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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101,193 | Preparation of single cell suspensions from human intestinal biopsies for single cell genomics applications | 1 | dx.doi.org/10.17504/protocols.io.q26g7bxqklwz/v5 | https://www.protocols.io/view/preparation-of-single-cell-suspensions-from-human-de3h3gj6 | Ran RZ Zhou, Oni Basu | TITLE: Preparation of single cell suspensions from human intestinal biopsies for single cell genomics applications
AUTHORS: Ran RZ Zhou, Oni Basu
[DESCRIPTION]
The protocol is adapted from Fujii's and Smillies's reports for single cell transcriptome analysis from human intestines. It provides details on acquirement of... | ["[Pre-Dissociation] Chill 1x PBS, wash media and dissociation media on ice. Samples are transfered with Advanced DMEM/F12 based media in 1.7 ml eppendorf tubes on ice. Once received in lab, samples are transfered to 35 mm dish using sharp-end forceps. Alternatively, tissues can be transferred to a 5 ml conical tube us... |
47,521 | MAPseq (Multiplexed Analysis of Projections by Sequencing) sample processing protocol | 4 | dx.doi.org/10.17504/protocols.io.bsm9nc96 | https://www.protocols.io/view/mapseq-multiplexed-analysis-of-projections-by-sequ-bsm9nc96 | Huiqing Zhan, Justus Kebschull, Anthony M. Zador | TITLE: MAPseq (Multiplexed Analysis of Projections by Sequencing) sample processing protocol
AUTHORS: Huiqing Zhan, Justus Kebschull, Anthony M. Zador
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes sample processing steps of MAPseq, a high-throughput mapping of single-neuron... | ["[RNA extraction]\nTissues are homogenized in 400ul of Trizol either with a Pellet Pestle Motor or with a tissue homogenizer, and then add 600ul of Trizol to make 1 ml of Trizol/sampleExtract RNA according to manufacturer’s protocol of Trizol ReagentDissolve RNA of each tissue sample into 13 ul of H2O", "[Reverse tran... |
19,223 | Instructions for recreating the elPrep 4.0.0 WES benchmarks | null | dx.doi.org/10.17504/protocols.io.wzxff7n | null | Charlotte Herzeel | TITLE: Instructions for recreating the elPrep 4.0.0 WES benchmarks
AUTHORS: Charlotte Herzeel
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes how to recreate the elPrep 4.0.0 benchmarks for WES data.</div></div>
[STEPS]
?. Configuration1.1 Hardware1.2 Software
These instruct... | ["Configuration1.1 Hardware1.2 Software\nThese instructions have been tested with elPrep v.4.0.1. 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 4.0.1", "Installatio... |
102,478 | Mutant generation in Streptococcus mitis strain B6 | 0 | dx.doi.org/10.17504/protocols.io.261ge5ezyg47/v1 | https://www.protocols.io/view/mutant-generation-in-streptococcus-mitis-strain-b6-dgbn3sme | Samantha King | TITLE: Mutant generation in Streptococcus mitis strain B6
AUTHORS: Samantha King
[DESCRIPTION]
This protocol is the methodology that we have successfully employed to generate and confirm insertion deletion mutants in Streptococcus mitis strain B6. Attached to the protocol is a file that includes primers for the MonX m... | ["[Streptococcus mitis B6 mutagenesis protocol] Creation of a plasmid construct", "[Streptococcus mitis B6 mutagenesis protocol] The regions upstream and downstream of the region to be deleted were amplified\nusing primers 1 and 2, and 3 and 4, respectively. These primers were designed\nto contain appropriate overhangs... |
57,310 | Quantification of rat stomach surface area | 1 | dx.doi.org/10.17504/protocols.io.6qpvr6dmbvmk/v1 | https://www.protocols.io/view/quantification-of-rat-stomach-surface-area-b376qrre | Madeleine Di Natale, Billie Hunne, Martin Stebbing, John Furness | TITLE: Quantification of rat stomach surface area
AUTHORS: Madeleine Di Natale, Billie Hunne, Martin Stebbing, John Furness
[DESCRIPTION]
This protocol describes the methods used to quantify the surface area of the rat stomach. Scale photographs of rat stomachs, which were perfusion fixed, were used to determine the s... | ["Experiments were conducted on 4 male and 4 female Sprague-Dawley rats of 185-360 g. Procedures were approved by the University of Melbourne Animal Ethics Committee. Rats were supplied with food and water ad libitum prior to the experiments.", "Rats were deeply anesthetised with an intraperitoneal injection of a mixtu... |
28,702 | Th2 Polarization of Mouse CD4+ Cells | null | dx.doi.org/10.17504/protocols.io.796hr9e | null | Sam Li | TITLE: Th2 Polarization of Mouse CD4+ Cells
AUTHORS: Sam Li
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. [Isolation of CD4+ Cells From Lymph Nodes]
Harvest lymph nodes (superficial cervical, mandibular, axillary, inguinal, and mesenteric) from mice.
?. [Isolation of CD4+ Cells From Lymph Nodes]
Tease ly... | ["[Isolation of CD4+ Cells From Lymph Nodes]\nHarvest lymph nodes (superficial cervical, mandibular, axillary, inguinal, and mesenteric) from mice.", "[Isolation of CD4+ Cells From Lymph Nodes]\nTease lymph nodes through a sterile 70-µm nylon cell strainer to obtain single-cell suspensions in complete RPMI containing 1... |
27,367 | Collecting eDNA from marine water samples in the field | 1 | dx.doi.org/10.17504/protocols.io.6yfhftn | https://www.protocols.io/view/collecting-edna-from-marine-water-samples-in-the-f-6yfhftn | Reindert Nijland | TITLE: Collecting eDNA from marine water samples in the field
AUTHORS: Reindert Nijland
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the process of collecting eDNA from marine water samples in the field and four different approaches for preservation of filters with eDNA as... | ["[Collection of eDNA from the water on a filter membrane]\nCollect water in an appropriate sterile, DNA free container.\nFor marine samples collected during scuba diving, we use a small hand-pump and a punch-balloon.", "[Collection of eDNA from the water on a filter membrane]\nFilter - with the 250 ml filters (0.8 mic... |
null | null | null | dx.doi.org/10.17504/protocols.io.mmpc45n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Forty SD male rats were divided into five groups randomly (n = 8 per group): the normal control (N) group, the normal saline group (NS), the light osteoarthritis group (A), the mild osteoarthritis group (B) and the heavy osteoarthritis group (C). On day 0, the rats in the A, ... | [] |
95,597 | UV Exposure Protocol | 4 | null | https://www.protocols.io/view/uv-exposure-protocol-c9kmz4u6 | Martin O Pollard | TITLE: UV Exposure Protocol
AUTHORS: Martin O Pollard
[DESCRIPTION]
A procedure utilising a UV crosslinker to expose isolated DNA to UV radiation with the aim of inducing lesions in the DNA typical of that kind of damage induced by UV.
[STEPS]
SECTION: UV treatment
1. Pipette 2.2 µL of which has a measured concent... | ["[UV treatment] Pipette 2.2 µL of which has a measured concentration of 227 µg/ml from stock tube to sterile plastic petri dish.", "[UV treatment] Dilute material in petri dish with 22.8 µL of buffer to achieve a target of 25 µL of DNA at 20 ng/µl yielding 0.5 µg of DNA. Gently mix but do not agitate vigorously.", ... |
52,397 | PCR and gel electropheresis | 4 | dx.doi.org/10.17504/protocols.io.bxempjc6 | https://www.protocols.io/view/pcr-and-gel-electropheresis-bxempjc6 | Ashwinuday | TITLE: PCR and gel electropheresis
AUTHORS: Ashwinuday
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol can be used to confirm genes or DNA of interest from a template using PCR. Also to amplify required amount of genes to larger amounts.</div></div>
[STEPS]
?. Prepare the working st... | ["Prepare the working stock solution of all the reagents required. If already prepared and stored, takeout from the refrigerator and thaw on ice.", "Prepare the following mixes each of total : - Itemsnegative controltest sampleultrapure water (from Milli-Q)40 ul39 ulpfu Buffer (10X)5 ul (1X)5 ul (1X)Forward primer (2... |
51,286 | Identifying the data elements and functionalities of clinical decision-support systems to administer medications for neonates and pediatrics: A systematic literature review protocol | 1 | dx.doi.org/10.17504/protocols.io.bwbwpape | https://www.protocols.io/view/identifying-the-data-elements-and-functionalities-bwbwpape | Somaye Norouzi, Zahra galavi, Leila Ahmadian | TITLE: Identifying the data elements and functionalities of clinical decision-support systems to administer medications for neonates and pediatrics: A systematic literature review protocol
AUTHORS: Somaye Norouzi, Zahra galavi, Leila Ahmadian
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div clas... | ["Review title and timescale1.Review titleIdentifying the data elements and functionalities of clinical decision-support systems to administer medications for neonates and pediatrics: A systematic literature review protocol.2. Orgignal langaage titleEnglish3. anticipated or actual start date10/07/20214. Anticipated com... |
58,244 | Conventional fixation method for Tetrahymena thermophila | 4 | null | https://www.protocols.io/view/conventional-fixation-method-for-tetrahymena-therm-b45cqy2w | miao.tian | TITLE: Conventional fixation method for Tetrahymena thermophila
AUTHORS: miao.tian
[DESCRIPTION]
A rapid and robust method for fixing Tetrahymena thermophila cells
[STEPS]
SECTION: General description of the method
1. It works for the IF of cytoplasm, nucleoplasm, and chromatin-bound proteins, FISH staining of rec... | ["[General description of the method] It works for the IF of cytoplasm, nucleoplasm, and chromatin-bound proteins, FISH staining of receptive sequences (e.g., telomeric repeats, TEs). Nuclear and cell morphology are nicely maintained.\n\nIt does not work for the IF of Cna1, γ-H2A.X, and tubulin.", "[Reagents] - 37% ... |
30,550 | gRNA design and cloning with SapI into Loop plasmid L2_lacZgRNA-Cas9-CsA | null | dx.doi.org/10.17504/protocols.io.93wh8pe | null | Eftychis Frangedakis, marta tomaselli, Susana Sauret-Gueto | TITLE: gRNA design and cloning with SapI into Loop plasmid L2_lacZgRNA-Cas9-CsA
AUTHORS: Eftychis Frangedakis, marta tomaselli, Susana Sauret-Gueto
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol explains how to design and clone the guide RNA target sequence into a L2 plasmid ready to ... | ["[Protocol for design of gRNA and cloning into L2 with SapI]\ngRNA oligo designOrder two oligos that contain the forward and reverse guide sequence plus the overhangs necessary for ligation (highlighted with bold) into L2_lacZgRNA-Cas9-CsA: oligo F: 5’- TCG-NNNNNNNNNNNNNNNNNNNN-gt 3’oligo R: 5’-AAAac-NNNNNNNNNNNNNNNN... |
31,722 | Isolation of Adult Pig Ventricular Myocytes | 1 | dx.doi.org/10.17504/protocols.io.ba8iihue | https://www.protocols.io/view/isolation-of-adult-pig-ventricular-myocytes-ba8iihue | Robert Harvey, Shailesh Agarwal | TITLE: Isolation of Adult Pig Ventricular Myocytes
AUTHORS: Robert Harvey, Shailesh Agarwal
[DESCRIPTION]
This protocol is for the isolation of adult pig ventricular myocytes.
