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 |
|---|---|---|---|---|---|---|---|
null | null | null | dx.doi.org/10.17504/protocols.io.hgsb3we | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Contact Dr. Steven Wilhelm (wilhelm@utk.edu) or Josh Stough (<a target="_blank"><span title="jstough@vols.utk.edu">jstough@vols.utk.edu</span></a>) for additional information regarding this protocol.</p>
[BEFORE_START]
<p>You will need:</p>
<p>Assembled sequencing dataset--t... | [] |
67,385 | Is It Safe To Use Fluxactive Complete Canada? | 1 | dx.doi.org/10.17504/protocols.io.dm6gpbn41lzp/v1 | https://www.protocols.io/view/is-it-safe-to-use-fluxactive-complete-canada-cd2zs8f6 | dfskoqia | TITLE: Is It Safe To Use Fluxactive Complete Canada?
AUTHORS: dfskoqia
[DESCRIPTION]
Product Name - Fluxactive Complete
Ingredients - Chinese Ginseng, Ginkgo Biloba
Health Benefits - The supplement promotes better prostate health
Side Effects - No serious side effects have been reported by users so far
Dosage -2 Cap... | [] |
42,160 | MAIT Cell Expansion in Donor Mice | 4 | dx.doi.org/10.17504/protocols.io.bmeqk3dw | https://www.protocols.io/view/mait-cell-expansion-in-donor-mice-bmeqk3dw | Timothy S C Hinks, Bonnie van Wilgenburg, Huimeng Wang, Liyen Loh, Marios Koutsakos, Katherine Kedzierska, Alexandra J. Corbett, Zhenjun Chen | TITLE: MAIT Cell Expansion in Donor Mice
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 3.1 of the "Study of MAIT Cell Activation in Vi... | ["Two days before infection streak out a plate of S. Typhimurium BRD509 (an attenuated vaccine strain [14]) on LB agar plates, containing and incubate plates at .\n[streptomycin]\n37 °C", "The day before infection, pick a single colony under flame and inoculate to with and leave static at (double contained if work... |
43,523 | Isolation and Phenotyping of Adult Mouse Microglial Cells | 1 | dx.doi.org/10.17504/protocols.io.bnrbmd2n | https://www.protocols.io/view/isolation-and-phenotyping-of-adult-mouse-microglia-bnrbmd2n | Kathleen Grabert, Barry W. McColl | TITLE: Isolation and Phenotyping of Adult Mouse Microglial Cells
AUTHORS: Kathleen Grabert, Barry W. McColl
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Microglia are the resident macrophages of the central nervous system parenchyma and fulfill crucial roles in brain development, homeostasis, and... | ["[Perfusion and Isolation of Mouse Brain]\nPerfuse animals transcardially with physiological saline (10 mL/min) until exudate runs clear (see Note 2).", "[Perfusion and Isolation of Mouse Brain]\nRemove brain and transfer into 50 mL Falcon tube containing either as whole brain, hemisphere, or brain region.\n[HBSS]", ... |
22,541 | 02: Parsing FASTA files | null | dx.doi.org/10.17504/protocols.io.z9mf946 | null | Frank Aylward | TITLE: 02: Parsing FASTA files
AUTHORS: Frank Aylward
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Week 1</div><div class = "text-block">Introduction to parsing FASTA files.</div><div class = "text-block">Commands to be entered into the command line are in bold. </div><div class = "text-block">He... | ["Today we will be looking at the genome of Yersinia pestis, which can be found on NCBI at this locationftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/009/065/GCA_000009065.1_ASM906v1Copy this URL into your browser and take a look at the files. These are publicly-available files that are made available from the Nationa... |
38,628 | Protocol of a systematic review with network meta-analysis: Chronic effects of physical exercise on blood pressure responsiveness to non-cardiopulmonary stress tests | 1 | dx.doi.org/10.17504/protocols.io.bhycj7sw | https://www.protocols.io/view/protocol-of-a-systematic-review-with-network-meta-bhycj7sw | Igor Mariano, Ana Luiza Amaral, Guilherme Morais Puga | TITLE: Protocol of a systematic review with network meta-analysis: Chronic effects of physical exercise on blood pressure responsiveness to non-cardiopulmonary stress tests
AUTHORS: Igor Mariano, Ana Luiza Amaral, Guilherme Morais Puga
[DESCRIPTION]
Laboratory stress tests can help compose the clinical profile... | ["[Background] Background \n\n Laboratory stress tests can help compose the clinical profile of individuals and predict, among others, the development of future cardiovascular events and depression [1]. These tests work by disturbing the individual's homeostasis in a controlled way to assess the body's responses t... |
99,785 | Library transfection | 0 | dx.doi.org/10.17504/protocols.io.dm6gpzjj1lzp/v1 | https://www.protocols.io/view/library-transfection-ddph25j6 | Raining Wang, Melinda Wheelock | TITLE: Library transfection
AUTHORS: Raining Wang, Melinda Wheelock
[DESCRIPTION]
This protocol details the transfection in 6-well plates.
[BEFORE_START]
Be sure that the HEK293T-LLP-iCasp9-blast cell line (Matreyek et al 2020) expresses BFP at a level of at least 98% before beginning a transfection (see Purity Sorti... | ["[Day -2] Two days before the planned transfection, passage HEK293T-LLP-iCasp9-blast culture and seed 2 T-175 flasks (more or less, depending on the number of cells needed).", "[Day 0] In the morning (or night before), lift and plate cells at 50% confluence in 4 6-well plates. Let the plates sit in the BSC for 30 min ... |
50,836 | Protocol-RNA-ISH | 1 | dx.doi.org/10.17504/protocols.io.bvvun66w | https://www.protocols.io/view/protocol-rna-ish-bvvun66w | Klaus Hirschbühl (Hematology and Oncology Medical Faculty University of Augsburg Augsburg Germany) | TITLE: Protocol-RNA-ISH
AUTHORS: Klaus Hirschbühl (Hematology and Oncology Medical Faculty University of Augsburg Augsburg Germany)
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:center">Protocol-RNA-ISH to the paper:</div></div><div class = "text-block"><... | [] |
71,517 | Demultiplexing Nanopore reads with LAST | 1 | dx.doi.org/10.17504/protocols.io.14egnxw4zl5d/v8 | https://www.protocols.io/view/demultiplexing-nanopore-reads-with-last-ch35t8q6 | David A Eccles | TITLE: Demultiplexing Nanopore reads with LAST
AUTHORS: David A Eccles
[DESCRIPTION]
This protocol is for a semi-manual method for read demultiplexing, as used after my presentation Sequencing DNA with Linux Cores and Nanopores to work out the number of reads captured by different barcodes.
This approach has now been... | ["[Combine read sequences] Combine all input reads into a single file\n\n \nNote: I'm using the pipe viewer command pv to produce a progress indicator while the command is running. If this command is not available, it can be replaced with cat with no change in function (apart from not showing progess).", "[Generating B... |
94,341 | SOP for BCA protein assay and western immunoblotting | 4 | dx.doi.org/10.17504/protocols.io.3byl4q4yovo5/v1 | https://www.protocols.io/view/sop-for-bca-protein-assay-and-western-immunoblotti-c8ddzs26 | Malu G Tansey | TITLE: SOP for BCA protein assay and western immunoblotting
AUTHORS: Malu G Tansey
[DESCRIPTION]
SOP for BCA protein assay and western immunoblotting
[STEPS]
SECTION: SDS-PAGE
3. Place gel cassette into tank and fill chamber to the fill line with running buffer. Fill cassette’s reservoir too.
SECTION: SDS-PAGE
4. Dis... | ["[SDS-PAGE] Place gel cassette into tank and fill chamber to the fill line with running buffer. Fill cassette’s reservoir too.", "[SDS-PAGE] Dislodge any bubbles in wells by triturating in well with a micropipette.", "[SDS-PAGE] Load appropriate volumes of samples and ladders. Load 4uL of ladder into the first well an... |
40,571 | Vezina Lab Mouse Castration Protocol | 1 | null | https://www.protocols.io/view/vezina-lab-mouse-castration-protocol-bju3knyn | Chad Vezina | TITLE: Vezina Lab Mouse Castration Protocol
AUTHORS: Chad Vezina
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Vezina Lab Mouse Castration Protocol 3/15/2010</div></div>
[STEPS]
?. [2 weeks prior to experiment]
Contact RARC (animal resource center) and reserve Isoflurane vaporizer and glass bead ... | ["[2 weeks prior to experiment]\nContact RARC (animal resource center) and reserve Isoflurane vaporizer and glass bead sterilizer.", "[2 days prior to experiment]\nCollect the following supplies and ensure that isofluorane and buprenorphine are in date: Betadine scrub, 32 oz (*RARC pharmacy)Surgical drape, non-sterile,... |
44,311 | Crosslinking of Cultured Cells | 4 | dx.doi.org/10.17504/protocols.io.bphxmj7n | https://www.protocols.io/view/crosslinking-of-cultured-cells-bphxmj7n | Eric L. Van Nostrand, Thai B. Nguyen, Chelsea Gelboin-Burkhart, Ruth Wang, Steven M. Blue, Gabriel A. Pratt, Ashley L. Louie, Gene W. Yeo | TITLE: Crosslinking of Cultured Cells
AUTHORS: Eric L. Van Nostrand, Thai B. Nguyen, Chelsea Gelboin-Burkhart, Ruth Wang, Steven M. Blue, Gabriel A. Pratt, Ashley L. Louie, Gene W. Yeo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Profiling of RNA binding protein targets in vivo provides critical ... | ["[Preparation of Cultured Cells for Crosslinking]\nAspirate the spent media and wash the plate with 1× DPBS (~ for a 15 cm plate) at . For suspension cells, pellet cells to remove spent media, and wash once with 1× DPBS.\n15 mL\n0 Room temperature", "[Preparation of Cultured Cells for Crosslinking]\nAspirate the super... |
null | null | null | dx.doi.org/10.17504/protocols.io.djt4nm | null | null | TITLE: No Title
AUTHORS:
[BEFORE_START]
Prepare High salt buffer, Carbonate buffer,Wash buffer,Protease inhibitors<br />Instruments you need: ULTRA-TURRAX Dispenser T10 basis S25 (IKA)(or other dispensers); Ultracentrifuge.
