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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null | null | null | dx.doi.org/10.17504/protocols.io.dtp6mm | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Preparation of both LB broth for growing bacteria and LB agar plates
[STEPS]
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null | null | null | dx.doi.org/10.17504/protocols.io.chtt6m | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol is for the "First Strand cDNA Synthesis Kit using ProtoScript II Reverse Transcriptase (M0368)".
[STEPS]
?.
?.
?.
?.
?. | [] |
97,473 | Protocol To Access Produce Images from the Imperfect Foods Dataverse on the Harvard Dataverse | 0 | dx.doi.org/10.17504/protocols.io.j8nlk85wdl5r/v1 | https://www.protocols.io/view/protocol-to-access-produce-images-from-the-imperfe-dbe92jh6 | Anjali Sharma | TITLE: Protocol To Access Produce Images from the Imperfect Foods Dataverse on the Harvard Dataverse
AUTHORS: Anjali Sharma
[DESCRIPTION]
In the face of the impending challenge of feeding a growing global population, one-third of all food produced ends up as waste. A notable contributor to this problem is the wastage ... | ["[Introduction] The produce images are stored in the imperferct foods dataverse (IFDverse) on the Harvard Dataverse. Decide on whether to search for produce on Harvard Dataverse, OR to use the link included in the annotated bibliography of the IFDverse.", "[Find Dataset for Produce and Type of Produce in Imperfect Foo... |
null | null | null | dx.doi.org/10.17504/protocols.io.e9hbh36 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This is part of the <a href="https://www.protocols.io/view/Collection-of-FOCUS-SubCell-Protocols-For-the-Enri-e9ebh3e" target="_blank">collection</a> of FOCUS™ SubCell protocols for the enrichment of subcellular fractions. Please refer to the appropriate protocol depending on... | [] |
91,261 | Reference pictures of hPSC cultured in defined conditions | 4 | dx.doi.org/10.17504/protocols.io.dm6gp32y5vzp/v1 | https://www.protocols.io/view/reference-pictures-of-hpsc-cultured-in-defined-con-c5c5y2y6 | Katarzyna Ludwik, Valeria Fernandez Vallone, Lyn Healy, Nathalie Lefort, Tamer Onder, Lisa Pavinato, Fatma Visal FVO OKUR, Harald Stachelscheid | TITLE: Reference pictures of hPSC cultured in defined conditions
AUTHORS: Katarzyna Ludwik, Valeria Fernandez Vallone, Lyn Healy, Nathalie Lefort, Tamer Onder, Lisa Pavinato, Fatma Visal FVO OKUR, Harald Stachelscheid
[DESCRIPTION]
Collection of reference images of hPSCs in different culture conditions and at differen... | ["[Example images of undifferentiated hPSCs in different culture conditions] Timepoints, matrix, and media used are labeled or indicated in Step description. \n\nThe standard morphology of undifferentiated hPSC colonies is distinctive and serves as an important criterion for assessing the pluripotent state of the cells... |
null | null | null | dx.doi.org/10.17504/protocols.io.cdks4v | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Please see the NEB website for more information.
[STEPS]
?.
?.
?.
?.
?.
?. | [] |
36,586 | Carbonate-Bicarbonate Buffer | null | dx.doi.org/10.17504/protocols.io.bfyijpue | https://www.protocols.io/view/carbonate-bicarbonate-buffer-bfyijpue | Neilier Junior | TITLE: Carbonate-Bicarbonate Buffer
AUTHORS: Neilier Junior
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">A buffer solution has the function of resisting changes in pH even when adding powerful acids or bases. However, in the physiological environment the buffered system also provides cofactors fo... | ["[Carbonate-Bicarbonate Buffer]\nMix sodium carbonate and sodium bicarbonate solutions in the proportions indicated. ABCDEFGHI1mL of Sodium carbonate4.09.516.022.027.533.038.542.52mL of Sodium bicarbonate46.040.534.028.022.517.011.57.53pH9.29.49.69.810.010.210.410.6\npH range: to (a) 0.1 M Sodium carbonate (anhydr... |
21,331 | Human Islet Microvasculature Immunofluorescence in Optically Cleared Samples | 1 | dx.doi.org/10.17504/protocols.io.y3tfynn | https://www.protocols.io/view/human-islet-microvasculature-immunofluorescence-in-y3tfynn | Martha Campbell Thompson, Elizabeth Butterworth Hosaka, Katelyn N Carty | TITLE: Human Islet Microvasculature Immunofluorescence in Optically Cleared Samples
AUTHORS: Martha Campbell Thompson, Elizabeth Butterworth Hosaka, Katelyn N Carty
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:left"><span>This protocol describes the imm... | ["[Stain the Tissue]\nIncubate the samples with primary antibodies on a rocker plate for 1-5 days at .\n0 Room temperature", "[Stain the Tissue]\nWash the tissue sections with 1xPBS for five times, minimum at .\n25 Room temperature", "[Imaging]\nThe following lasers were used for imaging each antigen in these images:... |
26,958 | scNMT-seq | null | dx.doi.org/10.17504/protocols.io.6jnhcme | null | Stephen Clark | TITLE: scNMT-seq
AUTHORS: Stephen Clark
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Here we describe the full wetlab protocol for scNMT-seq (single-cell nucleosome position, methylome and transcriptome sequencing), a plate-based single-cell multi-omic method.</div><div class = "text-block">In sc... | ["[Single-cell collection and methylase reaction]\nCollect single cells in Centrifuge at ≥1000g for ≥10s.\n[ of freshly prepared GpC methylase reaction mix (keep chilled on ice)]\nWe have successfully used both flow sorting and manual pipetting for single-cell collections.", "[Single-cell collection and methylase reac... |
63,867 | Bacterial Genomes Mining | 4 | dx.doi.org/10.17504/protocols.io.4r3l2obw4v1y/v1 | https://www.protocols.io/view/bacterial-genomes-mining-cak3scyn | contact.microbialtec | TITLE: Bacterial Genomes Mining
AUTHORS: contact.microbialtec
[DESCRIPTION]
The fast development of genome sequencing technologies and the power of advanced computational analyses of the DNA sequences dramatically increased the potential for natural product discovery. Our knowledge on the biosynthesis of secondary m... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.fi2bkge | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><strong>Experiment purpose is to monitor the time-course of a large-scale infection of host cyanobacteria by phage under variable media conditions and obtain samples for proteomic and transcriptomic analysis.</strong></p>
<p> </p>
<p><strong>15 Hourly Timepoints: 0, 1, 2, 3, ... | [] |
29,311 | Identification of different EEC types and nerve fiber types in human gastric mucosa | null | dx.doi.org/10.17504/protocols.io.8u7hwzn | null | Madeleine Di Natale, Josiane Fakhry, Martin Stebbing, Billie Hunne, John B. Furness | TITLE: Identification of different EEC types and nerve fiber types in human gastric mucosa
AUTHORS: Madeleine Di Natale, Josiane Fakhry, Martin Stebbing, Billie Hunne, John B. Furness
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Enteroendocrine cells are important regulators of gastrointestinal, ... | ["Stomach tissue is collected from patients who were undergoing gastric sleeve surgery for obesity at the Renown Regional Medical Center, Reno, Nevada.", "Sections of 12 μm thickness are cut, allowed to dry at room temperature for 1 h on microscope slides (SuperFrostPlus®; Grale Scientific, Vic, Australia) and incubate... |
null | null | null | dx.doi.org/10.17504/protocols.io.crav2d | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This is the protocol for immunoprecipitation using Protein A/G Magnetic Beads.
[BEFORE_START]
Use 25 µl of Protein A/G Magnetic Beads per 200 µl of crude cell lysate containing 200-500 µg of total protein in a standard immunoprecipitation protocol. I... | [] |
39,099 | ICV Surgery | 1 | null | https://www.protocols.io/view/icv-surgery-bie3kbgn | Sharona Sedighim, Molly Brennan, Olivier George | TITLE: ICV Surgery
AUTHORS: Sharona Sedighim, Molly Brennan, Olivier George
[STEPS]
?. [ICV Surgery Procedure]
Ears in ear bar (do NOT loosen the left bar)
?. [ICV Surgery Procedure]
Shave head
?. [ICV Surgery Procedure]
Put head up at 5 for ICV ONLY
?. [ICV Surgery Procedure]
Clean head with alcohol/iodine/alcohol
?.... | ["[ICV Surgery Procedure]\nEars in ear bar (do NOT loosen the left bar)", "[ICV Surgery Procedure]\nShave head", "[ICV Surgery Procedure]\nPut head up at 5 for ICV ONLY", "[ICV Surgery Procedure]\nClean head with alcohol/iodine/alcohol", "[ICV Surgery Procedure]\nIncision down the middle of the head, between the eyes",... |
null | null | null | dx.doi.org/10.17504/protocols.io.qvedw3e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol is used to clarity the process of total DNA extraction for our Betta splendens genome.</p>
[STEPS]
?.
