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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107,842 | QUINT Workflow Appendix | 4 | dx.doi.org/10.17504/protocols.io.36wgq3e6klk5/v2 | https://www.protocols.io/view/quint-workflow-appendix-dmja44ie | Michael X. Henderson | TITLE: QUINT Workflow Appendix
AUTHORS: Michael X. Henderson
[DESCRIPTION]
This protocol contains additional details for the modified QUINT workflow.
[STEPS]
SECTION: QuPath: Setting Stain Vectors
1. Draw a small rectangle over a characteristic DAB or hematoxylin stain.
SECTION: QuPath: Setting Stain Vectors
2. On Im... | ["[QuPath: Setting Stain Vectors] Draw a small rectangle over a characteristic DAB or hematoxylin stain.", "[QuPath: Setting Stain Vectors] On Image tab, double-click the Stain you would like to set. Click Yes on the prompt.", "[QuPath: Setting Stain Vectors] Give the new settings a unique name (Project ID). Click OK."... |
null | null | null | dx.doi.org/10.17504/protocols.io.j86crze | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Calculate various assembly statistics using the MetaQuast app on the CyVerse Discovery Environment.</p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
101,271 | Protocol for Making Soil | 0 | null | https://www.protocols.io/view/protocol-for-making-soil-de5x3g7n | Yuriani Palomino, Karma Terlik | TITLE: Protocol for Making Soil
AUTHORS: Yuriani Palomino, Karma Terlik
[DESCRIPTION]
This protocol outlines 3 soil recipes for their corresponding plant species: Phacelia parryi, P. campanularia, and Brassica rapa. In addition to the recipes, it also details the soil mixing process.
[STEPS]
SECTION: Soil Recipe for ... | ["[Soil Recipe for Phacelia campanularia] 1 part peat moss\n0.5 part vermiculite\n1.5 part sand\n3 parts perlite\n3 tbsp of fertilizer per 2 gallons of soil", "[Soil Recipe for Brassica rapa] 1 part peat moss\n1 part vermiculite\n1 part perlite\n3 tbsp of fertilizer per 2 gallons of soil", "[Soil Recipe for Phacelia pa... |
29,592 | FIB SEM protocol for anaerobic ciliates to visualize their prokaryotic endosymbionts and association with MROs | null | dx.doi.org/10.17504/protocols.io.85yhy7w | null | Johana Rotterova, Ivan Čepička | TITLE: FIB SEM protocol for anaerobic ciliates to visualize their prokaryotic endosymbionts and association with MROs
AUTHORS: Johana Rotterova, Ivan Čepička
[STEPS]
?. [Fixation of the cells]
Individually pick several hundreds of cells with a micropipette from 2 ml of a well-grown culture of the targeted ciliate stra... | ["[Fixation of the cells]\nIndividually pick several hundreds of cells with a micropipette from 2 ml of a well-grown culture of the targeted ciliate strain. Subsequently, follow fixation protocol by Rotterová et al. (2018) - see steps briefly described below or see full protocol \"Transmission electron microscopy proto... |
null | null | null | dx.doi.org/10.17504/protocols.io.imzcc76 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Mouse kidney tissues were harvested, fixed in 4% paraformaldehyde (PFA) and embedded in paraffin. All sections (3 micrometers in thickness) were stained with hematoxylin and eosin (H&E), periodic acid-Schiff (PAS, Thermo Scientific) or Masson’s trichrome staining (MTS, Si... | [] |
70,925 | RNA extraction from E. coli | 4 | dx.doi.org/10.17504/protocols.io.j8nlkw44wl5r/v1 | https://www.protocols.io/view/rna-extraction-from-e-coli-chhmt346 | An.Huang | TITLE: RNA extraction from E. coli
AUTHORS: An.Huang
[DESCRIPTION]
RNA extraction is a fundamental step in multiple experiments, for example, qPCR. This protocol helps conduct a simple RNA extraction procedure.
[STEPS]
SECTION: Preparation for experiment
1. Grow an overnight bacterial culture in the appropriate media... | ["[Preparation for experiment] Grow an overnight bacterial culture in the appropriate media at an appropriate temperature.", "[Preparation for experiment] In the following day, take 1 mLfrom overnight culture and add into 10 mL LB media. Grow until the OD600 reads at 0.6-1.0.", "[RNA extraction] Harvest 1.5 mL culture ... |
55,354 | ImmunoFACS | 1 | null | https://www.protocols.io/view/immunofacs-b2a2qage | Florian Noack, Silvia Vangelisti, Boyan Bonev | TITLE: ImmunoFACS
AUTHORS: Florian Noack, Silvia Vangelisti, Boyan Bonev
[DESCRIPTION]
Protocol to isolate distinct cell populations by immunostaining followed by FAC-sorting.
