseppe Manti
[DESCRIPTION]
This document is of vital importance for scientists attempting the culture of human
keratinocytes derived from skin, cornea, thymus, esophagus etc. Please strictly adhere
to the g... | ["[3T3J2 Growth Medium] Open DMEM bottle (ThermoFisher Scientific).", "[3T3J2 Growth Medium] Add 8 % (v/v) of bovine serum (ThermoFisher Scientific) (DO NOT use fetal calf serum!).", "Set up one flask at low density to maintain the line (5*10^5 cells at early passages, 10^5 cells at late passages). This flask should r... |
106,319 | Methods for xenograft tissue processing and capture for spatial transcriptomics using 10x-Genomics Visium platform | 0 | dx.doi.org/10.17504/protocols.io.4r3l2q1yxl1y/v1 | https://www.protocols.io/view/methods-for-xenograft-tissue-processing-and-captur-dj3p4qmn | Sandy S. Pineda, Hongyun Li, YuHong Fu, Glenda Halliday | TITLE: Methods for xenograft tissue processing and capture for spatial transcriptomics using 10x-Genomics Visium platform
AUTHORS: Sandy S. Pineda, Hongyun Li, YuHong Fu, Glenda Halliday
[DESCRIPTION]
This protocol details the process of preparing grafted mouse brain samples for spatial transcriptomics using 10X Genom... | ["[Tissue preparation] Selected 4% PFF-fixed & paraffin-embedded (FFPE) blocks of the xenograft mouse brains at the striatum level were cut in a rotary microtome (HistoCore MULTICUT R Rotary, Leica Biosystems) at 6µm thickness.\nFour tissue sections were cut and placed on each poly-prep slides (Millipore-Sigma, P0425).... |
84,692 | snm3C-seq3 | 1 | dx.doi.org/10.17504/protocols.io.kqdg3x6ezg25/v1 | https://www.protocols.io/view/snm3c-seq3-cwxuxfnw | Anna Bartlett, Rosa Castanon, Hanqing Liu, Yi Zhang, Chongyuan Luo, Joseph R. Ecker | TITLE: snm3C-seq3
AUTHORS: Anna Bartlett, Rosa Castanon, Hanqing Liu, Yi Zhang, Chongyuan Luo, Joseph R. Ecker
[DESCRIPTION]
We developed a single-nucleus multiomic sequencing technology (snm3C-seq3) to assay both the methylome and chromatin contacts from within the same cell. We further adapted this protocol to allo... | ["[Prepare Single Nuclei] Prepare stock solutions, stored at 4°C\n\n 1. NIM: Sucrose (250 mM), KCl (25 mM), MgCl2 (5 mM), Tris-Cl pH 8.0 (10 mM)\n 2. Dilutent: Tris-Cl pH 8.0 (120 mM), KCl (150 mM), MgCl2 (30 mM)", "[Prepare Single Nuclei] Prepare the following solutions fresh before each experiment\n\n1.... |
58,578 | Well-tempered Metadynamics protocol | 5 | null | https://www.protocols.io/view/well-tempered-metadynamics-protocol-b5fsq3ne | Vidya Niranjan, Akshay Uttarkar | TITLE: Well-tempered Metadynamics protocol
AUTHORS: Vidya Niranjan, Akshay Uttarkar
[DESCRIPTION]
Metadynamics is a technique in which the potential for one or more chosen variables ("collective variables") is modified by periodically adding a repulsive potential of Gaussian shape at the location given by particula... | ["Simulation system setup. \nIn the solvation tab\nThe complex is solvated in an orthorombhic box with the dimensions 10Å additional to the total size of the receptor complex.\nClick on minimize volume to obtain the optimal box dimensions.\n\n \n\nIn the Ions tab\nPlace ions based on the requirement of neutral, acidic... |
38,508 | Addgene Covid-19, Back To Work Training | 3 | dx.doi.org/10.17504/protocols.io.bhukj6uw | https://www.protocols.io/view/addgene-covid-19-back-to-work-training-bhukj6uw | Joanne Kamens, Addgene The Nonprofit Plasmid Repository | TITLE: Addgene Covid-19, Back To Work Training
AUTHORS: Joanne Kamens, Addgene The Nonprofit Plasmid Repository
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Disclaimer</span><span>: The SOP presented here has been designed by the Addgene nonprofit plasmid reposi... | [] |
73,145 | SPOT DNA Extraction from 142mm A/E 1µm Filters | 1 | dx.doi.org/10.17504/protocols.io.ewov1oqeklr2/v1 | https://www.protocols.io/view/spot-dna-extraction-from-142mm-a-e-1-m-filters-cjnzumf6 | Yi-Chun Yeh, Erin B Fichot, Alma E Parada | TITLE: SPOT DNA Extraction from 142mm A/E 1µm Filters
AUTHORS: Yi-Chun Yeh, Erin B Fichot, Alma E Parada
[DESCRIPTION]
Reference: Lie et al, 2013. Small-scale temporal and spatial variations in protistan community composition at the San Pedro Ocean Time-series station off the coast of southern California. Aquatic Mic... | ["[Day1] Prepare a 70°C water bath.", "[Day1] Prepare a razor blade, forceps, and a metal slab.", "[Day1] Cut the 142mm A/E filter into pieces on the metal slab and place it into a 50 ml falcon tube.", "[Day1] Add 6.2 ml of 2X lysis buffer and 500 µl of 0.5 mm zirconia/silica beads.", "[Day1] Bead-beat (vortex) for 1 m... |
19,481 | Parhyale hawaiensis embryo single cell dissociation | null | dx.doi.org/10.17504/protocols.io.w9zfh76 | null | Leo Blondel | TITLE: Parhyale hawaiensis embryo single cell dissociation
AUTHORS: Leo Blondel
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. [Coat all gear with BSA]
Prepare 1% BSA solution in ddH2OCoat 1 or more wells from 12 well plateCoat pasteur pipettes for embryo transfersIf using syringes for loading coat tubing... | ["[Coat all gear with BSA]\nPrepare 1% BSA solution in ddH2OCoat 1 or more wells from 12 well plateCoat pasteur pipettes for embryo transfersIf using syringes for loading coat tubing and syringes", "[Collect embryos]\nThis protocol was tested on embryos at 12hpf to 72hpf.From the collected females, harvest embryos in t... |
95,212 | Intact and clean nuclei isolation from wheat meristems | 4 | dx.doi.org/10.17504/protocols.io.yxmvm3renl3p/v1 | https://www.protocols.io/view/intact-and-clean-nuclei-isolation-from-wheat-meris-c88kzzuw | Isabel Faci, Maximillian RW Jones, Cristobal Uauy | TITLE: Intact and clean nuclei isolation from wheat meristems
AUTHORS: Isabel Faci, Maximillian RW Jones, Cristobal Uauy
[DESCRIPTION]
This protocol describes how to perform nuclei isolation from wheat meristem tissues (spikes and carpels/ovaries), specifically from flash-frozen tissues. With this protocol, we obtain ... | ["[Tissue collection] Next, for each sample, label 2 mL Eppendorf tubes for collection and place two nitrogen-cooled metallic steel beads (previously cleaned with 0.5 M HCl and 70% ethanol, diameter 3 mm) in each tube. For each sample, we will pool a number of meristematic spikes/ovaries/spikelets. Depending on the sta... |