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null | null | null | dx.doi.org/10.17504/protocols.io.jivcke6 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?. | [] |
98,534 | Generation of Immunodeficient Mice Bearing Human Immune Systems by the Engraftment of Hematopoietic Stem Cells | 4 | dx.doi.org/10.17504/protocols.io.36wgq4q43vk5/v2 | https://www.protocols.io/view/generation-of-immunodeficient-mice-bearing-human-i-dcge2tte | 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]
Immunodeficient mice are being used as recipients of human hematopoietic stem cells (HSC... | ["[Methods] Preparation of umbilical cord blood (UCB)", "[Methods] Allow histopaque and RPMI supplemented with 0.5% BSA to warm to room temperature.", "[Methods] Transfer UBC to 50 mL conical tubes (30 mls per tube).", "[Methods] Add hespan to each tube of UBC to a final concentration of 20% per volume and mix gently."... |
51,671 | Qubit (HS dsDNA Assay) | 1 | null | https://www.protocols.io/view/qubit-hs-dsdna-assay-bwpxpdpn | Wolfram Moebius | TITLE: Qubit (HS dsDNA Assay)
AUTHORS: Wolfram Moebius
[DESCRIPTION]
Qubit (HS dsDNA Assay)
[STEPS]
SECTION: Prepare working solution
1.
NOTE: This is suitable for small numbers of samples (i.e. less than 24), including the quantification of the final libraries using the next generation sequencing SOP.
Label the re... | ["[Prepare working solution] NOTE: This is suitable for small numbers of samples (i.e. less than 24), including the quantification of the final libraries using the next generation sequencing SOP.\n\nLabel the required number of 0.5 ml tubes for Standard 1, Standard 2 and all your samples (use only the specific Qubit As... |
34,645 | 10x Genomics Library Construction | null | dx.doi.org/10.17504/protocols.io.bd3vi8n6 | null | Graham J Etherington, Darren Heavens, David Baker, Ashleigh Lister, Rose McNelly, Gonzalo Garcia, Bernardo Clavijo, Iain Macaulay, Wilfried Haerty, Federica Di Palma | TITLE: 10x Genomics Library Construction
AUTHORS: Graham J Etherington, Darren Heavens, David Baker, Ashleigh Lister, Rose McNelly, Gonzalo Garcia, Bernardo Clavijo, Iain Macaulay, Wilfried Haerty, Federica Di Palma
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">10x Genomics Library Construction</d... | ["Input DNA (in this case Polecat) was diluted down from to using Qiagen EB and checked using a QuBit 2.0 Fluorometer (Thermo-Fisher). The sample was then diluted in half as it was denatured. Finally, of the diluted and denatured DNA was loaded onto the 10X chip which equated to .\n2.5 µl\n1.25 ng", "Gel beads, oil ... |
83,939 | Sample Collection and Processing for RNA Analysis | 1 | dx.doi.org/10.17504/protocols.io.n2bvj3r1plk5/v1 | https://www.protocols.click/view/sample-collection-and-processing-for-rna-analysis-cv8bw9sn | Xianjun Dong | TITLE: Sample Collection and Processing for RNA Analysis
AUTHORS: Xianjun Dong
[DESCRIPTION]
This protocol delineates the steps taken to collect frozen postmortem human brain samples and process them for RNA extraction and analysis.
[STEPS] | [] |
68,814 | Passaging of trophoblast organoids from full-term placental tissue. | 4 | dx.doi.org/10.17504/protocols.io.e6nvwkx8dvmk/v1 | https://www.protocols.io/view/passaging-of-trophoblast-organoids-from-full-term-cffntjme | Carolyn Coyne, henry.yang | TITLE: Passaging of trophoblast organoids from full-term placental tissue.
AUTHORS: Carolyn Coyne, henry.yang
[DESCRIPTION]
This protocol describes the passaging of trophoblast organoids isolated from full-term human placental tissue.
[STEPS]
SECTION: Reagents, Solutions and Materials prepared in advance:
1. a) Pre... | ["[Reagents, Solutions and Materials prepared in advance:] a) Pre-cool blunt 200 µl pipette tips (Fisher 02-707-134).\nb) Pre-warm multi-well TC plate (this protocol uses 24-well TC plate, cat# 3526, Costar) and Stem Pro Accutase (Gibco, Cat # A11105-01) supplemented with 10 µM Y-27632 (Sigma, Y0503-1MG; 100 × dilution... |
null | null | null | dx.doi.org/10.17504/protocols.io.dut6wm | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This procedure allows you to transform DNA into chemically competetent <em>E. coli</em>.
[BEFORE_START]
• Equilibrate a water bath to 42°C. <br />• Warm the vial of S.O.C medium to room temperature. <br />• Spread X-Gal onto LB agar plates with antibiotic, if desired for blue/w... | [] |
72,998 | Bird Measurements - ISL Peru | 1 | dx.doi.org/10.17504/protocols.io.rm7vzbxe2vx1/v1 | https://www.protocols.io/view/bird-measurements-isl-peru-cjieukbe | Jorge Luis Mendoza-Silva, Cristian Tirapelle, Mrinalini Watsa, Gideon Erkenswick | TITLE: Bird Measurements - ISL Peru
AUTHORS: Jorge Luis Mendoza-Silva, Cristian Tirapelle, Mrinalini Watsa, Gideon Erkenswick
[DESCRIPTION]
This protocol describes how to collect the relevant measurements during bird processing.
[GUIDELINES]
For an accurate description of measurements taken with birds, please refer t... | ["[Lengths] If requested: measure the total length of the bird using a tape measure or callipers. Align the bird's neck and measure from the tip of the beak to the tip of the tail. Avoid stretching the bird's neck when you are doing this.", "[Lengths] The wing measurements are taken from the fold of the closed wing to ... |
53,331 | Histological quantification of thickness of the mucosal and muscle layers of the rat stomach | 1 | dx.doi.org/10.17504/protocols.io.bybtpsnn | https://www.protocols.io/view/histological-quantification-of-thickness-of-the-mu-bybtpsnn | Madeleine R. Di Natale, Lauren Patten, Martin Stebbing, John Furness | TITLE: Histological quantification of thickness of the mucosal and muscle layers of the rat stomach
AUTHORS: Madeleine R. Di Natale, Lauren Patten, Martin Stebbing, John Furness
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The thickness, organization and relationships between the muscle layers of... | ["[Tissue Collection]\nStomach tissue is collected from adult Sprague-Dawley male and female rats. Rats are supplied with food and water ad libitum prior to any tissue collection. All procedures were approved by The Florey Institute of Neuroscience and Mental Health Animal Ethics Committee.", "[Histological Staining]\n... |
35,352 | TissueCyte Troubleshooting Guide | null | dx.doi.org/10.17504/protocols.io.beryjd7w | null | Allen Institute for Brain Science | TITLE: TissueCyte Troubleshooting Guide
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol outlines strategies to solve common problems that occur when setting up the TissueCyte 1000 system for normal operation.</div><div class = "text-block"><sp... | [] |
63,013 | Dynamic Light Scattering measurements | 4 | null | https://www.protocols.io/view/dynamic-light-scattering-measurements-b9sdr6a6 | arpine.sokratian | TITLE: Dynamic Light Scattering measurements
AUTHORS: arpine.sokratian
[DESCRIPTION]
Brief instrument guide for Dynamic Light Scattering Wyatt DynaPro followed by specific instructions to measure the size of sonicated amyloid fibrils
[STEPS]
SECTION: DLS overview
1.
SECTION: DLS overview
2.
SECTION: Sam... | ["[DLS overview]", "[DLS overview]", "[Sample preparation] Add 4 µLof diluted sample (ranges 0.1-0.5 mg/mL ) onto", "[Sample preparation]", "[Sample preparation] Load the cuvette into the DLS machine", "[Recording the size distribution] Connect the device and the detector software", "[Recording the size distribution]... |
99,812 | Artificial Cerebrospinal Fluid VIII (ACSF.VIII) | 1 | dx.doi.org/10.17504/protocols.io.yxmvmxy8ol3p/v4 | https://www.protocols.io/view/artificial-cerebrospinal-fluid-viii-acsf-viii-ddqc25sw | Allen Institute for Brain Science | TITLE: Artificial Cerebrospinal Fluid VIII (ACSF.VIII)
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
This protocol describes how to make Artificial Cerebrospinal Fluid VIII (ACSF.VIII). ACSF.VIII is used for multiple applications including incubation of fresh human brain slices prior to electrophysiologica... | [] |
57,698 | Random protocol | 4 | null | https://www.protocols.io/view/random-protocol-b4kaquse | Mark D D. Wilkinson | TITLE: Random protocol
AUTHORS: Mark D D. Wilkinson
[DESCRIPTION]
this is to explore the system
[STEPS]
1. 10 millimolar (mM)
3. 30 min
4. 6000 rpm, 30 min, 25 °C
2.
1.1.
| ["10 millimolar (mM)", "30 min", "6000 rpm, 30 min, 25 °C"] |
null | null | null | dx.doi.org/10.17504/protocols.io.f58bq9w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Preparation of BG-11 growth medium.</p>
[STEPS]
?.
?.
?.
?.