[STEPS]
2. Add freshly prepared 2% Formaldehyde (from a new vial) in PBS to a final concentration of 1% and incubate for 10 minutes at roo... | ["Add freshly prepared 2% Formaldehyde (from a new vial) in PBS to a final concentration of 1% and incubate for 10 minutes at room temperature with slow! rotation", "Add 2M glycine solution to a final concentration of 0.2M to quench the reaction and incubate 5 minutes at room temperature with slow! rotation", "Centrif... |
93,109 | Microglia validation by FACS-analysis | 4 | dx.doi.org/10.17504/protocols.io.81wgbxokqlpk/v1 | https://www.protocols.io/view/microglia-validation-by-facs-analysis-c66vzhe6 | Riana Lo Bu, Frank Soldner | TITLE: Microglia validation by FACS-analysis
AUTHORS: Riana Lo Bu, Frank Soldner
[DESCRIPTION]
This protocol describes the procedure for microglial precursor and mature microglia validation by Fluorescence-Activated Cell Sorting (FACS) analysis. Please refer to (https://doi.org/10.17504/protocols.io.4r3l22zbjl1y/v1) f... | ["[Microglial precursor validation] Harvest microglial precursors from flasks in STEP4 by collecting the media into 15 ml conical tubes and centrifuging it at150 rcf for 4 min.", "[Microglial precursor validation] Remove the supernatant and resuspend the cells in STEP4 media.", "[Microglial precursor validation] Count ... |
92,403 | Wet Aggregate Stability in Soil | 6 | dx.doi.org/10.17504/protocols.io.36wgq3jo5lk5/v2 | https://www.protocols.io/view/wet-aggregate-stability-in-soil-c6gtzbwn | Susan K Siragusa Ortman | TITLE: Wet Aggregate Stability in Soil
AUTHORS: Susan K Siragusa Ortman
[DESCRIPTION]
The wet sieving technique measures the percentage of water-stable aggregates in soils. It is a soil quality assessment analysis. Aggregate stability refers to the ability of soil aggregates to resist disintegration.
[STEPS]
1.
W... | ["Weigh and record the weights of numbered (use permanent marker) weigh dishes. I recommend setting up small trays as follows: 2 mm in front, 1-2mm in middle, and 0.5-1.0mm in back.\n Weigh up the appropriate amount of Aggregate Fractioned soil (refer to the chart for sample amounts). Tare out the plastic weigh dish ... |
null | null | null | dx.doi.org/10.17504/protocols.io.iehcbb6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The plasmids were constructed using standard methods; all sequences were verified by appropriate restriction digestion and/or sequencing. Human full-length <em>IGFBP2</em> cDNA from ASCs fused to a M2-Flag tag was produced with a standard PCR protocol. This sequence (Flag-<em... | [] |
60,467 | Creating Differential Transcript Expression Results with DESeq2 | 1 | dx.doi.org/10.17504/protocols.io.8epv51686l1b/v2 | https://www.protocols.io/view/creating-differential-transcript-expression-result-b7atrien | David A Eccles | TITLE: Creating Differential Transcript Expression Results with DESeq2
AUTHORS: David A Eccles
[DESCRIPTION]
Differential expression analysis of transcript count tables using DESeq2
[BEFORE_START]
You should have gene-annotated transcript count tables for multiple sequencing libraries, renamed to match the form of "<... | ["[Collating count data] Combine the transcript count data into a single data structure. To reduce confusion when this protocol is run multiple times, we declare an analysisDate variable to be used for output file names:\n\n\n \nWe also load libraries that will be used in the protocol:", "[Collating count data] Collect... |
63,813 | Nanodrop | 4 | null | https://www.protocols.io/view/nanodrop-cajdsci6 | Allyson Hirsch, George Testo | TITLE: Nanodrop
AUTHORS: Allyson Hirsch, George Testo
[DESCRIPTION]
The Thermo Scientific NanoDrop 8000 Spectrophotometer is a full-spectrum (220-750nm) instrument that accurately measures up to 8 individual 1 ul samples in one measurement cycle. The software allows the user to measure samples using either the full 8... | ["[Preparing & Blanking Nanodrop] Allow samples to efficiently thaw before starting (10 min)", "[Preparing & Blanking Nanodrop] Log into computer and open the Nanodrop program and select “Nucleic Acid.\"", "[Preparing & Blanking Nanodrop] Clean Nanodrop pedestals using molecular grade H2O.", "[Preparing &am... |
42,214 | Vulture Rehabilitation Manual | 2 | null | https://www.protocols.io/view/vulture-rehabilitation-manual-bmgek3te | Kerri Wolter | TITLE: Vulture Rehabilitation Manual
AUTHORS: Kerri Wolter
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Every single vulture species is under threat, not only in southern Africa, but across Africa and the globe. The dangers to the species vary by location, with most threats being anthropogenic. <... | [] |
90,334 | Vesicle Fusion on SiO2 Substrates | 1 | dx.doi.org/10.17504/protocols.io.36wgq3b4ylk5/v2 | https://www.protocols.io/view/vesicle-fusion-on-sio2-substrates-c4f6ytre | Nicole Voce, Paul Stevenson | TITLE: Vesicle Fusion on SiO2 Substrates
AUTHORS: Nicole Voce, Paul Stevenson
[DESCRIPTION]
This protocol outlines the steps to produce large area, uniform supported lipid bilayers on SiO2 substrates with or without patterned features.
[STEPS]
SECTION: Substrate cleaning
1. Clean plain SiO2 or TiO2-patterned substrat... | ["[Substrate cleaning] Clean plain SiO2 or TiO2-patterned substrates by sonicating them in a 1:1 IPA:Acetone mixture for ~2 minutes\nDry with a steady stream of N2", "[Substrate cleaning] Oxygen plasma clean the substrates for 2 minutes to remove any residual surface contamination", "[Vesicle prep] Prepare a 1.2 mg/mL ... |
62,591 | Development of a genome assembly strategy | 5 | dx.doi.org/10.17504/protocols.io.4r3l2oepxv1y/v1 | https://www.protocols.io/view/development-of-a-genome-assembly-strategy-b9c7r2zn | Khalid El Moussaoui | TITLE: Development of a genome assembly strategy
AUTHORS: Khalid El Moussaoui
[DESCRIPTION]
Before proceeding with genome assembly, it is necessary to determine the appropriate strategy. In the scientific literature on whole genome sequencing applied to dermatophytes, some authors indicate that they proceeded with SP... | ["[Set up the folders] Open a terminal window.", "[Set up the folders] Activate the previously created denovo_env environment by typing the following command in the terminal :", "[Set up the folders] Run this command to create the appropriate folders to the root of the user's directory (one folder per assembly strategy... |
54,167 | Megazyme Sucrose D-Glucose Assay Kit (K-SUCGL) | 4 | dx.doi.org/10.17504/protocols.io.by5xpy7n | https://www.protocols.io/view/megazyme-sucrose-d-glucose-assay-kit-k-sucgl-by5xpy7n | Likhithchandragiri | TITLE: Megazyme Sucrose D-Glucose Assay Kit (K-SUCGL)
AUTHORS: Likhithchandragiri
[DESCRIPTION]
Protocol for a colorimetric assay kit to determine sucrose and D-glucose concentrations by Megazyme.