[GUIDELINES]
This protocol is in compliance with the Guide for the Care and Use of Laboratory Animals as adopted by National Institutes of He... | ["Sedate adult pig (25 to 50 kg) with Telezol (500 mg, intramuscular). Administer atropine (1 mg, subcutaneous), to control salivary and bronchial secretions, and (200 mg, intravenous), to facilitate tracheal intubation. Anesthetize the animal with isoflurane (2-4%, inhalation).", "Shave the chest area and wash with be... |
45,891 | Sample Collection: Primate Feces for DNA/RNA | 4 | null | https://www.protocols.io/view/sample-collection-primate-feces-for-dna-rna-bq3bmyin | Alicia Rich | TITLE: Sample Collection: Primate Feces for DNA/RNA
AUTHORS: Alicia Rich
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">All of the methods and protocols for this project have been reviewed and approved by the Otterbein University Institutional Animal Care and Use Committee, Otterbein University's E... | ["[Sample Collection]\nGather fresh feces (\nIf it is not possible to gather fresh feces indirectly from a reliably identified individual, then follow the rectal swab directions in the direct sample collection procedure.\nAlways wear a facial covering and nitrile examination gloves while collecting samples.", "[Sample ... |
108,969 | GoT-ChA: Genotyping of Targeted loci with single-cell Chromatin Accessibility | 0 | dx.doi.org/10.17504/protocols.io.ewov19pn2lr2/v1 | https://www.protocols.io/view/got-cha-genotyping-of-targeted-loci-with-single-ce-dnnh5db6 | Franco Izzo, Robert M Myers, Saravanan Ganesan, Levan Mekerishvili, Sanjay Kottapalli, Tamara Prieto, Elliot O Eton, Theo Botella, Ivan Raimondi, Catherine Potenski, Dan A Landau | TITLE: GoT-ChA: Genotyping of Targeted loci with single-cell Chromatin Accessibility
AUTHORS: Franco Izzo, Robert M Myers, Saravanan Ganesan, Levan Mekerishvili, Sanjay Kottapalli, Tamara Prieto, Elliot O Eton, Theo Botella, Ivan Raimondi, Catherine Potenski, Dan A Landau
[DESCRIPTION]
Somatic mutations are crucial fo... | ["[Buffer Preparations] Pre-chill swing-bucket centrifuge to 4˚C", "[GoT-ChA on Permeabilized Whole Cells] Obtain all single cell suspensions (filter if needed) and measure viability and density (if\nviability is <90% proceed with live cell enrichment and/or use best judgement\ndepending on sample source / importance /... |
null | null | null | dx.doi.org/10.17504/protocols.io.qs8dwhw | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?. | [] |
45,912 | C-SOP-101: Bacterial Genomic DNA Isolation using the Nexttec 1-step Kit (96-plate format) | 4 | null | https://www.protocols.io/view/c-sop-101-bacterial-genomic-dna-isolation-using-th-bq3ymypw | Mihir Kekre | TITLE: C-SOP-101: Bacterial Genomic DNA Isolation using the Nexttec 1-step Kit (96-plate format)
AUTHORS: Mihir Kekre
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes an easy, convenient and rapid method of genomic DNA isolation and purification from Gram (+) and (-) bacterial... | ["[Before Starting]\nCreate an organised bench space by clearing away all clutter in order to maximize work efficiency. Avoid movements that will expose sterile materials to airborne contaminants.", "[Preparation of the Overnight Bacterial Suspension]\nRefer step 5 for Acinetobacter baumannii, Escherichia coli, Klebsie... |
68,379 | FIND-seq protocol v1.0 | 4 | dx.doi.org/10.17504/protocols.io.q26g74o78gwz/v1 | https://www.protocols.io/view/find-seq-protocol-v1-0-cez3tf8n | Iain C. Clark, Michael A. Wheeler, Hong-Gyun Lee, Liliana M. Sanmarco, Zhaorong Li, Shravan Thaploo, Carolina M. Polonio, Seung Won Shin, Giulia Scalisi, Joseph M. Rone, Federico Giovannoni, Stephanie E. J. Zandee, Alexandre Prat, Daniel C. Douek, Eli A. Boritz, Francisco J. Quintana, Adam R. Abate | TITLE: FIND-seq protocol v1.0
AUTHORS: Iain C. Clark, Michael A. Wheeler, Hong-Gyun Lee, Liliana M. Sanmarco, Zhaorong Li, Shravan Thaploo, Carolina M. Polonio, Seung Won Shin, Giulia Scalisi, Joseph M. Rone, Federico Giovannoni, Stephanie E. J. Zandee, Alexandre Prat, Daniel C. Douek, Eli A. Boritz, Francisco J. Quint... | ["[REAGENT SETUP] 20% (vol/vol) 1H-1H-2H-2H-Perfluoro-1-Octanol solution (Use this reagent immediately after preparation.)\n \n Reagent Reagent conc. Vol. PFO - 10 mL HFE-7500 - 40 mL Total 50 mL \n \n \n\n0.1% SPAN-80 in Hexane (Use this reagent immediately after preparation.)\n Reagent R... |
107,800 | Nuclei isolation from human brain cortex | 0 | dx.doi.org/10.17504/protocols.io.bp2l626bzgqe/v1 | https://www.protocols.io/view/nuclei-isolation-from-human-brain-cortex-dmhy437w | Xian Adiconis, Joshua Z Levin | TITLE: Nuclei isolation from human brain cortex
AUTHORS: Xian Adiconis, Joshua Z Levin
[DESCRIPTION]
This protocol can be used on flash-frozen or RNAlater-preserved brain cortex. It is based on a previously published method (1) with a few modifications including, 1) Adding Recombinant RNase Inhibitor into the EZ prep... | ["Prepare the following lysis buffers, wash buffer and resuspension buffer, and keep on ice.\nLysis buffer1\n \nLysis buffer2\n \nWash buffer (PBS with 0.01% BSA and 0.04 U/µl RNase Inhibitor)\n \n Nuclei resuspension buffer (PBS with 1% BSA and 0.2 U/µl RNase Inhibitor)", "Add 2 mLof cold Lysis buffer1 into an empty d... |
82,488 | ADI IsletCore Minimal Donor Criteria | 1 | dx.doi.org/10.17504/protocols.io.14egn2p7mg5d/v2 | https://www.protocols.click/view/adi-isletcore-minimal-donor-criteria-cusywwfw | Jocelyn E Manning Fox, James Lyon, Patrick MacDonald | TITLE: ADI IsletCore Minimal Donor Criteria
AUTHORS: Jocelyn E Manning Fox, James Lyon, Patrick MacDonald
[DESCRIPTION]
This SOP defines the pancreas donor profile acceptable for use by the Alberta Diabetes Institute IsletCore in their human islet isolation program.
ADI IsletCore receives pancreases from multiple Ca... | ["[ADI IsletCore Donor Inclusion Criteria] The following are ADI IsletCore inclusion criteria for pancreas donors for human islet isolation:\n\nA multi-organ donor or pancreas-only donor if the donor meets all the criteria for multi-organ donation\nAny type of donation (NDD, DCD, MAID)\nDCD warm ischemia time <30 minut... |
55,491 | Mitochondrial Antigen Presentation in RAW macrophages | 4 | dx.doi.org/10.17504/protocols.io.yxmvmk2x5g3p/v2 | https://www.protocols.click/view/mitochondrial-antigen-presentation-in-raw-macropha-b2fbqbin | Ahmed Fahmy, Tyler Cannon | TITLE: Mitochondrial Antigen Presentation in RAW macrophages
AUTHORS: Ahmed Fahmy, Tyler Cannon
[DESCRIPTION]
This protocol details methods for 3-day Mitochondrial Antigen Presentation Assay in a murine macrophage cell line (RAW) that expresses a glycoprotein B (gB) of herpes simplex virus 1 (HSV1) targeted to the mit... | ["[Day 1: cell plating] Prepare a 24 well plate:\nLabel appropriately (experimental condition – Heath shock (HS), controls, infection controls, etc. ) \nDuplicate labelled wells for the peptide control", "[Day 1: cell plating] Scrape RAW cells and resuspend (pipette up and down 8x).", "[Day 1: cell plating] Count RAW c... |
null | null | null | dx.doi.org/10.17504/protocols.io.rzkd74w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><span style="font-weight: 400;">This protocol is based on the fact that we struggled for a long time to obtain high purity DNA from the fungal material, especially from several rust species. We finally thought we made it when we obtained DNA with perfect QC measures using a <... | [] |
65,055 | Oxygen Evolution Measurement: Light Curve for Algae | 1 | dx.doi.org/10.17504/protocols.io.q26g74no9gwz/v1 | https://www.protocols.io/view/oxygen-evolution-measurement-light-curve-for-alga-cbr7sm9n | Steven J Burgess, Chandra Davies | TITLE: Oxygen Evolution Measurement: Light Curve for Algae
AUTHORS: Steven J Burgess, Chandra Davies
[DESCRIPTION]
Thanks to a lovely combination of trial and error I present to you an optimized* protocol for using an oxygen electrode to create a light curve for Ostrecoccus tauri. The light curve can be used to de... | ["[Prepare the electrolyte] Prepare the electrolyte", "[Prepare the electrolyte] Pour the salt into a 500 mL glass bottle", "[Prepare the electrolyte] Measure 100 mL of dH2O", "[Prepare the electrolyte] Pour the water into the same bottle as salt", "[Prepare the electrolyte] Close the lid and swirl the bottle with mild... |
43,118 | 3 Pre-imaging Setup for High Resolution AFM in Fluid | 1 | dx.doi.org/10.17504/protocols.io.bncnmave | https://www.protocols.io/view/3-pre-imaging-setup-for-high-resolution-afm-in-flu-bncnmave | Philip J. Haynes, Kavit H. S. Main, Alice Pyne | TITLE: 3 Pre-imaging Setup for High Resolution AFM in Fluid
AUTHORS: Philip J. Haynes, Kavit H. S. Main, Alice Pyne
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is part 3 of the "Atomic Force Microscopy of DNA and DNA-Protein Interactions" collection of protocols.</div><div class = "text-blo... | ["[Pre-imaging Setup for High Resolution AFM in Fluid]\nPrior to imaging, soak the chosen cantilever in a petri dish containing isopropanol:ethanol (1:1) for several hours and dry by blotting.", "[Pre-imaging Setup for High Resolution AFM in Fluid]\nEnsure cantilevers are totally dry before plasma cleaning in air for ... |
97,072 | HuBMAP | Digestion and scRNA Analysis of Skin | 0 | dx.doi.org/10.17504/protocols.io.bp2l62krzgqe/v1 | https://www.protocols.io/view/hubmap-digestion-and-scrna-analysis-of-skin-da2q2gdw | Arivarasan Karunamurthy, HJ Park | TITLE: HuBMAP | Digestion and scRNA Analysis of Skin
AUTHORS: Arivarasan Karunamurthy, HJ Park
[DESCRIPTION]
This method details digestion and scRNA analysis of the HuBMAP tissue skin specimens.