87,061 | Standard Operating Procedure (SOP) for Combined ICA and Systemic Administration of MPTP: The Overlesioned (Bilateral Asymmetric) Non-human Primate Model | 4 | dx.doi.org/10.17504/protocols.io.dm6gp3zw5vzp/v1 | https://www.protocols.io/view/standard-operating-procedure-sop-for-combined-ica-cy9vxz66 | Robert S Turner | TITLE: Standard Operating Procedure (SOP) for Combined ICA and Systemic Administration of MPTP: The Overlesioned (Bilateral Asymmetric) Non-human Primate Model
AUTHORS: Robert S Turner
[DESCRIPTION]
This standard operating procedure (SOP) describes safe methods for the use of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridi... | ["[Receipt and storage of MPTP] Place the package with MPTP into a chemical fume hood.", "[Receipt and storage of MPTP] Don appropriate personal protective equipment (Tyvek suit, half-mask respirator, bonnet, face shield, 2 pairs of nitrile gloves) and inspect the package to ensure no damage.", "[Receipt and storage of... |
null | null | null | dx.doi.org/10.17504/protocols.io.dak2cv | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
<p><strong>Primers:</strong></p>
<p>rpoC1_103: CAC TGC GGC AAA TAC AAA CG</p>
<p>rpoC1_360: TTT CAG GTC CTT GTG GTC AC<br /><br /></p>
<strong><strong>Reaction Mix:<br /></strong></strong>
<table style="width: 400px; height: 150px;">
<tbody>
<tr>
<td>Material</td>
<td>Amt.</td>... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.rh6d39e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Protocol for preparing NGFR-mNG2 tagged WM989 A6-G3 melanoma cells for sorting. </p>
[BEFORE_START]
<p>Warm trypsin, media and DPBS. </p>
[STEPS]
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67,277 | BeLiv [Official Website] 2022 | 1 | dx.doi.org/10.17504/protocols.io.8epv598qjg1b/v1 | https://www.protocols.io/view/beliv-official-website-2022-cdxms7k6 | sonoviveget | TITLE: BeLiv [Official Website] 2022
AUTHORS: sonoviveget
[DESCRIPTION]
Many individuals with diabetes battle with fluctuating glucose levels. Diabetes medications and insulin shots can help. Notwithstanding, certain individuals with diabetes search for regular choices to help glucose. As indicated by the US-based p... | [] |
79,007 | Standard M9 minimal medium | 4 | null | https://www.protocols.io/view/standard-m9-minimal-medium-crd7v29n | Andreas Sagen | TITLE: Standard M9 minimal medium
AUTHORS: Andreas Sagen
[DESCRIPTION]
M9 minimal media is a highly-referenced microbial growth medium used for the cultivation of E. coli. This buffered minimal microbial medium contains only salts and nitrogen, so it is traditionally supplemented with glucose, amino acids and vitamins... | ["[1 000 mL 10x M9 salt solution] In a bottle, fill with 800 mL deionized water", "[1 000 mL 10x M9 salt solution] Measure and add:\n 60 g Sodium phosphate (dibasic)\n 30 g Monopotassium phosphate\n 5 g Sodium chloride\n\nMaterials:", "[1 000 mL 10x M9 salt solution] Adjust pH to pH 7.4 using hydrogen chloride... |
47,416 | Automated QIAcube DNA Extraction | 4 | dx.doi.org/10.17504/protocols.io.5qpvoypkdg4o/v1 | https://www.protocols.io/view/automated-qiacube-dna-extraction-bsiyncfw | Clemens Scherzer | TITLE: Automated QIAcube DNA Extraction
AUTHORS: Clemens Scherzer
[DESCRIPTION]
This protocol explains the Standard Operating Protocol for automated extraction of DNA using QIAcube.
[BEFORE_START]
Based on 12 Samples.
DNA Q/C GOALS
1. Cary Concentration Assay
a. 260/280 = 1.8-2.0
b. Manual Purag... | ["[Part A: First Elution] Heat water bath to 37 °C before starting.", "[Part A: First Elution] Thaw Buffy Coat samples by gently agitating sample in water bath.", "[Part A: First Elution] Turn on QIAcube. Open door and remove reagent tray from QIAcube. Unscrew all caps and refill reagents where necessary. Do not exceed... |
77,397 | Virome harvesting from cheese microbiomes | 4 | dx.doi.org/10.17504/protocols.io.j8nlkw29xl5r/v1 | https://www.protocols.io/view/virome-harvesting-from-cheese-microbiomes-cptvvnn6 | Adair Borges | TITLE: Virome harvesting from cheese microbiomes
AUTHORS: Adair Borges
[DESCRIPTION]
This protocol details how we harvest the viral component, or virome, from cheese rind microbiomes. These viromes can be banked at 4 °C for short-term storage or -80 °C for long-term storage. Alternatively, one can extract DNA or RNA ... | ["[Virome extraction from cheese microbial community] Once the cheese sample is fully suspended, add 1 mL of chloroform to the sample. Close the conical tube, and seal the top with Parafilm. Shake the sample on a platform shaker for 1–2 h at room temperature.", "[Virome extraction from cheese microbial community] Move ... |
78,314 | Getting started with Micro-Meta App Tutorial | 5 | dx.doi.org/10.17504/protocols.io.36wgq7ddxvk5/v7 | https://www.protocols.io/view/getting-started-with-micro-meta-app-tutorial-cqqivvue | Alessandro Rigano, Mathias Hammer, Joel Ryan, Claire M. Brown, David Grunwald, Caterina Strambio De Castillia | TITLE: Getting started with Micro-Meta App Tutorial
AUTHORS: Alessandro Rigano, Mathias Hammer, Joel Ryan, Claire M. Brown, David Grunwald, Caterina Strambio De Castillia
[DESCRIPTION]
For quality, interpretation, reproducibility, and sharing value, microscopy images should be accompanied by detailed descriptions of... | ["[Before the tutorial] Video introduction", "[Tutorial - 1 - Download and Install Micro-Meta App] Download Micro-Meta App\n\nFollow the instructions in this step and in Video 3 of the tutorial series to download and install the stand-alone version of the Micro-Meta App.", "[Tutorial - 1 - Download and Install Micro-Me... |
37,900 | Dephosphorylation of 5´-ends of DNA using rSAP (M0371) | 1 | dx.doi.org/10.17504/protocols.io.bg9kjz4w | https://www.protocols.io/view/dephosphorylation-of-5-ends-of-dna-using-rsap-m037-bg9kjz4w | New England Biolabs | TITLE: Dephosphorylation of 5´-ends of DNA using rSAP (M0371)
AUTHORS: New England Biolabs
[DESCRIPTION]
Protocol for Dephosphorylation of 5´-ends of DNA using rSAP (M0371).