[GUIDELINES]
1. Store all reagent solutions as per the instructions given in the protocol. Keep the 1.65 mL working sto... | ["[Preparing the Reagents] To prepare Solution 1: Acetate Buffer, dissolve the contents of Bottle 1 (20 mL) to 400 mL in distilled water. \n\nStore at 4 °C", "[Preparing the Reagents] To prepare Solution 2: Beta-fructosidase, dissolve 1 mL of solution from Bottle 2 (20 mL) to 10 mL in distilled water. \n\nFor convenien... |
88,788 | UPitt TriState SenNet TMC H&E staining | 1 | dx.doi.org/10.17504/protocols.io.5qpvo3py7v4o/v1 | https://www.protocols.io/view/upitt-tristate-sennet-tmc-h-amp-e-staining-c2xuyfnw | Marta Bueno | TITLE: UPitt TriState SenNet TMC H&E staining
AUTHORS: Marta Bueno
[DESCRIPTION]
Hematoxylin and Eosin stains are the preferred method for histopathologic assessment of tissue sections.
Hematoxylin is used to illustrate nuclear detail in cells. Depth of coloration is not only related to the amount of DNA in the n... | ["[Staining Procedure] Prepare staining line with reagents in the staining train in the order of use.", "[Imaging] Slides will then be scanned by the Center for Biologic Imaging (CBI) using a VS200 slide scanner. Images can be acquired with brightfield scans at (10X, 20X).", "[Staining Procedure] Place slides into a xy... |
null | null | null | dx.doi.org/10.17504/protocols.io.equbdww | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Tris-glycine buffer solution
[STEPS]
?. | [] |
64,370 | Pharma Keto Gummies - Trusted Diet Formula or Cheap Brand? | 3 | dx.doi.org/10.17504/protocols.io.x54v9yo4mg3e/v1 | https://www.protocols.io/view/pharma-keto-gummies-trusted-diet-formula-or-cheap-ca4ssgwe | Tzachi H | TITLE: Pharma Keto Gummies - Trusted Diet Formula or Cheap Brand?
AUTHORS: Tzachi H
[DESCRIPTION]
Make a point to talk with an expert doctor or monetary specialist Pharma Keto Gummies to settling on any buying choice in the event that you use meds or have concerns following the survey subtleties shared previously.
[... | [] |
56,725 | Liquid chromatography-mass spectrometry method for isomer separation and detection of sugars, phophorylated sugars and organic acids | 1 | dx.doi.org/10.17504/protocols.io.b3mvqk66 | https://www.protocols.io/view/liquid-chromatography-mass-spectrometry-method-for-b3mvqk66 | Somnath Koley, Kevin L. Chu, Saba S. Gill, Doug K. Allen | TITLE: Liquid chromatography-mass spectrometry method for isomer separation and detection of sugars, phophorylated sugars and organic acids
AUTHORS: Somnath Koley, Kevin L. Chu, Saba S. Gill, Doug K. Allen
[DESCRIPTION]
This standard operating procedure is used to achieve effective separation of a wide range of polar... | ["[Abbreviations:] CE: collision energy \nCXP: collision cell exit potential \nddH2O: double-distilled water \nDP: declustering potential \nEP: entrance potential \nFW: fresh weight \nHILIC: hydrophilic interaction liquid chromatography\nHPLC: high-performance liquid chromatography \nID: isotopologue distribution \nLC-... |
33,170 | Marchantia high throughput imaging in multiwell plates | null | dx.doi.org/10.17504/protocols.io.bcmsiu6e | null | marta tomaselli, Marius Rebmann, Mihails Delmans | TITLE: Marchantia high throughput imaging in multiwell plates
AUTHORS: marta tomaselli, Marius Rebmann, Mihails Delmans
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol allows high throughput imaging of Marchantia gemmae, using a cheap setup made with broadly available lab equipme... | ["[Media preparation]\nPrepare 1/2 strength Gamborg media plus vitamin with 1.2% agar.", "[Plate set up]\nPour the media into your selected wells, making sure they are filled up to the top and they not contain any air bubble inside.\nThe number of wells to be filled depends on your requirements/ travelling range of th... |
null | null | null | dx.doi.org/10.17504/protocols.io.jtncnme | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol describes the preparation and use of ELISpot 96 well plates for measuring human IFNγ and Granzyme B production by immune cells (notably CD4 and CD8 T cells). Cells harvested from peripheral blood or other organs can be used, stimulated with antigen of interest (... | [] |
76,319 | Freely moving recording: Chronic recoverable Neuropixels in mice | 1 | dx.doi.org/10.17504/protocols.io.n92ldzz2ov5b/v5 | https://www.protocols.io/view/freely-moving-recording-chronic-recoverable-neurop-cnr7vd9n | Emily A Aery Jones | TITLE: Freely moving recording: Chronic recoverable Neuropixels in mice