?. | [] |
52,300 | Acute doses of beetroot juice supplementation on aerobic and anaerobic performance of trained male taekwondo athletes | 1 | dx.doi.org/10.17504/protocols.io.bxbkpikw | https://www.protocols.io/view/acute-doses-of-beetroot-juice-supplementation-on-a-bxbkpikw | Hossein Miraftabi, Zahra Avazpoor, Erfan Berjisian, Amir Sarshin, Sajjad Rezaei, Raúl Domínguez, Reid Reale, Emerson Franchini, Mohammad Hossein Samanipour, Majid S. Koozehchian, Mark E.T. Willems, Ramin Rafiei, Alireza Naderi | TITLE: Acute doses of beetroot juice supplementation on aerobic and anaerobic performance of trained male taekwondo athletes
AUTHORS: Hossein Miraftabi, Zahra Avazpoor, Erfan Berjisian, Amir Sarshin, Sajjad Rezaei, Raúl Domínguez, Reid Reale, Emerson Franchini, Mohammad Hossein Samanipour, Majid S. Koozehchian, Mark E.... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.extbfnn | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
<strong>Materials: </strong><br />• Sterile PBS <br />• Anti-human CD3 Antibody <br /> - Clone UCHT1 (LEAF™ format, Cat. No. 300413/300414/300432; Ultra-LEAF™ format, Cat. No. 300437/300438)<br /> - Clone OKT3 (LEAF™ format, Cat. No. 317303/317304/317315; Ultra-LEAF™ ... | [] |
82,765 | DAPI Staining Mouse Brain Sections | 1 | dx.doi.org/10.17504/protocols.io.3byl4jm6rlo5/v1 | https://www.protocols.io/view/dapi-staining-mouse-brain-sections-cu3mwyk6 | daphne.toglia, Holly Myers | TITLE: DAPI Staining Mouse Brain Sections
AUTHORS: daphne.toglia, Holly Myers
[DESCRIPTION]
This protocol details the steps for staining 4% PFA fixed mouse brain tissue sections with DAPI (4',6-diamidino-2-phenylindole), a fluorescent stain that can be used to label anatomic regions of interest in a mouse brain, allow... | ["[Before Staining] Wash the mouse brain sections for at least 3 times, 5 min each time in 1XPBS.", "[Staining with DAPI] Pipette diluted DAPI (see note below) into each well with a manual pipette and place well plate on a shaker at Room temperature. Each well should contain enough DAPI solution to fully submerge the ... |
null | null | null | dx.doi.org/10.17504/protocols.io.irbcd2n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol describes the affinity activity of microRNA93 through luciferase activity in 293T cells that have been transformed with a firefly luciferase coding sequence downstream of the BMP2 3'UTR. Using this methods we were able to idetificated microRNA93-5P binding the d... | [] |
81,629 | TS Spurrs - tissue fixed in Karnovsky's (TM - 013) | 4 | dx.doi.org/10.17504/protocols.io.8epv5j45jl1b/v1 | https://www.protocols.io/view/ts-spurrs-tissue-fixed-in-karnovsky-39-s-tm-013-ctx5wpq6 | sandra.crameri | TITLE: TS Spurrs - tissue fixed in Karnovsky's (TM - 013)
AUTHORS: sandra.crameri
[DESCRIPTION]
This method is used for conventional processing of tissue to Spurr's resin.
[GUIDELINES]
All time are minimum times, it is acceptable to go over time specified for any given step. Good place steps to leave overnight or... | ["[HEADER] SAN:\n\n\nSPEC No:\n\n\nOPERATOR & STEPS:\n\n\nOPERATOR & STEPS:", "[CONVENTIONAL] 2.5 % volume plus 4 % volume in 0.1 Molarity (m) for at least 40 min", "[CONVENTIONAL] Wash 0.1 Molarity (M) Sorenson's Phosphate Buffer pH 07.2 (300mosmol/kg) for 15 min", "[CONVENTIONAL] 1 % volume in buffer for 60 mi... |
36,547 | SPARC Pig1 acute wired ColoMOCA implantation | 1 | dx.doi.org/10.17504/protocols.io.bfxbjpin | https://www.protocols.io/view/sparc-pig1-acute-wired-colomoca-implantation-bfxbjpin | Dennis Bourbeau, Brett Hanzlicek, Margot Damaser | TITLE: SPARC Pig1 acute wired ColoMOCA implantation
AUTHORS: Dennis Bourbeau, Brett Hanzlicek, Margot Damaser
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"> In this study, we will be using Yorkshire Pigs, 50-70kg. The purpose of this study is to develop a tool to measure bowel fullness and activi... | ["[Anesthesia Preparation]\nAnesthesia Preparation Pigs will be initially anesthetized with an intramuscular dose of telazol (4.4−6.6 mg/kg). The animals will then be intubated orotracheally and maintained on isoflurane in oxygen (1-5%; depending on anesthetic depth). Anesthetic depth will be measured by the respons... |
76,395 | Potassium phosphate buffer (1.0 M, pH 6.2) | 4 | null | https://www.protocols.io/view/potassium-phosphate-buffer-1-0-m-ph-6-2-cnujveun | Andreas Sagen | TITLE: Potassium phosphate buffer (1.0 M, pH 6.2)
AUTHORS: Andreas Sagen
[DESCRIPTION]
Potassium phosphate buffers are buffers with a buffering capacity between 5.8 and 8.0, where it is possible to adjust the pH and buffer strength with different ratios of Sodium phosphate monobasic and Sodium phosphate dibasic.
[ST... | ["[500 mL Phosphate buffer (1.0 M, pH 6.2)] Fill a sterile 500 mL bottle with 400 mL distilled water", "[500 mL Phosphate buffer (1.0 M, pH 6.2)] Measure 12.035 g Sodium phosphate dibasic and 49.818 g Sodium phosphate monobasic\n\nMaterials:", "[500 mL Phosphate buffer (1.0 M, pH 6.2)] Add dry ingredients and mix for 5... |
42,801 | Proteins annotation of Nano-DESI MSI datasets | 1 | dx.doi.org/10.17504/protocols.io.bm2rk8d6 | https://www.protocols.io/view/proteins-annotation-of-nano-desi-msi-datasets-bm2rk8d6 | yang1832 , Julia Laskin | TITLE: Proteins annotation of Nano-DESI MSI datasets
AUTHORS: yang1832 , Julia Laskin
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Scope: </div><div class = "text-block">Annotate protein species detected by Nano-DESI IMS analysis.</div></div>
[STEPS]
?. Create mass list from the averaged spectru... | ["Create mass list from the averaged spectrum.", "Calculate the charge state of each multiply charged peaks based on the spacing between the isotopic peaks.", "Calculate the exact mass based on the m/z and charge state.", "Obtain CID data from each sample.", "Assign peaks by matching the exact mass and the CID spectrum... |
34,603 | Appendix 2: Optimization of Fragmentation Parameters | 1 | dx.doi.org/10.17504/protocols.io.14egn8exqg5d/v1 | https://www.protocols.io/view/appendix-2-optimization-of-fragmentation-parameter-bd2ji8cn | Dakota Betz | TITLE: Appendix 2: Optimization of Fragmentation Parameters
AUTHORS: Dakota Betz
[DESCRIPTION]
Fragmentation guidelines provided in the Library Construction Protocol: Enzymatic Fragmentation (step 1) may not result in the optimal library size distribution for your specific DNA samples. For this reason, precious sample... | ["Quantification of Input DNA\n\nThe Qubit fluorometer is recommended for the quantification of high-quality DNA, whereas the\nKAPA hgDNA Quantification and QC Kit provides both concentration and quality information for FFPE DNA.", "Handling of DNA Samples Containing EDTA", "For example:\n• If your DNA samples are in T... |
68,138 | Planet Microbe Semantic Web Application | 5 | dx.doi.org/10.17504/protocols.io.e6nvwkw19vmk/v1 | https://www.protocols.io/view/planet-microbe-semantic-web-application-cesitece | Kai Blumberg | TITLE: Planet Microbe Semantic Web Application
AUTHORS: Kai Blumberg
[DESCRIPTION]
Placeholder tutorial for the use of the Planet Microbe Semantic Web Application, accompanying the PhD dissertation work of Kai Blumberg.
[STEPS]
SECTION: Home Page
1. This protocol is a temporary place holder for the protocol to use ... | ["[Home Page] This protocol is a temporary place holder for the protocol to use the Planet Microbe Semantic Web API. This protocol is included as part of Kai Blumberg's PhD dissertation work. \n\nThis work is contained within this github repository: https://github.com/hurwitzlab/planet-microbe-semantic-web-analysis\n\... |
null | null | null | dx.doi.org/10.17504/protocols.io.cpxvpm | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Quick Ligation products may be transformed by many different methods. The following protocol is recommended by New England Biolabs.