[GUIDELINES]
Dephosphorylation of 5´- ends of DNA in Restriction Enzyme Reaction
The phosphate can be added directly into the digestion react... | ["Prepare a 20 µL reaction as follows: \nDNA1 pmol of DNA ends*CutSmart® Buffer (10X)2 µlrSAP1 unitH2O, purifiedto 20 µl**", "Incubate at 37 °C for 30 min.", "Stop reaction by heat-inactivation at 65 °C for 5 min."] |
42,940 | Creating sci-Space Grids for Spatial Barcoding | 1 | null | https://www.protocols.io/view/creating-sci-space-grids-for-spatial-barcoding-bm64k9gw | Sanjay Srivatsan, Mary Regier | TITLE: Creating sci-Space Grids for Spatial Barcoding
AUTHORS: Sanjay Srivatsan, Mary Regier
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Sci-Space is a technology for transferring spatially arrayed oligonucleotides onto tissue sections prior to single cell sequencing. The spatially arrayed oli... | ["[Casting dried agarose slides]\nTo prepare nuclease-free agarose, 3% w/v (SeaPlaque, Lonza, Bend, OR) was added to deionized water containing 0.1% v/v , incubated 2 hr at room temperature, and autoclaved at 15 psi on liquid cycle for at least 15 min to inactivate the remaining diethyl pyrocarbonate.", "[Casting drie... |
18,761 | Detection of single nucleotide polymorphisms with padlock probes | null | dx.doi.org/10.17504/protocols.io.wjhfcj6 | null | Tomasz Krzywkowski, Mats Nilsson | TITLE: Detection of single nucleotide polymorphisms with padlock probes
AUTHORS: Tomasz Krzywkowski, Mats Nilsson
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is for in situ detection of mRNAs and single nucleotide polymorphisms using padlock probes and rolling circle amplification.... | ["[Specimen Pretreatment: Adherent Cells]\nCulture cells in a flask until 80-90% confluence.", "[Specimen Pretreatment: Adherent Cells]\nWash cells twice with PBS, and dislodge cells by adding 1 mL/25 cm2 of 0.25% Trypsin-EDTA for 1-2 min.\n[Trypsin]", "[Specimen Pretreatment: Adherent Cells]\nResuspend the cells in ap... |
96,918 | Generation of knockout iPSCs using CRISPR-Cas9 genome editing | 0 | dx.doi.org/10.17504/protocols.io.36wgqnr33gk5/v1 | https://www.protocols.io/view/generation-of-knockout-ipscs-using-crispr-cas9-gen-davw2e7e | Nisha Mohd Rafiq, Pietro De Camilli | TITLE: Generation of knockout iPSCs using CRISPR-Cas9 genome editing
AUTHORS: Nisha Mohd Rafiq, Pietro De Camilli
[DESCRIPTION]
This protocol describes the genetic modification of induced pluripotent cells (iPSCs) using CRISPR-Cas9, including synthesis of gRNA plasmids, transfection, selection of clones, and sequencin... | ["[Molecular cloning] Design gRNAs using CHOPCHOP (https://chopchop.cbu.uib.no/). Specific gRNAs used in this study can be found in the method section of our manuscript.", "[Molecular cloning] Order gRNAs as complementary single stranded oligonucleotides (Integrated DNA Technologies). The indicated overhanging nucleoti... |
null | null | null | dx.doi.org/10.17504/protocols.io.kjecuje | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
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36,013 | Flow cytometry trait measurements (size, granularity and chlorophyll-a) of diatoms | 1 | dx.doi.org/10.17504/protocols.io.dm6gpr2x5vzp/v1 | https://www.protocols.io/view/flow-cytometry-trait-measurements-size-granularity-bfemjjc6 | Phoebe Argyle, Jana Hinners, Nathan Walworth, Sinead Collins, Naomi M. Levine, Martina Doblin | TITLE: Flow cytometry trait measurements (size, granularity and chlorophyll-a) of diatoms
AUTHORS: Phoebe Argyle, Jana Hinners, Nathan Walworth, Sinead Collins, Naomi M. Levine, Martina Doblin
[DESCRIPTION]
A method and guide for measuring size, relative granularity, and chlorophyll-a content in centric diatom cells. ... | ["[Sample preparation] Aliquot 200 µL of live, uniform culture and transfer to a round-bottom tissue culture plate. Agitate culture gently to suspend cells to create a uniform culture.", "[Sample preparation] Fix the cells with 20 µL (10 % volume) paraformaldehyde 8% solution, resulting in a final concentration of 0.... |
null | null | null | dx.doi.org/10.17504/protocols.io.hupb6vn | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
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98,294 | Tissue Fixation | HubMAP | JHU-TMC | 0 | dx.doi.org/10.17504/protocols.io.3byl4929jgo5/v2 | https://www.protocols.io/view/tissue-fixation-hubmap-jhu-tmc-db8w2rxe | Kyu Sang Han, Pei-Hsun Wu, Joel Sunshine, Ashley Kiemen, Miklhail James, Sashank Reddy, Denis Wirtz | TITLE: Tissue Fixation | HubMAP | JHU-TMC
AUTHORS: Kyu Sang Han, Pei-Hsun Wu, Joel Sunshine, Ashley Kiemen, Miklhail James, Sashank Reddy, Denis Wirtz
[DESCRIPTION]
First and most important - the original tissue sample must be of good quality. Factors such as warm
ischemic time, the time delay between tissue excisio... | ["[Tissue Fixation] Tissue is harvested using our protocol (Tissue Harvesting Protocol)", "[Tissue Fixation] The rate of penetration of formaldehyde depends on the size of the biopsy. Trimming is often required to facilitate fixation. Tissues placed in the tissue cassettes should be no thicker than 3-4mm because the in... |
70,241 | Phage DNA extraction with Monarch kit and digestion to single nucleosides | 1 | dx.doi.org/10.17504/protocols.io.3byl4j2p8lo5/v1 | https://www.protocols.io/view/phage-dna-extraction-with-monarch-kit-and-digestio-cgt9twr6 | Atanas Radkov, Adair Borges | TITLE: Phage DNA extraction with Monarch kit and digestion to single nucleosides
AUTHORS: Atanas Radkov, Adair Borges
[DESCRIPTION]
This protocol details high-molecular-weight DNA extraction from bacteriophages using the NEB Monarch HMW DNA Extraction Kit for Tissue. Following DNA extraction, DNA is digested down to... | ["[Nucleoside digestion] Use a Nucleoside Digestion Mix (NEB - M0649S) to digest 1 µg of DNA. Each reaction should contain 1 µL of Nucleoside Digestion Mix and 2 µL of 10× Nucleoside Digestion Mix buffer.", "[Nucleoside digestion] Perform reactions in 20 µL total volume and incubate at 37 °C for 1 h, followed by enzyme... |