AUTHORS: Emily A Aery Jones
[DESCRIPTION]
This protocol collection explains how to build a low-cost, lightweight system to implant 1 Neuropixels 1.0 probe or 2 Neuropixels 2.0 probes into mice, record during freely moving behavior, then recover th... | ["[Design the enclosure] Consider what acrylic to use (e.g. 1/4\" P95 matte black acrylic).\nUse black if you're planning to track LEDs in the dark or white if you're planning to track a Black6 mouse based on center of mass.\nUse matte finish to reduce reflections from LEDs and overhead lights.\nThicker material makes ... |
51,665 | Quick Fungal DNA extraction from colonies on plates | 1 | dx.doi.org/10.17504/protocols.io.bwprpdm6 | https://www.protocols.io/view/quick-fungal-dna-extraction-from-colonies-on-plate-bwprpdm6 | Johannes Debler | TITLE: Quick Fungal DNA extraction from colonies on plates
AUTHORS: Johannes Debler
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Adapted from </span><a href="https://doi.org/10.5423/PPJ.2009.25.1.108" style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;">Chi, M. ... | ["[Make stock solutions]\nAB11M TrisHCl pH 8.0 100 ml212.14 g Tris base or Trizma base3up to 100 ml deionised H2O4Adjust pHconcentrated HCl AB12M KCl (Potassium chloride)200 ml215.11 gKCl (Potassium chloride)3up to 200 mldeionised H2O AB1500 mM NaEDTA (pH 8.0)100 ml218.6 gEDTA disodium salt dihydrate3u... |
98,456 | CHCHD2 T61I Mouse Genotyping | 0 | dx.doi.org/10.17504/protocols.io.kxygxyejwl8j/v1 | https://www.protocols.io/view/chchd2-t61i-mouse-genotyping-dcdy2s7w | Szu-Chi Liao, Ken Nakamura | TITLE: CHCHD2 T61I Mouse Genotyping
AUTHORS: Szu-Chi Liao, Ken Nakamura
[DESCRIPTION]
To genotype CHCHD2 T61I point mutant mice by qPCR.
[STEPS]
SECTION: Mouse Tail Lysis
1. Materials
Isoflurane
Sanitized scissors
DirectPCR lysis reagent (mouse tail, Viagen Biotech, 102-T)
Proteinase K – Recombinant, PCR grade (Roch... | ["[Mouse Tail Lysis] Materials\nIsoflurane\nSanitized scissors\nDirectPCR lysis reagent (mouse tail, Viagen Biotech, 102-T) \nProteinase K – Recombinant, PCR grade (Roche, 03115844001)\nMicrocentrifuge tubes\nIncubator\nWater bath", "[Mouse Tail Lysis] Anesthetize mice with isoflurane.", "[Mouse Tail Lysis] Cut no long... |
30,803 | TRAP-SEQ_Sympathetic chain ganglia_Protocol | 1 | dx.doi.org/10.17504/protocols.io.babtiann | https://www.protocols.io/view/trap-seq-sympathetic-chain-ganglia-protocol-babtiann | Rui Zhang | TITLE: TRAP-SEQ_Sympathetic chain ganglia_Protocol
AUTHORS: Rui Zhang
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol describes steps to perform TRAP-SEQ with individually dissected sympathetic chain ganglia.</div></div>
[STEPS]
?. [Day 1 (Preparation of the affinity matrix)]
Calculate the... | ["[Day 1 (Preparation of the affinity matrix)]\nCalculate the amount of Dynabeads required on the basis of the ratios above. Note that the affinity matrix to be used in one particular experiment should be aliquotted to samples from a common source: either prepare all matrix in one larger tube or prepare batches in smal... |
103,177 | In vivo BioID protein purification | 0 | dx.doi.org/10.17504/protocols.io.8epv5r3z6g1b/v1 | https://www.protocols.io/view/in-vivo-bioid-protein-purification-dgzh3x36 | Shiyi Wang | TITLE: In vivo BioID protein purification
AUTHORS: Shiyi Wang
[DESCRIPTION]
In vivo BioID protein purification
[STEPS]
1. **Animal Preparation** - Breed genotype-matched animals (wild-type C57BL6 or LRRK2 G2019Ski/ki) to produce single-genotype litters. - For each genotype (WT or G2019S), prepare 6 pups for injection... | ["**Animal Preparation** - Breed genotype-matched animals (wild-type C57BL6 or LRRK2 G2019Ski/ki) to produce single-genotype litters. - For each genotype (WT or G2019S), prepare 6 pups for injection.", "**AAV Injection** - Inject 1 µL of AAVs carrying Astro-Ezrin-BioID (PHP.eB.GfaABC1D-Ezrin WT-BioID2-HA) or Astro-CYTO... |
62,096 | Oprah Keto Weight Loss : How To Buy This Extraordinary Product! | 1 | dx.doi.org/10.17504/protocols.io.bp2l6136dvqe/v1 | https://www.protocols.io/view/oprah-keto-weight-loss-how-to-buy-this-extraordina-b8vqrw5w | billhopey | TITLE: Oprah Keto Weight Loss : How To Buy This Extraordinary Product!
AUTHORS: billhopey
[DESCRIPTION]
Oprah Keto Weight Loss : Having a sound existence is the requested from various individuals. However, several lucky individuals figure out how to accomplish a sound life throughout everyday life.
