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 |
|---|---|---|---|---|---|---|---|
96,917 | Immunoblotting of I3 Neurons and dopaminergic neurons | 0 | dx.doi.org/10.17504/protocols.io.3byl49eqjgo5/v1 | https://www.protocols.io/view/immunoblotting-of-i3-neurons-and-dopaminergic-neur-davv2e66 | Nisha Mohd Rafiq, Pietro De Camilli | TITLE: Immunoblotting of I3 Neurons and dopaminergic neurons
AUTHORS: Nisha Mohd Rafiq, Pietro De Camilli
[DESCRIPTION]
This protocol describes the preparation of cell lysate from and iPSC-derived neurons (I3 Neurons, dopaminergic) and the immunoblotting procedure.
[STEPS]
SECTION: Cell culture and treatments
1. Grow... | ["[Cell culture and treatments] Grow I3 Neurons and dopaminergic (DA) neurons on six-well plates (3-5 × 105 cells/well).", "[Cell culture and treatments] After differentiation in their respective maturation media, wash the neurons with 1 mL ice-cold PBS.", "[Cell culture and treatments] Lyse the cells in 200 µL 1xRIPA... |
57,152 | Protocol collection: Dissociation and FACS isolation of embryonic and post-embryonic C. elegans intestine cells for RNA-seq analysis | 2 | dx.doi.org/10.17504/protocols.io.5jyl895jdv2w/v1 | https://www.protocols.io/view/protocol-collection-dissociation-and-facs-isolatio-b328qqhw | Robert TP Williams, Erin Osborne Nishimura | TITLE: Protocol collection: Dissociation and FACS isolation of embryonic and post-embryonic C. elegans intestine cells for RNA-seq analysis
AUTHORS: Robert TP Williams, Erin Osborne Nishimura
[DESCRIPTION]
This is a collection of protocols for the isolation of C. elegans intestine cells through FACS from embryo, L1, a... | [] |
55,114 | Kinovea tracking guide and distance calculation R script | 4 | dx.doi.org/10.17504/protocols.io.bz3ip8ke | https://www.protocols.io/view/kinovea-tracking-guide-and-distance-calculation-r-bz3ip8ke | Simon Benmaamar | TITLE: Kinovea tracking guide and distance calculation R script
AUTHORS: Simon Benmaamar
[DESCRIPTION]
This protocol can be used to determine the travelled distances of larvae on a black-stained agar plate. For this purpose, videos of the moving animals are recorded, the movement is then tracked using the Kinovea pro... | ["[Kinovea tracking guide] Start Kinovea program.\nImport video by clicking on File -> Open Video File.\nSet time format: Options -> Time markers format -> Total milliseconds.\nTo express distance in real life units add a line with the diagonal length of the black agar, then right click on the line -> Calibrate measure... |
108,112 | QuickNII Brain Atlas Registration | 4 | dx.doi.org/10.17504/protocols.io.e6nvwdme2lmk/v2 | https://www.protocols.io/view/quicknii-brain-atlas-registration-dmtq46mw | Michael X. Henderson | TITLE: QuickNII Brain Atlas Registration
AUTHORS: Michael X. Henderson
[DESCRIPTION]
This protocol describes QuickNII brain atlas registration.
[STEPS]
SECTION: QuickNII Brain Atlas Registration
1. Open the QuickNII program folder.
SECTION: QuickNII Brain Atlas Registration
2. Open Filebuilder. (FileBuilder loads yo... | ["[QuickNII Brain Atlas Registration] Open the QuickNII program folder.", "[QuickNII Brain Atlas Registration] Open Filebuilder. (FileBuilder loads your registration images by default settings without automated aligment, Skip to step 6 if using DeepSlice).", "[QuickNII Brain Atlas Registration] Navigate to the QVN fol... |
31,001 | Intracardiac perfusion with fixative for anatomical studies | null | dx.doi.org/10.17504/protocols.io.bahzib76 | https://www.protocols.io/view/intracardiac-perfusion-with-fixative-for-anatomica-bahzib76 | Janet Keast, Peregrine Osborne, Nicole Wiedmann | TITLE: Intracardiac perfusion with fixative for anatomical studies
AUTHORS: Janet Keast, Peregrine Osborne, Nicole Wiedmann
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is suitable for preserving tissues for anatomical studies of organs, ganglia, spinal cord or brain in adult rats. ... | ["[Preparation for perfusion]\nMake up the following solutions:Perfusion prewash solution: To 300 ml 0.9% sodium chloride (w/v) add 3.75 ml 1% sodium nitrite (w/v) and 0.11 ml heparin (5000 IU/ml). This is made up immediately prior to use.Perfusion fixative: 4% paraformaldehyde in 0.1M phosphate buffer, pH 7.4. This is... |
89,959 | W-4 WATER TESTING | 4 | dx.doi.org/10.17504/protocols.io.n92ldm2z8l5b/v1 | https://www.protocols.io/view/w-4-water-testing-c34fyqtn | REDI-NET Consortium | TITLE: W-4 WATER TESTING
AUTHORS: REDI-NET Consortium
[DESCRIPTION]
This protocol details standard operating procedure for water testing.
[BEFORE_START]
BEFORE START
Check the DNA and RNA concentrations in each sample of total nucleic acid (TNA) extraction.
If the concentrations are detectable, choose the sequencin... | ["[gDNA PREPARATION] When the RNA concentration of the sample is lower than the detectable range of the Qubit High Sensitivity Assay (<0.01 ng/ul), the sample is subjected to gDNA sequencing. The cDNA synthesis can be skipped.", "[gDNA PREPARATION] When the DNA concentration >10 ng/ul, calculate the required volume of ... |
83,738 | MGH Harvard SenNet Processing murine lung for paired single cell RNA-seq and mass spec | 4 | dx.doi.org/10.17504/protocols.io.e6nvwd6e9lmk/v1 | https://www.protocols.click/view/mgh-harvard-sennet-processing-murine-lung-for-pair-cvz2w78e | gshipkovenska | TITLE: MGH Harvard SenNet Processing murine lung for paired single cell RNA-seq and mass spec
AUTHORS: gshipkovenska
[DESCRIPTION]
Protocol for obtaining single cell suspension of murine lung.
[STEPS]
SECTION: Dissection
1. Euthanize mice by CO2 method.
SECTION: Dissection
2. Perfuse lungs via right ventricle.
SECTIO... | ["[Dissection] Euthanize mice by CO2 method.", "[Dissection] Perfuse lungs via right ventricle.", "[Dissection] Dissect out trachea and lungs and place in HBSS on ice.", "[Single cell suspension]", "[Count cells with heamocytometer] Count two samples each per lung and note down the exact number of cells. This informati... |
null | null | null | dx.doi.org/10.17504/protocols.io.ea9bah6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol is part of the VERVE holiday drive to collect exotic off-the-shelf laboratory recipes. More details <a href="https://www.protocols.io/g/verve-net/news/call-for-recipes" target="_blank">here</a>.<br /><br />Timing is everything when preparing a large meal. Unfortun... | [] |
95,932 | One step RT-ddPCR for probes to target eRNA samples : from sample preparation to droplet reading | 4 | dx.doi.org/10.17504/protocols.io.kxygx3j1zg8j/v1 | https://www.protocols.io/view/one-step-rt-ddpcr-for-probes-to-target-erna-sample-c9w4z7gw | Marine Vautier, Cecile Chardon, Cyrielle Galiegue, Isabelle Domaizon | TITLE: One step RT-ddPCR for probes to target eRNA samples : from sample preparation to droplet reading
AUTHORS: Marine Vautier, Cecile Chardon, Cyrielle Galiegue, Isabelle Domaizon
[DESCRIPTION]
The aim of this protocol is the digital droplet PCR (ddPCR) quantification of RNA target(s) using primer and probe sets. Re... | ["[Material preparation] Equipment decontamination:\n- Specific DNA-workstation: UV decontamination.\n\nTurn on the following equipments: \n- the QX200 droplet generator \n- the PX1 PCR plate sealer at 180 °C\n- the thermal cycler for PCR\n- the QX600 or QX200 droplet reader for ddPCR\n\nTubes annotation\n- One 0.5 mL ... |
46,714 | An Overview of Host Cell Protein | 4 | null | https://www.protocols.io/view/an-overview-of-host-cell-protein-bru2m6ye | 181830691 , hy | TITLE: An Overview of Host Cell Protein
AUTHORS: 181830691 , hy
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Host cell proteins are process-related impurities that are expressed by host cells used to produce biologic drug proteins. During the purification process, most HCP is removed, but residua... | [] |
28,725 | Protein expression in OnePot PURE cell-free system | null | dx.doi.org/10.17504/protocols.io.8avhse6 | null | Konstantinos Ragios | TITLE: Protein expression in OnePot PURE cell-free system
AUTHORS: Konstantinos Ragios
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">In this protocol we explain the procedure of protein expression in the OnePot PURE cell-free system.</div></div>
[STEPS]
?. [Protein expression]
For a 5μl reaction ... | ["[Protein expression]\nFor a 5μl reaction add to a tube 2μl of Energy solution, 0.65μl of Protein solution, 0.9μl of Ribosome solution, the DNA template (5nM final concentration in the reaction) and if needed add water to reach the final volume.\nThe minimum reaction volume is 5μl while the suggested one in 10μl. For ... |
70,308 | Conditions for growth of Rhodobacter sphaeroides in different media | 4 | dx.doi.org/10.17504/protocols.io.kxygx9emog8j/v1 | https://www.protocols.io/view/conditions-for-growth-of-rhodobacter-sphaeroides-i-cgwctxaw | Jaya K Yakha, Deborah K Hanson, Rosemarie Wilton, laible | TITLE: Conditions for growth of Rhodobacter sphaeroides in different media
AUTHORS: Jaya K Yakha, Deborah K Hanson, Rosemarie Wilton, laible
[DESCRIPTION]