39,154 | Opti-Prep density separation of viruses for metagenomics | 4 | dx.doi.org/10.17504/protocols.io.261geobqwl47/v1 | https://www.protocols.io/view/opti-prep-density-separation-of-viruses-for-metage-bigskbwe | Aditi K. Narayanan, Alon Philosof | TITLE: Opti-Prep density separation of viruses for metagenomics
AUTHORS: Aditi K. Narayanan, Alon Philosof
[DESCRIPTION]
Density purification of viruses from liquid suspensions to remove cells, cell debris, and contaminants related to growth media. Purified viruses can be used in a variety of downstream applications, ... | ["[Preparation of OptiPrep gradient] Prepare OptiPrep solutions at your chosen densities (OptiPrep Density Gradient Medium, Millipore Sigma, SKU:D1556). OptiPrep is a 60% w/v solution of iodixanol (density 1.32 g/mL). It comes sterile, with a rubber stopper in the top. Wipe the stopper with 70% ethanol and use a needle... |
91,459 | Purification of Methylglucose Lipopolysaccharides (MGLP) | 6 | dx.doi.org/10.17504/protocols.io.n92ldmjexl5b/v1 | https://www.protocols.io/view/purification-of-methylglucose-lipopolysaccharides-c5jby4in | Briana Marisco, Luisa M Nieto Ramirez, Karen Dobos | TITLE: Purification of Methylglucose Lipopolysaccharides (MGLP)
AUTHORS: Briana Marisco, Luisa M Nieto Ramirez, Karen Dobos
[DESCRIPTION]
Methylglucose lipopolysaccharides (mGLPs) are poly-methylated polysaccharides (PMPSs) that are acylated with short-chain fatty acids, uniquely synthesized by bacteria belonging to t... | ["[Total lipid extraction] Obtain approximately 100 g Mycobacterium tuberculosis (Mtb) cells and freeze dry by lyophilization.", "[Total lipid extraction] Determine the dry weight of the cells and transfer them to a 500 mL glass bottle.", "[Total lipid extraction] Delipidate cells by adding 10mL of 10:10:3 [vol/vol/v... |
11,434 | ROS staining | null | dx.doi.org/10.17504/protocols.io.peidjce | null | Magdalena Julkowska | TITLE: ROS staining
AUTHORS: Magdalena Julkowska
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol adapted from Shin et al., 2005 and Orman-Ligeza et al. 2016 (citing Shin)</div></div>
[STEPS]
?. [Transfer the seedlings from agar plates into nutrient solution containing DCF-DA (50 uM) for 30... | ["[Transfer the seedlings from agar plates into nutrient solution containing DCF-DA (50 uM) for 30 min. Preferably in darkness as DCF-DA is light sensitive]", "[wash with medium without DCF-DA and image fluorescence microscopy (460–500 nm bandpass excitation. Emission of 510– 560 nm bandpass]", "[wash with medium witho... |
93,770 | Preparation of Recording ACSF (artificial cerebrospinal fluid) for slice electrophysiology | 4 | dx.doi.org/10.17504/protocols.io.x54v9p4nmg3e/v1 | https://www.protocols.io/view/preparation-of-recording-acsf-artificial-cerebrosp-c7tiznke | Sarthak M. Singhal, thnasko | TITLE: Preparation of Recording ACSF (artificial cerebrospinal fluid) for slice electrophysiology
AUTHORS: Sarthak M. Singhal, thnasko
[DESCRIPTION]
Hnasko lab- preparation of Recording ACSF
Recording ACSF is used for incubating brain slices during cell-attached or whole-cell electrophysiological recordings of neurons... | ["Prepare 10X stock solution.", "Composition of 1 L of 10X Recording ACSF (in mM): 1250 NaCl, 25 KCl, 12 NaH2PO4, 125 d-glucose, 20 CaCl2 and 20 MgSO4.", "Composition of 1 L of 10X Recording ACSF (in g): 73.05 NaCl, 1.86 KCl, 1.44 NaH2PO4, 22.52 d-glucose, 2.94 CaCl2 and 4.93 MgSO4.", "Dissolve all salts in 1 L of ddH2... |
43,250 | V.3 - Direct wastewater RNA capture and purification via the "Sewage, Salt, Silica and SARS-CoV-2 (4S)" method | 4 | dx.doi.org/10.17504/protocols.io.bngsmbwe | https://www.protocols.io/view/v-3-direct-wastewater-rna-capture-and-purification-bngsmbwe | Oscar Whitney, Basem Al-Shayeb, Alex Crits-Cristoph, Mira Chaplin, Vinson Fan, Hannah Greenwald, Adrian Hinkle, Rose Kantor, Lauren Kennedy, Anna Maurer, Robert Tjian, Kara L. Nelson, UC Berkeley Wastewater-based epidemiology consortium | TITLE: V.3 - Direct wastewater RNA capture and purification via the "Sewage, Salt, Silica and SARS-CoV-2 (4S)" method
AUTHORS: Oscar Whitney, Basem Al-Shayeb, Alex Crits-Cristoph, Mira Chaplin, Vinson Fan, Hannah Greenwald, Adrian Hinkle, Rose Kantor, Lauren Kennedy, Anna Maurer, Robert Tjian, Kara L. Nelson, UC Berkel... | ["[Preparing RNA wash buffers]\nPrepareeach of two wash buffers - Wash buffer #1 (4S-WB1) and #2 (4S-WB2), for later use during cleanup of RNA bound to silica columns.\n1 L", "[Preparing RNA wash buffers]\n4S-WB1 composition: ABCD1ReagentOriginal molarity/%Final molarity/%Volume per liter of buffer2NaCl5 M1.5 M300 mL... |
null | null | null | dx.doi.org/10.17504/protocols.io.dmd425 | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
<strong>Materials:</strong> <br />- 10 place filter manifold<br /> - Towers (chilled overnight @ 4C) <br />- 5% (w/v) Trichloroacetic acid (TCA) (chilled overnight @ 4C) Usually 1L is enough for a single time series set <br />- 32 15ml centrifuge tubes <br />- Pump <br />- Scinti... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.p9ydr7w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div title="Page 4">
<div>
<div>
<p><span style="font-size: 9.000000pt; font-family: 'AdvHelv_R'; color: rgb(13.725000%, 12.157000%, 12.549000%);">Experimental set up for BONCAT coupled with fluorophore addition via copper (I)- catalysed azide-alkyne cycloaddition (i.e., click c... | [] |
97,460 | Drosophila melanogaster inoculation with Bd | 0 | dx.doi.org/10.17504/protocols.io.yxmvme7n6g3p/v1 | https://www.protocols.io/view/drosophila-melanogaster-inoculation-with-bd-dbeu2jew | Tatum S Katz, Alyssa Byer, Renwei Chen | TITLE: Drosophila melanogaster inoculation with Bd
AUTHORS: Tatum S Katz, Alyssa Byer, Renwei Chen
[DESCRIPTION]
Methods to inoculate D. melanogaster with Batrachochytrium dendrobatidis.
For manuscript Drosophila melanogaster is a possible vector of Batrachochytrium dendrobatidis under review at PLOS One.