Various are fat ... | ["[Oprah Keto Weight Loss]"] |
70,081 | A HABA dye based colorimetric assay to detect unoccupied biotin binding sites in a fusion protein containing avidin | 1 | dx.doi.org/10.17504/protocols.io.81wgby1w1vpk/v1 | https://www.protocols.io/view/a-haba-dye-based-colorimetric-assay-to-detect-unoc-cgn9tvh6 | Sonia Mukherjee, Pierre Leblanc, Mark Poznansky, Ann Sluder | TITLE: A HABA dye based colorimetric assay to detect unoccupied biotin binding sites in a fusion protein containing avidin
AUTHORS: Sonia Mukherjee, Pierre Leblanc, Mark Poznansky, Ann Sluder
[DESCRIPTION]
HABA (4'-hydroxyazobenzene-2-carboxylic acid) dye is an anionic dye which is used to assess the biotin binding si... | ["[Impact of biotin concentration on the displacement of HABA from Avidin in a colorimetric assay] Prepare Avidin-HABA complex:\nAdd 100 µL of a 12 micromolar (µM) Avidin stock solution to a 1.7 mL eppendorf tube containing 10.4 µL DPBS.", "[Impact of biotin concentration on the displacement of HABA from Avidin in a co... |
61,801 | Twist 96-Plex (Riptide) Library Prep | 4 | dx.doi.org/10.17504/protocols.io.j8nlkkm85l5r/v1 | https://www.protocols.io/view/twist-96-plex-riptide-library-prep-b8khrut6 | Katarina A Cohen, Khai-Minh H Nguyen, Oksana Polesskaya, Abraham Palmer | TITLE: Twist 96-Plex (Riptide) Library Prep
AUTHORS: Katarina A Cohen, Khai-Minh H Nguyen, Oksana Polesskaya, Abraham Palmer
[DESCRIPTION]
This protocol is designed for Twist 96-PLex Library Prep. We use the EPmotion 5075 to add sample barcodes (can also easily be done manually with a multichannel pipette). This is a... | ["[Adding Primer A with EPmotion] Fill ice pan with ice chips.", "[Adding Primer A with EPmotion] Defrost 4uL randomized/normalized sample plate from the \"EPMotion - Normalization and Randomization\" protocol on ice", "[Adding Primer A with EPmotion] Download and import and \nDepending on the GC content of the spe... |
91,855 | Ambulatory Testing - UroMOCA and ColoMOCA | 1 | dx.doi.org/10.17504/protocols.io.q26g7p931gwz/v1 | https://www.protocols.io/view/ambulatory-testing-uromoca-and-colomoca-c5xpy7mn | Brett Hanzlicek, Margot Damsaser, Dennis Bourbeau | TITLE: Ambulatory Testing - UroMOCA and ColoMOCA
AUTHORS: Brett Hanzlicek, Margot Damsaser, Dennis Bourbeau
[DESCRIPTION]
Ambulatory Recordings of Wireless Bladder (UroMOCA) and Colon (ColoMOCA) Devices in Pigs.
[STEPS]
SECTION: Ambulatory Testing
1. Place BluMOCA receiver radio into pocket on the pig jacket.
SECTIO... | ["[Ambulatory Testing] Place BluMOCA receiver radio into pocket on the pig jacket.", "[Ambulatory Testing] Wake the UroMOCA and ColoMOCA with the waker set between 9V-15V, 1.5A.", "[Ambulatory Testing] Plug the Bluetooth dongle into the computer.", "[Ambulatory Testing] Record from from the UroMOCA and ColoMOCA using L... |
null | null | null | dx.doi.org/10.17504/protocols.io.n4sdgwe | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Patterns of rabies virus spread within the central nervous system suggest that a thorough examination of the brain stem is critical for rabies diagnosis. Viral RNA is widespread in the brain of most animals positive for rabies. However, because virus spread may be unilateral,... | [] |
18,081 | DNA extraction (Salting out) | 1 | dx.doi.org/10.17504/protocols.io.vv9e696 | https://www.protocols.io/view/dna-extraction-salting-out-vv9e696 | Karen Guimaraes | TITLE: DNA extraction (Salting out)
AUTHORS: Karen Guimaraes
[BEFORE_START]
In microtubes containing tissue fragments, add 440μL of lysis buffer (10mM Tris-HCl, 2mM EDTA, 400mM NaCl, 2% SDS) and 10 µL of proteinase K (10mg/mL);
Incubate in a water bath at 55°C for approximately 1:30h or overnight;
Add 300µL of NaCl... | [] |
56,684 | Bogus Sample Prep Protocol | 1 | null | https://www.protocols.io/view/bogus-sample-prep-protocol-b3kkqkuw | Abby Moore | TITLE: Bogus Sample Prep Protocol
AUTHORS: Abby Moore
[DESCRIPTION]
This is a bogus protocol for assessing protocol development.
Here, I'll use the citation component to refer to a publication that might influence protocol development.
[BEFORE_START]
This is what you should know before you start the protocol ... | ["[This is my first section] Chill to °C . \n\nI used the reagent and temperature components in this step.", "[This is my first section] Combine 1 µL and 1 µL . \n\nI used the amount and reagent components in this step.", "[This is my first section] Centrifuge the using the following parameters 27000 rcf, 2 mi... |
97,589 | Nova-ST Spatial Transcriptomics protocol | 0 | dx.doi.org/10.17504/protocols.io.3byl4925jgo5/v1 | https://www.protocols.io/view/nova-st-spatial-transcriptomics-protocol-dbiv2ke6 | Suresh Poovathingal, Kristofer Davie, Stein Aerts | TITLE: Nova-ST Spatial Transcriptomics protocol
AUTHORS: Suresh Poovathingal, Kristofer Davie, Stein Aerts
[DESCRIPTION]
Nova-ST is a an open-source, high-resolution sequencing based spatial transcriptomics workflow. This method gives comparable resolution to BGI Stereoseq, SeqScope & PIXEL seq. Nova-ST is derived fro... | ["[Tissue preparation for spatial transcriptomics profiling] The first steps of the Nova-ST workflow starts with preparation of tissue for cryo-embedding. Follow the tissue preparation guidelines from 10X Genomics Visium Tissue Preparation guide\n\nOther useful video resources available from 10X Genomics:\nFlash Freezi... |
null | null | null | dx.doi.org/10.17504/protocols.io.crpv5m | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This is the blunting protocol for NEB PCR Cloning Kit (E1202)
[BEFORE_START]
Reaction volume may be scaled up or down as necessary.