This protocol provides a method for culturing Rhodobacter sphaeroides wildtype 2.4.1 and its KO strains in shake flask and BioTek Epoch 2, 48-well microplates. A... | ["[Conditions for growth of Rhodobacter sphaeroides in GYCC medium in shake flasks] Inoculate a GYCC agar plate from a glycerol stock containing appropriate antibiotic (if necessary) and incubate at 33 °C in an incubator in dark.", "[Conditions for growth of Rhodobacter sphaeroides in GYCC medium in shake flasks] After... |
51,111 | Protocol for detection of Salmonella Typhi and Salmonella Paratyphi A in Produce | 1 | dx.doi.org/10.17504/protocols.io.bv6fn9bn | https://www.protocols.io/view/protocol-for-detection-of-salmonella-typhi-and-sal-bv6fn9bn | Renuka Kapoor, Ashutosh Wadhwa, Christine Moe | TITLE: Protocol for detection of Salmonella Typhi and Salmonella Paratyphi A in Produce
AUTHORS: Renuka Kapoor, Ashutosh Wadhwa, Christine Moe
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The protocol describes method for qualitative detection (presence/ absence) of </span><span style = "fo... | ["[1. Processing of produce sample]\nThe following steps describe processing of produce samples up to enrichment stage.", "[2. Enrichment culture]\nThe following steps are for optional enrichment of the sample. If enrichment is not performed, the produce wash can be used directly for membrane filtration and DNA extract... |
55,977 | iNDI Transcription Factor-NGN2 differentiation of human iPSC into cortical neurons Version 1 | 4 | dx.doi.org/10.17504/protocols.io.8epv5969ng1b/v1 | https://www.protocols.io/view/indi-transcription-factor-ngn2-differentiation-of-b2whqfb6 | erika.laraflores, Andy Qi, Luke Reilly, Marianita Santiana, caroline.pantazis, michael.ward, Mark Cookson | TITLE: iNDI Transcription Factor-NGN2 differentiation of human iPSC into cortical neurons Version 1
AUTHORS: erika.laraflores, Andy Qi, Luke Reilly, Marianita Santiana, caroline.pantazis, michael.ward, Mark Cookson
[DESCRIPTION]
Induced pluripotent stem cell (iPSC)-derived neurons are an important tool for studying di... | ["[Medium Preparation] Induction Medium: \nFor day 0 to day 3\n \n Reagent Stock Final concentration Amount for 50mL of medium Knock out DMEM/F12 --------- ------- 48.5 mL N2 supplement 100X 1X 0.5 mL Non-essential amino acids (NEAA 100X ... |
19,562 | Supplemental I - Reagents for Homogenization Buffer | null | dx.doi.org/10.17504/protocols.io.xcifiue | null | Janne R. Hingst, Rie D. Bjerre, Jørgen F. P. Wojtaszewski, Jørgen Jensen | TITLE: Supplemental I - Reagents for Homogenization Buffer
AUTHORS: Janne R. Hingst, Rie D. Bjerre, Jørgen F. P. Wojtaszewski, Jørgen Jensen
[STEPS] | [] |
65,945 | Analysis of the reproducibility, transparency and quality of economic studies on pharmacological interventions in health included in clinical practice guidelines in Spain 2000-2020 | 3 | dx.doi.org/10.17504/protocols.io.bp2l6b395gqe/v3 | https://www.protocols.io/view/analysis-of-the-reproducibility-transparency-and-q-ccmzsu76 | juanruanoruiz , Pedro J Gómez Arias, Jesús Gay-Mimbrera, Macarena Aguilar-Luque, Beatriz Isla-Tejera | TITLE: Analysis of the reproducibility, transparency and quality of economic studies on pharmacological interventions in health included in clinical practice guidelines in Spain 2000-2020
AUTHORS: juanruanoruiz , Pedro J Gómez Arias, Jesús Gay-Mimbrera, Macarena Aguilar-Luque, Beatriz Isla-Tejera
[DESCRIPTION... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.k2bcyan | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><span style="font-weight: 400;">This protocol lyses symbiodinium cells with heat and pellets debris, producing material suitable as crude DNA template for robust PCRs. It is convenient for rapid strain identification from liquid cultures and from </span><em><span style="font-... | [] |
38,778 | nCoV-2019 sequencing protocol v3 (LoCost) | 1 | null | https://www.protocols.io/view/ncov-2019-sequencing-protocol-v3-locost-bh42j8ye | Josh Quick | TITLE: nCoV-2019 sequencing protocol v3 (LoCost)
AUTHORS: Josh Quick
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Amplicon sequencing protocol for SARS-CoV-2 v3 (LoCost)</div><div class = "text-block">We thank the ARTIC network, Oxford Nanopore Technologies, New England Biolabs, BCCDC, COG-UK, Ca... | ["[cDNA preparation]\nMix the following components in a PCR strip-tubes/plate. Gently mix by pipetting and pulse spin the tube to collect liquid. AB1ComponentVolume2LunaScript RT SuperMix (5X) 2 µL3Template RNA 8 µL4Total10 µL\nAB1ComponentVolume2LunaScript RT SuperMix (5X) 2 µL3Template RNA 8 µL4Total10 µL\nVir... |
21,220 | Vandy - Hyperinsulinemic-Hypoglycemic clamp | null | dx.doi.org/10.17504/protocols.io.yycfxsw | null | Li Kang | TITLE: Vandy - Hyperinsulinemic-Hypoglycemic clamp
AUTHORS: Li Kang
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span></div><div class = "text-block">Mice with catheters implanted in the jugular vein (infusions) and carotid artery (sampling) are used fo... | ["Surgical catheterization of the carotid artery and jugular vein in mice at least 5 days prior to the day of the study (refer to protocol for Surgical Catheterization of the Carotid Artery and Jugular Vein).", "Weigh mouse and start fast (suggested starting time between 7:00 and 8:00 AM) by placing mouse in a plastic ... |
50,685 | Supporting protocol for use-case 1: N-linked glycan m/z candidate detection in "M2aia - Interactive, fast and memory efficient analysis of 2D and 3D multi-modal mass spectrometry imaging data" | 5 | dx.doi.org/10.17504/protocols.io.bvq5n5y6 | https://www.protocols.io/view/supporting-protocol-for-use-case-1-n-linked-glycan-bvq5n5y6 | Jonas Cordes | TITLE: Supporting protocol for use-case 1: N-linked glycan m/z candidate detection in "M2aia - Interactive, fast and memory efficient analysis of 2D and 3D multi-modal mass spectrometry imaging data"
AUTHORS: Jonas Cordes
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">An N-glycan MALDI-MSI dataset ... | ["Open the Data view, e.g. from the menu: Window > Show View > DataOpen the Imaging tab in the Data view.enable TIC normalizationenable Savitzky-Golay smoothing with half-window-size of 10enable TopHat baseline correction with half-window-size of 50", "Load the dataset: File > Open File or Ctrl + OOpen the files: png... |
null | null | null | dx.doi.org/10.17504/protocols.io.mwgc7bw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Multicriteria desicion analysis (MCDA) is a tool used to perform quantitative benefit-risks assessment (BRA) anlysis in drugs, procedures and devices in health. It allows comparisons in the same indication, that allows quantitative BRA balances, is useful to shows results in ... | [] |
88,785 | Fluorescence-activated nuclei sorting (FANS) on human post-mortem cortex tissue enabling the isolation of distinct neural cell populations for multiple omic profiling | 4 | dx.doi.org/10.17504/protocols.io.36wgq4965vk5/v2 | https://www.protocols.io/view/fluorescence-activated-nuclei-sorting-fans-on-huma-c2xryfm6 | Stefania S Policicchio, Barry Chioza, Jonathan P Davies, Joe Burrage, Jonathan Mill, Emma L Dempster | TITLE: Fluorescence-activated nuclei sorting (FANS) on human post-mortem cortex tissue enabling the isolation of distinct neural cell populations for multiple omic profiling
AUTHORS: Stefania S Policicchio, Barry Chioza, Jonathan P Davies, Joe Burrage, Jonathan Mill, Emma L Dempster
[DESCRIPTION]
Increased understandi... | ["[Nuclear prep for FACS separation (using SOX10, IRF8, NeuN and Hoechst)] The protocol below yields at least 1,000,000 NeuN +ve, 1,000,000 SOX10 +ve, 400,000 IRF8 +ve (when the population is present) and 200,000 triple negative (NeuN-ve/SOX10-ve/IRF8-ve) nuclei per 500 mg of frozen human post-mortem cortex tissue. Rec... |
22,200 | Socio-demographic and lifestyle influences on falls among the elderly persons living in Gatanga Sub-County, Murang’a County, Central Kenya: A cross-section study | null | dx.doi.org/10.17504/protocols.io.zwyf7fw | null | Ernest Kimani, Simon Karanja, Lawrence Muthami | TITLE: Socio-demographic and lifestyle influences on falls among the elderly persons living in Gatanga Sub-County, Murang’a County, Central Kenya: A cross-section study
AUTHORS: Ernest Kimani, Simon Karanja, Lawrence Muthami
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">An estimated one-third of t... | [] |
85,679 | Leucine auxotrophy test of Fusarium graminearum strains | 4 | dx.doi.org/10.17504/protocols.io.q26g7p47qgwz/v1 | https://www.protocols.io/view/leucine-auxotrophy-test-of-fusarium-graminearum-st-cxwpxpdn | martin.urban | TITLE: Leucine auxotrophy test of Fusarium graminearum strains
AUTHORS: martin.urban
[DESCRIPTION]
This protocol outlines the methodology for preparing Leucine dropout medium, essential for assessing Leucine auxotrophy in Fusarium graminearum strains. The procedure involves the step-by-step preparation of the medium t... | ["Testing Fusarium graminearum strains for Leucine Auxotrophy \n\nMedia and supplements:\n\n Biotin (Supplier: Fluka/Merck) \n Biotin is essential for robust growth, particularly beneficial for vivid photography on minimal \n medium.\n\n Procedure:\nDissolve in water to achieve a 0.05% solution.\nAdd 20 µl o... |