[STEPS]
S... | ["[Protocol] Plate 0.5ml of treatment (10^6 zsps per fly or DI water) onto each agar plate", "Allow plates to dry so that no water is puddled on the surface", "Place 10 flies onto each plate", "Seal plates with parafilm and incubate at room temperature for 24 hours", "Transfer flies into fly vials (keeping all flies fr... |
61,519 | An optimized protocol for flow virometry (FVM)-based detection and enumeration of T4 bacteriophage | 1 | null | https://www.protocols.io/view/an-optimized-protocol-for-flow-virometry-fvm-based-b8bprsmn | Hannah Safford | TITLE: An optimized protocol for flow virometry (FVM)-based detection and enumeration of T4 bacteriophage
AUTHORS: Hannah Safford
[DESCRIPTION]
Flow virometry can support advanced water treatment and reuse by delivering near real-time information about viral water quality. Realizing the full potential of this techni... | ["[Preparation of purified, high-titer T4 stock] Propagate T4 and host from freeze-dried specimens.", "[Preparation of purified, high-titer T4 stock] Use propagated T4 and host to prepare purified, high-titer T4 stock for FVM.", "[Preparation of purified, high-titer T4 stock] Aliquot propagated specimens and store at -... |
96,343 | bHEV genotpying RT-PCR | 0 | null | https://www.protocols.io/view/bhev-genotpying-rt-pcr-dabx2apn | Siu Fung Ho | TITLE: bHEV genotpying RT-PCR
AUTHORS: Siu Fung Ho
[DESCRIPTION]
bHEV genotpying RT-PCR
[STEPS]
SECTION: Polyermase Chain Reaction
14. Setup mastermix in a 1.5 mL eppendorf tube. The following amounts are for a single reaction
Component Volume
2x Reaction Mix 25 µL
For... | ["[Polyermase Chain Reaction] Setup mastermix in a 1.5 mL eppendorf tube. The following amounts are for a single reaction\n\nComponent Volume\n2x Reaction Mix 25 µL \nForward Primer 10 μM 2 µL\nReverse Primer 10 μM 2 µL\nNuclease-free water 16 µL \nTotal ... |
27,394 | Loading Tn5 Enzyme with sci-protocol Oligonucleotides | 1 | dx.doi.org/10.17504/protocols.io.6zahf2e | https://www.protocols.io/view/loading-tn5-enzyme-with-sci-protocol-oligonucleoti-6zahf2e | Ryan Mulqueen, Andy Fields, Andrew Adey | TITLE: Loading Tn5 Enzyme with sci-protocol Oligonucleotides
AUTHORS: Ryan Mulqueen, Andy Fields, Andrew Adey
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Loading of Tn5 enzyme for sci-ATAC and s3 protocols.</div></div>
[STEPS]
?. [Prepare Reagents]
Prepare for protein dilution. ABCD1... | ["[Prepare Reagents]\nPrepare for protein dilution. ABCD1ReagentStock ConcentrationFinal ConcentrationAmount of Stock2HEPES-KOH (pH 7.2)1M100mM5mL3NaCl5M200mM2mL4Glycerol100%25%12.5mL5Triton-X100100%0.2%100uL6ddH2O30.4mL (to 50mL)7DTTDry2mM15.4 mg\n[2.125X Tn5 Dilution buffer]\nABCD1ReagentStock ConcentrationFinal ... |
47,004 | First-strand synthesis and touchdown PCR for SARS-CoV-2 | 3 | dx.doi.org/10.17504/protocols.io.br54m88w | https://www.protocols.io/view/first-strand-synthesis-and-touchdown-pcr-for-sars-br54m88w | Leonardo Caserta | TITLE: First-strand synthesis and touchdown PCR for SARS-CoV-2
AUTHORS: Leonardo Caserta
[STEPS] | [] |
50,944 | Human endometrium and endometriosis tissue dissociation for single-cell RNA sequencing | 4 | dx.doi.org/10.17504/protocols.io.bvy8n7zw | https://www.protocols.io/view/human-endometrium-and-endometriosis-tissue-dissoci-bvy8n7zw | Yuliana Tan, Diane Luo, Suleyman Bozal, Paul Robson, Elise Courtois | TITLE: Human endometrium and endometriosis tissue dissociation for single-cell RNA sequencing
AUTHORS: Yuliana Tan, Diane Luo, Suleyman Bozal, Paul Robson, Elise Courtois
[DESCRIPTION]
Tissue dissociation is critical step to ensure the quality of samples for single-cell RNA sequencing. To ensure recovery of most cells... | ["[Buffer and Enzymes Preparation] Prepare fresh digestion enzyme - Cold Active Protease (CAP) solution:", "[Viable Cell Sorting] Stain cells with viability dye (Propidium Iodide and Calcein Violet) following manufacturer's protocol, incubate 20 min.", "[Tissue Digestion with CAP] Mince the tissue to 1 mm2 cube with st... |
51,860 | Orange peel | Chitosan | Hemp | 1 | null | https://www.protocols.io/view/orange-peel-chitosan-hemp-bwvupe6w | Jil A Berenblum Phoenix Lai Esther Chang Anna Lu | TITLE: Orange peel | Chitosan | Hemp
AUTHORS: Jil A Berenblum Phoenix Lai Esther Chang Anna Lu
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Orange peel | Chitosan | Hemp</span></div></div>
[STEPS]
?. Remove the peel from an orange(we used Citrus Sinensis N... | ["Remove the peel from an orange(we used Citrus Sinensis Navel Oranges from Florida). While the peel is still fresh, blend it into small granules. The size of the granules can affect the characteristics of the end material.", "In a bowl, combine the Hemp Protein Powder , Gluten , and granulated Orange Peel Mix the in... |
17,598 | DNA extraction from avian faeces stored in ethanol | 1 | dx.doi.org/10.17504/protocols.io.ve6e3he | https://www.protocols.io/view/dna-extraction-from-avian-faeces-stored-in-ethanol-ve6e3he | James Nicholls | TITLE: DNA extraction from avian faeces stored in ethanol
AUTHORS: James Nicholls
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">DNA extraction from blue tit (Cyanistes caeruleus) faeces stored in ethanol.</span></div><div class = "text-block"><span>Methodology use... | ["Remove ~100-200 mg of blue tit faeces (typically 2-3 small fragments of faeces, each ~5 mm long) from storage tube, allow ethanol to evaporate off, and then place into a 2 mL round-bottomed centrifuge tube (Eppendorf 2 mL SafeLock tubes are good). Avoid using faeces that has lots of uric acid on it, or scrape off ur... |
null | null | null | dx.doi.org/10.17504/protocols.io.efrbbm6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol provides a method to predict phage community diversity using the algorithm PHACCS. Sequencing of viral communities often results in a high percent of unknown reads, largely due to our incomplete reference databases. To address this unknown factor of viromes, the al... | [] |
92,680 | FAST.R Installation and Launch with RStudio | 4 | dx.doi.org/10.17504/protocols.io.kxygx3464g8j/v1 | https://www.protocols.io/view/fast-r-installation-and-launch-with-rstudio-c6rgzd3w | Francesco Neri | TITLE: FAST.R Installation and Launch with RStudio
AUTHORS: Francesco Neri
[DESCRIPTION]
Step -by-step protocol to setup the R shiny application FAST.R for data analysis and visualization of FAST-generated data. This protocol is meant to be used within the FAST workflow
[STEPS]
SECTION: Install FAST.R with RStudio
1.... | ["[Install FAST.R with RStudio] If familiar with R and RStudio, see the FAST.R package page for installation and use.\n\nIf NOT familiar with R and RStudio, read instructions below", "[Install FAST.R with RStudio] Install FAST-R", "[Install FAST.R with RStudio] Download and install R and RStudio\nDownload from here. No... |
24,457 | Transformation of the chlorarachniophyte Amorphochlora amoebiformis by electroporation | null | dx.doi.org/10.17504/protocols.io.35hgq36 | null | Kodai Fukuba, Liz Cooney, Nick Irwin, Patrick J. Keeling, Yoshihisa Hirakawa | TITLE: Transformation of the chlorarachniophyte Amorphochlora amoebiformis by electroporation
AUTHORS: Kodai Fukuba, Liz Cooney, Nick Irwin, Patrick J. Keeling, Yoshihisa Hirakawa
[STEPS]
?. [Plasmid preparation]
Propagate plasmid DNA (pLaRGfp or its derivatives, such as pLaR182+GFP) in the Escherichia coli strain DH5... | ["[Plasmid preparation]\nPropagate plasmid DNA (pLaRGfp or its derivatives, such as pLaR182+GFP) in the Escherichia coli strain DH5α.", "[Plasmid preparation]\nPurify plasmid DNA from 200 mL culture of E. coli by a Qiagen Plasmid Maxi Kit (Qiagen).", "[Plasmid preparation]\nAdjust plasmid DNA concentration to 3-5 µg/µL... |
18,598 | FCA general dissociation protocol | null | dx.doi.org/10.17504/protocols.io.weefbbe | null | JONGEUN PARK | TITLE: FCA general dissociation protocol
AUTHORS: JONGEUN PARK
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is the protocol used for FCA_ImmunoP project</div></div>
[STEPS] | [] |
13,469 | RAD barcodes | 3 | null | https://www.protocols.io/view/rad-barcodes-rd5d286 | Tomasz Suchan | TITLE: RAD barcodes
AUTHORS: Tomasz Suchan
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">File listing 96 barcodes on SbfI-compatible P1 adapters we use for RAD-seq libraries.</div></div>
[STEPS] | [] |