[GUIDELINES]
Reaction volume may be scaled up or down as necessary. <br /><br />PCR generated DNA must be purified before blunting by using ... | [] |
63,902 | Tea Burn : It helps to increase the level of energy and strength! | 3 | dx.doi.org/10.17504/protocols.io.rm7vzy242lx1/v1 | https://www.protocols.io/view/tea-burn-it-helps-to-increase-the-level-of-energy-cam6sc9e | TeaBurnss | TITLE: Tea Burn : It helps to increase the level of energy and strength!
AUTHORS: TeaBurnss
[DESCRIPTION]
Tea Burn
[STEPS] | [] |
30,193 | FIXATIVE FOR MOSQUITO LARVAE | null | dx.doi.org/10.17504/protocols.io.9qrh5v6 | null | Rochelly da Silva Mesquita, Wanderli Pedro Tadei | TITLE: FIXATIVE FOR MOSQUITO LARVAE
AUTHORS: Rochelly da Silva Mesquita, Wanderli Pedro Tadei
[STEPS]
?. Accurately weigh of borax and dissolve it in of distilled water. Then, add of the formaldehyde solution and of glycerol, mix and bring to volume of with distilled water.
5 g
100 ml
10 ml
2.5 ml
1000 ml | ["Accurately weigh of borax and dissolve it in of distilled water. Then, add of the formaldehyde solution and of glycerol, mix and bring to volume of with distilled water.\n5 g\n100 ml\n10 ml\n2.5 ml\n1000 ml"] |
null | null | null | dx.doi.org/10.17504/protocols.io.irwcd7e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This is the reaction for the "Ligation Protocol with T4 DNA Ligase"
[STEPS]
?.
?.
?.
?.
?. | [] |
62,117 | Coverage of open citations in DOAJ journals - Protocol | 1 | dx.doi.org/10.17504/protocols.io.n92ldz598v5b/v3 | https://www.protocols.io/view/coverage-of-open-citations-in-doaj-journals-protoc-b8wdrxa6 | Constance Dami, Alessandro Bertozzi, Chiara Manca, Umut Kucuk | TITLE: Coverage of open citations in DOAJ journals - Protocol
AUTHORS: Constance Dami, Alessandro Bertozzi, Chiara Manca, Umut Kucuk
[DESCRIPTION]
This is the protocol for the research of the coverage of open citations in DOAJ journals.
Our goal is to find out:
about the coverage of articles from open access jour... | ["[Data Visualization] We visualize our results with python libraries. \nWe specifically visualize open_access_citations_by_year.json in a graph that specifies the number of citations in the y axis and the list of years in the x axis.", "[Publishing data] We publish all the CSV and JSON data that we gathered on our Dat... |
67,568 | Centriflaken: an automated data analysis pipeline for assembly and in silico analyses of food-borne pathogens from metagenomic samples | 5 | dx.doi.org/10.17504/protocols.io.kxygxzdbwv8j/v2 | https://www.protocols.io/view/centriflaken-an-automated-data-analysis-pipeline-f-cd8qs9vw | Kranti Konganti, Vishal Thovarai, Meghan Maguire, Julie A. Kase, Narjol Gonzalez-Escalona | TITLE: Centriflaken: an automated data analysis pipeline for assembly and in silico analyses of food-borne pathogens from metagenomic samples
AUTHORS: Kranti Konganti, Vishal Thovarai, Meghan Maguire, Julie A. Kase, Narjol Gonzalez-Escalona
[DESCRIPTION]
Rapid and comprehensive analysis of metagenomic data from any sa... | ["[Step 1] Create an account and Login:\n\nIf you do not already have an account on GalaxyTrakr, please create one by visiting this URL: https://account.galaxytrakr.org/Account/Register", "[Step 1] Once your account is activated, login by visiting https://galaxytrakr.org.", "[Step 2] Create a new history:\n \n\n \n\n\n... |
27,415 | Phenotypic analysis of circulating leukocytes | null | dx.doi.org/10.17504/protocols.io.6zxhf7n | null | John Davis Coakley | TITLE: Phenotypic analysis of circulating leukocytes
AUTHORS: John Davis Coakley
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Antibody panels for flow cytometry were prepared with specific antibodies for identification of lymphocyte populations, and antibodies specific to IL-23 receptor andIL-12 ... | ["Acquire blood sample from patient - 3mls EDTA", "Transfer 100mcl whole blood to each FACS tube (7 tubes per patient)", "Add Dead Cell Stain into each tube except tube 7 (unstained), vortex, and incubate for 15 minutes in the dark", "Resuspend with appropriate antibody cocktail (50mcl per tube) into each tube except 7... |
99,194 | Transmission Electron Microscopy of Native Nanodiscs | 0 | dx.doi.org/10.17504/protocols.io.x54v92ydml3e/v1 | https://www.protocols.io/view/transmission-electron-microscopy-of-native-nanodis-dc422yye | Caroline Brown, Snehasish Ghosh, Kallol Gupta | TITLE: Transmission Electron Microscopy of Native Nanodiscs
AUTHORS: Caroline Brown, Snehasish Ghosh, Kallol Gupta
[DESCRIPTION]
This is a protocol for conducting transmission electron microscopy of native nanodiscs to determine population size distribution and morphology.