[STEPS]
1. The fresh skin sample is digested enzymatically using Miltenyi Biotec Whole Skin Dissociation Kit, human for 2 h... | ["The fresh skin sample is digested enzymatically using Miltenyi Biotec Whole Skin Dissociation Kit, human for 2 hours and further dispersed using the Miltenyi gentleMACS Octo Dissociator.", "The resulting cell suspensions are filtered through 70 µm cell strainers twice and resuspended in phosphate-buffered saline (PBS... |
80,966 | Immunostaining of corticostriatal culture on fluid-walled dumbbells | 1 | dx.doi.org/10.17504/protocols.io.36wgqj8eyvk5/v1 | https://www.protocols.io/view/immunostaining-of-corticostriatal-culture-on-fluid-ctbewije | Quyen Do, Federico Nebuloni, Richard Wade-Martins | TITLE: Immunostaining of corticostriatal culture on fluid-walled dumbbells
AUTHORS: Quyen Do, Federico Nebuloni, Richard Wade-Martins
[DESCRIPTION]
This protocol describes the immunocytochemistry of the iPSC-derived corticostriatal culture on fluid-walled dumbbells.
[BEFORE_START]
Adherent cells are prone to peeling... | ["[Generation of the corticostriatal pathway coculture on fluid-walled dumbbells] Fabricate the fluid-walled dumbbells on 6 cm culture dishes as described in step 1 of Protocol: Fabrication of fluid-walled dumbbells and generation of the human corticostriatal pathway", "[Generation of the corticostriatal pathway cocult... |
55,515 | Perfusion Live Microscopy Using Zeiss LSM 780 and Ibidi Perfusion Sets with SPY650 DNA Dye | 1 | null | https://www.protocols.io/view/perfusion-live-microscopy-using-zeiss-lsm-780-and-b2f3qbqn | Emir Bora Akmeriç | TITLE: Perfusion Live Microscopy Using Zeiss LSM 780 and Ibidi Perfusion Sets with SPY650 DNA Dye
AUTHORS: Emir Bora Akmeriç
[DESCRIPTION]
Step by step protocol for setting up live microscopy experiments with Ibidi perfusion sets
[STEPS]
SECTION: Cell Seeding
1. Check whether HUVECs in T25/T75 are confluent
SECT... | ["[Cell Seeding] Check whether HUVECs in T25/T75 are confluent", "[Cell Seeding] Gelatinize 2 or 3 Ibidi 0.4 luer u-slides with 0.2% gelatin in water", "[Cell Seeding] Bring trypsin, PBS, media and FBS to to 37C inside cell culture incubator", "[Cell Seeding] Trypsinize dish and count cells. A minimum of 500k cells are... |
92,289 | Leaf Tissue and Crude Cell Wall Component Analysis | 1 | dx.doi.org/10.17504/protocols.io.3byl4q6jzvo5/v1 | https://www.protocols.io/view/leaf-tissue-and-crude-cell-wall-component-analysis-c6c9zaz6 | Lynn Doran, McBurke3 | TITLE: Leaf Tissue and Crude Cell Wall Component Analysis
AUTHORS: Lynn Doran, McBurke3
[DESCRIPTION]
Compositional analysis of moisture, sugar, and starch of leaf tissue and crude cell wall components including TFA-soluble hemicellulose, pectin, and cellulose/glycans.
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.ejybcpw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This is the quick version of the Monarch® Plasmid DNA Miniprep Kit Protocol (NEB #T1010). For the full protocol, please click <a href="https://www.neb.com/protocols/2015/11/20/monarch-plasmid-dna-miniprep-kit-protocol-t1010" target="_blank">here</a>.
[BEFORE_START]
<ul>
<li>For... | [] |
58,793 | Correlative Microscopy for Localization of Proteins In Situ: Pre-embedding Immuno-Electron Microscopy Using FluoroNanogold, Gold Enhancement, and Low- Temperature Resin | 1 | dx.doi.org/10.17504/protocols.io.b5nhq5b6 | https://www.protocols.io/view/correlative-microscopy-for-localization-of-protein-b5nhq5b6 | Daniela Boassa | TITLE: Correlative Microscopy for Localization of Proteins In Situ: Pre-embedding Immuno-Electron Microscopy Using FluoroNanogold, Gold Enhancement, and Low- Temperature Resin
AUTHORS: Daniela Boassa
[DESCRIPTION]
Immuno-electron microscopy (immuno-EM) is a technique that has been used widely to determine sub cellula... | ["Remove the culture medium from the MatTek dishes contain ing the cells and wash three times with HBSS pre-warmed up at 37 °C. Fix cells with pre-warmed fixative at 37 °C (4 % PFA, 4 % PFA + 0.1 % glut, 2 % PFA, 2 % PFA + 0.1 % glut) for 5 min at room temperature followed by 30 min over ice. All solutions and steps fr... |
null | null | null | dx.doi.org/10.17504/protocols.io.dy57y5 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?. | [] |
50,445 | Total lactate dehydrogenase calorimetric enzyme activity measurement | 4 | dx.doi.org/10.17504/protocols.io.bvhmn346 | https://www.protocols.io/view/total-lactate-dehydrogenase-calorimetric-enzyme-ac-bvhmn346 | Renuka Sriram | TITLE: Total lactate dehydrogenase calorimetric enzyme activity measurement
AUTHORS: Renuka Sriram
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Lactate Dehydrogenase is a key cytoplasmic enzyme that confers the observed Warburg effect in tumors. Its a tetrameric protein composed of combinations o... | ["[Pre-preparation]\nReaction buffer – Tris buffer @ , ,", "[Pre-preparation]\nMeasure and add the following: i.\t HCl Trisii.\tTris Baseiii. of NaCliv. Use solution to dissolve NADH and add (10 vials of each)\n1.57 g\n0.15 g\n1.64 g\n20 mg\n2 mg", "[Pre-preparation]\nTurn off stir plate and remove stir bar", ... |
78,924 | Colony PCR (E. coli) | 1 | dx.doi.org/10.17504/protocols.io.bp2l69ekrlqe/v1 | https://www.protocols.io/view/colony-pcr-e-coli-crbkv2kw | a.koh | TITLE: Colony PCR (E. coli)
AUTHORS: a.koh
[DESCRIPTION]
Fast and easy PCR to check for cloning inserts. This protocol is not suitable for downstream application of the amplified PCR products.
[STEPS]
1. Set up 1x PCR buffer mix
5X Green or Colorless GoTaq® Flexi Buffer: 10µl (1x)
PCR Nucleotide Mix, 10mM each: 1µl ... | ["Set up 1x PCR buffer mix\n5X Green or Colorless GoTaq® Flexi Buffer: 10µl (1x)\nPCR Nucleotide Mix, 10mM each: 1µl (0.2mM each dNTP)\nupstream primer: 2µl (1.0µM)\ndownstream primer: 2µl (1.0µM)\nGoTaq® G2 Flexi DNA Polymerase (5u/µl): 0.25µl (1.25u)\nMgCl2: 2ul (1 mM)\nNuclease-Free Water to: 50µl\n\nNote: Can reduc... |
60,118 | Getting started with Micro-Meta App Tutorial | 5 | null | https://www.protocols.io/view/getting-started-with-micro-meta-app-tutorial-b6xwrfpe | 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 descripti... | ["[Before the tutorial] Video introduction", "[Tutorial - 1 - Download and Install Micro-Meta App] Download Micro-Meta App\n\nFollow these instructions to download and install the stand-alone version of Micro-Meta App.", "[After the tutorial] Provide feedback\nAfter testing the Micro-Meta App, we would love to have you... |
32,562 | Cerebrovascular Reactivity and Cerebral Autoregulation are Improved in the Supine Posture Compared to Upright in Healthy Men and Women | null | dx.doi.org/10.17504/protocols.io.bb2siqee | null | Michelle E. Favre, Valerie Lim, Michael J. Falvo, Jorge M. Serrador | TITLE: Cerebrovascular Reactivity and Cerebral Autoregulation are Improved in the Supine Posture Compared to Upright in Healthy Men and Women
AUTHORS: Michelle E. Favre, Valerie Lim, Michael J. Falvo, Jorge M. Serrador
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Cerebrovascular reactivity ... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.hevb3e6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Protocol for transfer of RNA to nylon membrane for subsequent Northern Blot analysis.</p>
[STEPS]
?.