20,872 | Adult mouse lung cell dissociation (on ice) | null | dx.doi.org/10.17504/protocols.io.ymgfu3w | null | Andrew Potter | TITLE: Adult mouse lung cell dissociation (on ice)
AUTHORS: Andrew Potter
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol was used to dissociate adult (8-10 wk) mouse lung tissue. The entire procedure is carried out on ice (to reduce artifact gene expression changes) and takes about ha... | ["[Isolate tissue]\nUsing sterile forceps, transfer lung tissue to petri dish on ice. Remove excess DPBS using pipet. Mince lung tissue on petri dish on ice for 2 min until fine paste. Vigorously mince tissue using forceps to manipulate the tissue with one hand while using a grinding motion with the razor blade in the ... |
null | null | null | dx.doi.org/10.17504/protocols.io.n7bdhin | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>These are Expansion FISH (ExFISH) protocols for super-resolution imaging of RNA structure and location with diffraction-limited microscopes.</p>
<p> </p>
<p>Please select the appropriate protocol depending on your sample (cells or tissue).</p>
[STEPS] | [] |
86,179 | iNDI Maintenance protocol of iPSCs Version 1 | 4 | dx.doi.org/10.17504/protocols.io.q26g7py6kgwz/v1 | https://www.protocols.io/view/indi-maintenance-protocol-of-ipscs-version-1-cyebxtan | michael.ward, Erika Lara Flores, Mark Cookson | TITLE: iNDI Maintenance protocol of iPSCs Version 1
AUTHORS: michael.ward, Erika Lara Flores, Mark Cookson
[DESCRIPTION]
IPSC maintenance protocol
Matrigel procedure for coating plates
Vitronectin procedure for coating plates
Thawing iPSC
Splitting and Passaging iPSC
Freezing iPSC
[STEPS]
SECTION: Matrigel Coating
... | ["[Matrigel Coating] Aliquot concentrated Matrigel:\nGradually thaw a 5ml bottle of Matrigel on ice in a Styrofoam container\nPre-chill labeled Eppendorf tubes by placing in a cool rack on ice. \nBefore pipetting concentrated Matrigel into pre-chilled tubes, chill a 1 ml pipet tip by pipetting ice-cold KnockOut™ DMEM/F... |
19,547 | Enterovirus (EV) A71 real-time RT-PCR (EV-A71-TM2018) | null | dx.doi.org/10.17504/protocols.io.xb3fiqn | null | Ian Mackay, Judy Northill | TITLE: Enterovirus (EV) A71 real-time RT-PCR (EV-A71-TM2018)
AUTHORS: Ian Mackay, Judy Northill
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol aims to amplify enterovirus (EV) A71 viruses but not other viruses.</div><div class = "text-block">This protocol was designed by us.</div><div... | ["[Oligonucleotide sequences]\nAB1NameSequence 5'-3'2EVA71-VP4-For1TAYTAYAAAGAYTCBTATGCYG3EVA71-VP4-Rev1CCTTRACAGGRTTWGCRAACTT4EVA71-VP4-Rev2CTTTRACAGGRTTWGCAAATTT5EVA71-VP4-Rev3CCTTCACAGGGTTCGCAAACTT6EVA71-VP4-P1FAM - ACAGCVGGCAAGCAGAGYCTCAA - BHQ17EVA71-VP4-P2FAM - ACAGCRGGYAAACAGAGYCTCAA - BHQ18EVA71-VP4-P3FAM - ACT... |
77,005 | Submitting Genomes | 5 | null | https://www.protocols.io/view/submitting-genomes-cpfmvjk6 | emma.pearce | TITLE: Submitting Genomes
AUTHORS: emma.pearce
[DESCRIPTION]
Steps to submit a genome to NCBI through Bankit
[STEPS]
SECTION: Submitting to Bankit
1. Log into Bankit with UCSF username and password:
- Follow this link: https://www.ncbi.nlm.nih.gov/WebSub/?form=history&tool=genbank
- Choose more login options... | ["[Submitting to Bankit] Log into Bankit with UCSF username and password:\n - Follow this link: https://www.ncbi.nlm.nih.gov/WebSub/?form=history&tool=genbank\n - Choose more login options and select University of California, San Francisco", "[Submitting to Bankit] Select \"Start Bankit Submission\"", "[Submittin... |
42,855 | Deep SRE, Identification of Sterol Responsive Elements and Nuclear transcription factors Y proximity in human DNA by Convolutional Neural Network analysis. | 5 | dx.doi.org/10.17504/protocols.io.bm4fk8tn | https://www.protocols.io/view/deep-sre-identification-of-sterol-responsive-eleme-bm4fk8tn | Davide Noto | TITLE: Deep SRE, Identification of Sterol Responsive Elements and Nuclear transcription factors Y proximity in human DNA by Convolutional Neural Network analysis.
AUTHORS: Davide Noto
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The paper presents a novel strategy to identify putative binding sit... | ["[Deep SRE]\nSTEPS 1 to 5The first steps of the procedure are depicted in Figure 4. First, positive and negative TFChIP peaks are selected and stored in the ./neg and ./pos subdirs. Then peaks of SRE and NFY are extracted and compared to each other to check for a “SRE – 250 bp – NFY” couple where peaks are located wit... |
48,938 | collection 1 7.4 | 2 | null | https://www.protocols.io/view/collection-1-7-4-bt2inqce | Mariia Guliakina | TITLE: collection 1 7.4
AUTHORS: Mariia Guliakina
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">test 1</div></div>
[STEPS] | [] |
94,407 | Open field test for mice | 1 | dx.doi.org/10.17504/protocols.io.q26g7pk29gwz/v1 | https://www.protocols.io/view/open-field-test-for-mice-c8ffztjn | Csilla Novák, Andrés Mauricio Jaramillo Flautero, Matthias Prigge | TITLE: Open field test for mice
AUTHORS: Csilla Novák, Andrés Mauricio Jaramillo Flautero, Matthias Prigge
[DESCRIPTION]
The open field test is a classical test for the quantification of locomotor activity and anxiety-like behaviors in laboratory animals. This protocol is optimized for mice, and it includes the automa... | ["[Biobserve Viewer] Open Biobserve Viewer.", "[Biobserve Viewer] Make sure that the arena is well positioned in the middle of the view of the webcam.", "[Biobserve Viewer] Go to Configuration and Experiment. Set “stop experiment after: “ to 20 minutes. If you are alone, it is best to tick “Delayed start”, so you can s... |
null | null | null | dx.doi.org/10.17504/protocols.io.q56dy9e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div>
<p>Here we describe the standardised protocol used by the <a href="http://www.caboscience.org" target="_blank" rel="noopener noreferrer">Canadian Airborne Biodiversity Observatory</a> (CABO) to measure leaf spectral reflectance and transmittance, using an integrating spher... | [] |
31,591 | Rabies virus MinION sequencing protocol | null | dx.doi.org/10.17504/protocols.io.ba4figtn | null | Kirstyn Brunker, Josh Quick | TITLE: Rabies virus MinION sequencing protocol
AUTHORS: Kirstyn Brunker, Josh Quick
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a sample-to-sequence protocol for sequencing rabies virus genomes using the MinION platform ( may also be used with Illumina). This pipeline is feasible in low ... | ["[Primer pool preparation]\nIf required resuspend lyophilised primers at a concentration of each\nRABV primers for this protocol were designed using Primal Scheme and generate overlapping 400nt amplicons. There are currently primer schemes available for East Africa, Philippines and Peru, primer sequences are listed i... |
null | null | null | dx.doi.org/10.17504/protocols.io.evbbe2n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This is a widely used cleaning procedure for trace metal clean analyses. This procedure is specifically for the bottles used for measuring dissolved and labile cobalt using cathodic stripping voltammetry.
[GUIDELINES]
Make sure to use a fume hood when completing the steps invol... | [] |
19,235 | Protein Extraction of Symbiodiniaceae freshly isolated from Anthopleura elegantissima | null | dx.doi.org/10.17504/protocols.io.w2bfgan | null | Virginia Weis | TITLE: Protein Extraction of Symbiodiniaceae freshly isolated from Anthopleura elegantissima
AUTHORS: Virginia Weis
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. [Isolation of algal pellet from whole animal]
Obtain 25 frozen small Anthopleura elegantissima (You could use 10 medium or 3 large animals also... | ["[Isolation of algal pellet from whole animal]\nObtain 25 frozen small Anthopleura elegantissima (You could use 10 medium or 3 large animals also). Adjust the number of animals as needed.", "[Isolation of algal pellet from whole animal]\nPartially defrost and cut off pedal discs with a razor blade (keep the algal-rich... |
null | null | null | dx.doi.org/10.17504/protocols.io.hajb2cn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Thes protocols were original created by <a href=""http://www.whoi.edu/sbl/liteSite.do?litesite" target="_blank">Krista Longnecker</a> and <a href="http://jamesrco.github.io/" target="_blank">Jamie Collins</a> for creating lipsomes to be used in lipid photo-oxidation expe... | [] |
85,943 | Protocol for single cell and single nucleus prep for Cell Pellets/Multiple Myeloma (snRNA & snATAC) | 1 | dx.doi.org/10.17504/protocols.io.4r3l227oxl1y/v1 | https://www.protocols.io/view/protocol-for-single-cell-and-single-nucleus-prep-f-cx6xxrfn | Reyka Jayasinghe | TITLE: Protocol for single cell and single nucleus prep for Cell Pellets/Multiple Myeloma (snRNA & snATAC)
AUTHORS: Reyka Jayasinghe
[DESCRIPTION]
Protocol for single cell and single nucleus prep for Cell Pellets/Multiple Myeloma (snRNA & snATAC)
[STEPS]
SECTION: Reagents and Protocols
1.