33,575 | Plant and fungal DNA extraction using a QIAGEN QIAxtractor | null | dx.doi.org/10.17504/protocols.io.bc2fiybn | null | Laura Forrest, Michelle Hart, Alexandra Clark | TITLE: Plant and fungal DNA extraction using a QIAGEN QIAxtractor
AUTHORS: Laura Forrest, Michelle Hart, Alexandra Clark
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Here we describe a semi-robotic plate DNA extraction method that we have used at the Royal Botanic Garden Edinburgh (RBGE) to proce... | ["Lysis pre-treatment: in a trough mix 4 μl DX enzyme (kept at 4° C in the fridge) and 416 μl Tissue Digest (DXT) per sample (master mix 40.4 ml DXT and 392 μl DX enzyme per 96-sample plate); if extracting from fresh tissue rather than silica-dried or herbarium samples, substitute 4 μl DXT with 4 μl RNase A.", "Separat... |
69,719 | Multiplex fluorescent immunostaining of thin, fixed mouse brain tissue sections to characterize human iPSC-derived cell xenografts | 1 | dx.doi.org/10.17504/protocols.io.4r3l275mxg1y/v1 | https://www.protocols.io/view/multiplex-fluorescent-immunostaining-of-thin-fixed-cgbxtspn | Benjamin Trist, Louise Cottle | TITLE: Multiplex fluorescent immunostaining of thin, fixed mouse brain tissue sections to characterize human iPSC-derived cell xenografts
AUTHORS: Benjamin Trist, Louise Cottle
[DESCRIPTION]
This protocol describes our multiplex fluorescent immunohistochemistry protocol used to identify human iPSC-derived cells within... | ["[Day 1 (~3-4 hrs)] Pre-heat oven and Antigen Retrieval (AR) buffer to 70 °C.", "[Day 1 (~3-4 hrs)] Label scintillation vials to match labels on section storage plates (mouse and section series IDs, name, date etc.).", "[Day 1 (~3-4 hrs)] Transfer sections into scintillation vials using a transfer pipette or fine pain... |
58,649 | Processing of Radial K-space DW-MRI Data | 1 | dx.doi.org/10.17504/protocols.io.j8nlkkwj1l5r/v1 | https://www.protocols.io/view/processing-of-radial-k-space-dw-mri-data-b5hzq376 | Miguelrj , Hee Kwon Song, Stephen Pickup, Mamtaaryagupta , Rong Zhou | TITLE: Processing of Radial K-space DW-MRI Data
AUTHORS: Miguelrj , Hee Kwon Song, Stephen Pickup, Mamtaaryagupta , Rong Zhou
[DESCRIPTION]
The protocol includes reconstruction of diffusion weighted images from radial k-space data and using a 3-parameter fit to derive metrics of ADC and kurtosis index.
[STEPS]
1... | ["Image reconstruction\n\nRadially acquired diffusion-weighted images (DWIs) are reconstructed using the following steps:\n\nApply zero-order phase correction to each radial spoke using the average phase offset at the center slice of the lowest b-value image\nZerofill k-space by a factor of 2 to double field of view\nM... |
68,823 | RNA sequencing analysis of transcriptomic responses to vagal nerve stimulation in myenteric ganglia of porcine colon | 1 | dx.doi.org/10.17504/protocols.io.eq2lynmeqvx9/v1 | https://www.protocols.io/view/rna-sequencing-analysis-of-transcriptomic-response-cffxtjpn | Tao Li, Pu-Qing Yuan | TITLE: RNA sequencing analysis of transcriptomic responses to vagal nerve stimulation in myenteric ganglia of porcine colon
AUTHORS: Tao Li, Pu-Qing Yuan
[DESCRIPTION]
The region-dependent molecular characterization and influences by vagus nerve stimulation (VNS) influences in the porcine ENS has been little investiga... | ["Six castrated male Yucatan minipigs (3 of each controls and 3 with VNS) were fasted for 12 h and anaesthetized. Those with VNS underwent electrical stimulation of the celiac branch of the abdominal vagus nerve (2 Hz, 0.3-4 ms, 5 mA, 10 min) using pulse train.", "The proximal and distal colonic (pC, dC) pecimens with ... |
54,149 | Ligation and gel electrophoresis | 4 | dx.doi.org/10.17504/protocols.io.by5dpy26 | https://www.protocols.io/view/ligation-and-gel-electrophoresis-by5dpy26 | Chia-Hsien Shih | TITLE: Ligation and gel electrophoresis
AUTHORS: Chia-Hsien Shih
[DESCRIPTION]
This protocol is used for ligation of circular probe
[STEPS]
SECTION: Preparation
1. Dilute linear DNA into 10µM
SECTION: Preparation
2. Dilute T4 ligation primer into 10µM
SECTION: Protocol of Ligation
3. Add 11 µL of RNase-free water i... | ["[Preparation] Dilute linear DNA into 10µM", "[Preparation] Dilute T4 ligation primer into 10µM", "[Protocol of Ligation] Add 11 µL of RNase-free water into a eppendorf", "[Protocol of Ligation] Add 3 µL of 10X T4 Ligase buffer", "[Protocol of Ligation] Add 9 µL of 10µM T4 ligation primer", "[Protocol of Ligation] Add... |
84,050 | Cortical, Striatal and Dopaminergic Neurons Cultures Protocol | 1 | dx.doi.org/10.17504/protocols.io.rm7vzxn48gx1/v1 | https://www.protocols.click/view/cortical-striatal-and-dopaminergic-neurons-culture-cwbsxane | giulia.tombesi | TITLE: Cortical, Striatal and Dopaminergic Neurons Cultures Protocol
AUTHORS: giulia.tombesi
[DESCRIPTION]
This protocol describes how to obtain primary neuronal cultures from postnatal mice (P0-P1). It can be used to obtain pure cortical neurons cultures or stratal-cortical neurons and dopaminergic-cortical neurons c... | ["[Cells Dissociation] Snip the tissues into smaller pieces and place them in Papain solution. Use around 500 µL of Papain solution for 5 SN, around 1 mL of Papain solution for 5 striata and around 5 mL of Papain solution for 5-6 cortices.", "[Cells Dissociation] Triturate 10 times with a 5ml-pipette", "[Cells Dissocia... |
null | null | null | dx.doi.org/10.17504/protocols.io.t5teq6n | null | null | TITLE: No Title
AUTHORS:
[STEPS] | [] |
87,084 | Post-diagnosis dietary patterns among cancer survivors in relation to all-cause mortality and cancer-specific mortality: a systematic review and meta-analysis of cohort studies | 1 | dx.doi.org/10.17504/protocols.io.yxmvm3en5l3p/v1 | https://www.protocols.io/view/post-diagnosis-dietary-patterns-among-cancer-survi-czakx2cw | Maria-Eleni Spei, Ioannis Bellos, esamoli, Vassiliki Benetou | TITLE: Post-diagnosis dietary patterns among cancer survivors in relation to all-cause mortality and cancer-specific mortality: a systematic review and meta-analysis of cohort studies
AUTHORS: Maria-Eleni Spei, Ioannis Bellos, esamoli, Vassiliki Benetou
[DESCRIPTION]
This study aims to synthesize the latest evidence r... | ["Objective: To synthesize the latest evidence regarding the association of a priori and\na posteriori dietary patterns with robust outcome measures, such as total mortality and cancer-specific mortality.", "Eligibility criteria: Studies will be eligible to be included if: (i) they have a cohort design, prospective\nor... |
45,982 | C-SOP-401: Quality Control (QC) of DNA Libraries for Whole Genome Sequencing | 4 | null | https://www.protocols.io/view/c-sop-401-quality-control-qc-of-dna-libraries-for-bq56my9e | Mihir Kekre | TITLE: C-SOP-401: Quality Control (QC) of DNA Libraries for Whole Genome Sequencing
AUTHORS: Mihir Kekre
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:left">The success of fragmentation and size selection is best confirmed using an electrophoretic instrum... | ["[Before Starting]\nPrior to initiating the protocol, ensure that all active workbenches are cleaned with 80% ethanol, all relevant personal protective clothing is worn and the work area is prepared according to local GLP guidelines for molecular methods.Create an organised bench space by clearing away all clutter in ... |
null | null | null | dx.doi.org/10.17504/protocols.io.k92cz8e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><strong>Intended use:</strong></p>
<p>Kinetic system for Aspartate Aminotransferase (AST) or Glutamic oxalacetic trasminase (GOT) determination.</p>
<p><strong>Teste Principle:</strong></p>
<p><strong>AST</strong> catalyzes specifically the transfer of amino groups of asparc... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.njbdcin | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><strong>Objective </strong></p>
<p>To provide an in-depth and comprehensive overview of tick-borne rickettsioses among humans, livestock, wild animals and arthropods in Iran, a systematic review and meta-analysis will be performed. This review will capture the existing data r... | [] |
69,136 | Wet Chemistry RNA Isolation Method for Mature Cassava Leaf Tissue | 1 | null | https://www.protocols.io/view/wet-chemistry-rna-isolation-method-for-mature-cass-cfrqtm5w | Lynn Doran | TITLE: Wet Chemistry RNA Isolation Method for Mature Cassava Leaf Tissue
AUTHORS: Lynn Doran
[DESCRIPTION]
RNA extraction protocol for cassava for RNA of sufficient quality and quantity to perform RT-PCR gene expression studies.