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.q5ddy26 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div title="Page 1">
<div>
<div>
<p>Protocol for adult (8-10 week) mouse kidney dissociation.</p>
</div>
</div>
</div>
[BEFORE_START]
<div title="Page 1">
<p>Prepare <em>Bacillus Licheniformis</em> enzyme mix just prior to starting dissociation:</p>
<p> </p>
<table style="heigh... | [] |
81,163 | 5’ RACE-seq for RNA fragments with 5’ phosphate - library prep protocol | 4 | dx.doi.org/10.17504/protocols.io.n2bvj847wgk5/v1 | https://www.protocols.io/view/5-race-seq-for-rna-fragments-with-5-phosphate-libr-cthjwj4n | Marta.Gaglia, lea.gaucherand | TITLE: 5’ RACE-seq for RNA fragments with 5’ phosphate - library prep protocol
AUTHORS: Marta.Gaglia, lea.gaucherand
[DESCRIPTION]
This protocol will allow identification of fragments of RNA that have a 5' phosphate on a transcriptome-wide scale using an Illumina sequencing platform. Library preparation relies on liga... | ["[Procedure] RNA extraction\nExtract all RNA using RNeasy Qiagen kit.\nElute in 50 µl H2O.", "[Procedure] DNase treatment:\nAdd to each RNA sample:\n1.2 µl Turbo DNase\n1.5 µl RNasin\n6 µl 10x turbo DNase buffer\n1.3 µl H2O.\n(Total volume = 60 µl)\nIncubate at 37°C for 20 min.", "[Procedure] RNA extraction using phen... |
101,393 | Fast Green/Sirius Red Protocol For Leica ST5020 Automated Stainer | 1 | dx.doi.org/10.17504/protocols.io.ewov19djklr2/v1 | https://www.protocols.io/view/fast-green-sirius-red-protocol-for-leica-st5020-au-de9r3h56 | Angela Denn, Zbigniew Mikulski | TITLE: Fast Green/Sirius Red Protocol For Leica ST5020 Automated Stainer
AUTHORS: Angela Denn, Zbigniew Mikulski
[DESCRIPTION]
This Sirius Red Fast Green protocol is for the Leica ST5020 Automated multistainer. You can use it as a guide to developing your own protocol, catered to the needs of your researchers. This te... | ["[Fast Green/Sirius Red Stain] Arrange the reagents in the stainer according to the layout (note dark blue positions for FG/SR cups)", "[Fast Green/Sirius Red Stain] Program the FG/SR protocol into the ST5020 stainer according to the table below", "[Fast Green/Sirius Red Stain] Perform all required maintenance on the ... |
45,334 | Fluorescent Western Protocol | 4 | null | https://www.protocols.io/view/fluorescent-western-protocol-bqhwmt7e | Steven Burgess | TITLE: Fluorescent Western Protocol
AUTHORS: Steven Burgess
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Analysis of proteins using fluorescent immunoblot. </div><div class = "text-block"><span style = "font-weight:bold;">Note: </span><span style = "font-weight:bold;"> </span></div><div class = ... | ["Keep membranes in the black Western Blot incubation box for all steps, this is important after adding the secondary antibody because the signal is light-sensitive and will become bleached if not exposed to light for a long enough period.", "Wet with 1x PBS for min", "Rinse membrane with dH2O", "Discard PBS and incub... |
82,655 | Dilution-to-Extinction Experiment Protocol | 4 | dx.doi.org/10.17504/protocols.io.36wgq7d2ovk5/v2 | https://www.protocols.click/view/dilution-to-extinction-experiment-protocol-cux7wxrn | Shelby J Barnes, Michael Henson, Celeste Lanclos, Jordan Coelho, Cameron Thrash | TITLE: Dilution-to-Extinction Experiment Protocol
AUTHORS: Shelby J Barnes, Michael Henson, Celeste Lanclos, Jordan Coelho, Cameron Thrash
[DESCRIPTION]
Dilution-to-Extinction Experiment Protocol
[STEPS]
SECTION: Collection and Filtration
2. Culturing Hardware Preparation
SECTION: Inoculum Sample Enumeration
5. Samp... | ["[Collection and Filtration] Culturing Hardware Preparation", "[Inoculum Sample Enumeration] Sample Preparation", "[Medium Inoculation] All steps except incubation are performed inside a biosafety cabinet or laminar flow hood.", "[Collection and Filtration] Collect samples at any source of interest with sterile, acid-... |
79,903 | Processamento de actígrafos pré-coleta - ActTrust | 5 | dx.doi.org/10.17504/protocols.io.n92ld964xg5b/v4 | https://www.protocols.io/view/processamento-de-act-grafos-pr-coleta-acttrust-cr97v99n | Daniel Vartanian | TITLE: Processamento de actígrafos pré-coleta - ActTrust
AUTHORS: Daniel Vartanian
[DESCRIPTION]
Este protocolo faz parte do processo de coleta de dados actigráficos do Grupo Interdisciplinar de Pesquisa em Ritmos Biológicos (GIPERBIO). Ele foi desenvolvido para os actígrafos da empresa Condor Instruments. Algumas das... | ["[Conexão] Conecte o actígrafo ao computador.", "[Configuração] Verifique as configurações de coleta.", "[Carregamento] Carregue a bateria do actígrafo até aparecer o status CARREGADO no campo BATERIA.", "[Registro] Preencha e envie o formulário de processamento de actígrafos.", "[Finalização] Guarde o actígrafo dentr... |
null | null | null | dx.doi.org/10.17504/protocols.io.ef6bbre | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?. | [] |
92,975 | Expression and purification of LRRK2 constructs | 4 | dx.doi.org/10.17504/protocols.io.14egn314pl5d/v1 | https://www.protocols.io/view/expression-and-purification-of-lrrk2-constructs-c62pzgdn | Verena Dederer, Deep Chatterjee, Stefan Knapp, Sebastian Mathea | TITLE: Expression and purification of LRRK2 constructs
AUTHORS: Verena Dederer, Deep Chatterjee, Stefan Knapp, Sebastian Mathea
[DESCRIPTION]
Expression and purification of human LRRK2 and its variants from insect cells.
[BEFORE_START]
Buffers, beads, columns are chillled at 4°C prior to use.
[GUIDELINES]
if not oth... | ["[Protein expression and purification] exponentially growing SF9 cells (2x10^6 cells/mL in Lonza Insect-XPRESS medium) are transduced with high-titre bacculovirus suspension (encoding TEV cleavable N-terminally His6-Z-tagged human LRRK2).", "[Protein expression and purification] After shaking with at27 °Cfor 3960 min... |
43,640 | Importing live fungi to the US (UF Forest Entomology Lab) | 3 | dx.doi.org/10.17504/protocols.io.bnuymexw | https://www.protocols.io/view/importing-live-fungi-to-the-us-uf-forest-entomolog-bnuymexw | Demian F Gomez, You Li, Jiri Hulcr | TITLE: Importing live fungi to the US (UF Forest Entomology Lab)
AUTHORS: Demian F Gomez, You Li, Jiri Hulcr
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes how to hand-carry live fungi through airport customs into the United States for the UF Forest Entomology Lab.</div><div... | [] |
103,904 | RSV Nanopore Whole Genome Sequencing | 0 | null | https://www.protocols.io/view/rsv-nanopore-whole-genome-sequencing-dhp835rw | Rebecca Dewar, Martin McHugh, Seb Cotton, Goncalo Fernandes, Daniel Maloney, Kate Templeton | TITLE: RSV Nanopore Whole Genome Sequencing
AUTHORS: Rebecca Dewar, Martin McHugh, Seb Cotton, Goncalo Fernandes, Daniel Maloney, Kate Templeton
[DESCRIPTION]
This is the Nanopore sequencing protocol used with ARTIC RSV primers to sequence RSV samples in the Royal Infirmary of Edinburgh, which has been utilised in thi... | ["[Reverse Transcription (RT) using LunaScript RT SuperMix] Retrieve extracts based on run worksheet.", "[Reverse Transcription (RT) using LunaScript RT SuperMix] Invert tubes and pulse spin to 3000 rpm to remove drops from lids.", "[Reverse Transcription (RT) using LunaScript RT SuperMix] Switch on thermal cycler.", "... |
72,073 | WUSTL Senescence Network (SenNet) Biospecimen Collection SOP | 1 | dx.doi.org/10.17504/protocols.io.j8nlkww45l5r/v1 | https://www.protocols.io/view/wustl-senescence-network-sennet-biospecimen-collec-cimhuc36 | Daniel Rapp, Matthew Wyczalkowski | TITLE: WUSTL Senescence Network (SenNet) Biospecimen Collection SOP
AUTHORS: Daniel Rapp, Matthew Wyczalkowski
[DESCRIPTION]
This protocol describes the tissue collection and storing aspect of Washington University's Biospecimen core as part of the Cellular Senescence Network (SenNet).