[STEPS]
SECTION: Staining grids
1. Dilute na... | ["[Staining grids] Dilute nanodisc samples into single molecule range, typically around between 1:10 and 1:100 is the samples have been through size exclusion chromatography using dilution buffer (50 millimolar (mM) .", "[Staining grids] Glow-discharge carbon-coated copper grids (200 mesh) for 30 s seconds.", "[Stainin... |
31,580 | Somatic Signs of Withdrawal | 1 | null | https://www.protocols.io/view/somatic-signs-of-withdrawal-ba34igqw | Lauren Smith, Nathan Rizo, Lani Tieu, Olivier George | TITLE: Somatic Signs of Withdrawal
AUTHORS: Lauren Smith, Nathan Rizo, Lani Tieu, Olivier George
[STEPS]
?. [Procedure]
Place two observation cylinders on a surface
?. [Procedure]
Place one rat in each cylinder
?. [Procedure]
Set a timer to 30 minutes, at which point both observers will begin to watch the animals
?. [... | ["[Procedure]\nPlace two observation cylinders on a surface", "[Procedure]\nPlace one rat in each cylinder", "[Procedure]\nSet a timer to 30 minutes, at which point both observers will begin to watch the animals", "[Procedure]\nBehaviors to be tallied:JumpsTeeth ChatteringPtosisBlinksHead ShakesPaw TremorsAbdominal Con... |
108,104 | Protocol for the ‘Validated Entheses-based Reconstruction of Activity 2.0’ (VERA 2.0) Method: Semi-Automated Measurement of 3D Entheseal Changes | 0 | dx.doi.org/10.17504/protocols.io.5jyl82z8dl2w/v1 | https://www.protocols.io/view/protocol-for-the-validated-entheses-based-reconstr-dmtg46jw | Fotios Alexandros Karakostis | TITLE: Protocol for the ‘Validated Entheses-based Reconstruction of Activity 2.0’ (VERA 2.0) Method: Semi-Automated Measurement of 3D Entheseal Changes
AUTHORS: Fotios Alexandros Karakostis
[DESCRIPTION]
This protocol introduces the "Validated Entheses-based Reconstruction of Activity 2.0" (VERA 2.0), an advanced iter... | ["[Part 1 – Technical requirements and recommendations] Download and use the open-access software Meshlab Version 2023.12 or higher (https://www.meshlab.net/), since some steps of this protocol require functions not available in older versions of the software. If another 3D image processing software is used, please ens... |
28,249 | Protocol to immunostain Gastruloids (LSCB, EPFL) | 1 | dx.doi.org/10.17504/protocols.io.7tzhnp6 | https://www.protocols.io/view/protocol-to-immunostain-gastruloids-lscb-epfl-7tzhnp6 | Stefano Vianello, Mehmet Girgin, Giuliana Rossi, Matthias Lutolf | TITLE: Protocol to immunostain Gastruloids (LSCB, EPFL)
AUTHORS: Stefano Vianello, Mehmet Girgin, Giuliana Rossi, Matthias Lutolf
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Standard protocol used for immunostaining Gastruloids (aggregates of mouse embryonic stem cells) in the Lutolf Lab, EPFL.<... | ["[Fixing and primary antibody stain (D1)]\nHarvesting Gastruloids:", "[Fixing and primary antibody stain (D1)]\nUsing a cut P1000 tip to avoid accidental damage (cfr. \"Guidelines\"), collect Gastruloids from each well of the 96-well plate by placing the tip straight down to the bottom of each well, and aspirating up.... |
91,638 | Habituation and dishabituation (olfaction test) | 1 | dx.doi.org/10.17504/protocols.io.e6nvwdq9dlmk/v1 | https://www.protocols.io/view/habituation-and-dishabituation-olfaction-test-c5qwy5xe | Marina Lorente Picón, Núria Peñuelas, Ariadna Laguna, Miquel Vila | TITLE: Habituation and dishabituation (olfaction test)
AUTHORS: Marina Lorente Picón, Núria Peñuelas, Ariadna Laguna, Miquel Vila
[DESCRIPTION]
Habituation and dishabituation (olfaction test) for mice
[STEPS]
1. Individualize each mouse in a different cage with new bedding.
2. Present one cotton swab to the animal... | ["Individualize each mouse in a different cage with new bedding.", "Present one cotton swab to the animal for object habituation for 10 min.", "Present a second swab impregnated with water for 3 min.", "Measure the number of times the animal goes towards the second cotton swab and the time the animal spends sniffing it... |
83,495 | Immunofluorescent labeling of cultured cells | 1 | dx.doi.org/10.17504/protocols.io.eq2lyjzomlx9/v1 | https://www.protocols.click/view/immunofluorescent-labeling-of-cultured-cells-cvsfw6bn | Maryana Nissan, Divya.D.A Raj | TITLE: Immunofluorescent labeling of cultured cells
AUTHORS: Maryana Nissan, Divya.D.A Raj
[DESCRIPTION]
This protocol describes the process of Paraformaldehyde fixation [PFA-fixation] and immunofluorescent-labeling of cultured cells.
[STEPS]
1. Wash cells with 1X Phosphate-Buffered solution [1X PBS].
2. Fixate cel... | ["Wash cells with 1X Phosphate-Buffered solution [1X PBS].", "Fixate cells in 4% PFA for 15 minutes at room temperature [RT].", "Wash cells with 1X PBS twice, for 5 minutes each. Here, cells can be stored in 1X PBS at 4C for up to a week.", "Permeabilize cells with 1x PBS + 0.1% TriotonX-100 for 5 minutes at RT.", "Was... |
20,318 | Tranfection of SpCas9 containing plasmids to generate cell lines with Cas9 | null | dx.doi.org/10.17504/protocols.io.x36fqre | null | Binnypreet Kaur1, 2, Drahomíra Faktorová1, 2, Julius Lukeš1, 2, 3 | TITLE: Tranfection of SpCas9 containing plasmids to generate cell lines with Cas9
AUTHORS: Binnypreet Kaur1, 2, Drahomíra Faktorová1, 2, Julius Lukeš1, 2, 3
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>We electropoarted Spcas9 containing plasmid (pVY015) with </span><span style = "font-styl... | ["We electropoarted Spcas9 containing plasmid (pVY015) with Leishmania mexicana UTR under hygromycinselection marker as described in Protocol 7."] |
88,584 | Soil eDNA Extraction - Omega Mag-Bind / Opentrons OT-2 | 4 | null | https://www.protocols.io/view/soil-edna-extraction-omega-mag-bind-opentrons-ot-2-c2rgyd3w | Stephen Douglas Russell | TITLE: Soil eDNA Extraction - Omega Mag-Bind / Opentrons OT-2
AUTHORS: Stephen Douglas Russell
[DESCRIPTION]
This protocol uses Opentrons OT2 automation and the Omega Mag-Bind Environmental DNA 96 kit. It assumes you are starting with a dried soil sample in a 50mL tube that contains beads, per this protocol.