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64,353 | Tenaxtreme Male Enhancement® [100% Tena Xtreme] Price, Reviews, Scam? | 3 | dx.doi.org/10.17504/protocols.io.8epv59o5ng1b/v1 | https://www.protocols.io/view/tenaxtreme-male-enhancement-100-tena-xtreme-price-ca39sgr6 | H A | TITLE: Tenaxtreme Male Enhancement® [100% Tena Xtreme] Price, Reviews, Scam?
AUTHORS: H A
[DESCRIPTION]
Shockingly enough, not one demonstrated thing was absent from the Tenaxtreme Ingredients!
[STEPS] | [] |
68,666 | Operation of Software for Motion Correction of Cardiac MRI by Respiratory Phase | 5 | dx.doi.org/10.17504/protocols.io.36wgq72j5vk5/v1 | https://www.protocols.io/view/operation-of-software-for-motion-correction-of-car-cfa2tige | Steven Van Doren, Jia Xu, Zhijian Luan, Afia Shammi | TITLE: Operation of Software for Motion Correction of Cardiac MRI by Respiratory Phase
AUTHORS: Steven Van Doren, Jia Xu, Zhijian Luan, Afia Shammi
[DESCRIPTION]
Collection of real-time cardiac MRI scans during breathing is desirable for sick patients unable to hold their breath. The breathing motion in such scans can... | ["[Software setup] Install the software", "Copy the software package (a zip file) to a hard drive, for example, the C: drive", "[Software setup] Request licensing and price (academic or commercial) by corresponding author Steven Van Doren (vandorens@missouri.edu ) and/or the Technology Transfer Office of the University... |
57,205 | Step by step guide to tag endogenous genes with split-wrmScarlet and/or split-sfGFP in C. elegans | 1 | dx.doi.org/10.17504/protocols.io.b34vqqw6 | https://www.protocols.io/view/step-by-step-guide-to-tag-endogenous-genes-with-sp-b34vqqw6 | Jerome F Goudeau, Cynthia Kenyon, Maria Ingaramo | TITLE: Step by step guide to tag endogenous genes with split-wrmScarlet and/or split-sfGFP in C. elegans
AUTHORS: Jerome F Goudeau, Cynthia Kenyon, Maria Ingaramo
[DESCRIPTION]
Here is a step by step protocol describing our strategy to label endogenous proteins with split-sfGFP and/or split-wrmScarlet in C. elegans... | ["[Select a C. elegans strain expressing the split-fluorescent protein1-10 of your choice] Select a C. elegans strain expressing wrmScarlet1-10 and/or sfGFP1-10 in your tissue of interest\n\nSomatic split-sfGFP1-10:\nCF4587 muIs253[(Peft-3::sfGFP1-10::unc-54 3'UTR, Cbr-unc-119(+)] II; unc-119(ed3) III\n\nSomatic split-... |
47,266 | Expression and purification protocols of Homo sapiens GST-ATG4B recombinant protein | 4 | dx.doi.org/10.17504/protocols.io.bseanbae | https://www.protocols.io/view/expression-and-purification-protocols-of-homo-sapi-bseanbae | Dorotea Fracchiolla | TITLE: Expression and purification protocols of Homo sapiens GST-ATG4B recombinant protein
AUTHORS: Dorotea Fracchiolla
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes expression and purification procedures for obtaining GST-tagged human recombinant Autophagy specific de-ubiq... | ["[Protein expression]\nTransform into one aliquot () of chemically competent E.coli Rosetta pLyss cells according to standard protocol.\n[mini DNA plasmid SMC1392 (~100ng/µl)]\n50 µl", "[Protein expression]\nPlate cells on Amp/Cam Ty (or LB) plate and grow at .\n37 °C", "[Protein expression]\nThe following day, pick... |
90,590 | Protocol to isolate and fix nuclei from flash frozen female mouse gonads for IGVF | 4 | null | https://www.protocols.io/view/protocol-to-isolate-and-fix-nuclei-from-flash-froz-c4p6yvre | Elisabeth Rebboah | TITLE: Protocol to isolate and fix nuclei from flash frozen female mouse gonads for IGVF
AUTHORS: Elisabeth Rebboah
[DESCRIPTION]
This protocol describes isolation of nuclei from left and right 10 week old mouse ovary and oviduct (pooled tissue ID: 26) from 8 founder strains (B6J, AJ, 129S1J, NZOJ, WSBJ, NODJ, PWKJ, a... | ["[Setup] Label tubes.", "[Setup] Pre-chill centrifuge to 4C.", "[Setup] Prepare ice buckets.", "[Setup] Prepare 35 ml lysis buffer on ice in a 50 mL conical tube. Distribute 2 mL into 8 gentleMACS C Tubes on ice. Add 175 ul RNase inhibitor to the lysis buffer aliquot the day of the experiment.", "[Setup] Prepare 3.5 m... |
23,966 | Neuropathy Phentoyping Protocols - In Situ Hybridization | null | dx.doi.org/10.17504/protocols.io.3m6gk9e | null | Eva Feldman | TITLE: Neuropathy Phentoyping Protocols - In Situ Hybridization
AUTHORS: Eva Feldman
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span></div><div class = "text-block"><span style = "font-weight:bold;">Phenotyping of Rodents for the Presence of Diabetic ... | ["[Day 1: All solutions, reagents, tips, tubes etc must be RNase FREE!!!]\nList all information concerning slides used, label slides as appropriate 1. Set dry bath at 70ºC and thaw formamide for step 12. 2. Retrieve slides from -80ºC and place directly into a slide rack in a dish containing 4% paraformaldehyde for 2 mi... |
40,791 | ELISA for quantification of IL-28 in human serum. | 6 | dx.doi.org/10.17504/protocols.io.bj3xkqpn | https://www.protocols.io/view/elisa-for-quantification-of-il-28-in-human-serum-bj3xkqpn | Angel Justiz-Vaillant | TITLE: ELISA for quantification of IL-28 in human serum.
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Interleukins (IL) are a type of cytokine first thought to be expressed by leukocytes alone but have later been found to be produced by many other body cells. ... | ["An anti-human IL-28 coating antibody is adsorbed onto the microwells by incubation overnight at 4°C with carbonate-bicarbonate buffer.", "Add 50 µl of human serum. Human IL-28 present in the serum sample binds to antibodies adsorbed into the microwells.", "The microplate is blocked with 3% non-fat milk-PBS buffer and... |
12,970 | Sequencing library preparation | null | dx.doi.org/10.17504/protocols.io.qwidxce | 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: Sequencing library preparation
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'kra... | [] |
45,541 | SEM Critical Point Dryer JIAM Protocol | 4 | null | https://www.protocols.io/view/sem-critical-point-dryer-jiam-protocol-bqqdmvs6 | Elizabeth Fozo | TITLE: SEM Critical Point Dryer JIAM Protocol
AUTHORS: Elizabeth Fozo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">SEM Critical Point Dryer Protocol at JIAM</div></div>
[STEPS]
?. [Protocol for using the critical point dryer at JIAM]
Power on the machine at least 5 minutes before using (Suggest ... | ["[Protocol for using the critical point dryer at JIAM]\nPower on the machine at least 5 minutes before using (Suggest doing this during the last dehydration step).", "[Protocol for using the critical point dryer at JIAM]\nMake sure the O-ring between the cover (with 3 screws) and the chamber is in good shape.", "[Prot... |
61,795 | Region velocity estimation and visulization with seurat | 5 | dx.doi.org/10.17504/protocols.io.eq2lynejrvx9/v1 | https://www.protocols.io/view/region-velocity-estimation-and-visulization-with-s-b8kbrusn | Chen Zhang | TITLE: Region velocity estimation and visulization with seurat
AUTHORS: Chen Zhang
[DESCRIPTION]
Example pipeline of region velocity estimation and visulization of steady-state model and dynamical model using EM algorithm in R with Seurat to pretreat scRNA-seq data
[STEPS]
SECTION: Read expression matrices in R
1. ... | ["[Read expression matrices in R] library(Regionvelocity) data(cell_e_gexp_sper_pb) data(cell_i_gexp_sper_pb) data(cell_RNA_gexp_sper_pb)", "[Alternative step of step 1 to get data from example data of Region velocity package] library(Regionvelocity) data(cell_e_gexp_sper_pb) data(cell_i_gexp_sper_pb) data(cell_RNA_ge... |
20,710 | UC Davis - Total Cholesterol (TC) Protocol | null | dx.doi.org/10.17504/protocols.io.ygeftte | null | Peter Havel | TITLE: UC Davis - Total Cholesterol (TC) Protocol
AUTHORS: Peter Havel
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">Cholesterol esters are enzymatically hydrolysed by cholesterol esterase to cholesterol and free fa... | ["Add 5 µl of calibrator and sample to each well.", "Add 300 µl of reagent to each well. Incubate at 37°C for 5 minutes. Read at 540 nm.", "Subtract blank readings from final readings. The assay will be linear so the unknown samples can be calculated as (Sample Absorbance ÷ Calibrator Absorbance) × Calibrator Concentr... |
82,908 | Quantifying Synaptic Colocalizations with SynBot (Manual Thresholding) | 5 | dx.doi.org/10.17504/protocols.io.kxygx9rjog8j/v1 | https://www.protocols.click/view/quantifying-synaptic-colocalizations-with-synbot-m-cu74wzqw | Justin T Savage, Juan Ramirez, Dolores Irala, Cagla Eroglu | TITLE: Quantifying Synaptic Colocalizations with SynBot (Manual Thresholding)
AUTHORS: Justin T Savage, Juan Ramirez, Dolores Irala, Cagla Eroglu
[DESCRIPTION]
Protocol for quantifying synapse numbers using the manual thresholding method in SynBot.