[STEPS]
1. Specimens to be coll... | ["Specimens to be collected:\n\n1.) Skin (peri-incisional) 2x1cm\n2.)Liver Tissue 1cm3\n3.) Liver Tissue 1cm3a abdominal (omentum) and/or subcutaneous, 2 x 2cm3\n4.) Bone Marrow\n5.) Blood", "[Skin/Liver/Fats collection] Third piece of each tissue type will be Flash frozen in Liquid Nitrogen. See step 10.", "[Skin/Live... |
50,343 | Statistical Considerations and Analysis Plan (Part 9 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.bvefn3bn | https://www.protocols.io/view/statistical-considerations-and-analysis-plan-part-bvefn3bn | Stephen.Gitelman , Jeffrey A. Bluestone | TITLE: Statistical Considerations and Analysis Plan (Part 9 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 9 of "Safety and Effic... | [] |
57,752 | COVID-19 ARTIC v4.1 Illumina library construction and sequencing protocol - tailed method | 1 | dx.doi.org/10.17504/protocols.io.j8nlk4b36g5r/v2 | https://www.protocols.io/view/covid-19-artic-v4-1-illumina-library-construction-b4myqu7w | DNA Pipelines R&D, Benjamin Farr, Diana Rajan, Emma Betteridge, Lesley Shirley, Michael Quail, Naomi Park, Nicholas Redshaw, Iraad F Bronner, Louise Aigrain, Scott Goodwin, Scott Thurston, Stefanie Lensing, James Bonfield, Keith James, Nicholas Salmon, Charlotte Beaver, Rachel Nelson, David K. Jackson, Alex Ald... | TITLE: COVID-19 ARTIC v4.1 Illumina library construction and sequencing protocol - tailed method
AUTHORS: DNA Pipelines R&D, Benjamin Farr, Diana Rajan, Emma Betteridge, Lesley Shirley, Michael Quail, Naomi Park, Nicholas Redshaw, Iraad F Bronner, Louise Aigrain, Scott Goodwin, Scott Thurston, Stefanie Lensing, ... | ["[cDNA generation] Important! This step must be performed in a RNase free, pre-PCR environment in which post PCR COVID-19 amplicons are not present, to minimise risk of sample contamination.\n\nDecontaminate bench surfaces, pipettes and gloves with RNase ZAP before starting work. Keep reagents and samples chilled thro... |
17,333 | Glucose-Stimulated Glucagon Secretion using Biorep Perifusion Machine - Mouse Islets | 1 | dx.doi.org/10.17504/protocols.io.u6veze6 | https://www.protocols.io/view/glucose-stimulated-glucagon-secretion-using-biorep-u6veze6 | Aliya Spigelman, Jocelyn Manning Fox, Patrick Macdonald | TITLE: Glucose-Stimulated Glucagon Secretion using Biorep Perifusion Machine - Mouse Islets
AUTHORS: Aliya Spigelman, Jocelyn Manning Fox, Patrick Macdonald
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. [Day before experiment]
Isolate mouse islets as described in Mouse Islet Isolation protocol.
?. [Day b... | ["[Day before experiment]\nIsolate mouse islets as described in Mouse Islet Isolation protocol.", "[Day before experiment]\nPick the isolated mouse islets into Mouse Islet Culture Media (>90% islet purity). Mouse Islet Culture Media500 mL RPMI (11.1mMglucose) Gibco 1875-11950 mL FBS Canadian Origin Gibco12483-0205 mL... |
106,552 | Nuclei counting after Trypan Blue staining | 0 | dx.doi.org/10.17504/protocols.io.5jyl82838l2w/v1 | https://www.protocols.io/view/nuclei-counting-after-trypan-blue-staining-dkay4sfw | Carmen Abaurre, Ka Wai Lee, Ernest Arenas | TITLE: Nuclei counting after Trypan Blue staining
AUTHORS: Carmen Abaurre, Ka Wai Lee, Ernest Arenas
[DESCRIPTION]
Nuclei counting after Trypan Blue staining
[GUIDELINES]
Be wary of nuclei integrity when counting for snRNA-seq. Some minor blebbing of nuclei can still be considered acceptable, but broken up nuclei are... | ["Prepare nuclei suspension from samples.", "In order to increase accuracy, prepare duplicates or triplicates per sample.", "Add 9 μl of 0.4% Trypan Blue to a 0.2 ml tube", "Add 1 µl of nuclei suspension to the Trypan Blue solution. Do not dispense to the walls of the tube.", "Mix slowly by pipetting up and down 10 tim... |
23,919 | Global NeuroSurg 1 Study: Determining the Global Outcomes of Traumatic Brain Injury in low-, middle-, and high- income countries: A prospective, international cohort study | null | dx.doi.org/10.17504/protocols.io.3kpgkvn | null | Ahmed Negida, Zoe Teton, Hieder Al-Shami, Ahmed Hegazy, Ahmed M. Raslan | TITLE: Global NeuroSurg 1 Study: Determining the Global Outcomes of Traumatic Brain Injury in low-, middle-, and high- income countries: A prospective, international cohort study
AUTHORS: Ahmed Negida, Zoe Teton, Hieder Al-Shami, Ahmed Hegazy, Ahmed M. Raslan
[DESCRIPTION]
<div class = "text-blocks"><div class = "text... | [] |
92,455 | Environmental DNA (eDNA) 12S Metabarcoding Illumina MiSeq NGS Protocol with size selection | 1 | dx.doi.org/10.17504/protocols.io.eq2lyj1kelx9/v2 | https://www.protocols.io/view/environmental-dna-edna-12s-metabarcoding-illumina-c6ifzcbn | Kathleen Pitz, Jacoby Baker | TITLE: Environmental DNA (eDNA) 12S Metabarcoding Illumina MiSeq NGS Protocol with size selection
AUTHORS: Kathleen Pitz, Jacoby Baker
[DESCRIPTION]
This sequencing protocol is intended to directly follow and use the PCR products of the protocol:
"Environmental DNA (eDNA) 12S Metabarcoding PCR Protocol (with Platinum ... | ["[MIOP: Minimum Information about an Omics Protocol] MIOP Term\nValue\n \nmethodology category\n\n \nproject\n\n \npurpose\n\n \nanalyses\n\n \ngeographic location\n\n \nbroad-scale environmental context\n\n \nlocal environmental context\n\n \nenvironmental medium\n\n \ntarget\n\n \ncreator\n\n \nmaterials required\... |
68,330 | Mouse Ischemia Experiment | 1 | dx.doi.org/10.17504/protocols.io.ceyitfue | https://www.protocols.io/view/mouse-ischemia-experiment-ceyitfue | gagandeep kaur, Irfan_Rahman | TITLE: Mouse Ischemia Experiment
AUTHORS: gagandeep kaur, Irfan_Rahman
[DESCRIPTION]
The objective of this protocol is to understand the effect of cold ischemia time on cellular senescence in mouse lung and heart tissues.
The sampling of lung and heart tissues will be done based on equal weights. 6 pieces weighing ar... | ["[Lung Tissue Dissociation] Immediately transfer the tubes to MACS Tissue Dissociator and run user-defined program named m_lung_01_02 for mouse lungs and m_heart_01.01 for mouse heart.", "[Lung Tissue Dissociation] 1) Mince tissue finely, place into 50ml GentleMACS C-tube with liberase enzymatic cocktail a. Fo... |
52,413 | Harvesting Tobacco Seeds | 4 | dx.doi.org/10.17504/protocols.io.bxe5pjg6 | https://www.protocols.io/view/harvesting-tobacco-seeds-bxe5pjg6 | Lynn Doran | TITLE: Harvesting Tobacco Seeds
AUTHORS: Lynn Doran
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol for harvesting seeds from research tobacco plants.</div></div>
[STEPS]
?. Inspect pollinating bag for any damage that could indicate cross-pollination. Discard any plants that look like the... | ["Inspect pollinating bag for any damage that could indicate cross-pollination. Discard any plants that look like the pollination bag may have been damaged.", "Inspect the inflorescence. Seed development is complete when the plant begins to die back and the majority of the seed pods have turned brown.", "Clip the stem... |
20,499 | Ultra-deep, long-read nanopore sequencing of mock microbial community standards | null | dx.doi.org/10.17504/protocols.io.x9tfr6n | null | Josh Quick, Sam Nicholls, Nick Loman, Shuiquan Tang | TITLE: Ultra-deep, long-read nanopore sequencing of mock microbial community standards
AUTHORS: Josh Quick, Sam Nicholls, Nick Loman, Shuiquan Tang
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Background: Long sequencing reads are information-rich: aiding de novo assembly and reference mapping, a... | ["[Prepare standard]\nTransfer orto a Eppendorf tube.\n[Microbial Community Standard]\n[Microbial Community Standard II (Log distribution)]\n1.5 ml\nEach 75 ul of the even community is expected to yield 2000 ng and the log community 220 ng therefore a larger starting volume of the later is required.", "[Retain supernat... |
79,440 | Handling and Sampling Small Nonhuman Primates - ISL Peru | 1 | dx.doi.org/10.17504/protocols.io.5qpvor1exv4o/v1 | https://www.protocols.io/view/handling-and-sampling-small-nonhuman-primates-isl-crtqv6mw | Mrinalini Watsa, Cristian Tirapelle, Alice Poirier, Alexandra Sacco, Priscila Peralta-Aguilar, Efstathia Robakis, Ishaan Raghunandan, Gideon Erkenswick | TITLE: Handling and Sampling Small Nonhuman Primates - ISL Peru
AUTHORS: Mrinalini Watsa, Cristian Tirapelle, Alice Poirier, Alexandra Sacco, Priscila Peralta-Aguilar, Efstathia Robakis, Ishaan Raghunandan, Gideon Erkenswick
[DESCRIPTION]
Program Timing:
Trap habituation begins in May. Trapping and sample collection... | ["[Preparatory phase] The functionality of the trap(s) is checked the day before a trapping event. Ideally, minimal modifications to trap placement, positioning, and operation are made on the day of capture.\n\nMULTI-COMPARTMENT TRAPS: A string is tied to the outside of each door of the multi-compartment trap (made of ... |
29,612 | 10X Genomics Single-Nucleus RNA-Sequencing for Transcriptomic Profiling of Adult Human Tissues | null | dx.doi.org/10.17504/protocols.io.86khzcw | null | Sarah Urata, Blue Lake, Dinh Diep, Masato Hoshi, Sanjay Jain, Kun Zhang | TITLE: 10X Genomics Single-Nucleus RNA-Sequencing for Transcriptomic Profiling of Adult Human Tissues
AUTHORS: Sarah Urata, Blue Lake, Dinh Diep, Masato Hoshi, Sanjay Jain, Kun Zhang
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">10X Genomics Single Cell 3' (v3) RNA sequencing is a microdroplet-bas... | ["[Isolate Nuclei]\nResuspend nuclei in to of PBS + 0.1% RNase Inhibitor (volume depends on target concentration)\n100 µl\n1 ml", "[Isolate Nuclei]\nCount nuclei (e.g. BioRad T20 Cell Counter)", "[Isolate Nuclei]\nCheck nuclei integrity under fluorescent microscope using DAPI channel. Nuclei should appear distinct, h... |
19,565 | Harvesting OP50 for C. elegans liquid culture | null | dx.doi.org/10.17504/protocols.io.xcmfiu6 | null | Vidur Sabharwal | TITLE: Harvesting OP50 for C. elegans liquid culture
AUTHORS: Vidur Sabharwal
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. [Harvesting OP50]
After 8 hr incubation, use 2 ml of E. coli OP50 LB culture to inoculate each of 3 x 250 ml LB. Place flasks in shaking incubator (180 rpm) O/N.