All lysis buffers shou... | ["[Reagents and Protocols] All lysis buffers should\nbe prepared fresh and stored at 4oC. \n\nBuffers based on Nuclei Isolation from Mouse Brain Tissue for\nSingle Cell ATAC Sequencing Protocol from 10X\n\n\nRelevant 10X Protocols:\n\nNuclei Isolation for Single Cell ATAC\nSequencing\nNuclei Isolation from Mouse Brain ... |
null | null | null | dx.doi.org/10.17504/protocols.io.s2wegfe | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Bruce McDonald 1990 modified from Murray and Thompson</p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.etgbejw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
For use in <a href="https://www.protocols.io/view/Preparation-of-Denaturing-Agarose-Gel-for-RNA-Anal-es4begw" target="_blank">Preparation of Denaturing Agarose Gel for RNA Analysis</a>.
[STEPS]
?.
?.
?.
?. | [] |
39,786 | RNA in situ hybridization on pancreatic sections using RNAscope® technology | 1 | dx.doi.org/10.17504/protocols.io.e6nvw9367gmk/v1 | https://www.protocols.io/view/rna-in-situ-hybridization-on-pancreatic-sections-u-bi4ikgue | Caroline CT Tremblay, Julien Ghislain, Vincent Poitout | TITLE: RNA in situ hybridization on pancreatic sections using RNAscope® technology
AUTHORS: Caroline CT Tremblay, Julien Ghislain, Vincent Poitout
[DESCRIPTION]
This protocol describes the steps for performing RNA in situ hybridization simultaneously for two targets using RNAscope Multiplex Fluorescent reagent Kit ... | ["[Preparation of cryosections] Tissue fixation\n\n \nHarvest the pancreas and place it in a 50 ml Falcon tube containing 30 mL of cold 4 % PFA (12 mL of 10 % PFA + 18 mL of PBS). \nFix for 240 min at 4 °C in the dark. \nThen, working in a chemical hood, delicately remove the pancreas with forceps and place it on bro... |
53,645 | Effect of postoperative coffee consumption on postoperative ileus after abdominal surgery: An updated systematic review and meta-analysis (protocol) | 1 | dx.doi.org/10.17504/protocols.io.bymmpu46 | https://www.protocols.io/view/effect-of-postoperative-coffee-consumption-on-post-bymmpu46 | Jun Watanabe, Atsushi Miki, Kazuhiko Kotani, Naohiro Sata | TITLE: Effect of postoperative coffee consumption on postoperative ileus after abdominal surgery: An updated systematic review and meta-analysis (protocol)
AUTHORS: Jun Watanabe, Atsushi Miki, Kazuhiko Kotani, Naohiro Sata
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style ... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.fyvbpw6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div class="page" title="Page 1">
<div class="layoutArea">
<div class="column">
<p>The SensiFAST™ Probe Lo-ROX Kit has been developed for fast, highly reproducible real-time PCR and has been validated on commonly used real-time PCR instruments. The kit has been formulated for us... | [] |
89,625 | Immunohistochemistry Protocol for Free-floating Fixed Tissue with Tyramine Signal Amplification (TSA) | 1 | dx.doi.org/10.17504/protocols.io.j8nlkom2dv5r/v1 | https://www.protocols.io/view/immunohistochemistry-protocol-for-free-floating-fi-c3rzym76 | Jeffrey Kordower, Yaping Chu, Jeremy Molina | TITLE: Immunohistochemistry Protocol for Free-floating Fixed Tissue with Tyramine Signal Amplification (TSA)
AUTHORS: Jeffrey Kordower, Yaping Chu, Jeremy Molina
[DESCRIPTION]
Immunohistochemistry protocol for staining free-floating fixed tissue with Tyramine signal amplification (TSA) in the Kordower Laboratory. TSA ... | ["[DAY 1 (3.5hrs)] Wash sections (6 x 5 min) in Dilution Media (DM) (0.2 Molarity (M)TBS plus 0.05 % volumeTriton X-100).", "[DAY 1 (3.5hrs)] Endogenous peroxidase inhibition (20 min). 0.1 Molarity (M) Sodium meta-periodate in TBS.\n100 mL 0.2 Molarity (m)Tris-buffered saline (TBS)\n2.13 g sodium meta-periodate", "[DAY... |
108,094 | Prokaryotes/Eukaryotes 16S-V4V5 rRNA Metabarcoding PCR protocol for NGS Illumina sequencing | 4 | dx.doi.org/10.17504/protocols.io.36wgq42o3vk5/v2 | https://www.protocols.io/view/prokaryotes-eukaryotes-16s-v4v5-rrna-metabarcoding-dms646he | Sarah Romac | TITLE: Prokaryotes/Eukaryotes 16S-V4V5 rRNA Metabarcoding PCR protocol for NGS Illumina sequencing
AUTHORS: Sarah Romac
[DESCRIPTION]
Nowadays metabarcoding approaches allow to explore the diversity of different communities using next-generation sequencing (NGS).
Here we describe the 16S-V4V5 DNA amplification method... | ["[Tagged Primer Design and preparation] We use the prokaryotic 16SV4V5 primer set 515fY- 926r from Parada et al. 2016.", "[Tagged Primer Design and preparation]", "[Tagged Primer Design and preparation] Lyophilized Tagged-primers are obtained at Eurogentec, using the RP-Cartridge Gold purification.\n\nWork always unde... |
88,113 | 602.2 Donor Acceptance Criteria for URMC HTC SenNet Inclusion | 4 | dx.doi.org/10.17504/protocols.io.dm6gp394dvzp/v1 | https://www.protocols.io/view/602-2-donor-acceptance-criteria-for-urmc-htc-senne-c2aryad6 | Gloria S Pryhuber | TITLE: 602.2 Donor Acceptance Criteria for URMC HTC SenNet Inclusion
AUTHORS: Gloria S Pryhuber
[DESCRIPTION]
Purpose and Scope of the Procedure
Standardize process for receiving lung donations
Scope: Coordination of screening, acceptance and receipt of tissue for research programs
Principles
Lung donations reject... | ["[Review Case: accept or decline based on eligibility] Take referral call or BRINDL screening report", "[Review Case: accept or decline based on eligibility] Review Eligibility Criteria", "[Review Case: accept or decline based on eligibility] Start Case Record in BRINDL Inventory Screening Log", "[Review Case: accept ... |
null | null | null | dx.doi.org/10.17504/protocols.io.mnbc5an | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>In this protocol, the incubation of <em>Synechocystis</em> sp. PCC 6803 colonies on agarplates and further incubation in flasks for further plate reader measurements for fluorescence detection are described. The protocol was handed over by Anna Behle MSc.</p>
[BEFORE_START]
... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.kvwcw7e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The appropriate use of clinically accurate diagnostic tests is essential for the detection of pertussis, a poorly controlled vaccine-preventable disease. The purpose of this study was to estimate the sensitivity and specificity of different diagnostic criteria including cultu... | [] |
48,858 | Sample run SOP for ECD/FID/TCD | 1 | null | https://www.protocols.io/view/sample-run-sop-for-ecd-fid-tcd-btx2npqe | Sparky Jr. | TITLE: Sample run SOP for ECD/FID/TCD
AUTHORS: Sparky Jr.
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Sample run SOP for ECD/FID/TCD by Sparky Jr.</div></div>
[STEPS]
?. [Startup]
Open HP ChemStation using the shortcut on the desktop
?. [Startup]
Start each instrument listed in the Utilities me... | ["[Startup]\nOpen HP ChemStation using the shortcut on the desktop", "[Startup]\nStart each instrument listed in the Utilities menu:SparkyJrECD/FID", "[Sample Run]\nTo run samples on the ECD/FID GC with HP 7694 Headspace Autosampler (Sparky Jr.):", "[Sample Run]\nCreate a sequenceSequence ParametersSequence OutputSeque... |
52,183 | Efficacy of Inspiratory Muscle Training for Hypertension: a systematic review and meta-analysis protocol | 1 | dx.doi.org/10.17504/protocols.io.bw7xphpn | https://www.protocols.io/view/efficacy-of-inspiratory-muscle-training-for-hypert-bw7xphpn | Yoshito Kadoya, Shunsuke Taito, Kayoko Morio, Natsumi Saka | TITLE: Efficacy of Inspiratory Muscle Training for Hypertension: a systematic review and meta-analysis protocol
AUTHORS: Yoshito Kadoya, Shunsuke Taito, Kayoko Morio, Natsumi Saka
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">.</div></div>
[STEPS]
?. | [] |
47,101 | Coating plates with Matrigel for ES/iPS culture | 1 | dx.doi.org/10.17504/protocols.io.br85m9y6 | https://www.protocols.io/view/coating-plates-with-matrigel-for-es-ips-culture-br85m9y6 | Jiuchun Zhang, Harper JW | TITLE: Coating plates with Matrigel for ES/iPS culture
AUTHORS: Jiuchun Zhang, Harper JW
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is about coating plates with matrigel.</div></div>
[STEPS]
?. Chill .
[PBS]
on ice
Skip this step if you have PBS in the fridge already.