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
93,072 | ROBIN: A unified nanopore-based sequencing assay integrating real-time, intraoperative methylome classification and next-day comprehensive molecular brain tumour profiling for ultra-rapid tumour diagnostics | 6 | dx.doi.org/10.17504/protocols.io.bp2l6xepklqe/v1 | https://www.protocols.io/view/robin-a-unified-nanopore-based-sequencing-assay-in-c65qzg5w | Simon Deacon, Inswasti Cahyani, Matthew Loose | TITLE: ROBIN: A unified nanopore-based sequencing assay integrating real-time, intraoperative methylome classification and next-day comprehensive molecular brain tumour profiling for ultra-rapid tumour diagnostics
AUTHORS: Simon Deacon, Inswasti Cahyani, Matthew Loose
[DESCRIPTION]
Background
Advances in our technolog... | ["[Tissue Selection] Open tissue pot in Category 3 MSC and weigh total mass on petri dish.", "[DNA Extraction from Brain Tissue] Homogenize tissue using vortexer at full speed for 5 min.", "[Tissue Selection] Dissect out representative tumour tissue weighing 5-25 mg, then place in Tissue Disruption Tube.", "[Tissue Sel... |
20,649 | Case - Lipid Analysis Assay by GC-mass spectrometry | null | dx.doi.org/10.17504/protocols.io.yehftb6 | null | Henri Brunengraber | TITLE: Case - Lipid Analysis Assay by GC-mass spectrometry
AUTHORS: Henri Brunengraber
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary</span></div><div class = "text-block"><span>A known quantity of tissue / plasma is hydrolyzed and extracted after adding kn... | ["Pipette 1ml KOH ethanol solution (1N KOH in 70% EtOH) for every 100mg of tissue or 100 μl of plasma use glass screw top tubes (may use less tissue/plasma)", "Internals standards (IS): add 25 μl of 1mg/ml heptadecanoic acid (C17:0) and cholesterol-d7 for every 100μl of tissue (note: adjust added amount of internal sta... |
62,346 | Preparation of Bacteria Glycerol Stocks | 1 | null | https://www.protocols.io/view/preparation-of-bacteria-glycerol-stocks-b85iry4e | Stephane Fadanka, Shalo Minette, Nadine Mowoh | TITLE: Preparation of Bacteria Glycerol Stocks
AUTHORS: Stephane Fadanka, Shalo Minette, Nadine Mowoh
[DESCRIPTION]
This protocol is meant to provide researchers with a step by step procedure on how to prepare glycerol stocks in order to preserve and store bacteria for long term.
Bacterial glycerol stocks are im... | ["[Preparing liquid culture of the bacteria to be stored] Prepare LB following this protocol depending on the desired amount of LB and subsequent number of glycerol stock tubes needed.\n\nUsing an inoculating wire loop, pick up some bacteria colonies from a culture plate and inoculate in an Erlenmeyer flask containing ... |
null | null | null | dx.doi.org/10.17504/protocols.io.h4ub8ww | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Protocol Immunohistochemistry free-floating sections with anti-doublecortin antibody for avian tissue.</p>
[STEPS]
?.
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88,929 | Yale Murine TMC - Immunofluorescence Protocol | 1 | dx.doi.org/10.17504/protocols.io.8epv5xenng1b/v1 | https://www.protocols.io/view/yale-murine-tmc-immunofluorescence-protocol-c239ygr6 | Yun-Hee Youm, Yufeng Liu, Vishwa Deep Dixit | TITLE: Yale Murine TMC - Immunofluorescence Protocol
AUTHORS: Yun-Hee Youm, Yufeng Liu, Vishwa Deep Dixit
[DESCRIPTION]
Immunofluorescence staining of mouse tissues
[STEPS]
SECTION: Immunofluorescence Staining
1. Take out the slides to a slide holder and warm slides on a 37°C heater for 5-10 min. Grouping: usually m... | ["[Immunofluorescence Staining] Take out the slides to a slide holder and warm slides on a 37°C heater for 5-10 min. Grouping: usually maximum two antibodies (with secondary antibody red + green) + nuclear staining for one slide. Set negative control for each secondary antibody to detect any non-specific background."... |
null | null | null | dx.doi.org/10.17504/protocols.io.dmh435 | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
Ingridients stocks can be batch made and sterilize by filtering through 0.22 μm filter. Lysis buffer sets are recommended to make freshly. If you are doing ChIP routinely, you can also batch make lysis buffer sets, filter through 0.22 μm filter and store @ 4 °... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.k3ccyiw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div class="page" title="Page 2">
<div class="layoutArea">
<div class="column">
<p>This is a sample Mobility Shift Protocol (NFκB). Each oligo labeled with IRDye 700 provided by LI-COR® Biosciences for EMSA reactions will have an optimized protocol to measure the protein-DNA int... | [] |
71,469 | Immunocytochemistry for CASR in iPSc-derived dopaminergic neurons | 4 | dx.doi.org/10.17504/protocols.io.ewov1onyplr2/v1 | https://www.protocols.click/view/immunocytochemistry-for-casr-in-ipsc-derived-dopam-ch2mt8c6 | Peter Kilfeather | TITLE: Immunocytochemistry for CASR in iPSc-derived dopaminergic neurons
AUTHORS: Peter Kilfeather
[DESCRIPTION]
CASR immunocytochemistry protocol to accompany Kilfeather, Khoo et al., 2023: Single cell spatial transcriptomic and translatomic profiling of dopaminergic neurons in health, ageing and disease
[STEPS]
S... | ["[Day 1] Fix the iPSC derived neurons in 4% PFA.", "[Day 1] Permeabilise cells for 10 min in a solution of 5% NDS, 1% BSA and 0.5% Triton-X 100.", "[Day 1] Block in a solution of 5% NDS and 1% BSA for 1 h.", "[Day 1] Incubate cells for 16 h O/N at 4°C with the following primary antibodies: CASR (Abcam Cat# ab79038, RR... |
86,978 | 811.1 CODEXV1 Staining and Imaging Protocol | 4 | dx.doi.org/10.17504/protocols.io.261ged5pov47/v1 | https://www.protocols.io/view/811-1-codexv1-staining-and-imaging-protocol-cy7axzie | Jeffrey Purkerson, Gloria S Pryhuber, heidie_huyck | TITLE: 811.1 CODEXV1 Staining and Imaging Protocol
AUTHORS: Jeffrey Purkerson, Gloria S Pryhuber, heidie_huyck
[DESCRIPTION]
This protocol describes multiplexed immunofluorescent staining and imaging of FFPE lung tissue sections utilizing the Phenocycler-Keyence 800 platform (Akoya Biosciences). The approach is based... | ["[Lung section preparation] Bake Sections to promote tissue adherence to coverslips.", "[Labeling of lung tissue sections with antibody-barcode conjugates] Deparaffination and Rehydration\nIncubate coverslips placed in a coverslip staining rack in Coppin Jars containing xylene (3X) followed by a descending ethanol ser... |
42,177 | Transcriptomics | 1 | dx.doi.org/10.17504/protocols.io.bme9k3h6 | https://www.protocols.io/view/transcriptomics-bme9k3h6 | Andreea S | TITLE: Transcriptomics
AUTHORS: Andreea S
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The potato root secretes root exudates, a mixture of organic molecules out of which solanine is found in the highest concentration (range of ug/ml). Also, solanine is a molecule specifically found in the ... | ["[Sample preparation]\nDilute an overnight culture of B. mycoides to OD600=0.05 in LB. Divide the culture in 2 parts.Supplement one of them with solanine (concentration range from to ) . Keep the other one as a negative control.", "[Sample preparation]\nCulture the cells for\n30 33", "[Sample preparation]\nCollect c... |
37,781 | Mouse Cardiac Perfusion Fixation and Brain Collection | 1 | dx.doi.org/10.17504/protocols.io.bg5vjy66 | https://www.protocols.io/view/mouse-cardiac-perfusion-fixation-and-brain-collect-bg5vjy66 | Allen Institute for Brain Science | TITLE: Mouse Cardiac Perfusion Fixation and Brain Collection
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the procedures for intracardiac perfusion fixation of postnatal mice, including anesthesia, exsanguination, fixation, brain ... | [] |
23,201 | Quantitative fluorescent polymerase chain reaction (QF-PCR) for the rapid prenatal diagnosis of common fetal aneuploidies | null | dx.doi.org/10.17504/protocols.io.2v9ge96 | null | Predrag Noveski, Marija Terzic, Marija Vujovic, Maja Kuzmanovska, Emilija Sukarova Stefanovska, Dijana Plaseska-Karanfilska | TITLE: Quantitative fluorescent polymerase chain reaction (QF-PCR) for the rapid prenatal diagnosis of common fetal aneuploidies
AUTHORS: Predrag Noveski, Marija Terzic, Marija Vujovic, Maja Kuzmanovska, Emilija Sukarova Stefanovska, Dijana Plaseska-Karanfilska
[DESCRIPTION]
<div class = "text-blocks"><div class = "te... | ["[Main QF-PCR reaction]\nТhis section describes the main QF-PCR reaction and consists of the following steps:2.1) Prepare QF-PCR multiplex primer mix;2.2) Perform PCR reaction;2.3) Capillary electrophoresis of the PCR product and analysis of the results.", "[DNA isolation from amniocytes/chorionic villi/blood]\nPerfom... |
60,232 | Amplify iTracer Barcode and Scars from 10x cDNA | 4 | null | https://www.protocols.io/view/amplify-itracer-barcode-and-scars-from-10x-cdna-b63grgjw | Ashley Maynard, Sophie Jansen, Giovanna Brancati | TITLE: Amplify iTracer Barcode and Scars from 10x cDNA
AUTHORS: Ashley Maynard, Sophie Jansen, Giovanna Brancati
[DESCRIPTION]
Induced pluripotent stem cell (iPSC)-derived organoids provide models to study human organ development. Single-cell transcriptomics enable highly resolved descriptions of cell states within... | ["[Set up Reaction 1 (Root PCR)] Make reaction master mix: \n Component 1x rxn 17x rxn 2x Phusion Ready Mix 25 10uM 10x Root PCR GFP F Primer 2.5 10uM 10x Universal R Primer 2.5 100% DMSO 1.5 EvaGreen 0.75 cDNA prod... |
85,752 | Essential surgeries for the electrophysiological recording from a behaving non-human primate brain 1 (Head fixation post and recording chamber implantation) | 1 | dx.doi.org/10.17504/protocols.io.5jyl8p9yrg2w/v1 | https://www.protocols.io/view/essential-surgeries-for-the-electrophysiological-r-cxyyxpxw | Daisuke Kase, Witold J Lipski, Devin R Harsch, Robert S Turner | TITLE: Essential surgeries for the electrophysiological recording from a behaving non-human primate brain 1 (Head fixation post and recording chamber implantation)
AUTHORS: Daisuke Kase, Witold J Lipski, Devin R Harsch, Robert S Turner
[DESCRIPTION]
The implantation of a head fixation post and recording chamber is the... | ["[Planning for the head fixation post and recording chamber implantation] Calculate the coordinates of the target brain area relative to the ear bar zero.", "[Planning for the head fixation post and recording chamber implantation] Attach the chamber holder bar to the stereotaxic arm.", "[Planning for the head fixatio... |
null | null | null | dx.doi.org/10.17504/protocols.io.hg2b3ye | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Sonication procedure implemented to reduce labyrinthulomycete cell aggregation from culture for subsequent growth analyses. </p>
[STEPS]
?.