37 °C
?. [Harvestin... | ["[Harvesting OP50]\nAfter 8 hr incubation, use 2 ml of E. coli OP50 LB culture to inoculate each of 3 x 250 ml LB. Place flasks in shaking incubator (180 rpm) O/N.\n37 °C", "[Harvesting OP50]\nWeigh 3 x 50 ml centrifuge tubes and write weight of the empty tube on the tube.", "[Harvesting OP50]\nDay 2. Using a serologi... |
26,100 | Determination of Clostridium sp. contamination level | 1 | dx.doi.org/10.17504/protocols.io.bp2l64q2rvqe/v1 | https://www.protocols.io/view/determination-of-clostridium-sp-contamination-leve-5qug5ww | Eva Petrova, Roey Angel | TITLE: Determination of Clostridium sp. contamination level
AUTHORS: Eva Petrova, Roey Angel
[DESCRIPTION]
adopted from Dr Tomasz Grenda (2018)
[STEPS]
1. Prepare 10g of sample and resuspend it in 90ml of saline solution (0.85% NaCl).
10 g
90 mL
2. Subject suspension to decimal dilutions in saline solution (see G... | ["Prepare 10g of sample and resuspend it in 90ml of saline solution (0.85% NaCl). \n10 g \n90 mL", "Subject suspension to decimal dilutions in saline solution (see Guidelines), prepare at least 5 levels.", "After sample preparation, dispense 10ml of TPGY broth into tubes (number of tubes depends on the number of sample... |
107,584 | Quantitative targeted metabolomics for ASO mouse model using Biocrates Q500 Platform | 0 | dx.doi.org/10.17504/protocols.io.261ge5pwyg47/v2 | https://www.protocols.io/view/quantitative-targeted-metabolomics-for-aso-mouse-m-dma842hw | Siamak MahmoudianDehkordi | TITLE: Quantitative targeted metabolomics for ASO mouse model using Biocrates Q500 Platform
AUTHORS: Siamak MahmoudianDehkordi
[DESCRIPTION]
Using the biocrates MxP‱ Quant 500 kit (biocrates life science AG, Innsbruck, Austria), a commercially available targeted metabolomics kit, we assessed 630 metabolites across 26 ... | ["[Sample Preparation] A total of 226 samples were prepared for quantification with mass spectrometry (MS)-based metabolomics: 23 plasma samples, 69 gut content samples (23 cecal contents, 23 colon contents, and 23 duodenum contents), and 134 tissue samples (88 brain, 23 colon, and 23 duodenum)", "[Sample Preparation] ... |
null | null | null | dx.doi.org/10.17504/protocols.io.f4wbqxe | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div class="page" title="Page 14">
<div class="layoutArea">
<div class="column">
<p>The EPIK™ miRNA Panel Assays protocol is a two‐step protocol consisting of:</p>
<p> </p>
<div class="page" title="Page 14">
<table>
<tbody>
<tr>
<td>
<div class="layoutArea">
<div class="column">... | [] |
43,955 | Kasson Lab DNA Extraction | 4 | dx.doi.org/10.17504/protocols.io.q26g78413lwz/v1 | https://www.protocols.io/view/kasson-lab-dna-extraction-bn6tmhen | Angie Macias, Matthew T Kasson, Brian Lovett | TITLE: Kasson Lab DNA Extraction
AUTHORS: Angie Macias, Matthew T Kasson, Brian Lovett
[DESCRIPTION]
This is a routine protocol for extracting DNA from various fungi. This extraction method is suitable for follow-up molecular work such as PCR amplification.
[STEPS]
SECTION: Before you begin
1. Turn on hot water bath,... | ["[Before you begin] Turn on hot water bath, set to 65 °C.", "[Before you begin] Pull two Eppendorf 1.5 mL centrifuge tubes per sample.", "[Before you begin] Label both sets of tubes with (short) sample names.", "[Before you begin] Label one tube set for each sample with an \"I\" for .", "[Before you begin] Add 600 µL... |
81,166 | Purification of influenza A virus RNA from cell supernatant to check sequences | 4 | dx.doi.org/10.17504/protocols.io.36wgqj8wxvk5/v1 | https://www.protocols.io/view/purification-of-influenza-a-virus-rna-from-cell-su-cthnwj5e | Marta.Gaglia, lea.gaucherand | TITLE: Purification of influenza A virus RNA from cell supernatant to check sequences
AUTHORS: Marta.Gaglia, lea.gaucherand
[DESCRIPTION]
We use this protocol to isolate RNA from influenza A virus-containing cell supernatant and monitor maintenance of sequence insertions or mutations
[STEPS]
1. Influenza A virus extr... | ["Influenza A virus extraction from cell supernatant using QIAamp Viral RNA Mini Kit\nFollow the manufacturer's protocol using a starting cell supernatant volume of 140 µl.\nElute in 60 µl buffer AVE.", "DNase treatment using Qiagen RNase-free DNase set:\nMake mastermix of DNase and buffer. For each sample:\n10 µl buff... |
31,727 | cAMP Regulated Cl- Current Protocol | 1 | dx.doi.org/10.17504/protocols.io.ba8pihvn | https://www.protocols.io/view/camp-regulated-cl-current-protocol-ba8pihvn | Robert Harvey, Shailesh Agarwal | TITLE: cAMP Regulated Cl- Current Protocol
AUTHORS: Robert Harvey, Shailesh Agarwal
[DESCRIPTION]
cAMP Regulated Cl- Current Protocol
[STEPS]
1. Membrane currents were recorded from isolated pig ventricular myocytes using the whole-cell configuration of the patch clamp technique.
2. Isolated cells were placed in a p... | ["Membrane currents were recorded from isolated pig ventricular 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 contain... |
null | null | null | dx.doi.org/10.17504/protocols.io.hjwb4pe | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div>
<div>
<p>This protocol is from 'Flower Ca<sup>2+</sup> channel in CME and ADBE' of Yao CK et al.</p>
<div>
<div>
<p> </p>
<p>Please see the manuscript for the full method details.</p>
</div>
</div>
</div>
</div>
[BEFORE_START]
<p>You'll need: </p>
<p> </p>
<p><strong>0 mM... | [] |
61,103 | DNA extraction and Nanopore library prep from single wild-caught drosophilids | 1 | dx.doi.org/10.17504/protocols.io.dm6gpbdn8lzp/v2 | https://www.protocols.io/view/dna-extraction-and-nanopore-library-prep-from-sing-b7wprpdn | Bernard Y Kim | TITLE: DNA extraction and Nanopore library prep from single wild-caught drosophilids
AUTHORS: Bernard Y Kim
[DESCRIPTION]
We have been assembling the genomes of many Drosophila species. This protocol fork allows for the sequencing of single wild-caught flies using Nanopore MinION sequencers, in contrast to our previou... | ["[(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 fly to a 1.5 mL LoBind tube.", "[(Optional) Hydration of ethanol-fixed tissue] Add 500 µL Buffer STE to the tube with the fly.", "[(Optional) Hydration of et... |
64,766 | Use of Interviewer-Administered Telephone Surveys during Infectious Disease Outbreaks, Epidemics, and Pandemics: A Scoping Review Protocol | 1 | dx.doi.org/10.17504/protocols.io.36wgq7poyvk5/v1 | https://www.protocols.io/view/use-of-interviewer-administered-telephone-surveys-cbg6sjze | Sayaka Arita, Mouhamadou Faly Ba, Zoumana Traoré, Emmanuel Bonnet, Adama Faye, Valery Ridde | TITLE: Use of Interviewer-Administered Telephone Surveys during Infectious Disease Outbreaks, Epidemics, and Pandemics: A Scoping Review Protocol
AUTHORS: Sayaka Arita, Mouhamadou Faly Ba, Zoumana Traoré, Emmanuel Bonnet, Adama Faye, Valery Ridde
[DESCRIPTION]
Introduction: Emergence of modern technology and digita... | ["[Review questions] Review questions\n\nThe following research question was formulated: What are some main characteristics of interviewer-administered telephone surveys during infectious disease outbreaks, epidemics, and pandemics? The additional questions are set to explore the methods and implementation challenges i... |
94,014 | Protocol for 3D bioprinting functional human brain tissues | 4 | dx.doi.org/10.17504/protocols.io.e6nvwdyjdlmk/v1 | https://www.protocols.io/view/protocol-for-3d-bioprinting-functional-human-brain-c726zqhe | Yuanwei Yan, Mathivanan, Su-Chun Zhang | TITLE: Protocol for 3D bioprinting functional human brain tissues
AUTHORS: Yuanwei Yan, Mathivanan, Su-Chun Zhang
[DESCRIPTION]
Detailed protocol for 3D bioprinting functional human brain tissues
[STEPS]
SECTION: Reagents
1.