?. Take cul... | ["Chill .\n[PBS]\non ice\nSkip this step if you have PBS in the fridge already.", "Take culture dishes you want to coat out of their package and place them inside a tissue culture hood.", "Thaw desired number of Matrigel aliquots either or at .\non ice\n0 Room temperature\nKeep in mind that matrigel will solidify at r... |
43,310 | NEB Instant Sticky-end Ligase Master Mix-CHEM 584 | 1 | dx.doi.org/10.17504/protocols.io.bninmcde | https://www.protocols.io/view/neb-instant-sticky-end-ligase-master-mix-chem-584-bninmcde | Ken Christensen, Harold Bien | TITLE: NEB Instant Sticky-end Ligase Master Mix-CHEM 584
AUTHORS: Ken Christensen, Harold Bien
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Taken directly from NEB's website, this is the protocol for using their optimized sticky-end ligation and transformation. For more information, see </... | ["[Preparation]\nPlace master mix tube on ice and flick a few times to mix.", "[Ligation]\nCombine 20–100 ng of vector with a 3-fold molar excess of insert and q.s. to 5μl with dH2O.\n5 µl", "[Ligation]\nAdd 5 μl of Instant Sticky-end Ligase Master Mix, mix thoroughly by pipetting up and down 7-10 times, and place on i... |
36,616 | Intraperitoneal Injection in an Adult Mouse | null | dx.doi.org/10.17504/protocols.io.bfzgjp3w | https://www.protocols.io/view/intraperitoneal-injection-in-an-adult-mouse-bfzgjp3w | Allen Institute for Brain Science | TITLE: Intraperitoneal Injection in an Adult Mouse
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the general procedure used for intraperitoneal injection in adult mice.</div><div class = "text-block"><span style = "font-weight:bold... | [] |
34,615 | Dephosphorylation of 5´-ends of DNA using Antarctic Phosphatase (NEB #M0289) | 1 | dx.doi.org/10.17504/protocols.io.bd2xi8fn | https://www.protocols.io/view/dephosphorylation-of-5-ends-of-dna-using-antarctic-bd2xi8fn | New England Biolabs | TITLE: Dephosphorylation of 5´-ends of DNA using Antarctic Phosphatase (NEB #M0289)
AUTHORS: New England Biolabs
[DESCRIPTION]
This is the protocol for dephosphorylation of 5'-ends of DNA using AnP (Antarctic Phosphatase - M0289).
[GUIDELINES]
Dephosphorylation of 5' -ends of DNA in Restriction Enzyme Reaction
The... | ["Prepare a 20 µL reaction as follows:", "Incubate at 37 °C for 30 min.", "Stop reaction by heat-inactivation at 80 °C for 2 min."] |
73,978 | BCA analysis of hydrolyzable proteins in pollen using the Pierce BCA assay kit | 6 | dx.doi.org/10.17504/protocols.io.261ge3rwwl47/v1 | https://www.protocols.io/view/bca-analysis-of-hydrolyzable-proteins-in-pollen-us-ckg2utye | Mark J. Carroll | TITLE: BCA analysis of hydrolyzable proteins in pollen using the Pierce BCA assay kit
AUTHORS: Mark J. Carroll
[DESCRIPTION]
This protocol quantifies total protein contents of small amounts of pollen (10 mg) using the bicinchoninic acid (BCA) assay of the Pierce BCA protein assay kit (Thermo Scientific product number ... | ["[Acid Hydrolysis of Pollen] Dry down the pollen sample in a freeze dryer.", "[Acid Hydrolysis of Pollen] Weigh out 10.0 mg of pollen into a crimp cap vial. Place the sample vials into a 24 well plate (acts as a vial holder).", "[Acid Hydrolysis of Pollen] Warning – read the precautions and hazards regarding handling ... |
98,946 | Fast-scan cyclic voltammetry to assess dopamine release in ex vivo mouse brain slices while optogenetically activating astrocytes | 1 | dx.doi.org/10.17504/protocols.io.x54v92j44l3e/v1 | https://www.protocols.io/view/fast-scan-cyclic-voltammetry-to-assess-dopamine-re-dcva2w2e | Shinil Raina, Bradley M Roberts, Stephanie J Cragg | TITLE: Fast-scan cyclic voltammetry to assess dopamine release in ex vivo mouse brain slices while optogenetically activating astrocytes
AUTHORS: Shinil Raina, Bradley M Roberts, Stephanie J Cragg
[DESCRIPTION]
This protocol is to assess whether optogenetically activating astrocytes affects the dopamine concentration ... | ["[Preparation of ex vivo mouse brain slices] Prepare cutting solution, chill and oxygenate (see Materials).", "[Preparation of ex vivo mouse brain slices] Prepare vibratome settings: 300 μm slices, 0.44 mm/s speed, Δ1.45 mm vibration. Chill plate and buffer tray in freezer, rinse razor blade in acetone.", "[Preparatio... |
null | null | null | dx.doi.org/10.17504/protocols.io.c8nzvd | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Preparation of the trace metal mixture for addition to seawater for the cultivation of marine cyanobacteria, <em>Prochlorococcus</em> and <em>Synechococcus</em>
[BEFORE_START]
Prepare the six trace metal stock solutions as described in the Primary Trace Metal Stocks protocol:<b... | [] |
62,713 | Microglia FACS staining after isolation (from UCSD) | 4 | dx.doi.org/10.17504/protocols.io.dm6gpbxp8lzp/v1 | https://www.protocols.io/view/microglia-facs-staining-after-isolation-from-ucsd-b9gzr3x6 | rabdelha | TITLE: Microglia FACS staining after isolation (from UCSD)
AUTHORS: rabdelha
[DESCRIPTION]
This protocol details about microglia FACS staining after isolation (from UCSD).
[GUIDELINES]
Gating Notes
live vs dead
FSC vs SSC
singles vs. doublets.
CD11B (high) vs. CD45 (low).
CX3CR1 (optional) gate on positive cells.... | ["[Protocol] Resuspend cells staining buffer (300 µL of HBSS+EDTA+BSA).\nResuspend in a 15-ml falcon tube.", "[Protocol] Add Fc Block (~1:100 dilution) and incubate for 15 min at 4 °C or in the fridge.\nAdd this to cells resuspended in the HBSS.", "[Protocol] Take ~5% of cells for unstained control, put on ice.", "[Pro... |
81,788 | Cryomiller SOP | 1 | dx.doi.org/10.17504/protocols.io.5qpvormjzv4o/v1 | https://www.protocols.click/view/cryomiller-sop-ct44wqyw | Lorenzo Lucherini | TITLE: Cryomiller SOP
AUTHORS: Lorenzo Lucherini
[DESCRIPTION]
Standard of procedure for cryomiller Retsch at the Soft Materials Laboratory (EPFL)
[STEPS]
SECTION: Refill the N2 dewar
2. Use two wrenches to unscrew the N2 pipe from the dewar. Firmly push downwards both wrenches at the same time.
SECTION: Refill t... | ["[Refill the N2 dewar] Use two wrenches to unscrew the N2 pipe from the dewar. Firmly push downwards both wrenches at the same time.", "[Refill the N2 dewar] Place the dewar in the lift and block the wheels. Pull the red strap in front of the door of the lift and send the lift to floor 0.", "[Refill the N2 dewar] Hand... |
92,040 | Fixation and embedding of organoids for histology | 4 | dx.doi.org/10.17504/protocols.io.5qpvo3w6xv4o/v1 | https://www.protocols.io/view/fixation-and-embedding-of-organoids-for-histology-c55gy83w | Tatiana Karakasheva | TITLE: Fixation and embedding of organoids for histology
AUTHORS: Tatiana Karakasheva
[DESCRIPTION]
This is a modification of a previously published protocol for fixation and pre-embedding of 3D organoids prior to embedding into paraffin and sectioning for histology (see Reference). This new protocol is simplified, ye... | [] |
76,686 | Autofluorescence Microscopy QC for Multimodal Molecular Imaging | 1 | dx.doi.org/10.17504/protocols.io.e6nvwjm5dlmk/v1 | https://www.protocols.click/view/autofluorescence-microscopy-qc-for-multimodal-mole-cn5nvg5e | Katerina V Djambazova, Nathan Heath Patterson, Lukasz Migas, Angela R.S. Kruse, Melissa Farrow, Raf Van De Plas, Jeff Spraggins | TITLE: Autofluorescence Microscopy QC for Multimodal Molecular Imaging
AUTHORS: Katerina V Djambazova, Nathan Heath Patterson, Lukasz Migas, Angela R.S. Kruse, Melissa Farrow, Raf Van De Plas, Jeff Spraggins
[DESCRIPTION]
Autofluorescence QC is performed prior to collecting on-tissue AF. Fluorescence intensity can be... | ["[Autofluorescence Microscopy QC] Fluorescence QC is collected prior to any on-tissue AF collection.\n\nUse fluorescence calibration slides - StarLight Calibration Slides - Bang Laboratories \nDAPI (excitation-360nm, emission-450nm), Dragon green (excitation-480nm, emission-520nm), and Envy green (excitation-525nm, em... |
41,428 | Electroporation Protocol | 1 | dx.doi.org/10.17504/protocols.io.bkpukvnw | https://www.protocols.io/view/electroporation-protocol-bkpukvnw | Ken Christensen | TITLE: Electroporation Protocol
AUTHORS: Ken Christensen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol may be used with electrocompetent cells prepared by you according to </span><a href="https://www.protocols.io/view/Making-your-own-electrocompetent-cells-imsv6m" style = "text... | ["Turn on electroporator and set to 1.7-2.5 kv (optimize for strain), 200 ohms and 25 µF", "Place recovery SOC in 37°C water bath", "Pre-warm LB-antibiotic plates at 37°C", "Thaw cells on ice for 10 min or use freshly made cells", "Place appropriate number of microcentrifuge tubes and 1 mm-electroporation cuvettes on i... |