[STEPS]
SECTION: Installation
1. Install/Update FIJI. The newest vers... | ["[Installation] Install/Update FIJI. The newest version of Fiji can be found at https://fiji.sc/ Some features may not function properly if your Fiji is not up to date.", "[Installation] Visit the Syn_Bot GitHub repository (https://github.com/Eroglu-Lab/Syn_Bot) and download the ilastik4ij_Syn_Bot-1.8.2-SNAPSHOT.jar f... |
62,634 | Mycology media | 1 | dx.doi.org/10.17504/protocols.io.e6nvw536wvmk/v2 | https://www.protocols.io/view/mycology-media-b9eir3ce | Yin-Tse Huang | TITLE: Mycology media
AUTHORS: Yin-Tse Huang
[DESCRIPTION]
Mycology media
[STEPS]
1. WA+C agar
Water agar + chloramphenicol (氯黴素 kill bacteria): As an environmental isolating media
2. PDA+C agar
potato dextrose agar + chloramphenicol (氯黴素 kill bacteria): Use when WA+C agar is not working
5. Emerson YpSs Aga... | ["WA+C agar \nWater agar + chloramphenicol (氯黴素 kill bacteria): As an environmental isolating media", "PDA+C agar\npotato dextrose agar + chloramphenicol (氯黴素 kill bacteria): Use when WA+C agar is not working", "Emerson YpSs Agar: For chytrids", "10% Unclarified V8 Agar\nCombine 100 ml V8 juice and 900 ml of distilled ... |
29,404 | Immunohistochemistry Protocol for Beta Amyloid Products using USA Detection Kit | null | dx.doi.org/10.17504/protocols.io.8x4hxqw | null | Sam Li | TITLE: Immunohistochemistry Protocol for Beta Amyloid Products using USA Detection Kit
AUTHORS: Sam Li
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. Clear Slides: Remove paraffin and hydrate the tissueNote: If using frozen sections, allow slides to come to room temperature for 15 minutes & proceed to ste... | ["Clear Slides: Remove paraffin and hydrate the tissueNote: If using frozen sections, allow slides to come to room temperature for 15 minutes & proceed to step (F) only A. Xylene - 5 minutes in each of (3) different 250 mL containersB. 100% alcohol - 5 minutes in each of (3) different 250 mL containersC. 95% alcohol - ... |
50,237 | HyDrop-RNA v1.0 | 1 | null | https://www.protocols.io/view/hydrop-rna-v1-0-bva5n2g6 | Suresh Poovathingal, Florian De Rop, Stein Aerts | TITLE: HyDrop-RNA v1.0
AUTHORS: Suresh Poovathingal, Florian De Rop, Stein Aerts
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Step-by-step protocol for performing HyDrop-RNA. The duration of each step assumes an experienced protocol user. For a first-time user, we recommend doubling the expected ... | ["[Microfluidics Preparation]\nSetting up the Microfluidic FrameworkThese steps need to happen in advance before the run can be started, as time between the preparation of the cell resuspension in RT mix and actual encapsulation needs to be minimised to preserve cell viability.", "[Microfluidics Preparation]\nBoot up ... |
40,806 | ELISA for quantification of IL-39 in human serum. | 6 | dx.doi.org/10.17504/protocols.io.bj4ekqte | https://www.protocols.io/view/elisa-for-quantification-of-il-39-in-human-serum-bj4ekqte | Angel Justiz-Vaillant | TITLE: ELISA for quantification of IL-39 in human serum.
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Interleukins (IL) are a type of cytokine first thought to be expressed by leukocytes alone but have later been found to be produced by many other body cells.... | ["An anti-human IL-39 coating antibody is adsorbed onto the microwells by incubation overnight at 4°C with carbonate-bicarbonate buffer.", "Add 50 µl of human serum. Human IL-39 present in the serum sample binds to antibodies adsorbed into the microwells.", "The microplate is blocked with 3% non-fat milk-PBS buffer and... |
62,443 | Next Optimal Male Enhancement | 3 | dx.doi.org/10.17504/protocols.io.4r3l2oe6jv1y/v1 | https://www.protocols.io/view/next-optimal-male-enhancement-b88jrzun | H Douglas Morris | TITLE: Next Optimal Male Enhancement
AUTHORS: H Douglas Morris
[DESCRIPTION]
One way to do this is to offer employees an environment that promotes healthy and active lifestyles.
[STEPS] | [] |
43,638 | Media for Fungal Culturing | 3 | dx.doi.org/10.17504/protocols.io.bnuwmexe | https://www.protocols.io/view/media-for-fungal-culturing-bnuwmexe | Jiri Hulcr, You Li, Sawyer Adams, Demian F Gomez | TITLE: Media for Fungal Culturing
AUTHORS: Jiri Hulcr, You Li, Sawyer Adams, Demian F Gomez
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the different media for fungal culturing.</div><div class = "text-block"><span>This protocol is part of the Bark Beetle Mycobiome (BBM) ... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.n5tdg6n | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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34,744 | Title: Ultrasound Use and its Impact on Clinical Decisions in the Accident and Emergency Department at Georgetown Public Hospital Corporation | null | dx.doi.org/10.17504/protocols.io.bd6yi9fw | https://www.protocols.io/view/title-ultrasound-use-and-its-impact-on-clinical-de-bd6yi9fw | Davendra Kissoon, Sri Devi Jagjit, Jordan Rupp, Brian Bales, Jeremy Boyd | TITLE: Title: Ultrasound Use and its Impact on Clinical Decisions in the Accident and Emergency Department at Georgetown Public Hospital Corporation
AUTHORS: Davendra Kissoon, Sri Devi Jagjit, Jordan Rupp, Brian Bales, Jeremy Boyd
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.hetb3en | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol describes the transfection of mammalian cells with <em>in vitro</em> transcribed, unmodified, non-charged tRNAs. We have used this method successfully to raise intrinsic tRNA concentrations in HeLa<sup>1</sup> and N2a cells<sup>2</sup>. Furthermore, tRNAs synthe... | [] |
50,190 | Generation of Immunodeficient Mice Bearing Human Immune Systems by the Engraftment of Hematopoietic Stem Cells | 4 | dx.doi.org/10.17504/protocols.io.bu9nnz5e | https://www.protocols.io/view/generation-of-immunodeficient-mice-bearing-human-i-bu9nnz5e | Suheyla Hasgur, Ken Edwin Aryee, Leonard D. Shultz, Dale L. Greiner, and Michael A. Brehm | TITLE: Generation of Immunodeficient Mice Bearing Human Immune Systems by the Engraftment of Hematopoietic Stem Cells
AUTHORS: Suheyla Hasgur, Ken Edwin Aryee, Leonard D. Shultz, Dale L. Greiner, and Michael A. Brehm
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Immunodeficient mice are bein... | ["[Methods]\nPreparation of umbilical cord blood (UCB)", "[Methods]\nAllow histopaque and RPMI supplemented with 0.5% BSA to warm to room temperature.", "[Methods]\nTransfer UBC to conical tubes (30 mls per tube).\n50 mL", "[Methods]\nAdd hespan to each tube of UBC to a final concentration of 20% per volume and mix ge... |
25,407 | Primary Human Fibroblast Cell Culture | null | dx.doi.org/10.17504/protocols.io.427gyhn | null | Aparna Kumar, Faria Zafar, Birgitt Schuele | TITLE: Primary Human Fibroblast Cell Culture
AUTHORS: Aparna Kumar, Faria Zafar, Birgitt Schuele
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Growing and maintaining primary human skin fibroblast cell cultures.</div><div class = "text-block">Additional links for protocols can be found:</div><div ... | ["[Preparing for Culturing]\nStore cryovials in liquid nitrogen storage tank upon arrival. Place vials in dry ice when ready to work with cells (do not thaw immediately).", "[Preparing for Culturing]\nWarm up AmnioMax media in water bath, wipe bottle with 70% alcohol before placing in a biosafety cabinet. Aliquot of t... |
null | null | null | dx.doi.org/10.17504/protocols.io.cieubd | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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85,430 | Plant material collection protocol for eastern hemlock (Tsuga canadensis) to assess chemical and expression profiles associated with HWA resistance | 1 | dx.doi.org/10.17504/protocols.io.rm7vzbryrvx1/v4 | https://www.protocols.click/view/plant-material-collection-protocol-for-eastern-hem-cxnwxmfe | Vidya S Vuruputoor, karlfetter, victoriaburton, Jill Wegrzyn | TITLE: Plant material collection protocol for eastern hemlock (Tsuga canadensis) to assess chemical and expression profiles associated with HWA resistance
AUTHORS: Vidya S Vuruputoor, karlfetter, victoriaburton, Jill Wegrzyn
[DESCRIPTION]
This protocol was developed by the PCG team for sampling needle and branch tissu... | ["[TreeSnap Observation] TreeSnap is a mobile application that can run on both Apple OS and Android that utilizes the phone’s GPS to collect location information and present a set of standardized questions to the collector on basic traits of the tree, including image data. This is the application of choice for this pr... |
86,512 | Mouse Stereotaxic Surgery for Alpha Synuclein Pre-formed Fibrils (PFFs) Injection in the Dorsal Striatum | 4 | null | https://www.protocols.io/view/mouse-stereotaxic-surgery-for-alpha-synuclein-pre-cyqqxvvw | null | TITLE: Mouse Stereotaxic Surgery for Alpha Synuclein Pre-formed Fibrils (PFFs) Injection in the Dorsal Striatum
AUTHORS:
[DESCRIPTION]
This protocol describes the steps for performing stereotaxic surgery in mice. It is applicable to intracranial injections of PFFs into the dorsal striatum of the mouse brain.