1. Thrombin (T7009, Sigma)
2. Fibrinogen (F3879, Sigma)
3. Aprotinin (A1153, Sigma)
4. ... | ["[Reagents] 1. Thrombin (T7009, Sigma) \n2. Fibrinogen (F3879, Sigma) \n3. Aprotinin (A1153, Sigma) \n4. CaCl2 (C7902, Sigma) \n5. Deionized (DI) water \n6. Dulbecco’s phosphate buffered saline (DPBS) (14190144, ThermoFisher Scientific) \n7. Transglutaminase (TG) from lyophilized Moo Glue powder (Modernist Pantry; ME,... |
33,103 | Quick Emulsion PCR Extraction Protocol | null | dx.doi.org/10.17504/protocols.io.bcjpiumn | null | Vijay K Chaudhary, Vaishali Verma, Amita Gupta, Vijay K. Chaudhary | TITLE: Quick Emulsion PCR Extraction Protocol
AUTHORS: Vijay K Chaudhary, Vaishali Verma, Amita Gupta, Vijay K. Chaudhary
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Emulsion PCR (ePCR) is an important technique that permits amplification of DNA molecules in physically separated picoliter volume... | ["Vigourously vortex the tube for 1 min.", "Transfer entire emulsion PCR mixture (100 µl + the overlaid mineral oil) to a fresh 1.5 ml microfuge tube and add 500 µl of QIA PB purification buffer (5 x volume) directly the tube. For larger ePCR mixture, appropriate volume of PB buffer can be added.", "Load the entire sus... |
68,955 | Disposal of Environmental Samples from Water Bodies Infested with Zebra Mussels | 4 | dx.doi.org/10.17504/protocols.io.eq2lynoymvx9/v2 | https://www.protocols.io/view/disposal-of-environmental-samples-from-water-bodie-cfj3tkqn | Malcolm A Barnard, Stephen Powers | TITLE: Disposal of Environmental Samples from Water Bodies Infested with Zebra Mussels
AUTHORS: Malcolm A Barnard, Stephen Powers
[DESCRIPTION]
Zebra Mussels (Dreissena polymorpha) are a highly invasive species that have been invading water bodies around the United States and beyond. This protocol for sample disposal... | ["[Sample Killing] Pour all environmental sample water from bottles into a dish pan.", "[Sample Killing] Save the bottles for acid washing\n \n.", "[Sample Killing] Add 50 mL of bleach per 1 L of sample water.", "Let the bleached sample sit for a minimum of four hours if not until the next day.", "[Sample Disposal] Dis... |
63,615 | 2% Agarose Gel | 4 | null | https://www.protocols.io/view/2-agarose-gel-cac7sazn | George Testo | TITLE: 2% Agarose Gel
AUTHORS: George Testo
[DESCRIPTION]
Agarose gel electrophoresis is a method of gel electrophoresis used in biochemistry, molecular biology, genetics, and clinical chemistry to separate a mixed population of macromolecules such as DNA or proteins in a matrix of agarose, one of the two main compon... | ["[Pouring a Standard 2% Agarose Gel] Measure 1g of Agarose.", "[Pouring a Standard 2% Agarose Gel] Mix agarose powder with 49mL of DI water and 1mL of 50x TAE in a microwavable flask.", "[Pouring a Standard 2% Agarose Gel] Microwave for 1-3 minutes until the agarose is completely dissolved.", "[Pouring a Standard 2% A... |
75,837 | Multiplexed snRNA-seq from frozen human brain samples | 4 | dx.doi.org/10.17504/protocols.io.kqdg369keg25/v2 | https://www.protocols.io/view/multiplexed-snrna-seq-from-frozen-human-brain-samp-cna5vag6 | Marcos Nascimento | TITLE: Multiplexed snRNA-seq from frozen human brain samples
AUTHORS: Marcos Nascimento
[DESCRIPTION]
This is a protocol to save your experiment and successfully demultiplex nuclei using CellPlex, the cholesterol-modified-oligo (CMO) barcodes from 10x Genomics on your nuclei from snap-frozen tissue.
Generally speaki... | ["[Preparation] Check if the Rotor SW32Ti rotor is at 4°C", "[Preparation] Prepare your working area: Clean the workbench and pipettes with RNAse Zap.", "[Preparation] Add RNAse inhibitor (Sigma cat.# 3335402001) to LB and WRB (0.2U/ul).", "[Preparation] Put lysis buffer and sucrose solutions on ice.", "[Nuclei Isolati... |
66,322 | Bridport Health Liver Support:-(SCAM EXPOSED 2022) | 3 | dx.doi.org/10.17504/protocols.io.x54v9ynj1g3e/v1 | https://www.protocols.io/view/bridport-health-liver-support-scam-exposed-2022-cczssx6e | bridporthealth | TITLE: Bridport Health Liver Support:-(SCAM EXPOSED 2022)
AUTHORS: bridporthealth
[DESCRIPTION]
The body is built to withstand a lot of chaos, but most people take it for granted. Whether drinking alcohol serves as a social lubricant or a symptom of depression, it can lead to addiction for some people. With these ye... | [] |
107,044 | ChAT Immunofluorescent Staining of medulla oblongata fixed sections | 1 | dx.doi.org/10.17504/protocols.io.kqdg32nzpv25/v1 | https://www.protocols.io/view/chat-immunofluorescent-staining-of-medulla-oblonga-dksc4waw | Pietro La Vitola | TITLE: ChAT Immunofluorescent Staining of medulla oblongata fixed sections
AUTHORS: Pietro La Vitola
[DESCRIPTION]
This protocol is designed for choline acetyltransferase (ChAT) staining using the Millipore AB144P (RRID:AB_2079751) antibody. Tissue stained with this protocol include 30μm free-floating mouse brain sec... | ["[ChAT Immunofluorescent Staining of medulla oblongata fixed sections] Wash tissue slices in tris-buffer saline (TBS: 0.05M Trizma base and 0.15M NaCl; pH: 7.6) for 10 minutes. Repeat x3.", "[ChAT Immunofluorescent Staining of medulla oblongata fixed sections] Incubate in blocking buffer (5% donkey serum, 2% BSA, 0.5%... |
null | null | null | dx.doi.org/10.17504/protocols.io.gvybw7w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
A collection of protocols designed to guide the user in processing a viral metagenome from raw sequence data to assembly, and subsequent analysis. The user uses <em>actual</em> reads from <a href="https://github.com/MicroB3-IS/osd-analysis" target="_blank">Ocean Sampling Day (20... | [] |
63,821 | Forward Primer Reconstitution | 4 | null | https://www.protocols.io/view/forward-primer-reconstitution-cajmsck6 | Allyson Hirsch, George Testo | TITLE: Forward Primer Reconstitution
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, it... | ["[Preparing Forward Primer] Vortex and spin down primer tube: this breaks up the solidified primer at the bottom of the tube and brings the primer debris up from the bottom of the tube.", "[Preparing Forward Primer] Look for nM (nanoMoles) on the printed primer label and circle. \n\nEx: 779 µL", "[Preparing Forward Pr... |
93,197 | NCBI Bacterial Pathogen Data Curation Protocol: SOP for Editing GenomeTrakr Submissions | 1 | dx.doi.org/10.17504/protocols.io.36wgq5jb5gk5/v5 | https://www.protocols.io/view/ncbi-bacterial-pathogen-data-curation-protocol-sop-c69mzh46 | Tina Lusk Pfefer, Ruth Timme, Candace Hope Bias, Errol Strain, Maria Balkey | TITLE: NCBI Bacterial Pathogen Data Curation Protocol: SOP for Editing GenomeTrakr Submissions
AUTHORS: Tina Lusk Pfefer, Ruth Timme, Candace Hope Bias, Errol Strain, Maria Balkey
[DESCRIPTION]
PURPOSE: After data are submitted to NCBI submitters often encounter the need to update, retract, or replace these records. T... | ["[BioProject Curation for BioProjects linked to NCBI Pathogen Detection] How to make edits to BioProject records:", "[BioProject Curation for BioProjects linked to NCBI Pathogen Detection] To edit Title, Organism, Description, URL, or publications for your BioProject, follow steps 1-6 below.\n\n1. Click on the \"Manag... |
42,619 | Using rhythmic auditory stimuli to modulate resilience to perturbations during walking in healthy young adults | 3 | dx.doi.org/10.17504/protocols.io.bmu3k6yn | https://www.protocols.io/view/using-rhythmic-auditory-stimuli-to-modulate-resili-bmu3k6yn | Deepak Ravi | TITLE: Using rhythmic auditory stimuli to modulate resilience to perturbations during walking in healthy young adults
AUTHORS: Deepak Ravi
[STEPS] | [] |
63,425 | Oplexx Keto | 3 | dx.doi.org/10.17504/protocols.io.j8nlkk2e1l5r/v1 | https://www.protocols.io/view/oplexx-keto-b969r9h6 | H H | TITLE: Oplexx Keto
AUTHORS: H H
[DESCRIPTION]
we are here to help you out. We do have the supplement that will easily counter all the extra fat from your body tone.
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.g5bby2n | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.d9699d | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
In this protocol we show how to perform the taxonomic biomarker discovery operation using <a href="https://bitbucket.org/nsegata/lefse" target="_blank">LEfSe</a>.
[BEFORE_START]
REQUIREMENTS: <a href="https://bitbucket.org/nsegata/lefse" target="_blank">LEfSe</a> installed (and... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.rted6je | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?. | ["ATP and NAD+ and NADH metabolites were extracted from female third instar wandering larvae harbouring Alstonville and Dahomey mtDNA raised on 1:2 P:C and 1:16 P:C diets (7 replicates per mitotype-diet combination)", "The extracted metabolites were analysed using liquid chromatography (LC) electrospray ionisation tand... |
null | null | null | dx.doi.org/10.17504/protocols.io.rvad62e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p> </p>
<p>Coffee is considered as a major source of dietary antioxidants; some are present in the green bean, whereas others are generated during roasting. Coffee roasting, the process of the heating of green coffee beans transforming them into black coffee beans, transforms ... | [] |
28,448 | MojoSort™ Human CD4 T Cell Selection Protocol | null | dx.doi.org/10.17504/protocols.io.7z8hp9w | null | Sam Li | TITLE: MojoSort™ Human CD4 T Cell Selection Protocol
AUTHORS: Sam Li
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Product description and procedure summary:</span><span>
This kit is designed for the sequential positive selection of CD4</span><span style = "vertic... | ["Prepare cells from your tissue of interest or blood without lysing erythrocytes. Kits for human samples have been optimized for PBMCs, please prepare the cells using a suitable method.", "In the final wash of your sample preparation, resuspend the cells in MojoSort™ Buffer by adding up to 4 mL in a 5 mL (12 x 75 mm) ... |
66,626 | Myco Nootropic Brain Gummies:-Does it really work? Review after 30 days Use | 3 | dx.doi.org/10.17504/protocols.io.rm7vzyd98lx1/v1 | https://www.protocols.io/view/myco-nootropic-brain-gummies-does-it-really-work-r-cdbas2ie | brainmyconootropic | TITLE: Myco Nootropic Brain Gummies:-Does it really work? Review after 30 days Use
AUTHORS: brainmyconootropic
[DESCRIPTION]
Myco Nootropic Brain Gummies is a versatile high-potency nootropic supplement manufactured in the UK and USA by Wolfson Brands. In common with all the other top nootropic products, Myco Nootro... | [] |
32,117 | Healthy Control Recruitment and Enrollment | null | dx.doi.org/10.17504/protocols.io.bbkvikw6 | null | Alyssa Ward, Gracie Gordon, Jimmie Ye | TITLE: Healthy Control Recruitment and Enrollment
AUTHORS: Alyssa Ward, Gracie Gordon, Jimmie Ye
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The Immune Cell Census aims to collect expression data from 1000 blood samples collected from healthy individuals. This protocol outlines our inclusion/exc... | ["[Participant Recruitment]\nOur study team maintains fliers that direct participants to the immunecensus.org website and give our study email address (immunecensus@ucsf.edu). After participants express interest, we schedule a phone screen.", "[Phone Screen]\nEnsure participants understand that the de-identified (no na... |
93,183 | Positive test extract (PTE) aliquots | 3 | dx.doi.org/10.17504/protocols.io.n92ldm1enl5b/v1 | https://www.protocols.io/view/positive-test-extract-pte-aliquots-c687zhzn | Anna Schmidt, Matthias Meyer | TITLE: Positive test extract (PTE) aliquots
AUTHORS: Anna Schmidt, Matthias Meyer
[DESCRIPTION]
This document describes the preparation of FluidX tubes containing positive test extract (PTE). It is part of the library preparation workflow of the Ancient DNA Core Unit of the MPI-EVA.