null | null | null | dx.doi.org/10.17504/protocols.io.gk8buzw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This is a DNA extraction protocol from sea cucumber (Apostichopus japonicus) body-wall tissue. It accompanies the following <em>GigaScience</em> publication:</p>
<p> </p>
<p>Jihoon Jo, et al. (2016): Draft genome of the sea cucumber Apostichopus japonicus and genetic polymor... | [] |
75,979 | Isolation and Amplification of SARS-CoV-2 RNA from Nasopharyngeal Specimen | 4 | dx.doi.org/10.17504/protocols.io.q26g7y32kgwz/v1 | https://www.protocols.io/view/isolation-and-amplification-of-sars-cov-2-rna-from-cnfjvbkn | Frank Twum Aboagye, Maame Ekua Acquah | TITLE: Isolation and Amplification of SARS-CoV-2 RNA from Nasopharyngeal Specimen
AUTHORS: Frank Twum Aboagye, Maame Ekua Acquah
[DESCRIPTION]
COVID-19 caused by the SARS-CoV-2 was declared a global pandemic by the World Health Organization in March 2020. Classical symptoms associated with the infection include fever,... | ["[RNA Extraction Protocol (Zymo Quick-RNA Viral Kit)] Vortex the specimen for 30 s at 3000 rpm and allow it to sit on the bench for 1 minute", "[RNA Extraction Protocol (Zymo Quick-RNA Viral Kit)] Aliquot 200 µL of the specimen into a sterile 1.5 mL microcentrifuge tube", "[RNA Extraction Protocol (Zymo Quick-RNA Vira... |
43,632 | Microtome Dissection of Beetles | 3 | dx.doi.org/10.17504/protocols.io.bnuqmevw | https://www.protocols.io/view/microtome-dissection-of-beetles-bnuqmevw | Jiri Hulcr | TITLE: Microtome Dissection of Beetles
AUTHORS: Jiri Hulcr
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes how visualize internal structures, from mandibular mycangia, to beetle heads or bodies.</div><div class = "text-block"><span>This protocol is part of the Bark Beetle Myc... | [] |
55,424 | Surface protein biotinylation | 4 | dx.doi.org/10.17504/protocols.io.b2c8qazw | https://www.protocols.io/view/surface-protein-biotinylation-b2c8qazw | Daehun Park, Pietro De Camilli | TITLE: Surface protein biotinylation
AUTHORS: Daehun Park, Pietro De Camilli
[DESCRIPTION]
This protocol describes surface protein labeling with biotin using EZ-Link Sulfo-NHSLC-Biotin. This chemical reacts with primary amines such as lysine but does not permeate cell membranes because of the charge. Thus, it only b... | ["[Surface protein biotinylation] Wash cells with ice-cold PBS.", "[Surface protein biotinylation] Discard biotin containing medium. Quench and remove unbound biotin using 50 millimolar (mM) glycine in ice-cold PBS for 10 min at4 °C.", "[Surface protein biotinylation] Wash 2-3 times with ice-cold PBS.", "[Surface prote... |
42,022 | Code of Conduct | 1 | dx.doi.org/10.17504/protocols.io.bmaek2be | https://www.protocols.io/view/code-of-conduct-bmaek2be | Emma Ganley, Irina Makkaveeva, Lenny Teytelman | TITLE: Code of Conduct
AUTHORS: Emma Ganley, Irina Makkaveeva, Lenny Teytelman
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Code of Conduct for protocols.io employees.</div></div>
[STEPS]
?. [General Conduct]
This code of conduct outlines our expectations for all protocols.io team members. Plea... | ["[General Conduct]\nThis code of conduct outlines our expectations for all protocols.io team members. Please keep the following expectations about behavior in mind, whether interacting with someone in person or remotely. Following this code of conduct is essential for a welcoming and safe environment. You should tak... |
26,142 | A Whole-heart Provider for Compartmental Modeling Antibody Services | null | dx.doi.org/10.17504/protocols.io.5r6g59e | null | Echo Han | TITLE: A Whole-heart Provider for Compartmental Modeling Antibody Services
AUTHORS: Echo Han
[STEPS]
?. About Creative Biolabs Firstly started up at the beginning of 21 century in New York, USA, Creative Biolabs was set up by a group of biological scientists who are devoted to the development of antibodies. Aiming at ... | ["About Creative Biolabs Firstly started up at the beginning of 21 century in New York, USA, Creative Biolabs was set up by a group of biological scientists who are devoted to the development of antibodies. Aiming at facilitating drug or scientific research, high-tech antibody maturation platforms like PreciAb™, compre... |
93,387 | Small Scale purification test for expression of human PINK1 in insect cells | 4 | dx.doi.org/10.17504/protocols.io.n2bvj3mxxlk5/v1 | https://www.protocols.io/view/small-scale-purification-test-for-expression-of-hu-c7fjzjkn | Verena Dederer, Olawale G. Raimi, Miratul M K Muqit, Stefan Knapp, Sebastian Mathea | TITLE: Small Scale purification test for expression of human PINK1 in insect cells
AUTHORS: Verena Dederer, Olawale G. Raimi, Miratul M K Muqit, Stefan Knapp, Sebastian Mathea
[DESCRIPTION]
Purified, recombinant proteins are essential for biochemical characterization and structural studies. However, every protein is u... | ["[Section 1: Cloning of human PINK1 constructs into pFB-6HZB] Amplify region of interest from human PINK1 gene (OHu25380D; Genscript) with primers\nendcoding 5’TACTTCCAATCCATG extension for forward and 5’TATCCACCTTTACTGTCA extension for reverse primers.", "[Section 1: Cloning of human PINK1 constructs into pFB-6HZB] D... |
67,834 | MIDAS 2 Protocol | 2 | dx.doi.org/10.17504/protocols.io.6qpvr6jzpvmk/v1 | https://www.protocols.io/view/midas-2-protocol-ceg2tbye | miriam.goldman , chunyu.zhao | TITLE: MIDAS 2 Protocol
AUTHORS: miriam.goldman , chunyu.zhao
[DESCRIPTION]
The Metagenomic Intra-Species Diversity Analysis System 2 (MIDAS2) is a scalable pipeline that identifies single nucleotide variants (SNVs) and gene copy number variants (CNVs) in metagenomes using comprehensive reference databases built fr... | [] |
83,399 | High-throughput phenotyping of green canopy area during nematode infection | 4 | dx.doi.org/10.17504/protocols.io.kqdg39167g25/v1 | https://www.protocols.click/view/high-throughput-phenotyping-of-green-canopy-area-d-cvpfw5jn | Jaap-Jan Willig, Devon Sonneveld, Joris J.M. van Steenbrugge, Laurens Deurhof, Casper C. van Schaik, Misghina G. Teklu, Aska Goverse, Jose L. Lozano Torres, Geert Smant, Mark G. Sterken | TITLE: High-throughput phenotyping of green canopy area during nematode infection
AUTHORS: Jaap-Jan Willig, Devon Sonneveld, Joris J.M. van Steenbrugge, Laurens Deurhof, Casper C. van Schaik, Misghina G. Teklu, Aska Goverse, Jose L. Lozano Torres, Geert Smant, Mark G. Sterken
[DESCRIPTION]
Nematode migration, feeding ... | ["Fill 200mL pots with silversand.", "Place the pots in the steel frames.", "Once all the pots are filled with silversand, cover them with the black nonreflective foamed PVC coversheet.", "Sow 2 to 5 Arabidopsis seeds per pot using a toothpick.", "Prior to sowing, silver sand was watered with Hyponex for five minutes."... |
73,200 | MycoFluor Mycoplasma Detection | 1 | dx.doi.org/10.17504/protocols.io.bp2l692nklqe/v1 | https://www.protocols.io/view/mycofluor-mycoplasma-detection-cjqqumvw | Ali Albalakhi, Ning Xia | TITLE: MycoFluor Mycoplasma Detection
AUTHORS: Ali Albalakhi, Ning Xia
[DESCRIPTION]
MycoFluor™ Mycoplasma Detection produces a fast and simple fluorescence microscopic assay that identifies mycoplasma infection in cell cultures. In order to detect mycoplasma, the fluorescent MycoFluor™ reagent is added to the cultur... | ["[Protocol Testing of Culture Media] Take about 4mL of cell medium directly form the culture dish in which the cells have been growing centrifuge the sample at 1300 x g for 10min to pellet any cells and debris", "[Protocol Testing of Culture Media] Carefully transfer 1mL of supernatant into labeled microcentrifuge tub... |
20,854 | An 8-week resistance training protocol is effective in adapting quadriceps but not patellar tendon shear modulus | null | dx.doi.org/10.17504/protocols.io.ykwfuxe | null | Pietro Mannarino, Liliam Fernandes Oliveira, Thiago Torres da Matta | TITLE: An 8-week resistance training protocol is effective in adapting quadriceps but not patellar tendon shear modulus
AUTHORS: Pietro Mannarino, Liliam Fernandes Oliveira, Thiago Torres da Matta
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Habitual loading and resistance training (RT) can lead... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.tuienue | null | null | TITLE: No Title
AUTHORS:
[STEPS]
SECTION: Preparation of plasma-derived EVs and isolation of RNA
?.