?.
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25,616 | 14 SDS-PAGE | null | dx.doi.org/10.17504/protocols.io.49qgz5w | null | TJUSLS China | TITLE: 14 SDS-PAGE
AUTHORS: TJUSLS China
[STEPS]
?. Mount the gels in the vertical electrophoresis apparatus.
?. Load samples under the cathode buffer. Apply 10μL sample volumes to 0.7 × 5 mm sample wells.
10 µl
?. Set running conditions appropriate to your type of gel. We usually set 200V to run at the beginning, aft... | ["Mount the gels in the vertical electrophoresis apparatus.", "Load samples under the cathode buffer. Apply 10μL sample volumes to 0.7 × 5 mm sample wells.\n10 µl", "Set running conditions appropriate to your type of gel. We usually set 200V to run at the beginning, after 10 minutes change the voltage into 300V for ano... |
77,635 | Library preparation (dsDNA single indexing, non-UDG, no split) | 1 | dx.doi.org/10.17504/protocols.io.n92ldpjexl5b/v1 | https://www.protocols.io/view/library-preparation-dsdna-single-indexing-non-udg-cp3bvqin | Marcel Keller, Christiana L Scheib | TITLE: Library preparation (dsDNA single indexing, non-UDG, no split)
AUTHORS: Marcel Keller, Christiana L Scheib
[DESCRIPTION]
Protocol for the preparation of single indexed double-stranded DNA libraries for Illumina sequencing, optimized for ultra-short ancient DNA molecules, modified from Meyer & Kircher (2010) Col... | ["[Blunt End Repair] Use 1.5 ml ER tube to set up the Blunt End Repair Master Mix on ice .", "[Blunt End Repair] Add 20 µl Master Mix to each tube of the ER strip.", "[Blunt End Repair] Vortex and spin down DNA extracts, add 30 µl of template DNA or water to each tube.", "[Blunt End Repair] Mix carefully by resuspendin... |
51,445 | Rapid quantification of cellulose nanocrystals by Calcofluor White fluorescence staining | 1 | dx.doi.org/10.17504/protocols.io.bwgvpbw6 | https://www.protocols.io/view/rapid-quantification-of-cellulose-nanocrystals-by-bwgvpbw6 | Roi Peretz, Hadas Mamane, Elizaveta Sterenzon, Yoram Gerchman | TITLE: Rapid quantification of cellulose nanocrystals by Calcofluor White fluorescence staining
AUTHORS: Roi Peretz, Hadas Mamane, Elizaveta Sterenzon, Yoram Gerchman
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:left">Cellulose nanocrystals (CNCs) have ... | ["[Standard calibration curve]\nFor calibration curve, prepare different CNC solutions in DI water (up to 0.5% w/v).", "[Standard calibration curve]\nIn flat-bottomed black 96 plate, place 100 µL of sample, 20 µL of 5M KOH and 80 µL of CW reagent (in this order). KOH is needed for basic conditions (pH=12-13).", "[Stand... |
29,496 | Bacterial Transformation Protocol | 1 | null | https://www.protocols.io/view/bacterial-transformation-protocol-82yhyfw | Olivier George, Sierra Simpson | TITLE: Bacterial Transformation Protocol
AUTHORS: Olivier George, Sierra Simpson
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Transformation of bacteria to amplify DNA for cloning, virus production, or other molecular biology techniques. </div></div>
[STEPS]
?. Transfer competent cells (DH5a) f... | ["Transfer competent cells (DH5a) from -80 to wet ice for 5-10 min or until thawed.", "Add 1ng to 50ng of DNA directly to cells. Incubate for 10 minutes on ice.", "Heat shock cells for 45 seconds at 42C in a heat block. (Do not go over 45 seconds!) You can kill bacteria by keeping them at high temps for too long.", "Tr... |
35,845 | Simple Way to Make Homemade Cloth Masks: Fabrics Treated with NaCl and Starch Solution | null | dx.doi.org/10.17504/protocols.io.be9djh26 | https://www.protocols.io/view/simple-way-to-make-homemade-cloth-masks-fabrics-tr-be9djh26 | M Mehedi Hasan Rocky, Mohammad Amzad Hossain Bhuyan, Shamim Akhtar | TITLE: Simple Way to Make Homemade Cloth Masks: Fabrics Treated with NaCl and Starch Solution
AUTHORS: M Mehedi Hasan Rocky, Mohammad Amzad Hossain Bhuyan, Shamim Akhtar
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:left">This protocol describes a simple ... | ["[Step by Step]\nCloth size specification: Cut out a piece of rectangular cloth sheet for a mask (width from 18 to 21 inches and length from 30 to 40 inches) from a cotton/linen woven cloth/napkin fabric. Fold over all sides ¼ inch and stitch down.", "[Step by Step]\nClean the cloth sheet for the mask with a normal de... |
34,851 | RNA Extraction Without a Kit | null | dx.doi.org/10.17504/protocols.io.beabjaan | null | Addgene The Nonprofit Plasmid Repository | TITLE: RNA Extraction Without a Kit
AUTHORS: Addgene The Nonprofit Plasmid Repository
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes RNA extraction without a kit. To see the full abstract and additional resources, visit </div><div class = "text-block"><a href="https://www.ad... | ["[Homogenization/Lysis]\nHomogenize or lyse tissues or cells in Solution D.\nFor tissues: use of Solution D per of cells. For cultured cells: use of Solution D per 1 X 107 cells.", "[Homogenization/Lysis]\nAllow sample(s) to sit at for to allow for dissociation of the nucleoprotein complexes.\n0 Room temperatu... |
null | null | null | dx.doi.org/10.17504/protocols.io.s2vege6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>ed. Petteri Karisto 2018</p>
[STEPS]
?.
?.
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94,801 | Processing of raw Stereo-seq data, quality control and cell type identification | 4 | dx.doi.org/10.17504/protocols.io.j8nlkoq25v5r/v1 | https://www.protocols.io/view/processing-of-raw-stereo-seq-data-quality-control-c8trzwm6 | Peter Kilfeather | TITLE: Processing of raw Stereo-seq data, quality control and cell type identification
AUTHORS: Peter Kilfeather
[DESCRIPTION]
Processing of raw Stereo-seq data, quality control and cell type identification methods from Kilfeather, Khoo et al., 2024
[STEPS]
SECTION: Protocol
1. Raw gene-by-spot data per sample were a... | ["[Protocol] Raw gene-by-spot data per sample were aggregated to create a 2-dimensional image of RNA signal for each sample using custom Python (v3.9.0, RRID:SCR_008394) scripts. To segment individual cells, each image was subjected to a processing pipeline written in Python (workflow illustrated in Supplementary Figur... |
null | null | null | dx.doi.org/10.17504/protocols.io.gvmbw46 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div class="page" title="Page 2">
<div class="layoutArea">
<div class="column">
<p>Two-dimensional gel electrophoresis (2DE) is a powerful and well-established method for high-resolution profiling of proteins. This technique separates complex protein mixtures based on two indepe... | ["[Direct Fluorescent-labeled Sample] Prior to beginning labeling, all desired sample pre-processing (e.g. fractionation, purification, enrichment, etc.) should be performed. This includes preparing the sample in a preservative-free phosphate buffer at pH 8.5 (see appropriate LI-COR labeling protocol for details). For ... |
20,712 | UC Davis - Comprehensive Laboratory Animal Monitoring System (CLAMS) | null | dx.doi.org/10.17504/protocols.io.yggfttw | null | Peter Takeuchi, Trina Knotts | TITLE: UC Davis - Comprehensive Laboratory Animal Monitoring System (CLAMS)
AUTHORS: Peter Takeuchi, Trina Knotts
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">Energy expenditure is measured using an indirect respira... | ["Recommend acclimation to MBP Vivarium Room 115 for one week prior to study. a. Animals will be placed in single housing (duplex cages: one cage with clear divider) after transfer. While acclimating in the MBAL animal room the mice will be introduced to the sifted powdered version of their normal accustomed rodent ch... |
null | null | null | dx.doi.org/10.17504/protocols.io.dmc42v | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Bacterial viruses (phages) influence global biogeochemical cycles by modulating bacterial mortality, metabolic output and evolution. However, our understanding of phage infections is limited by few methods and environmentally-relevant model systems. Prior work showed that Cellul... | [] |
48,100 | Chemical Oxygen Demand (COD) Protocol | 1 | null | https://www.protocols.io/view/chemical-oxygen-demand-cod-protocol-bs8cnhsw | William Brigman | TITLE: Chemical Oxygen Demand (COD) Protocol
AUTHORS: William Brigman
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Version 2.0 (COD station 1</span><span style = "vertical-align:super;">st</span><span> lab and analytical trailer)</span></div><div class = "text-block"><span style = ":UNDERLI... | ["Fill out the COD data sheet, record the sample identification number and COD vial number.", "For samples with moderate to low COD (such as constructed wetlands) use the 1,500 mg/L COD vials.For samples with high COD (such as lagoons) use the 15,000 mg/L COD vials.", "Turn on COD block heater digester (DRB 200-HACH) (... |
98,492 | ImmPRESS Polymer Detection Following BaseScope In Situ Hybridization | 0 | dx.doi.org/10.17504/protocols.io.kqdg325rzv25/v1 | https://www.protocols.io/view/immpress-polymer-detection-following-basescope-in-dce42tgw | madalynn.erb Erb | TITLE: ImmPRESS Polymer Detection Following BaseScope In Situ Hybridization
AUTHORS: madalynn.erb Erb
[DESCRIPTION]
Protocol for performing ImmPRESS immunostaining with alkaline phosphatase labeling after BaseScope In Situ Hybridization mouse brain sections.