[STEPS] | [] |
92,337 | FASTQ alignment, gene counts, and differential expression analysis and functional annotation of DEGs | 5 | dx.doi.org/10.17504/protocols.io.dm6gp3mzdvzp/v1 | https://www.protocols.io/view/fastq-alignment-gene-counts-and-differential-expre-c6erzbd6 | Rebecca Wallings | TITLE: FASTQ alignment, gene counts, and differential expression analysis and functional annotation of DEGs
AUTHORS: Rebecca Wallings
[DESCRIPTION]
FASTQ alignment, gene counts, and differential expression analysis and functional annotation of DEGs
[STEPS]
SECTION: FASTQ alignment, gene counts, and differential expre... | ["[FASTQ alignment, gene counts, and differential expression analysis] FASTQ files were aligned against the mouse genome (GRCm39) and GRCm39.107 annotation using STAR to generate BAM files. Gene counts were generated from BAM files using Rsamtools (Bioconductor package) and the summarizeOverlaps function with the Genom... |
35,749 | Large (Klenow) Fragment Blunting (M0210) | 1 | dx.doi.org/10.17504/protocols.io.be6djha6 | https://www.protocols.io/view/large-klenow-fragment-blunting-m0210-be6djha6 | New England Biolabs | TITLE: Large (Klenow) Fragment Blunting (M0210)
AUTHORS: New England Biolabs
[DESCRIPTION]
Protocol for blunting ends by 3' overhang removal and fill-in of 3' recessed (5' overhang) ends using DNA Polymerase I, Large (Klenow) Fragment (M0210)
[STEPS]
1. DNA should be dissolved in 1 X or T4 DNA Ligase Reaction buff... | ["DNA should be dissolved in 1 X or T4 DNA Ligase Reaction buffer supplemented with 33 Micromolar (µM) each dNTP.", "Add 1 unit of Klenow per microgram DNA.", "Incubate for 15 min at 25 °C.", "Stop reaction by adding EDTA to a final concentration of 10 Milimolar (mM).", "Heat for 20 min at 75 °C."] |
67,416 | F1 Keto GummiesBody Weight Reduction Formula Reviews, Official Store , price and where to buy ? | 3 | dx.doi.org/10.17504/protocols.io.5qpvobmnxl4o/v1 | https://www.protocols.io/view/f1-keto-gummiesbody-weight-reduction-formula-revie-cd3ys8pw | mickleputh | TITLE: F1 Keto GummiesBody Weight Reduction Formula Reviews, Official Store , price and where to buy ?
AUTHORS: mickleputh
[DESCRIPTION]
The rising number of affected people is what's going on to focus in on this issue really.
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.r67d9hn | null | null | TITLE: No Title
AUTHORS:
[STEPS] | [] |
56,839 | Mouse Islet Perifusion (3-stimuli protocol) | 1 | dx.doi.org/10.17504/protocols.io.n2bvj6yenlk5/v1 | https://www.protocols.io/view/mouse-islet-perifusion-3-stimuli-protocol-b3rfqm3n | Islet and Pancreas Analysis Core | TITLE: Mouse Islet Perifusion (3-stimuli protocol)
AUTHORS: Islet and Pancreas Analysis Core
[DESCRIPTION]
Our perifusion setup consists of 4 independently-driven channels, which allows for up to 4 different groups of islets to be studied simultaneously. Each channel has an intake catheter, a peristaltic pump, a cham... | ["[General Perifusion Startup] Fill perifusion water bath with deionized water to about 1 inch from the top and set the temperature to 37 °C.", "[Preparation of Base Perifusion Media and Secretagogues] Prepare base perifusion media by combining reagents below in a 1-L Erlenmeyer flask. Add 1 L of deionized water and mi... |
null | null | null | dx.doi.org/10.17504/protocols.io.cjeujd | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<strong>Peroxide Value Method</strong><br /><br /> Brief description: This method for peroxide value determination of lipids is based on the original International Dairy Federation standard method. The basic principal of the method is that ferrous(Fe2+) ions are oxidized to ferr... | [] |
45,315 | 3.1 Human iPSC Culture | 1 | dx.doi.org/10.17504/protocols.io.bqhbmt2n | https://www.protocols.io/view/3-1-human-ipsc-culture-bqhbmt2n | Evelyn J. Sauter, Lisa K. Kutsche, Simon D. Klapper, Volker Busskamp | TITLE: 3.1 Human iPSC Culture
AUTHORS: Evelyn J. Sauter, Lisa K. Kutsche, Simon D. Klapper, Volker Busskamp
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This is part 3.1 of the "</span><a href="https://www.protocols.io/private/C65DB81838BC11EBA61A0A58A9FEAC2A/protocols" style = "text-decora... | ["[3.1 Human iPSC Culture]\nFor the coating of cell culture plates, resuspend one aliquot of Matrigel in the appropriate amount of cold coating medium (see Note 1). Add the Matrigel solution to the cell culture plates and distribute equally so that the entire well is covered (see Note 6).", "[3.1 Human iPSC Culture]\nT... |
12,975 | DNA and RNA backups | null | dx.doi.org/10.17504/protocols.io.qwpdxdn | null | Adriana Alberti, Julie Poulain, Stefan Engelen, Karine Labadie, Sarah Romac, Isabel Ferrera, Guillaume Albini, Jean-Marc Aury, Caroline Belser, Alexis Bertrand, Corinne Cruaud, Corinne Da Silva, Carole Dossat, Frédéric Gavory, Shahinaz Gas, Julie Guy, Maud Haquelle, E'krame Jacoby, Olivier Jaillon, Arnaud Lemainque, E... | TITLE: DNA and RNA backups
AUTHORS: Adriana Alberti, Julie Poulain, Stefan Engelen, Karine Labadie, Sarah Romac, Isabel Ferrera, Guillaume Albini, Jean-Marc Aury, Caroline Belser, Alexis Bertrand, Corinne Cruaud, Corinne Da Silva, Carole Dossat, Frédéric Gavory, Shahinaz Gas, Julie Guy, Maud Haquelle, E'krame Jacoby, ... | ["After nucleic acids extractions, prepare two RNA aliquots and three DNA aliquots for each sample. - RNA: use one aliquot for the library preparation and sequencing process, and store the second one as a backup. If RNA quantity is - DNA: use the first aliquot for the librayr preparation and the second one for backu... |
null | null | null | dx.doi.org/10.17504/protocols.io.rsvd6e6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<p>The protocol aims explicitly to amplify BFV viruses and not other viruses.</p>
<p>The assay targets the E2 gene region and is designed as a qualitative test for investigating BFV infection of humans... | [] |
57,225 | Total RNA and DNA from Microalgae | 1 | null | https://www.protocols.io/view/total-rna-and-dna-from-microalgae-b35hqq36 | Yingyu Hu, Zoe V Finkel | TITLE: Total RNA and DNA from Microalgae
AUTHORS: Yingyu Hu, Zoe V Finkel
[DESCRIPTION]
Here we describe a protocol for extracting and quantifying bulk RNA and DNA from microalgae, which is adapted from Berdalet E. et al. (2005).