?. | ["[Preparation of plasma-derived EVs and isolation of RNA] {\"blocks\":[{\"key\":\"5a05i\",\"text\":\" MiRCURY Exosome Isolation Kit-Serum and Plasma (Exiqon, Denmark) was used for isolation of plasmatic EVs. Briefly, 600 ml of plasma was treated with thrombin for 5 minutes at room temperature to remove clotting facto... |
34,792 | Brain-wide delivery of Janelia Fluor HaloTag ligand dyes for tracking protein turnover in mice | null | dx.doi.org/10.17504/protocols.io.bd8gi9tw | null | Boaz Mohar, Karel Svoboda | TITLE: Brain-wide delivery of Janelia Fluor HaloTag ligand dyes for tracking protein turnover in mice
AUTHORS: Boaz Mohar, Karel Svoboda
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">These protocols are part of a yet unpublised paper by the same title.</div></div>
[STEPS] | [] |
74,981 | P7b.- REVISIÓN Y CONTROL DEL PROCESO DE PRESENTACIÓN PLANES DE INVESTIGACIÓN | 1 | dx.doi.org/10.17504/protocols.io.81wgby46yvpk/v1 | https://www.protocols.io/view/p7b-revisi-n-y-control-del-proceso-de-presentaci-n-cmgdu3s6 | cgarcia | TITLE: P7b.- REVISIÓN Y CONTROL DEL PROCESO DE PRESENTACIÓN PLANES DE INVESTIGACIÓN
AUTHORS: cgarcia
[DESCRIPTION]
Atendiendo a las particularidades de la Aplicación LAUREA ACADEMIC, el proceso de presentación del Plan de Investigación inicial por parte de los doctorandos, actualmente queda únicamente bajo la supervis... | ["[P7b.- REVISIÓN Y CONTROL DEL PROCESO DE PRESENTACIÓN PLANES DE INVESTIGACIÓN] DESCRIPCIÓN DEL PROCESO\n\nEn la primera semana de cada mes, la Secretaría de la EIDUCAM enviará un informe de estado de inscripciones de Planes de Investigación a las Comisiones Académicas. En este informe incluirá la siguiente informació... |
55,647 | RNA/DNA extraction from plankton natural samples using NucleoSpin RNA + RNA/DNA Buffer kits (Macherey Nagel) | 4 | dx.doi.org/10.17504/protocols.io.b2j7qcrn | https://www.protocols.io/view/rna-dna-extraction-from-plankton-natural-samples-u-b2j7qcrn | Sarah Romac | TITLE: RNA/DNA extraction from plankton natural samples using NucleoSpin RNA + RNA/DNA Buffer kits (Macherey Nagel)
AUTHORS: Sarah Romac
[DESCRIPTION]
This protocol has been developped for simultaneous nucleic acid (RNA and DNA) extraction from environmental water samples collected by filtration on polycarbonate 47mm... | ["[Lysis] Lyse your plankton filter samples following the protocol :\n\nhttps://www.protocols.io/edit/cryogrinding-protocol-mecanic-lysis-of-142mm-filte-beqpjdvn", "[Lysis] Depending of the plankton size fraction samples you have, select :\n\n1 - RNA/DNA extraction using NucleoSpin RNA MIDI kit regarding [>20µ] size fr... |
48,747 | PCLS Whole Mounts | 4 | null | https://www.protocols.io/view/pcls-whole-mounts-btujnnun | Morrisey Lab | TITLE: PCLS Whole Mounts
AUTHORS: Morrisey Lab
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">PCLS Whole Mounts</div><div class = "text-block">**done at room temperature**</div></div>
[STEPS] | [] |
59,703 | Recombinant Antibody Affinity Purification with Protein A or Protein G | 4 | dx.doi.org/10.17504/protocols.io.14egn76yyv5d/v1 | https://www.protocols.io/view/recombinant-antibody-affinity-purification-with-pr-b6ixrcfn | Addgene The Nonprofit Plasmid Repository | TITLE: Recombinant Antibody Affinity Purification with Protein A or Protein G
AUTHORS: Addgene The Nonprofit Plasmid Repository
[DESCRIPTION]
This protocol describes how to affinity purify recombinant antibodies from cell culture supernatant using Protein A or Protein G columns.
[BEFORE_START]
See the Materials secti... | ["[Affinity chromatography] Add 1 part Protein A/G binding buffer to 1 part tissue culture supernatant and mix well.", "[Affinity chromatography] Equilibrate filtered tissue culture supernatant containing the recombinant antibody to Room temperature (see Transfection for Recombinant Antibody protocol).", "[Affinity chr... |
91,872 | Vu, M-A. T. et al (2024) Targeted micro-fiber arrays for measuring and manipulating localized multi-scale neural dynamics over large, deep brain volumes during behavior | 2 | dx.doi.org/10.17504/protocols.io.bp2l6xyrklqe/v1 | https://www.protocols.io/view/vu-m-a-t-et-al-2024-targeted-micro-fiber-arrays-fo-c5x8y7rw | Mai-Anh Vu | TITLE: Vu, M-A. T. et al (2024) Targeted micro-fiber arrays for measuring and manipulating localized multi-scale neural dynamics over large, deep brain volumes during behavior
AUTHORS: Mai-Anh Vu
[DESCRIPTION]
This collection contains eight protocols detailing methods used in Vu, M-A. T. et al (2024) Targeted micro-fi... | [] |
86,871 | Organoids dehydration and Organoids embedding in paraffin | 4 | null | https://www.protocols.io/view/organoids-dehydration-and-organoids-embedding-in-p-cy3xxypn | Gabriela Vallejo Flores, Annika Fendler | TITLE: Organoids dehydration and Organoids embedding in paraffin
AUTHORS: Gabriela Vallejo Flores, Annika Fendler
[DESCRIPTION]
This protocol is for Organoids dehydration and Organoids embedding adapted from Fendler, A., et al. Research Square (2020).
[BEFORE_START]
Melt the paraffin at 65 °C during 3-6 hrs in the o... | ["[Dehydration] Table 1. Dehydration steps of organoids in agarose beads", "[Embedding]", "[Embedding] With a forceps, carefully transfer the agarose block into a paraffin embedding jar\n(metal)", "[Embedding] Transfer the embedded jar to a cooling plate, and place the plastic embedding cassette on top on the embedding... |
96,325 | PBMCs Processing for Single Cell Multiome ATAC + Gene Expression Sequencing | 0 | dx.doi.org/10.17504/protocols.io.j8nlko7w6v5r/v1 | https://www.protocols.io/view/pbmcs-processing-for-single-cell-multiome-atac-gen-dabd2ai6 | Weiyan Jia, Etiena Basner-Tschakarjan, William Beggs, Derek Kelly, Ning Xie, Yuanqing Feng, Sarah Tishkoff | TITLE: PBMCs Processing for Single Cell Multiome ATAC + Gene Expression Sequencing
AUTHORS: Weiyan Jia, Etiena Basner-Tschakarjan, William Beggs, Derek Kelly, Ning Xie, Yuanqing Feng, Sarah Tishkoff
[DESCRIPTION]
This protocol was designed for the workflow of the Multiome assay on 16 PBMC samples using the 10X Next GE... | ["[1. Thawing PBMCs( ~ 2 hrs, Benzonase treatment )] Remove cryovials from liquid nitrogen storage and place them on dry ice.", "[1. Thawing PBMCs( ~ 2 hrs, Benzonase treatment )] Warm The medium to 37°C in a water bath and prepare the washing Medium.", "[1. Thawing PBMCs( ~ 2 hrs, Benzonase treatment )] Thaw frozen vi... |
null | null | null | dx.doi.org/10.17504/protocols.io.ngmdbu6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol describes the untargeted polar analysis of urine samples from cows and calves, with special emphasis on the coverage of thyreostats. Extraction started with 3 mL urine and was in essence based on liquid-liquid extraction with ethyl acetate. Analysis of extracts ... | [] |
54,617 | RNA Quality Control Non-Denaturing Agarose "Bleach" Gel | 1 | dx.doi.org/10.17504/protocols.io.bzjzp4p6 | https://www.protocols.io/view/rna-quality-control-non-denaturing-agarose-34-blea-bzjzp4p6 | Lynn Doran | TITLE: RNA Quality Control Non-Denaturing Agarose "Bleach" Gel
AUTHORS: Lynn Doran
[DESCRIPTION]
To evaluate the quality of RNA without the use of toxic chemicals, samples are run in a non-denaturing agarose "bleach" gel and product segregation is used to estimate RNA integrity.
Be aware that in a non-dena... | ["Empty and rinse the gel electrophoresis tank with distilled water at least three times.", "Dry the tank with paper towels.", "Treat the gel electrophoresis tank, the gel casting system, the gel tray, and the gel comb with RNase Away. Set up the gel tray and the gel casting system.", "Prepare fresh 0.5X TAE.", "Measu... |
28,986 | Confocal imaging of live larval zebrafish for assessing peripheral neuropathy | null | dx.doi.org/10.17504/protocols.io.8i2huge | null | Sandra Rieger | TITLE: Confocal imaging of live larval zebrafish for assessing peripheral neuropathy
AUTHORS: Sandra Rieger
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">This protocol describes a method to mount live 8 day-old zebra... | ["Mounting of larvae for imagingBefore mounting, select fluorescent larvae under a fluorescent stereomicroscope. For this, add a few drops of tricaine stock to the dish in which the larvae are raised and wait until larvae are anesthetized. Assess anesthesia by touching larvae with a pipette tip. If no response is obser... |
101,696 | Brain Tissue RNA Extraction -- University of Minnesota TMCs | 0 | dx.doi.org/10.17504/protocols.io.bp2l62dmdgqe/v1 | https://www.protocols.io/view/brain-tissue-rna-extraction-university-of-minnesot-dfi83khw | David A Bernlohr, Hector Martell Martinez | TITLE: Brain Tissue RNA Extraction -- University of Minnesota TMCs
AUTHORS: David A Bernlohr, Hector Martell Martinez
[DESCRIPTION]
RNA extraction protocol from snap frozen tissues and/or cell pellets adapted from PureLink RNA Mini Kit and PureLink with TRIzol Reagent protocols (attached). Protocol here used with neur... | ["[Preparation] Choose and locate samples: box year and number, slot number.", "[Preparation] Spray benchtop with 70% ethanol or RNase away.", "[Preparation] Fill two containers with dry ice. One for the tools in step #4. Second for holding tissue samples.", "[Preparation] Wipe cutting board, razor, and forceps all wit... |
63,873 | Clinical CBD Gummies: Reviews, Ingredients, Shark Tank, Pain & Is It Scam Or Trusted? | 3 | dx.doi.org/10.17504/protocols.io.j8nlkk2xdl5r/v1 | https://www.protocols.io/view/clinical-cbd-gummies-reviews-ingredients-shark-tan-cak9scz6 | kairee.jeriko | TITLE: Clinical CBD Gummies: Reviews, Ingredients, Shark Tank, Pain & Is It Scam Or Trusted?