[STEPS]
SECTION: Day 1
1. Complete BaseScope in situ hybrid... | ["[Day 1] Complete BaseScope in situ hybridization using 35um mouse brain sections. Do not dry slides.\nFor BaseScope protocol see : (dx.doi.org/10.17504/protocols.io.5qpvo364zv4o/v1)", "[Day 1] Wash slides 2 times in PBS at room temp 5 minutes each wash", "[Day 1] Incubate sections in rabbit anti TH (1:500) in 0.4% BS... |
null | null | null | dx.doi.org/10.17504/protocols.io.uc4esyw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><span style="font-weight: 400;">Most noncommercial tradition DNA extraction protocols result in a crude DNA preparation. If the DNA is intended to be used for a high-end application like Nanopore sequencing, it requires a thorough clean-up and size selection before it could b... | ["[Make beads stock solution] {\"blocks\":[{\"key\":\"9vmf5\",\"text\":\"For 10 mL beads stock solution:\\u00a0\",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[],\"entityRanges\":[],\"data\":[]},{\"key\":\"7i6bp\",\"text\":\" \",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[],\"entityRanges\":[],\... |
40,420 | Competitive enzyme-linked immunosorbent assay for investigating SpL binding to mammalian and avian immunoglobulins | 6 | dx.doi.org/10.17504/protocols.io.bjqckmsw | https://www.protocols.io/view/competitive-enzyme-linked-immunosorbent-assay-for-bjqckmsw | Angel Justiz-Vaillant | TITLE: Competitive enzyme-linked immunosorbent assay for investigating SpL binding to mammalian and avian immunoglobulins
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This ELISA was based on the theory that antibodies present in different samples would compete with... | ["This ELISA is based on the theory that antibodies present in different samples would compete with human IgG for binding to SpL, resulting in inhibition of human IgG-SpL interactions.", "The samples tested are commercially prepared pooled sera from skunk, coyote, raccoon, duck, and also commercially prepared purified ... |
93,747 | Induction of aggregation in alpha-synuclein-expressing cells by treatment with preformed fibrils (PFFs) | 1 | dx.doi.org/10.17504/protocols.io.eq2lyjbbplx9/v1 | https://www.protocols.io/view/induction-of-aggregation-in-alpha-synuclein-expres-c7stznen | Cole S Sitron, Victoria A Trinkaus, F Ulrich Hartl | TITLE: Induction of aggregation in alpha-synuclein-expressing cells by treatment with preformed fibrils (PFFs)
AUTHORS: Cole S Sitron, Victoria A Trinkaus, F Ulrich Hartl
[DESCRIPTION]
This protocol details how to efficiently produce alpha-synuclein aggregates in cells by templating the misfolding of intracellular alp... | ["[Induction of alpha synuclein aggregation] Seed cells into plates such that they are ~25% confluent the following day.", "[Induction of alpha synuclein aggregation] On the following day, warm PBS and OptiMEM to 37 °C, thaw an aliquot of PFFs, and (if using) allow lipofectamine to reach Room temperature.", "[Induction... |
null | null | null | dx.doi.org/10.17504/protocols.io.gg5bty6 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
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?.
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98,851 | Fluorescence assay for Enterovirus A71 3C protease activity measurement | 1 | dx.doi.org/10.17504/protocols.io.14egn6zjql5d/v1 | https://www.protocols.io/view/fluorescence-assay-for-enterovirus-a71-3c-protease-dcsb2wan | Charline Giroud, oleg.fedorov | TITLE: Fluorescence assay for Enterovirus A71 3C protease activity measurement
AUTHORS: Charline Giroud, oleg.fedorov
[DESCRIPTION]
This protocol details the fluorescence assay for Enterovirus A71 (EV-A71) 3C protease activity measurement. This method is intended to measure the activity of viral proteases by using a s... | ["[EV-A71 3C Pro IC50 Measurement] Assay buffer: 50 millimolar (mM)Tris pH 7.0, 150 millimolar (mM) NaCl, 10 % (v/v) glycerol and 1 millimolar (mM) TCEP (optional).\nIncubation: 60 min at Room temperature.\nEV-A71 3C: protein stocks were stored at -80C and used as 2x solution ( 5 micromolar (µM), 22.5 micromolar (µM) f... |
58,123 | Run Clearmap 1 docker | 5 | dx.doi.org/10.17504/protocols.io.eq2lynnkrvx9/v1 | https://www.protocols.io/view/run-clearmap-1-docker-b4zjqx4n | Moritz Negwer | TITLE: Run Clearmap 1 docker
AUTHORS: Moritz Negwer
[DESCRIPTION]
This protocol is a supplement to our upcoming publication "FriendlyClearMap: An optimized toolkit for mouse brain mapping and analysis".
In this protocol, we describe in detail how to run Clearmap1 in a Docker container.
[STEPS]
SECTION: Docker Se... | ["[Docker Setup] On Windows: \nIf you haven't already, download and set up Docker Desktop for Windows. This requires administrator privileges and will also install the Windows Subsystem for Linux (WSL2). \n\nDownload: \nhttps://www.docker.com/products/docker-desktop \n\nThen, download the docker container from our repo... |
79,876 | Generation of induced pluripotent stem cells and gene correction | 1 | dx.doi.org/10.17504/protocols.io.5jyl8jo89g2w/v1 | https://www.protocols.io/view/generation-of-induced-pluripotent-stem-cells-and-g-cr9cv92w | michela.deleidi | TITLE: Generation of induced pluripotent stem cells and gene correction
AUTHORS: michela.deleidi
[DESCRIPTION]
iPSC generation and gene correction (CRISPR-CAS9) protocol
[STEPS]
SECTION: Generation of induced pluripotent stem cells and gene correction
1. Skin fibroblasts were reprogrammed by nucleofection with pCXLE-... | ["[Generation of induced pluripotent stem cells and gene correction] Skin fibroblasts were reprogrammed by nucleofection with pCXLE- hOct3/4 (RRID:Addgene_27076), pCXLE-hSK (RRID:Addgene_27078),using the Amaxa nucleofection kit for human dermal fibroblasts (Lonza, VPD-100) and program P-022 of the Nucleofector 2b (Lonz... |
null | null | null | dx.doi.org/10.17504/protocols.io.heub3ew | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol is part of the manuscript: <a href="http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2000862" target="_blank">Gonçalves et al. Commensal bacteria and essential amino acids control food choice behavior and reproduction. Plos Biology. 2017 Apr ... | [] |
16,193 | yeast single cell RNA-seq (yscRNA-seq) | null | dx.doi.org/10.17504/protocols.io.t29eqh6 | null | Mariona Nadal, Saiful Islam, Wu Wei, Pablo Latorre, Michelle Nguyen, Eulàlia de Nadal, Francesc Posas, Lars M. Steinmetz | TITLE: yeast single cell RNA-seq (yscRNA-seq)
AUTHORS: Mariona Nadal, Saiful Islam, Wu Wei, Pablo Latorre, Michelle Nguyen, Eulàlia de Nadal, Francesc Posas, Lars M. Steinmetz
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. [Cell growth]
Grow the desired pre-inoculum of your desired yeast strain in their c... | ["[Cell growth]\nGrow the desired pre-inoculum of your desired yeast strain in their corresponding media O/N.To profile exponentially growing cells, we recommend the initial culture not to grow over OD660=1", "[Cell growth]\nNext morning. Dilute your cells to OD660= 0.05 in the corresponding media and allow for at leas... |
46,276 | Protocol for "Thriving during COVID-19: Predictors of Psychological Well-Being and Ways of Coping” | 1 | dx.doi.org/10.17504/protocols.io.brfcm3iw | https://www.protocols.io/view/protocol-for-34-thriving-during-covid-19-predictor-brfcm3iw | dguess | TITLE: Protocol for "Thriving during COVID-19: Predictors of Psychological Well-Being and Ways of Coping”
AUTHORS: dguess