RNA and DNA are extracted from microalgae samples and then quantified by fluorochrome ... | ["[Day 1: Freeze-dry samples] Freeze dry samples and blank filters. Freeze at -80 °C until processed.", "[Day 1: Prepare primary solutions] Turn on UV light in biosafety cabinet for 15 min and clean working surface with decontamination solution.", "[Day 1: Prepare primary solutions] Prepare Tris buffer 5 mM pH 8.0", ... |
54,516 | Padrões de arquivamento para Revisões Sistemáticas e Quantitativas da Literatura (RSQL) | 3 | dx.doi.org/10.17504/protocols.io.bzgup3ww | https://www.protocols.io/view/padr-es-de-arquivamento-para-revis-es-sistem-ticas-bzgup3ww | Daniel Vartanian | TITLE: Padrões de arquivamento para Revisões Sistemáticas e Quantitativas da Literatura (RSQL)
AUTHORS: Daniel Vartanian
[DESCRIPTION]
Este protocolo foi criado para o programa de Revisões Sistemáticas e Quantitativas da Literatura (RSQL) científica do Grupo Interdisciplinar de Pesquisa em Sono (GIPSO), mas ele pode ... | [] |
101,652 | GEM Generation and Barcoding | 0 | dx.doi.org/10.17504/protocols.io.5jyl82d16l2w/v1 | https://www.protocols.io/view/gem-generation-and-barcoding-dfhu3j6w | Heidi Monroe, Nayra Cardenes, Melanie Königshoff, koenigshoffm, Robert Lafyatis | TITLE: GEM Generation and Barcoding
AUTHORS: Heidi Monroe, Nayra Cardenes, Melanie Königshoff, koenigshoffm, Robert Lafyatis
[DESCRIPTION]
The Chromium Single Cell Gene Expression Solution upgrades short read sequencers to deliver a scalable microfluidic platform for 3’ digital gene expression by profiling 500-10,000 ... | ["[GEM Generation and Barcoding] Prepare Master Mix on ice. Pipette mix 15× and centrifuge briefly.\n \nMaster Mix:", "[GEM Generation and Barcoding] Add 31.9 µL master mix into each tube of a PCR 8-tube strip on ice .", "[GEM Generation and Barcoding] Assemble Chromium Next GEM Chip", "[GEM Generation and Barcoding] C... |
null | null | null | dx.doi.org/10.17504/protocols.io.qpadvie | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This year´s interlab study allows participants to fulfil Bronze medal requirements. </p>
<p>For this purposes a set of experiments has to be performed, which in the end will be compared and validated with other team´s data. </p>
<p>Part of this Challenge are the Calibration p... | [] |
63,222 | Post-IMS H&E Staining for Pancreas or Eye Cryosections | 1 | null | https://www.protocols.io/view/post-ims-h-e-staining-for-pancreas-or-eye-cryosect-b9ywr7xe | Angela Kruse, Diane Saunders, Jamie Allen, Carrie Romer, Danielle Gutierrez, Alvin Powers, Jeff Spraggins | TITLE: Post-IMS H&E Staining for Pancreas or Eye Cryosections
AUTHORS: Angela Kruse, Diane Saunders, Jamie Allen, Carrie Romer, Danielle Gutierrez, Alvin Powers, Jeff Spraggins
[DESCRIPTION]
This protocol for H&E staining can be applied to either fixed or unfixed frozen cryosections.
[STEPS]
SECTION: H&E ... | ["[H&E Staining] Incubate in 95% alcohol for 1 min , then wash, dipping until clear.", "[H&E Staining] Incubate in hematoxylin for 30 s , then wash until clear.", "[H&E Staining] Dip 3-4x in bluing solution, then wash for 30 s", "[H&E Staining] Dip 3-4x in 95% alcohol.", "[H&E Staining] Dip 1-2x in ... |
86,204 | Induction of starvation stress | 1 | dx.doi.org/10.17504/protocols.io.5jyl8pjq7g2w/v1 | https://www.protocols.io/view/induction-of-starvation-stress-cye4xtgw | Louise Uoselis | TITLE: Induction of starvation stress
AUTHORS: Louise Uoselis
[DESCRIPTION]
Induction of starvation stress using EBSS in HeLa cells
[STEPS]
SECTION: Day 1
1. Seed cells, aiming for a confluency of 90 – 100% at the time of treatment the next day.
SECTION: Day 2
2. Feed cells for 60 min in an appropriate volume of st... | ["[Day 1] Seed cells, aiming for a confluency of 90 – 100% at the time of treatment the next day.", "[Day 2] Feed cells for 60 min in an appropriate volume of standard growth media.", "[Day 2] Remove the media, and wash each well 3 times with an ample amount of room temperature PBS (eg. Wash with 3 mL of PBS per well o... |
23,387 | Instructional tutorial for using demuxlet | null | dx.doi.org/10.17504/protocols.io.233ggqn | null | Hyun Min Kang, Meena Subramaniam, Sasha Targ, Michelle Nguyen, Lenka Maliskova, Elizabeth McCarthy, Eunice Wan, Simon Wong, Lauren Byrnes, Cristina M Lanata, Rachel E Gate, Sara Mostafavi, Alexander Marson, Noah Zaitlen, Lindsey A Criswell, Chun Jimmie Ye | TITLE: Instructional tutorial for using demuxlet
AUTHORS: Hyun Min Kang, Meena Subramaniam, Sasha Targ, Michelle Nguyen, Lenka Maliskova, Elizabeth McCarthy, Eunice Wan, Simon Wong, Lauren Byrnes, Cristina M Lanata, Rachel E Gate, Sara Mostafavi, Alexander Marson, Noah Zaitlen, Lindsey A Criswell, Chun Jimmie Ye
[DESC... | ["[Getting Started]\nPlease select between the two following options: 1. Installating from Docker2. Installing from source", "[Getting Started]\nRunning demuxlet from dockerWe have created a docker container at yimmieg/demuxlet to run demuxlet through docker.You can run it with$ docker run -v path/to/tutorial:/data yim... |
99,250 | NCBI submission protocol (BioSample/SRA) | 1 | dx.doi.org/10.17504/protocols.io.rm7vzjyj5lx1/v1 | https://www.protocols.io/view/ncbi-submission-protocol-biosample-sra-dc6s2zee | Ruth Timme, Emma Griffiths, Bryan Wee | TITLE: NCBI submission protocol (BioSample/SRA)
AUTHORS: Ruth Timme, Emma Griffiths, Bryan Wee
[DESCRIPTION]
PURPOSE: This document provides detailed instructions on how to submit raw sequence data and associated contextual data for pathogens to NCBI while adhering to the INSDC standard data structure, "Pathogen DOM,... | ["[Establish submission environment at NCBI] Set up a new NCBI submission environment for your laboratory:\n\n1.1: Create an NCBI user account\n1.2: Set up an NCBI submission user group for your lab\n1.4: Bookmark the link to your submission portal\n1.5. Identify or establish new BioProjects (detailed in Step 3)\n\n\nR... |
97,722 | Immunofluorescence Staining and High Content Imaging | 0 | null | https://www.protocols.io/view/immunofluorescence-staining-and-high-content-imagi-dbn22mge | David Sirkin, Gregory Tracy, Hanwen Zhang, Lilia Peyton, Ada McCarroll, Jubao Duan | TITLE: Immunofluorescence Staining and High Content Imaging
AUTHORS: David Sirkin, Gregory Tracy, Hanwen Zhang, Lilia Peyton, Ada McCarroll, Jubao Duan
[DESCRIPTION]
This protocol offers a description of immunofluorescence staining and high content imaging of iPSC induced neurons using the ImageXpress Micro Confocal H... | ["[Immunofluorescence Staining] Wash iPSC derived neurons twice with 1X PBS and fix with 4% PFA for 30 min in a 96 well optical bottom plate with a polymer base.", "[Immunofluorescence Staining] Store fixed neurons at 4C in 1x PBS with 0.02% sodium azide.", "[Immunofluorescence Staining] Aspirate sodium azide with pipe... |
null | null | null | dx.doi.org/10.17504/protocols.io.cixufm | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<a href="http://store.p212121.com/ampicillin-sodium-salt/" target="_blank">Ampicillin</a> is a β-lactam antibiotic routinely used in bacterial selection procedures to select for bacteria (usually E. coli) that have been transformed with an ampicillin resistance plasmid... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.ezdbf26 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol aims to achieve an isotopic labeling of mixotrophic algae using <sup>15</sup>N and <sup>13</sup>C labeled heat-killed bacteria. It was developped to be used with the mixorophic chrysophyte <em>Ochromonas</em> to asses the sources of carbon and nitrogen of this a... | [] |
52,114 | Long-read plant genome assembly and annotation: quality assessment | 5 | null | https://www.protocols.io/view/long-read-plant-genome-assembly-and-annotation-qua-bw5spg6e | Scott Ferguson, Ashley Jones, Justin Borevitz | TITLE: Long-read plant genome assembly and annotation: quality assessment
AUTHORS: Scott Ferguson, Ashley Jones, Justin Borevitz
[DESCRIPTION]
With the introduction of long-read, third generation sequencing (e.g. Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio) and associated bioinformatics tools... | ["[Genome quality assessment] Having assembled a genome we want to assess how good it is. The three major considerations here are contiguity, accuracy and completeness.\n\nContiguity we can assess with numerical statistics: \nN50.\nE-size.\nnumber of sequences.\nN50 and E-size are both ways of trying to express genome ... |
91,037 | Preparation of ex-vivo brain slices for physiology experiments | 4 | null | https://www.protocols.io/view/preparation-of-ex-vivo-brain-slices-for-physiology-c455yy86 | enrico.zampese | TITLE: Preparation of ex-vivo brain slices for physiology experiments
AUTHORS: enrico.zampese
[DESCRIPTION]
This protocols describes the procedure to obtain ex-vivo mouse brain slices with a vibratome.
This protocol is originally meant to collect mibrain coronal slices but can be adapted to other brain regions/configu... | ["[Before the procedure:] A few hours/day before the procedure it is recommended to prepare some slicing solution and freeze it (~200ml).", "[Before the procedure:] Break the pre-frozen slicing solution into a large beaker and add freshly-made slicing solution. With the help of the immersion blender transform the froze... |
75,403 | Manual de configuración Audiomoth 1.2.0 - Guía de 8+1 pasos | 1 | dx.doi.org/10.17504/protocols.io.14egn2wdqg5d/v1 | https://www.protocols.io/view/manual-de-configuraci-n-audiomoth-1-2-0-gu-a-de-8-cmvju64n | Jaime Pacheco | TITLE: Manual de configuración Audiomoth 1.2.0 - Guía de 8+1 pasos
AUTHORS: Jaime Pacheco
[DESCRIPTION]
Esta pequeña guía está dedicada a toda persona o institución interesada en incorporar las evaluaciones acústicas pasivas de murciélagos u otro grupo de fauna silvestre (e incluso evaluación de paisaje sonoro) emplea... | ["[Manual de configuración Audiomoth 1.2.0 Guía de 8+1 pasos] Paso 2\nColocar las tres (3) pilas AA en la parte posterior del Audiomoth 1.2.0.", "[Manual de configuración Audiomoth 1.2.0 Guía de 8+1 pasos] Paso 1\nPreparar todo el equipamiento necesario para la preparación y configuración considerando los siguientes el... |
86,627 | Protocol to isolate and fix nuclei from flash frozen mouse kidneys for IGVF | 4 | null | https://www.protocols.io/view/protocol-to-isolate-and-fix-nuclei-from-flash-froz-cyubxwsn | Elisabeth Rebboah | TITLE: Protocol to isolate and fix nuclei from flash frozen mouse kidneys for IGVF
AUTHORS: Elisabeth Rebboah
[DESCRIPTION]
This protocol describes isolation of nuclei from 10 week old mouse kidneys from 8 founder strains (B6J, AJ, 129S1J, NZOJ, WSBJ, NODJ, PWKJ, and CASTJ), preparation of a single nucleus suspension,... | ["[Setup] Label tubes.", "[Setup] Pre-chill centrifuge to 4C.", "[Setup] Prepare ice buckets.", "[Setup] Prepare lysis buffer in a 50 ml conical tube on ice. Distribute 2.5 ml into 8 gentleMACS C Tubes on ice. Add RNase inhibitor to the lysis buffer aliquot the day of the experiment.", "[Setup] Prepare RSB in a 50 ml c... |
41,012 | Protocol for capture and concentration of viruses from wastewater samples (up to 50 mL) using Magnetic Nanotrap® particles. | 4 | null | https://www.protocols.io/view/protocol-for-capture-and-concentration-of-viruses-bkauksew | Anurag Patnaik, Ben Lepene, Alex Barclay | TITLE: Protocol for capture and concentration of viruses from wastewater samples (up to 50 mL) using Magnetic Nanotrap® particles.