AUTHORS: kairee.jeriko
[DESCRIPTION]
Why is the discomfort much more astonishing is that often while bodily ache happens, them eats the whole consideration, after which it reminiscence, concentrate, plus all the other m... | [] |
42,400 | Plasmodium berghei ookinete culture | 4 | dx.doi.org/10.17504/protocols.io.bmm8k49w | https://www.protocols.io/view/plasmodium-berghei-ookinete-culture-bmm8k49w | Benito Recio Totoro | TITLE: Plasmodium berghei ookinete culture
AUTHORS: Benito Recio Totoro
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-style:italic;">Plasmodium</span><span style = "font-style:italic;font-style:italic;"> </span><span style = "font-style:italic;">berghei</span><span> is one o... | ["[Mice infections for passages.]\nMice are inoculated via intraperitoneally (IP) with no more than either from a cryopreserved stock or by passage from other mice.From cryopreserved stock: allow the blood-cryopreservation solution to thaw slowly and inoculate IP.Passage form another mouse: The number of parasites pe... |
28,296 | Quantification of Gel Bands by an Image J Macro, Band/Peak Quantification Tool | null | dx.doi.org/10.17504/protocols.io.7vghn3w | null | Kenji Ohgane, Hiromasa Yoshioka | TITLE: Quantification of Gel Bands by an Image J Macro, Band/Peak Quantification Tool
AUTHORS: Kenji Ohgane, Hiromasa Yoshioka
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol offers an Image J macro/plugin that enable easy quantification of bands on western blots, dot blots, and fluore... | ["[Installation of ImageJ and the macro]\nDown load the following ImageJ macro file (_BandPeakQuantification.ijm) and place in a directory under the ImageJ plugins directory.\nFor example, save the ijm file in“Applications> ImageJ > plugins”. With the“_”character at the start of the filename, ImageJ automatically recog... |
null | null | null | dx.doi.org/10.17504/protocols.io.qh7dt9n | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?... | [] |
6,450 | Ti (III) Reagent | null | dx.doi.org/10.17504/protocols.io.iisccee | null | Steven Wilhelm | TITLE: Ti (III) Reagent
AUTHORS: Steven Wilhelm
[DESCRIPTION]
<p>Used for washing off extracellular iron.</p>
<p> </p>
<p>Please contact Dr. Steven Wilhelm (wilhelm@utk.edu) for any additional information regarding this protocol.</p>
[STEPS]
?. [Chelator Solution]
Per 250 mL, add 4.65 g of Na2EDTA into distilled or ... | ["[Chelator Solution]\nPer 250 mL, add 4.65 g of Na2EDTA into distilled or Milli-Q water.\n[Na2EDTA]", "[Chelator Solution]\nAdd 3.68 g of Na3 Citrate.\n[Na3 Citrate]", "[Salts]\nAdd 2.5 mL of 0.1 M KCl.\n[of 0.1 M KCl]", "[Salts]\nAdd 3.0 g of NaCl (s).\n[NaCl]", "[Salts]\nAdd 7.77 mL of 20% TiCl3 while stirring after... |
99,495 | Immunofluorescence labelling and imaging of cholinergic interneurons in post-mortem human brain tissues | 0 | dx.doi.org/10.17504/protocols.io.eq2lywn5qvx9/v1 | https://www.protocols.io/view/immunofluorescence-labelling-and-imaging-of-cholin-ddef23bn | Alan K. L. Liu, Laura Parkkinen | TITLE: Immunofluorescence labelling and imaging of cholinergic interneurons in post-mortem human brain tissues
AUTHORS: Alan K. L. Liu, Laura Parkkinen
[DESCRIPTION]
This protocol details immunofluorescence labelling and imaging of cholinergic interneurons along with striatal astrocytes in formalin-fixed paraffin-embe... | ["[Collection and fixation of post-mortem human brain tissues] Collect 6 µm-thick sections of formalin-fixed paraffin-embedded (FFPE) tissues containing the anterior basal ganglia at the level of nucleus accumbens.", "[Collection and fixation of post-mortem human brain tissues] Place tissue sections in an oven at 70°C ... |
63,334 | Preparation of organotypic cerebellar cultures | 4 | dx.doi.org/10.17504/protocols.io.6qpvr67bbvmk/v1 | https://www.protocols.io/view/preparation-of-organotypic-cerebellar-cultures-b94er8te | Laura Lossi, adalberto.merighi | TITLE: Preparation of organotypic cerebellar cultures
AUTHORS: Laura Lossi, adalberto.merighi
[DESCRIPTION]
This protocol describes the basics to prepare organotypic cerebellar cultures using the membrane interface method.
[BEFORE_START]
Be sure to have all your tool and solutions ready. Working areas must be clean ... | ["[Tissue sampling] Euthanize mice at the required post-natal age with an overdose of intraperitoneal sodium pentobarbital (60 mg ⁄ 100 g body weight).", "[Tissue sampling] Quickly remove the brain from the skull while the head is kept submerged in the ice-cooled cutting solution and isolate the cerebellum under the st... |
48,414 | My test protocol | 1 | null | https://www.protocols.io/view/my-test-protocol-bth6nj9e | Abby Moore | TITLE: My test protocol
AUTHORS: Abby Moore
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is an illegitimate protocol used for testing purposes.</div></div>
[STEPS]
?. [substance combination]
These are my instructions on how to combine substances to make media. Here, I made a tag for NGMA .... | ["[substance combination]\nThese are my instructions on how to combine substances to make media. Here, I made a tag for NGMA . I can specify this cat no because it will always be the same.I can also include a field to fill out the substance type, but I would prefer to set a default value for this key instead of having... |
100,001 | Zeiss AxioImager 63X Z-Stack Image Capture | 1 | dx.doi.org/10.17504/protocols.io.kqdg35kzqv25/v3 | https://www.protocols.io/view/zeiss-axioimager-63x-z-stack-image-capture-ddv92696 | Allen Institute for Brain Science | TITLE: Zeiss AxioImager 63X Z-Stack Image Capture
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
This protocol describes the system that is used to capture Z stack images which are reassembled post-processing into 3D reconstructions.
Note: Research reported in this publication was supported by the National ... | [] |
88,524 | Overlap PCR | 4 | dx.doi.org/10.17504/protocols.io.bp2l6x8zrlqe/v1 | https://www.protocols.io/view/overlap-pcr-c2pkydkw | NUS iGEM | TITLE: Overlap PCR
AUTHORS: NUS iGEM
[DESCRIPTION]
2023 NUS-Singapore iGEM team followed this protocol to combine DNA fragments with overlapping regions, thereby reducing the number of fragments used in the Gibson Assembly and thus, improving the success rate of the Gibson Assembly. These overlapping regions are creat... | ["Determine the volume ratio for each DNA fragment required in the reaction to calculate the appropriate volume for each DNA fragment. The final sample volume is 47 µL, with 25 µL being the KOD OneTM PCR Master Mix (Blue). Therefore, the remaining volume (22 µL) will be allocated to the gene fragments and DI Water for ... |
10,838 | Prescholers' causal reasoning | 1 | dx.doi.org/10.17504/protocols.io.ntwdepe | https://www.protocols.io/view/prescholers-39-causal-reasoning-ntwdepe | Tessa Van Schijndel, Kim Huijpen, Ingmar Visser, Maartje Raijmakers | TITLE: Prescholers' causal reasoning
AUTHORS: Tessa Van Schijndel, Kim Huijpen, Ingmar Visser, Maartje Raijmakers
[DESCRIPTION]
1 Protocol
2-5 Scoring forms (versions 1A, 1B, 2A and 2B)
For communication regarding the translation of the documents the authors can be contacted.
[STEPS] | [] |
73,500 | Whole blood T cell assay for NHPs, containment protocol | 4 | dx.doi.org/10.17504/protocols.io.bp2l692prlqe/v1 | https://www.protocols.io/view/whole-blood-t-cell-assay-for-nhps-containment-prot-cjz4up8w | Jonathan Audet, Courtney Meilleur | TITLE: Whole blood T cell assay for NHPs, containment protocol
AUTHORS: Jonathan Audet, Courtney Meilleur
[DESCRIPTION]
This is a protocol used to perform T cell assays using whole blood (collected in EDTA tubes) or cells from bronchoalveolar lavage (BAL). We have successfully used this protocol for rhesus macaques, ... | ["[Preparations] Prepare the staining mix. (for 1 sample:)\n\n \n Supplier Antibody Clone Channel Volume per test BD Biosciences CD45 D058-1283 BUV395 1.25 BD Biosciences CD3 SP34-2 BUV496 5 BD Biosciences CD8 RPA-T8 BUV563 1.25 BD Biosciences CD16 3G8 BUV737 5 BD Bioscie... |
91,357 | Novel Object Recognition Test | 1 | dx.doi.org/10.17504/protocols.io.81wgbx99qlpk/v1 | https://www.protocols.io/view/novel-object-recognition-test-c5f5y3q6 | Marina Lorente Picón, Núria Peñuelas, Ariadna Laguna, Miquel Vila | TITLE: Novel Object Recognition Test
AUTHORS: Marina Lorente Picón, Núria Peñuelas, Ariadna Laguna, Miquel Vila
[DESCRIPTION]
Novel Object Recognition Test for mice
[STEPS]
1. Individualize each mouse in a different cage with new bedding.
2. Expose the animal to two identical objects for habituation.
3. After 24h ch... | ["Individualize each mouse in a different cage with new bedding.", "Expose the animal to two identical objects for habituation.", "After 24h change one of the two objects for a new one.", "Measure the time the animal spends exploring the new object and the old\nobject.", "Calculate the discrimination index using the fo... |
47,949 | Total Cellular RNA Purification Protocol from Animal Tissue (Trizol + RNeasy) | 4 | null | https://www.protocols.io/view/total-cellular-rna-purification-protocol-from-anim-bs3mngk6 | Loyal Goff | TITLE: Total Cellular RNA Purification Protocol from Animal Tissue (Trizol + RNeasy)
AUTHORS: Loyal Goff
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol provides an optimaized, high-quality total RNA extraction method that balances time and RNA-yield effectively by combining the phase ... | ["[Sample Homogenization]\nBegin with tissue stored at (for each TRIzol you will use).\n50 mg\n-80 °C\n1 mL", "[Sample Homogenization]\nPlace tissue in liquid nitrogen and grind to a powder with a frozen mortar and pestle.", "[Sample Homogenization]\nLiquid nitrogen will evaporate, but prior to tissue thawing, add TR... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.