[STEPS]... | ["Prepare drugs and sonicated PFF", "Surgery room setup", "Mouse preparation with anesthesia.", "Surgery", "Drilling and skull preparation.", "Inject PFF using Nanoject II Auto-Nanoliter Injector at the desired rate and desired volume. We inject 2 µL 5 µg/µL at the rate of 2 µL", "Closing/Suturing\nAfter completion ... |
25,046 | In vitro transcription, capping, and 2'-O methylation of long RNAs | null | dx.doi.org/10.17504/protocols.io.4pwgvpe | null | Stephen Floor | TITLE: In vitro transcription, capping, and 2'-O methylation of long RNAs
AUTHORS: Stephen Floor
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is for in vitro transcription of long RNAs off plasmid or PCR product templates. It is assumed that the template has been gel purified, is th... | ["[PCR amplification of template]\nPrimer design: pA60 txn rev TTT TTT TTT TTT TTT TTT TTT TTT TTT TTT TTT TTT TTT TTT TTT TTT TTT TTT TTT TTT CTG CAGpA60 txn fwd CGG CCA GTG AAT TCG AGC TCT AAT ACG ACT CAC TAT AGGnote: if using a different template, substitute the reverse and forward primers for primers that will ampl... |
46,683 | Bioanalyzer Operation for IVT Products | 1 | dx.doi.org/10.17504/protocols.io.brt3m6qn | https://www.protocols.io/view/bioanalyzer-operation-for-ivt-products-brt3m6qn | Allen Institute for Brain Science | TITLE: Bioanalyzer Operation for IVT Products
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is used to operate the Bioanalyzer which is used as a quality control step for IVT products. Peak size, shape, and sample concentration are recorded ... | [] |
106,743 | 3D Microfluidic Platforms for Extracellular Vesicle Isolation, Characterization, Downstream Analysis and In Vitro Treatment | 0 | dx.doi.org/10.17504/protocols.io.4r3l2qzqpl1y/v1 | https://www.protocols.io/view/3d-microfluidic-platforms-for-extracellular-vesicl-dkgx4txn | Emeli Chatterjee, Scott Lindsay, Tyler Ostrander, Marta Garcia-Contreras, Hawa S. Ndiaye, John Sauld, Gautam Mahajan, Louise C. Laurent, Prabhleen Singh, Saumya Das, Priyadarshini Pantham | TITLE: 3D Microfluidic Platforms for Extracellular Vesicle Isolation, Characterization, Downstream Analysis and In Vitro Treatment
AUTHORS: Emeli Chatterjee, Scott Lindsay, Tyler Ostrander, Marta Garcia-Contreras, Hawa S. Ndiaye, John Sauld, Gautam Mahajan, Louise C. Laurent, Prabhleen Singh, Saumya Das, Priyadarshini ... | ["Organ-on-a-chip", "Liver-on-chip:\nFollow Manufacturer’s protocol for seeding chip with hepatocytes, Kupffer cells,\nStellate cells, and liver endothelial\ncells (Emulate, inc.).\nKidney-on-chip:\nFollow Manufacturer’s protocol for seeding chip with RPTECs and RMVECs\n(Emulate, inc.).", "Treatment of cells with extr... |
55,836 | Membrane Filtration for SARS-CoV-2 Viral Capture | 4 | dx.doi.org/10.17504/protocols.io.yxmvmno85g3p/v1 | https://www.protocols.io/view/membrane-filtration-for-sars-cov-2-viral-capture-b2r4qd8w | Caleb Centrell, Jamie VanTassell, Julia Raymond, Marlene K Wolfe, Pengbo, Christine Moe | TITLE: Membrane Filtration for SARS-CoV-2 Viral Capture
AUTHORS: Caleb Centrell, Jamie VanTassell, Julia Raymond, Marlene K Wolfe, Pengbo, Christine Moe
[DESCRIPTION]
This protocol describes how to perform membrane filtration vacuum technology with wastewater grab samples to allow for SARS-CoV-2 RNA extraction.
[BE... | ["[Preparation] Prepare and collect all supplies necessary for the number of samples that will be concentrated using membrane filtration.", "[Sample Processing Procedure] Remove the grab sample from the 4°C refrigerator and place under the sterilized biological hood.", "[Sample Processing Procedure] Aseptically pour 30... |
108,740 | A protocol for the differentiation of the common monkeypox virus (all clades) and its mutation (1b clade) by real-time PCR | 0 | dx.doi.org/10.17504/protocols.io.5qpvokz4zl4o/v1 | https://www.protocols.io/view/a-protocol-for-the-differentiation-of-the-common-dnfc5biw | Sudhir Bhatia, Gudrun Baersch | TITLE: A protocol for the differentiation of the common monkeypox virus (all clades) and its mutation (1b clade) by real-time PCR
AUTHORS: Sudhir Bhatia, Gudrun Baersch
[DESCRIPTION]
The monkeypox virus was first isolated in Copenhagen in 1958. It causes similar lesions to smallpox and should be distinguished from ot... | ["Thaw one tube each: A, B, C, D1 and D2. If the kit is not in use, store them at -20°C. Keep tubes away from sunlight.", "Mark your microtubes with a sample number, positive and negative Control. \nAll samples must be carried out for tube A and in parallel for tube C.", "Thaw tube A. Add 8µl of Tube A to each tube. Ot... |
95,566 | Smell discrimination test | 0 | dx.doi.org/10.17504/protocols.io.36wgq3wwxlk5/v1 | https://www.protocols.io/view/smell-discrimination-test-c9jnz4me | daniel.dautan daniel, Per Svenningsson | TITLE: Smell discrimination test
AUTHORS: daniel.dautan daniel, Per Svenningsson
[DESCRIPTION]
Behavioral test to assess smell discrimination in mice.
[STEPS]
1. Transfer the cage into the experimental room at least 1h before testing. Always maintain the cage in a ventilated cage rack to avoid smell contamination.
2... | ["Transfer the cage into the experimental room at least 1h before testing. Always maintain the cage in a ventilated cage rack to avoid smell contamination.", "Set the open field before starting experiment. The open field is a dark-grey box of 40 x 40 cm with clean floor and a light suspended above the center. A maximum... |
86,451 | Mouse Ovariectomy | 1 | dx.doi.org/10.17504/protocols.io.14egn338zl5d/v1 | https://www.protocols.io/view/mouse-ovariectomy-cyntxven | Sabina Marciano, Roberta Marongiu | TITLE: Mouse Ovariectomy
AUTHORS: Sabina Marciano, Roberta Marongiu
[DESCRIPTION]
This protocol outlines the steps to perform an Ovariectomy in a mouse
[STEPS]
1. Anesthetize the mouse with Ketamine ( 100 µL / 100 g )
2. Apply eye ointment
3. Shave and disinfect the area below the ribs
4. Disinfect the surgical tools... | ["Anesthetize the mouse with Ketamine ( 100 µL / 100 g )", "Apply eye ointment", "Shave and disinfect the area below the ribs", "Disinfect the surgical tools", "Place the mouse on the side", "Align 2 tweezers with the arms/legs and use the crossing point as a reference for the\nincision", "Perform a small incision and ... |
46,951 | Freezing and Formalin Fixation of Tissue | 1 | dx.doi.org/10.17504/protocols.io.br4fm8tn | https://www.protocols.io/view/freezing-and-formalin-fixation-of-tissue-br4fm8tn | Jamie Allen, Maya Brewer, Elizabeth Neumann, Carrie Romer, Danielle Gutierrez, Mark deCaestecker, Jeff Spraggins | TITLE: Freezing and Formalin Fixation of Tissue
AUTHORS: Jamie Allen, Maya Brewer, Elizabeth Neumann, Carrie Romer, Danielle Gutierrez, Mark deCaestecker, Jeff Spraggins
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Scope:</div><div class = "text-block">To describe the procedure for freezing fres... | ["[Documentation and Preparation]\nPlace a layer of dry ice in to box and add enough isopentane to make a slurry.", "Label embedding molds and add a small amount of CMC to each one (barely cover the bottom).", "Remove sample container from ice and document on sample sheet any information that is written on the lid.", "... |
100,753 | X-region PolyU/UC mutagenesis | 0 | dx.doi.org/10.17504/protocols.io.8epv5rxy6g1b/v1 | https://www.protocols.io/view/x-region-polyu-uc-mutagenesis-demr3c56 | Carolina Lopez | TITLE: X-region PolyU/UC mutagenesis
AUTHORS: Carolina Lopez
[DESCRIPTION]
Protocol to PCR and in vitro transcribe the HCV X region w/out mutagenesis
[STEPS]
SECTION: HCV X-region PolyU/UC PCR - T7 in vitro transcription
1. PCR:
1) Thaw component and cDNA, spin down before use
2) Assemble reaction: Master Mix: 10X (... | ["[HCV X-region PolyU/UC PCR - T7 in vitro transcription] PCR:\n1) Thaw component and cDNA, spin down before use\n2) Assemble reaction: Master Mix: 10X (each reaction assemble 3 tubes)\n \n Total: 50 µL\n\n3) Run PCR", "[II.\tIn vitro transcription:] ➢\tSpin-down all reagents \n➢\tKeep the 10X Reaction Bu... |
20,643 | Serial killer pore investigation: protocol for analyzing fatigue failure pores in additively manufactured Ti6Al4V | null | dx.doi.org/10.17504/protocols.io.yebftan | null | Muofhe Tshibalanganda, Anton du Plessis, Stephan le Roux | TITLE: Serial killer pore investigation: protocol for analyzing fatigue failure pores in additively manufactured Ti6Al4V
AUTHORS: Muofhe Tshibalanganda, Anton du Plessis, Stephan le Roux
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol outlines the steps followed to determine a potentia... | ["[Before Scanning]\nWrap the sample inside a bubble wrap for support. Make sure the marked threaded grip is facing up.This is to know which side is up when analysing.", "[Sample mounting]\nLoad the sample on a foam (e.g. florist oasis).", "[Scanning Stettings]\nThe sample was scanned using the scanned using Phoenix V|... |
105,075 | Mouse Tissue mtDNA Copy Number Protocol | 0 | dx.doi.org/10.17504/protocols.io.14egn6jwzl5d/v1 | https://www.protocols.io/view/mouse-tissue-mtdna-copy-number-protocol-diut4ewn | Livia Hecke Morais, Jack Devine | TITLE: Mouse Tissue mtDNA Copy Number Protocol
AUTHORS: Livia Hecke Morais, Jack Devine
[DESCRIPTION]
Mouse Tissue mtDNA Copy Number Protocol developed in the Picard lab at Departments of Psychiatry and Neurology, Robert N Butler Columbia Aging Center, Columbia
University Irving Medical Center, New York, NY, USA