AUTHORS: Anurag Patnaik, Ben Lepene, Alex Barclay
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol provides a method for Magnetic Nanotrap® particle-based... | ["[Virus capture]\nPlace a 50 mL conical tube on a tube rack.", "[Virus capture]\nAdd of wastewater sample to the conical tube.\n50 mL", "[Virus capture]\nLet the wastewater sample sit on the benchtop at for . This will allow large aggregates to settle at the bottom of the tube.\n0 Room temperature", "[Virus captu... |
null | null | null | dx.doi.org/10.17504/protocols.io.k3xcypn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The presence and structure of EFNs in <em>Opuntia robusta</em> had not been investigated. We used light, scanning-electron, and transmission-electron microscopy to examine morphology, anatomy, and ultrastructure of the secretory spines in areoles in female and hermaphrodite i... | [] |
60,195 | Synthesis of colloidal dextran-conjugated superparamagnetic iron nanoparticles (SPIONs) | 6 | dx.doi.org/10.17504/protocols.io.eq2lyn69pvx9/v1 | https://www.protocols.io/view/synthesis-of-colloidal-dextran-conjugated-superpar-b62brgan | William Hancock-Cerutti, Arun Kumar Tharkeshwar, Shawn M Ferguson, Pietro De Camilli | TITLE: Synthesis of colloidal dextran-conjugated superparamagnetic iron nanoparticles (SPIONs)
AUTHORS: William Hancock-Cerutti, Arun Kumar Tharkeshwar, Shawn M Ferguson, Pietro De Camilli
[DESCRIPTION]
This method describes the synthesis and usage of dextran-conjugated superparamagnetic iron nanoparticles (SPIONs... | [] |
89,961 | S-4 SOIL TESTING | 4 | dx.doi.org/10.17504/protocols.io.dm6gp3xbdvzp/v1 | https://www.protocols.io/view/s-4-soil-testing-c34hyqt6 | REDI-NET Consortium | TITLE: S-4 SOIL TESTING
AUTHORS: REDI-NET Consortium
[DESCRIPTION]
This protocol details standard operating procedure for soil testing.
[BEFORE_START]
BEFORE START
Check the DNA and RNA concentrations in each sample of total nucleic acid (TNA) extraction.
If the concentrations are detectable, choose the sequencing ... | ["[gDNA PREPARATION] When the RNA concentration of the sample is lower than the detectable range of the Qubit High Sensitivity Assay (<0.01 ng/ul), the sample is subjected to gDNA sequencing. The cDNA synthesis can be skipped.", "[gDNA PREPARATION] When the DNA concentration >10 ng/ul, calculate the required volume of ... |
61,648 | Mitogenome (or other Multi-gene) Maximum Likelihood Phylogenetic Analyses | 1 | dx.doi.org/10.17504/protocols.io.bp2l613kzvqe/v1 | https://www.protocols.io/view/mitogenome-or-other-multi-gene-maximum-likelihood-b8fqrtmw | Dakota Betz | TITLE: Mitogenome (or other Multi-gene) Maximum Likelihood Phylogenetic Analyses
AUTHORS: Dakota Betz
[DESCRIPTION]
A guide to doing maximum likelhood whole mitogenome (or multigene) analyses in RaXML. This was written after Avery's instructions!
[STEPS]
1. Create text files in FASTA format with all of each of the g... | ["Create text files in FASTA format with all of each of the genes you want to use (i.e. Pilargidae_12S.txt, Gastropods_ATP6.txt, etc.). Make sure the same organism has the same name for ALL of the genes (spaces included - there should be none, but sometimes they sneak up on you).", "Open Mesquite, create a new file, ma... |
21,828 | Sub-Cloning Primer Design and PCR | null | dx.doi.org/10.17504/protocols.io.zjcf4iw | null | Abby Jurgensmeier, Moriah Beck | TITLE: Sub-Cloning Primer Design and PCR
AUTHORS: Abby Jurgensmeier, Moriah Beck
[STEPS]
?. Combine the following in a small PCR tube: AB11 uLForward Primer (10 uM)21 uLReverse Primer (10 uM)31uLTemplate DNA (may need adjustment for at least 20 ng; remember to adjust water volume!)41 uLdNTPs50.25 uLTaq Polymerase65 u... | ["Combine the following in a small PCR tube: AB11 uLForward Primer (10 uM)21 uLReverse Primer (10 uM)31uLTemplate DNA (may need adjustment for at least 20 ng; remember to adjust water volume!)41 uLdNTPs50.25 uLTaq Polymerase65 uL10X Thermopol Buffer741.75 uLddH20\nAB11 uLForward Primer (10 uM)21 uLReverse Primer (10 u... |
15,197 | Rice medium | null | dx.doi.org/10.17504/protocols.io.s35egq6 | null | Roscoff Culture Collection | TITLE: Rice medium
AUTHORS: Roscoff Culture Collection
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Used for heterotrophic protists.</div></div>
[STEPS]
?. Filter 1L of seawater aged for at least two months on prefilter and filter 0.2 µm
?. Heat seawater during 20 min at 100°C
?. Add 40 graism o... | ["Filter 1L of seawater aged for at least two months on prefilter and filter 0.2 µm", "Heat seawater during 20 min at 100°C", "Add 40 graism of rice", "Autoclave 3 times the medium (let temperature decrease between each round of autoclaving)"] |
29,171 | ChroPlate - ProteinG | null | dx.doi.org/10.17504/protocols.io.8qthvwn | null | Alexandra Ehl, David Frommholz, Nadine Stefanczyk | TITLE: ChroPlate - ProteinG
AUTHORS: Alexandra Ehl, David Frommholz, Nadine Stefanczyk
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Purification Guide for the Isolation of Antibodies with ChroPlate Filtration Plates by DALEX Biotech.</span></div><div class = "tex... | ["[Load and Wash]\nPlace the ChroPlate on a clean deep-well plate. Add up to 1.5 ml sample to every well. Centrifuge 2 - 10 minutes at 400 g in a swing-out rotor.\nIt is advisable to keep the flow-through and wash fractions for later analysis, e.g. SDS-PAGE.The centrifugation time depends on the sample's volume and vis... |
104,255 | Hydrogel Microparticles as Force Sensors: Synthesis and Application in Phagocytosis Studies | 0 | dx.doi.org/10.17504/protocols.io.q26g71dqqgwz/v1 | https://www.protocols.io/view/hydrogel-microparticles-as-force-sensors-synthesis-dh2738hn | Alvja Mali, Youri Peeters, Mangala Srinivas, Daan Vorselen | TITLE: Hydrogel Microparticles as Force Sensors: Synthesis and Application in Phagocytosis Studies
AUTHORS: Alvja Mali, Youri Peeters, Mangala Srinivas, Daan Vorselen
[DESCRIPTION]
We provide a protocol for the synthesis of tuneable hydrogel microparticles (HMPs), and their application to measure forces during phagocy... | ["[Deformable Acrylamide co-Acrylic acid Microparticle (DAAM-particle) synthesis] Prepare the extrusion equipment", "[Deformable Acrylamide co-Acrylic acid Microparticle (DAAM-particle) synthesis] Flask selection: Check if the flask ensures a proper fit of the SPG module. Allow N2 atmosphere regulation by creating a cl... |
89,505 | Optical densitometry of neuronal fibers | 4 | dx.doi.org/10.17504/protocols.io.8epv5x3nng1b/v1 | https://www.protocols.io/view/optical-densitometry-of-neuronal-fibers-c3m9yk96 | Núria Peñuelas | TITLE: Optical densitometry of neuronal fibers
AUTHORS: Núria Peñuelas
[DESCRIPTION]
Optical densitometry of striatal neuronal fibers in the rodent brain
[STEPS]
1. Scan the immunostained serial coronal sections covering different caudorostral levels of the brain regions (for striatum, 4 sections/animal) with an Epso... | ["Scan the immunostained serial coronal sections covering different caudorostral levels of the brain regions (for striatum, 4 sections/animal) with an Epson Perfection v750 Pro scanner.", "Open the resulting images in ImageJ (RRID:SCR_003070,https://imagej.net/).", "With the free hand selections tool, draw the region o... |
28,908 | Feeding T75, T150, and 6wp Backup | 1 | dx.doi.org/10.17504/protocols.io.8gkhtuw | https://www.protocols.io/view/feeding-t75-t150-and-6wp-backup-8gkhtuw | Andrea Argouarch | TITLE: Feeding T75, T150, and 6wp Backup
AUTHORS: Andrea Argouarch
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol includes feeding of T75 flask, T150 flask, or the back up 6 well plate.</div></div>
[STEPS]
?. [Observations]
Observe cell morphology and outgrowth
?. [Observations]
Feed ever... | ["[Observations]\nObserve cell morphology and outgrowth", "[Observations]\nFeed every 2-3 days until 90-100% confluent", "[Preparation]\nTurn off UV lights and clean hood with 70% ethanol", "[Preparation]\nClean items with 70% ethanol and bring into hood a. Sterile Filtered Media with PenStrep", "[Preparation]\nWrit... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.