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">COVID-19 has led to global dramatic shifts in daily life. Following the biopsychosocial model of health, the goal of the current ... | ["Survey administered online: \"Psychological Well-Being during COVID-19\"", "Data collected in SPSS format for the survey on \"Psychological Well-Being during COVID-19\" (N = 938 U.S. participants)"] |
null | null | null | dx.doi.org/10.17504/protocols.io.jw9cph6 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
39,550 | Efficacy of Simulation-Based Education for intravascular catheterization :protocol for a systematic review and meta- analysis | 1 | dx.doi.org/10.17504/protocols.io.biu6keze | https://www.protocols.io/view/efficacy-of-simulation-based-education-for-intrava-biu6keze | Hiromu Okano, Takuya Mayumi, Yuki Kataoka, Masahiro Banno, Yasushi Tsujimoto, Akihiro Shiroshita, Shunsuke Taito, Joho Tokumine | TITLE: Efficacy of Simulation-Based Education for intravascular catheterization :protocol for a systematic review and meta- analysis
AUTHORS: Hiromu Okano, Takuya Mayumi, Yuki Kataoka, Masahiro Banno, Yasushi Tsujimoto, Akihiro Shiroshita, Shunsuke Taito, Joho Tokumine
[DESCRIPTION]
<div class = "text-blocks"><div cla... | [] |
40,075 | SEM imaging of Bacteria | 3 | dx.doi.org/10.17504/protocols.io.bjdjki4n | https://www.protocols.io/view/sem-imaging-of-bacteria-bjdjki4n | avinash.kale | TITLE: SEM imaging of Bacteria
AUTHORS: avinash.kale
[STEPS] | [] |
56,560 | Pilot Exercise: Generating the Illumina SampleSheet and sharing data via BaseSpace | 1 | null | https://www.protocols.io/view/pilot-exercise-generating-the-illumina-samplesheet-b3gqqjvw | Ruth Timme, Maria Balkey, Tunc Kayikcioglu, Candace Bias, Cameron Boerner, James Pettengill | TITLE: Pilot Exercise: Generating the Illumina SampleSheet and sharing data via BaseSpace
AUTHORS: Ruth Timme, Maria Balkey, Tunc Kayikcioglu, Candace Bias, Cameron Boerner, James Pettengill
[DESCRIPTION]
This protocol describes the required steps to generate Illumina SampleSheet and provides guidelines for sharing... | ["[Generating Sequencing SampleSheet] Create your SampleSheet using Excel or a text editor. Name your sample sheet according your internal protocols, and use a *.csv extension. The sample sheet is organized in sections titled Header, Reads, Settings and Data. Section headings are case-sensitive and shown in brac... |
null | null | null | dx.doi.org/10.17504/protocols.io.d7n9md | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<span style="color: #333333; font-family: helvetica, sans-serif; font-size: 14px; line-height: 21px;">Bambus2 is a scaffolding module that can be applicable to metagenomics settings. MetaVelvet uses a novel graph splitting algorithm during contiging process, and uses the scaffol... | [] |
59,750 | Isolation of high molecular weight genomic DNA from Entomophthora muscae | 4 | null | https://www.protocols.io/view/isolation-of-high-molecular-weight-genomic-dna-fro-b6kercte | Carolyn Elya | TITLE: Isolation of high molecular weight genomic DNA from Entomophthora muscae
AUTHORS: Carolyn Elya
[DESCRIPTION]
Obtaining quality genomic material from Entomophthoralean fungi has proven extremely difficult. This protocol describes a method that has been successfully used to obtain high molecular weight genomic D... | ["[Fungal culture] Fungal culture can be established from glycerol freezer stock or from a sporulating cadaver following methods outlined in Hajek et al, 2012. Cultures are grown in supplemented with added 5% FBS (e.g., ) , which will henceforth be referred to as Grace's + 5% FBS.", "[Fungal culture] From -80C glyce... |
88,189 | What is the existing evidence base for adult medical Same Day Emergency Care in UK NHS hospitals? A scoping review protocol | 1 | dx.doi.org/10.17504/protocols.io.3byl4qz7rvo5/v1 | https://www.protocols.io/view/what-is-the-existing-evidence-base-for-adult-medic-c2c5yay6 | Sue Dean, Julian Barratt | TITLE: What is the existing evidence base for adult medical Same Day Emergency Care in UK NHS hospitals? A scoping review protocol
AUTHORS: Sue Dean, Julian Barratt
[DESCRIPTION]
Objectives
Same Day Emergency Care (SDEC) is a new model of care, which has emerged over the
past 5 years, building upon prior ambulator... | ["[Introduction] INTRODUCTION\n\n\nAmbulatory care is an umbrella term used in the UK to describe acute hospital care that is distinct from outpatient, accident and emergency, urgent treatment centres, or inpatient\ncare, and is sometimes referred to as ambulatory emergency care (AEC) (1). In other countries, particula... |
null | null | null | dx.doi.org/10.17504/protocols.io.vgse3we | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol includes a computational pipeline used in assembly and annotation of Kiwifruit Actinidia eriantha genome.
[STEPS]
SECTION: Illumina raw reads cleaning
?.
SECTION: PacBio assembly
?.
SECTION: Polish of PacBio assembly with Illumina reads
?.
SECTION: Scaffold anc... | ["[Illumina raw reads cleaning] {\"blocks\":[{\"key\":\"c6joq\",\"text\":\"1) Deduplication with super_deduper (https:\\/\\/github.com\\/dstreett\\/Super-Deduper) (Optional)\",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[],\"entityRanges\":[{\"offset\":37,\"length\":41,\"key\":0}],\"data\":[]},{\"key\":\"e... |
31,600 | Human Pancreas Optical Clearing by iDISCO and VISIKOL | null | dx.doi.org/10.17504/protocols.io.ba4qigvw | null | Martha Campbell Thompson, Malavika Nair | TITLE: Human Pancreas Optical Clearing by iDISCO and VISIKOL
AUTHORS: Martha Campbell Thompson, Malavika Nair
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Optical clearing of tissues to improve deep tissue microscopy was described over a century ago and methods have improved considerably f... | ["[Permeabilization]\nOn a shaker, wash the fixed tissue 2x30 minutes in 1X PBS at room temperature.", "[Permeabilization]\nDehydrate the tissue in increasing grades of methanol, 50%-80%-100% MeOH, for 1 hour each at room temperature.", "[Permeabilization]\nPlace the tissue in 5% H2O2/20% DMSO/MeOH overnight on a shake... |
46,412 | Isolation and phenotypic characterization of antibiotic resistant E.coli and Salmonella from food animal feces | 4 | dx.doi.org/10.17504/protocols.io.brjkm4kw | https://www.protocols.io/view/isolation-and-phenotypic-characterization-of-antib-brjkm4kw | Rosine Manishimwe, Paola M. Moncada, Marie Bugarel, H. Morgan Scott, Guy H. Loneragan | TITLE: Isolation and phenotypic characterization of antibiotic resistant E.coli and Salmonella from food animal feces
AUTHORS: Rosine Manishimwe, Paola M. Moncada, Marie Bugarel, H. Morgan Scott, Guy H. Loneragan
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol was designed to hel... | ["[DAY 1 : Preparation of fecal samples]\nFor each fecal sample Use a wooden scoopula to weight of feces\n10 g", "[DAY 1 : Preparation of fecal samples]\nTransfer the feces in a 710mL Whirl Pak® bag (Whirl-Pak, Madison, Wisconsin) with a filter", "[DAY 1 : Preparation of fecal samples]\nAdd of to the bag\n90 mL",... |
null | null | null | dx.doi.org/10.17504/protocols.io.fb4biqw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Explore and compare two strains of <em>Dehalococcoides mccartyi</em> to discover putative gene(s) responsible for complete dechlorination of PCE to nontoxic end product, ethylene.</p>
<p> </p>
[BEFORE_START]
<p>If you do not have an existing JGI SSO account, make your reques... | [] |
51,727 | Test protocol II | 1 | null | https://www.protocols.io/view/test-protocol-ii-bwrppd5n | Abby Moore | TITLE: Test protocol II
AUTHORS: Abby Moore
[DESCRIPTION]
This is a test protocol
[STEPS]