[ST... | ["[Consumables, with catalog numbers:] BD Vacutainer Tubes (BD #363083)\nTris HCl (Sigma #T3253)\nTween 20, 10% (Sigma #P1379)\nNuclease free water (Thermofisher Scientific #AM9939)\nProteinase K (20 mg/mL) (Thermofisher Scientific #AM2548)\nStericup Quick Release-GV Sterile Vacuum Filtration System – 500 mL (Millipore... |
9,379 | ATPase activity assay | null | dx.doi.org/10.17504/protocols.io.mebc3an | null | Anika Wiegard, Christin Köbler, Katsuaki Oyama, Anja K. Dörrich, Chihiro Azai, Kazuki Terauchi, Annegret Wilde, Ilka Maria Axmann | TITLE: ATPase activity assay
AUTHORS: Anika Wiegard, Christin Köbler, Katsuaki Oyama, Anja K. Dörrich, Chihiro Azai, Kazuki Terauchi, Annegret Wilde, Ilka Maria Axmann
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol can be used to analyse ATPase activity of KaiC proteins. Produced ADP ... | ["[Preparation of running buffer]\nfill a 1l bottle with 963.4 ml MilliQadd 5.8 ml phosphoryc acid (17.2 M stock Nacalai tesque, CAS 121-44-8) [for pH adjustment] --> final concentration = 100 mMadd 20.8 ml trimethylamine (7.15M stock, Nacalai tesque, CAS 7664-38-2) [counter-ion] --> final concentration = 150 mMadd 10... |
34,638 | Optimization of Fragmentation Temperature | 1 | dx.doi.org/10.17504/protocols.io.e6nvw9o5dgmk/v1 | https://www.protocols.io/view/optimization-of-fragmentation-temperature-bd3ni8me | Dakota Betz | TITLE: Optimization of Fragmentation Temperature
AUTHORS: Dakota Betz
[DESCRIPTION]
The standard fragmentation temperature is 37°C. If you are fragmenting high-quality genomic DNA, any other
high-complexity DNA sample, or FFPE DNA to a mode fragment length <500 bp, it is unlikely that you will have to
change or optimi... | ["To determine the optimal fragmentation parameters for low-complexity samples, or high-complexity samples\nwhen the desired mode fragment length is >500 bp:", "Set up four replicate reactions with a non-precious, bulk sample that is representative of the actual samples\nto be processed.", "Fragment two of the samples ... |
37,779 | Post Patch Clamp Slice Fixation | 1 | dx.doi.org/10.17504/protocols.io.bg5tjy6n | https://www.protocols.io/view/post-patch-clamp-slice-fixation-bg5tjy6n | Allen Institute for Brain Science | TITLE: Post Patch Clamp Slice Fixation
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the process to fix recorded/filled cells from mouse and human brain slices with 4% PFA/2.5% Glutaraldehyde in PBS for future histochemical process... | [] |
57,186 | ToLA Assembly Pipeline 1 | 5 | null | https://www.protocols.io/view/tola-assembly-pipeline-1-b34aqqse | Marcela Uliano-Silva, Ksenia Krasheninnikova, Shane A. McCarthy | TITLE: ToLA Assembly Pipeline 1
AUTHORS: Marcela Uliano-Silva, Ksenia Krasheninnikova, Shane A. McCarthy
[DESCRIPTION]
Here you find the first assembly pipeline developed by the Tree of Life Assembly Team (ToLA) to assemble the genomes sequenced in the first 2 years of the Darwin Tree of Life Project (DToL), which ... | ["[Reads trimming] Pacbio Hifi reads trimming\n\nInput your Pacbio Hifi reads to HiFiAdapterFilt (https://github.com/sheinasim/HiFiAdapterFilt)\n\nHiFiAdapterFilt will convert .bam to .fastq and remove reads with remnant PacBio adapter sequences."] |
43,299 | Measure chlorophyll-a and pheophytin-a by Turner Designs | 4 | null | https://www.protocols.io/view/measure-chlorophyll-a-and-pheophytin-a-by-turner-d-bnibmcan | Yingyu Hu | TITLE: Measure chlorophyll-a and pheophytin-a by Turner Designs
AUTHORS: Yingyu Hu
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Here we describe a protocol for measuring chlorophyll-a and pheophytin-a from microalgae by using Turner Designs (10-AU)</div></div>
[STEPS]
?. [Prepare Chlorophyll-a s... | ["[Prepare Chlorophyll-a standard]\nPrimary stock: ≅10 mg/L", "[Prepare reagent]\nSaturated magnesium carbonate solution", "[Extract chlorophyll sample and blank]\nExtract samples on the filter", "[Daily calibrate]\nAllow Turner to warm-up for at least 15 minutes.", "[Prepare reagent]\n90% buffered acetone", "[Prepare ... |
19,365 | Bioinformatic pipeline for studying transcriptome and regulome dynamics during neural differentiation | null | dx.doi.org/10.17504/protocols.io.w6dfha6 | null | Zhouchun Shang, Dongsheng Chen, Quanlei Wang, Shengpeng Wang | TITLE: Bioinformatic pipeline for studying transcriptome and regulome dynamics during neural differentiation
AUTHORS: Zhouchun Shang, Dongsheng Chen, Quanlei Wang, Shengpeng Wang
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Here we present a bioinformatic pipeline for dissecting transcriptional r... | ["[Raw data description]\nSingle cell RNA-seq: 50bp single-end sequencing was performed using the BGISEQ-500 platformBulk RNA-seq: 50bp single-end sequencing was performed using the BGISEQ-500 platformAssay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) was sequenced on BGISEQ-500 platform", "[Assess ... |
94,410 | Locomotion test for mice | 1 | dx.doi.org/10.17504/protocols.io.6qpvr3njzvmk/v1 | https://www.protocols.io/view/locomotion-test-for-mice-c8fiztke | Csilla Novák, Andrés Mauricio Jaramillo Flautero, Matthias Prigge | TITLE: Locomotion test for mice
AUTHORS: Csilla Novák, Andrés Mauricio Jaramillo Flautero, Matthias Prigge
[DESCRIPTION]
The locomotion test is an open field test in darkness, so it does not aim to measure anxiety, only locomotor activity.
[STEPS]
SECTION: Behaviour
1. Transport the mice to the behaviour room and pu... | ["[Behaviour] Transport the mice to the behaviour room and put the mice in individual cages.", "[Behaviour] Leave them in the lobby in darkness or with red light for at least 30 minutes.", "[Behaviour] Turn on the red lights in the room.", "[Behaviour] Place a 50x50 cm arena on the table.", "[Behaviour] Clean the arena... |
86,289 | Mouse Brain Tissue Collection and Analysis | 4 | dx.doi.org/10.17504/protocols.io.3byl4qj4zvo5/v1 | https://www.protocols.io/view/mouse-brain-tissue-collection-and-analysis-cyhrxt56 | Robert Edwards, Shweta Jain | TITLE: Mouse Brain Tissue Collection and Analysis
AUTHORS: Robert Edwards, Shweta Jain
[DESCRIPTION]
This protocol describes the dissection and collection of coronal sections of the striatum and midbrain from a mouse brain. The tissue can be used in a number of applications and here we describe two: the measurement c... | ["[Tissue dissection] Euthanize mice by inhalation of CO2", "[Tissue dissection] Decapitate mouse and remove brain", "[Tissue dissection] Place brain into a rodent brain matrix (RBM-2000C, Protech International Inc.)", "[Tissue dissection] By inserting razor blades into the slots of the brain matrix, collect two 1 mm c... |
95,363 | Precision thin sectioning of silica phytoliths by Focused Ion Beam (FIB-SEM) | 4 | dx.doi.org/10.17504/protocols.io.n2bvj37qplk5/v1 | https://www.protocols.io/view/precision-thin-sectioning-of-silica-phytoliths-by-c9dbz22n | Djanira Rodrigues Negrao, Julio Criginski Cezar, Fabiano E. Montoro, Jian Wang, Charles W. Rice, Carlos Driemeier | TITLE: Precision thin sectioning of silica phytoliths by Focused Ion Beam (FIB-SEM)
AUTHORS: Djanira Rodrigues Negrao, Julio Criginski Cezar, Fabiano E. Montoro, Jian Wang, Charles W. Rice, Carlos Driemeier
[DESCRIPTION]
Phytoliths are microbodies of biogenic silica made by many plant species in all ecosystems over th... | ["[Plant material] The outer layer of the plant tissue (here we used sugarcane stalk) must contain numerous phytoliths. To extract sugarcane phytoliths, we manually peeled the stalk into strips of 2 mm thickness. These strips are subsequently cut into pieces of 1 cm2 using a clean scissor. The plant material was then p... |
52,294 | ADAPTACIÓN DE CULTIVOS CELULARES SIN AMBIENTE DE CO2, DESCONGELACIÓN, MANTENIMIENTO Y ENSAYOS DE PLAQUEO VIRAL. | 4 | dx.doi.org/10.17504/protocols.io.bxbepije | https://www.protocols.io/view/adaptaci-n-de-cultivos-celulares-sin-ambiente-de-c-bxbepije | Delia Piedad Recalde-Reyes, Carlos Andrés Rodríguez Salazar, Jhon Carlos Castaño Osorio | TITLE: ADAPTACIÓN DE CULTIVOS CELULARES SIN AMBIENTE DE CO2, DESCONGELACIÓN, MANTENIMIENTO Y ENSAYOS DE PLAQUEO VIRAL.
AUTHORS: Delia Piedad Recalde-Reyes, Carlos Andrés Rodríguez Salazar, Jhon Carlos Castaño Osorio
[DESCRIPTION]
Este método de cultivo celular es una adaptación para cultivo de líneas celulares eucario... | ["Preparación de medios de cultivo.\n\n\nEl medio de cultivo a utilizar dependerá de cada una de las líneas celulares como se observa en la tabla 1 y se debe suplementar empleando: Antibiótico antimicótico 1X, Suero fetal bovino 10%, Caldo Triptosa fosfato 10%, cabe destacar que el medio MEM para las células HepG2 pued... |
33,606 | Single cell isolation and monoclonal culture establishment of Acanthamoeba castellanii using migration on agar plates | null | dx.doi.org/10.17504/protocols.io.bc3eiyje | null | Morgan Colp | TITLE: Single cell isolation and monoclonal culture establishment of Acanthamoeba castellanii using migration on agar plates
AUTHORS: Morgan Colp
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Isolation of single </span><span style = "font-style:italic;">Acanthamoeba castellanii </span><span>... | ["[E. coli preparation]\nGrow 24 hour culture of E. coli K-12 in LB", "[E. coli preparation]\nPellet E. coli and resuspend in an equal volume of water or Page's Amoeba Saline in 15 mL Falcon tube", "[Plate set-up]\nPour PAS agar into several (3 to 5) Petri plates per 10 cells planned to isolate and let set.", "[Plate s... |
40,792 | ELISA for quantification of IL-29 in human serum. | 6 | dx.doi.org/10.17504/protocols.io.bj3ykqpw | https://www.protocols.io/view/elisa-for-quantification-of-il-29-in-human-serum-bj3ykqpw | Angel Justiz-Vaillant | TITLE: ELISA for quantification of IL-29 in human serum.