*Low recovery was achieved using Qiagen RNeasy kit. Typical recoveries using the mini... | [] |
46,604 | Genotyping of polymorphisms rs1801133 in MTHFR, rs1051266 in SLC19A1 and rs1805087 in MTR | 1 | dx.doi.org/10.17504/protocols.io.brrkm54w | https://www.protocols.io/view/genotyping-of-polymorphisms-rs1801133-in-mthfr-rs1-brrkm54w | Nayane Soares de Lima, Caroline Christine Pincela da Costa , Rômulo Morais Azevedo, Angela Adamski Reis, Rodrigo da Silva Santos | TITLE: Genotyping of polymorphisms rs1801133 in MTHFR, rs1051266 in SLC19A1 and rs1805087 in MTR
AUTHORS: Nayane Soares de Lima, Caroline Christine Pincela da Costa , Rômulo Morais Azevedo, Angela Adamski Reis, Rodrigo da Silva Santos
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div clas... | ["[DNA extraction]\n.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\tThe DNA samples were extracted from peripheral blood and submitted to DNA purification using the commercial extraction kit, following the prot... |
50,301 | Study Medications (Part 5 of Safety and Efficacy of Imatinib for Preserving Beta-Cell Function in New-onset Type 1 Diabetes Mellitus) | 1 | dx.doi.org/10.17504/protocols.io.bvc5n2y6 | https://www.protocols.io/view/study-medications-part-5-of-safety-and-efficacy-of-bvc5n2y6 | Stephen.Gitelman , Jeffrey A. Bluestone | TITLE: Study Medications (Part 5 of Safety and Efficacy of Imatinib for Preserving Beta-Cell Function in New-onset Type 1 Diabetes Mellitus)
AUTHORS: Stephen.Gitelman , Jeffrey A. Bluestone
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is Part 5 of "Safety and Efficacy of Imatinib for Preserv... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.gwubxew | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Protocol for cell separation, enumeration, and sorting of low biomass samples for SIP-NanoSIMS preparations. </p>
[BEFORE_START]
<ol>
<li>Clean 12 spoons
<ol>
<li>soaked in bleach ~15min, then rinse with 0.2um MQ, then Sonicate 15 min, then rinse, then bring water cup with s... | [] |
45,426 | Modified pH drop protocol (K+) | 4 | null | https://www.protocols.io/view/modified-ph-drop-protocol-k-bqksmuwe | Elizabeth Fozo | TITLE: Modified pH drop protocol (K+)
AUTHORS: Elizabeth Fozo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Modified pH drop protocol (K</span><span style = "vertical-align:super;">+</span><span style = "vertical-align:super;">)</span></div></div>
[STEPS]
?. [To prepare the K+ electrode for... | ["[To prepare the K+ electrode for use:]\nRemove the rubber caps.", "[Do slope check for electrode performance:]", "[Standard curve:]\n0mM (no K+) = 9mL water + 1mL 1M NaCl", "[Modified pH drop protocol:]\nRead pH & mV readings atdesired intervals.", "[To prepare the K+ electrode for use:]\nFill with 0.1M NaCl filling ... |
82,336 | shRNA plasmids | 3 | dx.doi.org/10.17504/protocols.io.yxmvm288bg3p/v1 | https://www.protocols.io/view/shrna-plasmids-cum8wu9w | Shiyi Wang | TITLE: shRNA plasmids
AUTHORS: Shiyi Wang
[DESCRIPTION]
How to make shRNA plasmids
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.cpvvn5 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Basic Protocol for culturing Neuro2a cells.
[GUIDELINES]
<strong>The following are taken directly from the vendor website, I use high glucose DMEM instead of Eagle's MEM. </strong><br /><br /><strong>Complete Growth Medium</strong> The base medium for this cell line is ATCC-for... | [] |
58,212 | Gallyas-silver stain | 4 | dx.doi.org/10.17504/protocols.io.b44cqysw | https://www.protocols.io/view/gallyas-silver-stain-b44cqysw | Christiana.bjorkli , María José Lagartos Donate | TITLE: Gallyas-silver stain
AUTHORS: Christiana.bjorkli , María José Lagartos Donate
[DESCRIPTION]
Simplified Gallyas-silver staining protocol that works for pathological staining in rodent and human tissue
[STEPS]
SECTION: Solutions that can be made in advance and stored in a fume hood
2.