1. Use 80:20 MeOH:H2O for this step. This is not easy to access by machine.
2. If you haven't already, make a solution with the following components:
80 % volume
20 % volume
3. If you haven't already, make a solution w... | ["Use 80:20 MeOH:H2O for this step. This is not easy to access by machine.", "If you haven't already, make a solution with the following components:\n\n80 % volume \n20 % volume", "If you haven't already, make a solution with the following components:\n\n80 % volume \n20 % volume", "Use this piece of equipment:", "... |
92,562 | RNA-seq of primary human fibroblasts cultured on soft and stiff ECM | 4 | dx.doi.org/10.17504/protocols.io.e6nvwd447lmk/v1 | https://www.protocols.io/view/rna-seq-of-primary-human-fibroblasts-cultured-on-s-c6mszc6e | Brian D. Cosgrove, Lexi Bounds, Carson Key Taylor, Alan L. Su, Anthony J. Rizzo, Alejandro Barrera, Andrea R Daniel, Gregory E. Crawford, Brenton D. Hoffman, Charles A. Gersbach | TITLE: RNA-seq of primary human fibroblasts cultured on soft and stiff ECM
AUTHORS: Brian D. Cosgrove, Lexi Bounds, Carson Key Taylor, Alan L. Su, Anthony J. Rizzo, Alejandro Barrera, Andrea R Daniel, Gregory E. Crawford, Brenton D. Hoffman, Charles A. Gersbach
[DESCRIPTION]
This protocols describes methods for RNA-se... | ["[Cell culture and soft hydrogel processing] Culture primary human neonatal fibroblasts (HFF cells, ATCC CRL-2097) in DMEM with 10% FBS, 1% AntiAnti, and 1% NEAA (Sigma) on tissue culture plastic (TCP).", "[Cell culture and soft hydrogel processing] Use polyacrylamide hydrogel 35 and 150 mm PetriSoft EasyCoat dishes (... |
58,478 | Assessment of membrane lipid state at the natural killer cell immunological synapse | 4 | dx.doi.org/10.17504/protocols.io.b5cnq2ve | https://www.protocols.io/view/assessment-of-membrane-lipid-state-at-the-natural-b5cnq2ve | Yu Li, Jordan S. Orange | TITLE: Assessment of membrane lipid state at the natural killer cell immunological synapse
AUTHORS: Yu Li, Jordan S. Orange
[DESCRIPTION]
The plasma membrane is a fluid structure that protects cells as one of their first barriers and actively participates in numerous biological processes in many ways including throu... | ["Introduction\n\nThe plasma membrane is composed of a complex collection of phospholipids, sterols and membrane proteins which is dynamic in its constitution. It provides cells basic protections against external stress and regulates the exchange between the intra- and extra-cellular environments. It also actively part... |
82,534 | U54 SCENT Normal Lung Donor Tissue Collection Procedure | 1 | null | https://www.protocols.click/view/u54-scent-normal-lung-donor-tissue-collection-proc-cuuewwte | Matthew Hartwig, Sarah Casalinova* | TITLE: U54 SCENT Normal Lung Donor Tissue Collection Procedure
AUTHORS: Matthew Hartwig, Sarah Casalinova*
[DESCRIPTION]
This document outlines the acceptance criteria and workflow for notification, screening, acceptance and logistics of donor lung collection between Duke University Medical Center and our local Organ ... | ["[Inclusion Criteria - Adults and Pediatrics] Inclusion Criteria:\n • All ages (if donor is ≤ 18yo refer to peds exclusion list)\n • Brain Dead (DBD) or Death by Circulatory Death (DCD)\n • Is the donor research consented?\n\nExclusion Criteria - Adults:\n • PCR COVID+ Donors (must have at least 1 follow u... |
54,821 | Creating Planet Microbe Data Packages | 5 | dx.doi.org/10.17504/protocols.io.bzsdp6a6 | https://www.protocols.io/view/creating-planet-microbe-data-packages-bzsdp6a6 | Kai Blumberg, Alise J J. Ponsero, Bonnie Hurwitz | TITLE: Creating Planet Microbe Data Packages
AUTHORS: Kai Blumberg, Alise J J. Ponsero, Bonnie Hurwitz
[DESCRIPTION]
Marine microbial ecology requires the systematic comparison of biogeochemical and sequence data to analyze environmental influences on the distribution and variability of microbial communities. With e... | ["[Validate datapackage.json] Optional Step, run GoodTables validation for constraints\n\nThis is based on the original goodtables script avaiable from: https://goodtables.readthedocs.io/en/latest/\n\nFirst install the goodtables library using pip:\npip install goodtables\n\nExample call using the script\ngoodtables OS... |
92,696 | Protocol for assembly of a serine integrase-based platform for functional validation of genetic switch controllers in eukaryotic cells-Animal | 1 | dx.doi.org/10.17504/protocols.io.bp2l6xzjdlqe/v1 | https://www.protocols.io/view/protocol-for-assembly-of-a-serine-integrase-based-c6ryzd7w | Marco A. de Oliveira, Lilian H. Florentino, Thais T. Sales, Rayane N. Lima, Luciana R. C. Barros, Cintia G. Limia, Mariana S. M. Almeida, Maria L. Robledo, Leila M. G. Barros, Eduardo O. Melo, Daniela M. Bittencourt, Stevens K. Rehen, Martín H. Bonamino, Elibio Rech | TITLE: Protocol for assembly of a serine integrase-based platform for functional validation of genetic switch controllers in eukaryotic cells-Animal
AUTHORS: Marco A. de Oliveira, Lilian H. Florentino, Thais T. Sales, Rayane N. Lima, Luciana R. C. Barros, Cintia G. Limia, Mariana S. M. Almeida, Maria L. Robledo, Leila ... | ["[Cell Passage ● Timing 30 min] Cultivate bovine fibroblast cells at 5.0x105 cells per culture flask with a 75 cm2 surface area. Well area coverage, between 60-80% confluence. It takes approximately 8-10 days.", "[Cell Passage ● Timing 30 min] Before starting dissociation, place the working aliquot of 0.05% trypsin an... |
83,716 | Lipid (Oil Red O) Staining | 4 | dx.doi.org/10.17504/protocols.io.5qpvo3n9bv4o/v1 | https://www.protocols.click/view/lipid-oil-red-o-staining-cvzcw72w | Laura.SabioRodriguez | TITLE: Lipid (Oil Red O) Staining
AUTHORS: Laura.SabioRodriguez
[DESCRIPTION]
Lipid droplets (LDs) are dynamic, ubiquitously present lipid-storage organelles, predominantly present in the adipocytes. Triglycerides, neutral lipids, and cholesterol esters stored in LDs are the largest sources of energy. The presence... | ["[Procedure] Fixation\nRemove the medium and gently wash the cells twice with . Add to the cells and incubate for 30 min.\nNote: Do not add formalin directly onto the cells. Pipette onto the wall and mix gently rotating.", "[Procedure] All components:\nUse 100 µL for a 96 well plate\nUse 2 mL for a 6 well plate\nUs... |
42,649 | in situ hybridization | 4 | null | https://www.protocols.io/view/in-situ-hybridization-bmvzk676 | 张 雪 | TITLE: in situ hybridization
AUTHORS: 张 雪
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. [Day1]
复水：75%MetOH+25%PBT 1ml shake for 5min
?. [Day1]
50%MetOH+50%PBT 5min
?. [Day1]
25%MetOH+75%PBT 5min
?. [Day1]
100%PBT 5min 1/4
融化PK
?. [Day1]
100%PBT 5min 2/4
?. [Day1]
100%PBT 5min 3/4
?. [Day1]
100%PBT 5min 4... | ["[Day1]\n复水：75%MetOH+25%PBT 1ml shake for 5min", "[Day1]\n50%MetOH+50%PBT 5min", "[Day1]\n25%MetOH+75%PBT 5min", "[Day1]\n100%PBT 5min 1/4\n融化PK", "[Day1]\n100%PBT 5min 2/4", "[Day1]\n100%PBT 5min 3/4", "[Day1]\n100%PBT 5min 4/4", "[Day1]\n透化：Proteinase K: PBT = 1 : 1000 (终浓度10µg/ml），24h前：不消化；24h：5min；36h：10min；48h：15... |
80,864 | Interviewing for Art as an Act of Resistance | 1 | dx.doi.org/10.17504/protocols.io.5qpvorzo9v4o/v1 | https://www.protocols.io/view/interviewing-for-art-as-an-act-of-resistance-cs78whrw | angelabelulia | TITLE: Interviewing for Art as an Act of Resistance
AUTHORS: angelabelulia
[DESCRIPTION]
To gain insight and explore how art has served as an act of resistance against French Colonization in French Polynesia
[STEPS]
1. Understand the purpose of the interview: To gain insight and personal experiences into how music h... | ["Understand the purpose of the interview: To gain insight and personal experiences into how music has served as an act of resistance against French Colonization in French Polynesia", "Identify the stakeholders: local artists, cultural leaders/elders and community organizations", "Ask for permission and consent to rese... |
106,619 | Immunofluorescence and microscopy_reformatted | 0 | dx.doi.org/10.17504/protocols.io.4r3l2qz83l1y/v1 | https://www.protocols.io/view/immunofluorescence-and-microscopy-reformatted-dkc34syn | Isabel Lam, Alain Ndayisaba, Vikram Khurana | TITLE: Immunofluorescence and microscopy_reformatted
AUTHORS: Isabel Lam, Alain Ndayisaba, Vikram Khurana
[DESCRIPTION]
Immunofluorescence and microscopy_reformatted
[STEPS] | [] |
33,948 | Protein Expression Using BL21(DE3) (C2527) | 1 | dx.doi.org/10.17504/protocols.io.bdd4i28w | https://www.protocols.io/view/protein-expression-using-bl21-de3-c2527-bdd4i28w | New England Biolabs | TITLE: Protein Expression Using BL21(DE3) (C2527)
AUTHORS: New England Biolabs
[DESCRIPTION]
This protocol explains methods for Protein Expression Using BL21(DE3) Competent E. coli (C2527).
You can find the protocol for a large-scale Protein Expression here.
[GUIDELINES]
BL21(DE3) Genotype:
fhuA2 [lon] ompT gal (... | ["Transform expression plasmid into BL21(DE3).", "Plate on antibiotic selection plates.", "Incubate at 37 °C.", "Resuspend a single colony in 10 mL.", "Incubate at 37 °C until OD600 reaches 0.4–0.8.", "Induce with 4 µL or 40 µL of 100 Milimolar (mM) (final concentration of 40 or 400 µM).", "Induce for 3-5 hours at 37... |
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