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Interleukins (IL) are a type of cytokine first thought to be expressed by leukocytes alone but have later been found to be produced by many other body cells. ... | ["An anti-human IL-29 coating antibody is adsorbed onto the microwells by incubation overnight at 4°C with carbonate-bicarbonate buffer.", "Add 50 µl of human serum. Human IL-29 present in the serum sample binds to antibodies adsorbed into the microwells.", "The microplate is blocked with 3% non-fat milk-PBS buffer and... |
null | null | null | dx.doi.org/10.17504/protocols.io.kj5cuq6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Protocol for performing ATAC-seq on nuclei isolated from <em>Drosophila melanogaster</em> stage 5 embryos that were flash frozen and then cut in half along the anterior-posterior midline. Data from this protocol are presented in the following paper: https://www.biorxiv.org/co... | [] |
20,309 | Development of a doubled haploid mapping population of Pyropia yezoensis and measurement of the economic characters of blade | null | dx.doi.org/10.17504/protocols.io.x3vfqn6 | null | Linbin Huang, Xinghong Yan | TITLE: Development of a doubled haploid mapping population of Pyropia yezoensis and measurement of the economic characters of blade
AUTHORS: Linbin Huang, Xinghong Yan
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-style:italic;">Pyropia yezoensis</span><span> is one of the most... | ["[Preparation of conchocelis]\nStock culture of free-living conchocelis of Pyropia yezoensis wild-type strain Py-LS and red-type pigmentation mutant Py-HT were maintained in the laboratory, at under 10 µmol photons m–2 s–12 (10:14 LD) provided by cool-white, 40-W fluorescent lamps, in an SEBC bottle with culture medi... |
61,436 | FLOUR-seq | 4 | dx.doi.org/10.17504/protocols.io.yxmvmnpm6g3p/v1 | https://www.protocols.io/view/flour-seq-b784rryw | Zhichao Chen | TITLE: FLOUR-seq
AUTHORS: Zhichao Chen
[DESCRIPTION]
We presented three barcoded technologies (BD Rhapsody) that are accessible to most researchers: high-throughput single-cell ONT full-length RNA sequencing (FLOUR-seq). FLOUR-seq combines BD Rhapsody and nanopore sequencing to detect the RNA panorama (including nasce... | ["[mouse testis cell dissociation] The mouse testis were dissociated to single cells refer to Adult mouse testis cell dissociation (on ice).", "[Priming and treating the BD Rhapsody Cartridge] Prime and treat the BD Rhapsody Cartridge (Cat. No. 400000847).", "[Loading cells in cartridge] Dilute 20000 cells with cold Sa... |
56,830 | Fluorescent Western Protocol | 4 | dx.doi.org/10.17504/protocols.io.b3q6qmze | https://www.protocols.io/view/fluorescent-western-protocol-b3q6qmze | Steven J Burgess, Lynn Doran | TITLE: Fluorescent Western Protocol
AUTHORS: Steven J Burgess, Lynn Doran
[DESCRIPTION]
Analysis of proteins using fluorescent immunoblot.
Note:
- The choice of secondary antibody depends on the choice of primary antibody, whether it is derived from a mouse (monoclonal) or a rabbit (polyclonal).
- It is advi... | ["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 2 min min", "Rinse membrane with dH2O", "Discard PBS and ... |
57,746 | Thawing, Passaging and Freezing of hPSCs on MEFs | 2 | dx.doi.org/10.17504/protocols.io.b4msqu6e | https://www.protocols.io/view/thawing-passaging-and-freezing-of-hpscs-on-mefs-b4msqu6e | Hanqin Li, Oriol Busquets, Steven Poser, Dirk Hockemeyer, Frank Soldner | TITLE: Thawing, Passaging and Freezing of hPSCs on MEFs
AUTHORS: Hanqin Li, Oriol Busquets, Steven Poser, Dirk Hockemeyer, Frank Soldner
[DESCRIPTION]
This collection contains protocols which describe the standard procedure of culturing human pluripotent stem cells (hPSCs) on inactivated mouse embryonic fibroblasts (... | [] |
50,767 | Terra Troubleshooting | 5 | null | https://www.protocols.io/view/terra-troubleshooting-bvtpn6mn | Yuan Li, Jill V Hagey, Michael Weigand, Technical Outreach and Assistance for States Team | TITLE: Terra Troubleshooting
AUTHORS: Yuan Li, Jill V Hagey, Michael Weigand, Technical Outreach and Assistance for States Team
[DESCRIPTION]
This protocol contains step-by-step instructions and tips for troubleshooting issues you may encounter while using Terra. If your problem cannot be addressed with this protoc... | ["[The workflow status is “Failed” for a sample, why?] To start troubleshooting the workflow (Titan in this case) for a failed sample, click on the 'JOB HISTORY' panel in the workspace page. It should bring you to the following page:\n\n \nClick on the job submission that contains the failed sample under the 'Submissi... |
null | null | null | dx.doi.org/10.17504/protocols.io.kxacxie | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?. | [] |
47,954 | Probiotics | 4 | dx.doi.org/10.17504/protocols.io.bs3sngne | https://www.protocols.io/view/probiotics-bs3sngne | Sulav Indra Paul | TITLE: Probiotics
AUTHORS: Sulav Indra Paul
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Gut probiotic improves growth and health of </span><span style = "font-style:italic;">B. gonionotus</span><span> fishes</span></div></div>
[STEPS]
?. [Euthanasia methods]
Pure clove oil was first diss... | ["[Euthanasia methods]\nPure clove oil was first dissolved in ethyl alcohol in 1:9 ratio (clove oil: ethyl alcohol)", "[Euthanasia methods]\nThis solution then diluted in water in order to obtain concentrations of 0.05 mL (50 mg), and 0.20 mL (200 mg) of clove oil per 500 mL of water", "[Euthanasia methods]\nFor hemato... |
20,372 | U Mass -Lactate | null | dx.doi.org/10.17504/protocols.io.x5ufq6w | null | Jason Kim | TITLE: U Mass -Lactate
AUTHORS: Jason Kim
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">This experiment involves a spectrophotometric measurement using Roche Cobas Clinical Chemistry Analyzer. Serum lactate levels a... | ["Perform daily quality control assessment of instrumentation before analysis.", "Load each sample into a specialized micro-sample cup for the clinical chemistry analyzer.", "Select Lactate test on display and run the analysis.", "Collect and analyze the data."] |
null | null | null | dx.doi.org/10.17504/protocols.io.e3ibgke | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol has been optimized to remove washing steps after antibody cocktail and nanobeads incubations, resulting in a shorter and more convenient protocol. This procedure is optimized for the isolation of 10<sup>7</sup> to 2 x 10<sup>8</sup> cells per tube from human per... | [] |
99,629 | Pre-Imaging Solid Growth Medium - Yeast | 0 | dx.doi.org/10.17504/protocols.io.8epv5r9wjg1b/v1 | https://www.protocols.io/view/pre-imaging-solid-growth-medium-yeast-ddim24c6 | Mathias Hammer, Ammeret Rossouw, Azra Lari, Ben Montpetit, David Grunwald | TITLE: Pre-Imaging Solid Growth Medium - Yeast
AUTHORS: Mathias Hammer, Ammeret Rossouw, Azra Lari, Ben Montpetit, David Grunwald
[DESCRIPTION]
This protocol describes the steps to prepare solid culture medium for Saccharomyces cerevisiae.
This solid medium is used for cultures that are going to be investigated by fl... | ["[Preparation of ~20 agar plates of yeast pre-imaging growth medium] Compound medium for autoclave", "[Preparation of ~20 agar plates of yeast pre-imaging growth medium] Fill a 500 ml flask with 444 mLddH2O. \nAdd a magnetic stirring bar and place the flask on a stirring hot plate.", "[Preparation of ~20 agar plates o... |
40,985 | Determination of IgM concentration by the Mancini test. | 6 | dx.doi.org/10.17504/protocols.io.bj9zkr76 | https://www.protocols.io/view/determination-of-igm-concentration-by-the-mancini-bj9zkr76 | Angel Justiz-Vaillant | TITLE: Determination of IgM concentration by the Mancini test.
AUTHORS: Angel Justiz-Vaillant
[STEPS]
?. An appropriate anti-IgM antiserum (antibody) is poured in the center well of an agar-containing plate.
?. Carefully circular wells are cut and detached from the plates.
?. A series of standards containing known co... | ["An appropriate anti-IgM antiserum (antibody) is poured in the center well of an agar-containing plate.", "Carefully circular wells are cut and detached from the plates.", "A series of standards containing known concentrations of IgM are placed in separate wells, while “unknown” human serum samples and control are pla... |
46,021 | Isolation of Nuclei from Adult_Human_Brain_Tissue | 1 | dx.doi.org/10.17504/protocols.io.bq7dmzi6 | https://www.protocols.io/view/isolation-of-nuclei-from-adult-human-brain-tissue-bq7dmzi6 | Allen Institute for Brain Science | TITLE: Isolation of Nuclei from Adult_Human_Brain_Tissue
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Isolation of nuclei from frozen adult human brain tissue or thawed and microdissected brain tissue sections for FPCR and/or RNA-seq analysis. </div><div... | [] |
50,742 | CD34+ isolation from human bone marrow | 4 | dx.doi.org/10.17504/protocols.io.bvswn6fe | https://www.protocols.io/view/cd34-isolation-from-human-bone-marrow-bvswn6fe | Mohsen Khosravi-Maharlooei, Markus Holzl, Austin Chen, Megan Sykes | TITLE: CD34+ isolation from human bone marrow
AUTHORS: Mohsen Khosravi-Maharlooei, Markus Holzl, Austin Chen, Megan Sykes
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol details the steps for isolating CD34+ cells from human bone marrow. The CD34+ cells isolated from this protocol can ... | ["Transfer the content of the collection bag into a sterile flask", "Add BM Medium to the bag and rinse it thoroughly\n250 mL", "Transfer the content of the collection bag into the sterile flask", "Layer of the suspension over of Histopaque\n35 mL\n15 mL", "Centrifuge the tubes for 30 minutes without brake at RT\n500... |
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