SECTION: Solutions that ... | ["[Solutions that can be made in advance and stored in a fume hood]", "[Solutions that can be made in advance and stored in a fume hood] Make 4% of NaOH (sodium hydroxide) - use gloves, store in fume hood", "[Solutions that can be made in advance and stored in a fume hood]", "[Solutions that can be made in advance and ... |
36,053 | HuBMAP UF TMC - Single Cell RNA Seq (10x Genomics) Library Preparation and Sequencing | null | dx.doi.org/10.17504/protocols.io.bffvjjn6 | https://www.protocols.io/view/hubmap-uf-tmc-single-cell-rna-seq-10x-genomics-lib-bffvjjn6 | Franchesca Farris, Maigan Brusko | TITLE: HuBMAP UF TMC - Single Cell RNA Seq (10x Genomics) Library Preparation and Sequencing
AUTHORS: Franchesca Farris, Maigan Brusko
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is for the generation of 3' (chemistry version 3) cDNA libraries from individual cells via droplet gen... | ["[GEM Generation & Barcoding]\nPreparation of Single Cell Master Mix: a. Prepare Master Mix on ice. Pipette mix 15x and centrifuge briefly. b. Add 33.4 µl Master Mix into each tube of a PCR 8-tube strip on ice.", "[GEM Generation & Barcoding]\nLoad Chromium Chip B: a. Assemble Chromium Chip B in a 10x Chip H... |
null | null | null | dx.doi.org/10.17504/protocols.io.etpbemn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This tutorial was based off of the paper The microbes we eat: abundance and taxonomy of microbes consumed in a day's worth of meals for three diet types. <span style="font-weight: 400;">The article provides those interested in bioinformatics, food science, or microbiology inform... | [] |
97,509 | CODA (part 3): deep learning tissue structures labeling | HuBMAP | JHU-TMC | 0 | dx.doi.org/10.17504/protocols.io.81wgbz1x3gpk/v1 | https://www.protocols.io/view/coda-part-3-deep-learning-tissue-structures-labeli-dbgd2js6 | Kyu Sang Han, Pei-Hsun Wu, Joel Sunshine, Ashley Kiemen, Sashank Reddy, Denis Wirtz | TITLE: CODA (part 3): deep learning tissue structures labeling | HuBMAP | JHU-TMC
AUTHORS: Kyu Sang Han, Pei-Hsun Wu, Joel Sunshine, Ashley Kiemen, Sashank Reddy, Denis Wirtz
[DESCRIPTION]
In this section, we describe steps to create a basic semantic segmentation algorithm using CODA. CODA uses a modified resnet50 net... | ["[Deep learning multi-labelling of tissue structures using training on manual annotations] Choose the biological structures you wish to segment in your images. Semantic segmentation algorithms must classify every pixel of every image with a label, so your list must be exhaustive. For example, in lung histology you cou... |
68,786 | ES cells general methods | 4 | dx.doi.org/10.17504/protocols.io.e6nvwkxz9vmk/v1 | https://www.protocols.io/view/es-cells-general-methods-cfestjee | Rebecca Berrens | TITLE: ES cells general methods
AUTHORS: Rebecca Berrens
[DESCRIPTION]
general methods for mouse ES cell culturing
[BEFORE_START]
All media should be warmed up to37 °C in a water-bath before use.
Spray all the bottles (except new culture flasks or tubes) before putting into the hood.
[STEPS]
SECTION: Reactivating ce... | ["[Reactivating cells from liquid nitrogen stock] Spray a tube with 70% EtOH and wipe off. Transfer all thawed cells (~1ml) into the 15ml Falcon tube.", "[Reactivating cells from liquid nitrogen stock] Drop by drop, and swirl from time to time, add 9ml ES complete medium or EC10 medium. Final volume of cells is 10ml. (... |
82,571 | Immunohistochemistry for FOXP3+ staining in Breast Cancer Tissue | 6 | dx.doi.org/10.17504/protocols.io.eq2ly7m6elx9/v1 | https://www.protocols.click/view/immunohistochemistry-for-foxp3-staining-in-breast-cuvjww4n | Freda Halim | TITLE: Immunohistochemistry for FOXP3+ staining in Breast Cancer Tissue
AUTHORS: Freda Halim
[DESCRIPTION]
These are protocols used for study of FOXP3+ Cell Count in Luminal B Her-2 negative BC patients. We used using paraffin sections of 66 samples and stained the slides for FOXP3+ antibody, using primary antibody cl... | ["[Deparaffinization and Rehydration] Incubate slides in Xylenes for 3 minutes", "[Deparaffinization and Rehydration] Incubate slides in Xylenes", "[Deparaffinization and Rehydration] Incubate slides in Xylenes", "[Deparaffinization and Rehydration] Rehydrate slides in 100% Ethanol", "[Deparaffinization and Rehydration... |
33,146 | LCMS-SOP Determination of Microcystins in Water Samples by High Performance Liquid Chromatography (HPLC) with Single Quadrupole Mass Spectrometry (MS) | 3 | dx.doi.org/10.17504/protocols.io.bck2iuye | https://www.protocols.io/view/lcms-sop-determination-of-microcystins-in-water-sa-bck2iuye | Gregory L Boyer | TITLE: LCMS-SOP Determination of Microcystins in Water Samples by High Performance Liquid Chromatography (HPLC) with Single Quadrupole Mass Spectrometry (MS)
AUTHORS: Gregory L Boyer
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This standard operating procedure is used to determine and quantify m... | [] |
58,949 | Overall protocol for top-down CZE-MS/MS of human small intestine tissue | 1 | dx.doi.org/10.17504/protocols.io.b5tdq6i6 | https://www.protocols.io/view/overall-protocol-for-top-down-cze-ms-ms-of-human-s-b5tdq6i6 | Jeannie Camarillo, Bryon Drown, Neil Kelleher | TITLE: Overall protocol for top-down CZE-MS/MS of human small intestine tissue
AUTHORS: Jeannie Camarillo, Bryon Drown, Neil Kelleher
[DESCRIPTION]
Overview description of the process for acquiring top-down capillary zone electrophoresis MS/MS data on human small intestine tissue
[STEPS]
SECTION: Tissue Collection... | ["[Tissue Collection] Small intestine tissue was provided by Stanford University TMC. Tissue was collected according to the following: \n\nhttps://dx.doi.org/10.17504/protocols.io.bin8kdhw", "[Sample Preparation]", "[Data Acquisition]", "[Data Analysis]"] |
78,515 | Carbon nanotube (CNT) yarn fabrication for chronic interfacing with the autonomic nervous system | 1 | dx.doi.org/10.17504/protocols.io.n2bvj8enpgk5/v1 | https://www.protocols.io/view/carbon-nanotube-cnt-yarn-fabrication-for-chronic-i-cqwtvxen | Grant Mccallum, Xiaohong Sui, Chen Qiu, Joseph Marmerstein, Yang Zheng, Thomas Eggers, Chuangang Hu, Liming Dai, Dominique Durand | TITLE: Carbon nanotube (CNT) yarn fabrication for chronic interfacing with the autonomic nervous system
AUTHORS: Grant Mccallum, Xiaohong Sui, Chen Qiu, Joseph Marmerstein, Yang Zheng, Thomas Eggers, Chuangang Hu, Liming Dai, Dominique Durand
[DESCRIPTION]
The ability to reliably and safely communicate chronically wit... | ["[Carbon nanotube (CNT) yarn fabrication] VA-MWCNT arrays (with MWCNTs of ca.250 μm in length andca.30 nm in diameter) (Fig. 1a), were first synthesized on Fe/Al-coated Si/SiO2 wafers using a low pressure chemical vapor deposition (CVD) method according to our previously reported procedure52.", "[Carbon nanotube (CNT)... |
25,006 | NEBNext® Ultra™ II End Repair/dA-Tailing Module (NEB #E7546) | null | dx.doi.org/10.17504/protocols.io.4nngvde | null | Menna Teffera, New England Biolabs | TITLE: NEBNext® Ultra™ II End Repair/dA-Tailing Module (NEB #E7546)
AUTHORS: Menna Teffera, New England Biolabs
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The NEBNext Ultra II End Repair/dA-Tailing Module is optimized to convert 500 pg-1 μg of fragmented DNA to repaired DNA having 5 ́ phosphor... | ["[NEBNext End Prep]\nMix the following contents in a sterile nuclease-free tube: AB1ComponentVolume2(green) NEBNext Ultra II End Prep Enzyme Mix3 µl3(green) NEBNext Ultra II End Prep Reaction Buffer7 µl4Fragmented DNA50 µl5Total Volume60 µl\nAB1ComponentVolume2(green) NEBNext Ultra II End Prep Enzyme Mix3 µl3(green) ... |
null | null | null | dx.doi.org/10.17504/protocols.io.chut6v | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?. | [] |
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