[STEPS]
... | ["[Initial Preparation] This protocol makes use of the Opentrons Omega Mag-Bind Environmental 96 protocol found here. \n\nThis protocol also assumes you have a dried soil sample in a 50 mL tube with beads already included per the sister sample collection protocol.", "[Sample Preparation - Omega Protocol] Place the 50 m... |
50,787 | Nanoblade production | 4 | null | https://www.protocols.io/view/nanoblade-production-bvubn6sn | maxime.smits , Simone Giovannozzi, Louise Medaer | TITLE: Nanoblade production
AUTHORS: maxime.smits , Simone Giovannozzi, Louise Medaer
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Nanoblades are virus-like particles that are able to transiently deliver a Cas9 protein together with a gRNA, without integration of DNA in the genome.</div></div>
[... | ["[DAY 0]\nSEEDING Petri-dishes (PD)", "[DAY 0]\nSeed HEK293T cells in a 10 cm PD in DMEM 2% FCS + 500 µL Gentamycin", "[DAY 0]\nIncubate on 37 °C at 5% CO2", "[DAY 1]\nTRANSFECTION of transfer, packaging, and envelop plasmids", "[DAY 1]\nBefore starting, measure the DNA concentration and the purity of the plasmids in ... |
null | null | null | dx.doi.org/10.17504/protocols.io.h68b9hw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The protocol describes the transformation of the choanoflagellate <em>Salpingoeca rosetta</em> using a Nucleofector 4d Device and SF kit from Lonza. Plasmids that use <em>S. rosetta</em> promoters and regulatory elements to drive the expression of luciferase and fluorescent p... | [] |
74,116 | Mental health, mobility and climate change: a scoping review protocol | 1 | dx.doi.org/10.17504/protocols.io.5qpvor9dbv4o/v1 | https://www.protocols.io/view/mental-health-mobility-and-climate-change-a-scopin-ckmcuu2w | Jean Marc Goudet, Faria Binte Arif, Helal Uddin Ahmed, Valery Ridde | TITLE: Mental health, mobility and climate change: a scoping review protocol
AUTHORS: Jean Marc Goudet, Faria Binte Arif, Helal Uddin Ahmed, Valery Ridde
[DESCRIPTION]
Objective:
This scoping review aims to map the knowledge gap on mental health – mobilities – climate change nexus. This will allow us to better underst... | ["[Introduction] Climate-induced (im)mobility[1]is a field that has emerged during the 70’s(1). It is deeply focused on the consequences of sudden and slow-onset climate hazards(2)on mobilities. Mobility, on the other hand, is perceived as an opportunity to adapt to environmental changes(3), but is more complex for peo... |
null | null | null | dx.doi.org/10.17504/protocols.io.tc4eiyw | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?. | [] |
53,012 | Transforming the marine bacterium Ruegeria pomeroyi using tri-parental mating | 4 | dx.doi.org/10.17504/protocols.io.yxmvmk6o6g3p/v1 | https://www.protocols.io/view/transforming-the-marine-bacterium-ruegeria-pomeroy-bxzupp6w | Cherry Gao, Christopher R. Reisch, Mary Ann Moran, Roman Stocker | TITLE: Transforming the marine bacterium Ruegeria pomeroyi using tri-parental mating
AUTHORS: Cherry Gao, Christopher R. Reisch, Mary Ann Moran, Roman Stocker
[DESCRIPTION]
This protocol describes a tri-parental mating method for transforming the model marine bacterium Ruegeria pomeroyi DSS-3 with a desired recombinan... | ["[Execution] Prepare 5 mL of the three bacterial strains for tri-parental mating:\n\n(1) wildtype R. pomeroyi (1/2 YTSS medium, 30 °C with shaking);\n\n(2) helper E. coli containing the pRK600 plasmid (LB medium amended with 15 µg/mL , 37 °C with shaking)\n\n (3) donor E. coli containing the constructed plasmid (... |
95,656 | Untargeted metabolomics of Tagless Lyso-IP | 1 | dx.doi.org/10.17504/protocols.io.kxygx3jm4g8j/v1 | https://www.protocols.io/view/untargeted-metabolomics-of-tagless-lyso-ip-c9ngz5bw | Wentao Dong, Eshaan S Rawat, Daniel Saarela, Monther Abu-Remaileh | TITLE: Untargeted metabolomics of Tagless Lyso-IP
AUTHORS: Wentao Dong, Eshaan S Rawat, Daniel Saarela, Monther Abu-Remaileh
[DESCRIPTION]
Lysosomal biology is increasingly implicated in neurodegenerative diseases and health. It has traditionally been difficult to profile the metabolomic homeostasis of the lysosome in... | ["[Untargeted metabolomics of Tagless Lyso-IP] This method is following successful isolation of lysosomes the Tagless Lyso-IP method as described\nin: dx.doi.org/10.17504/protocols.io.x54v9yp51g3e/v1 (Tagless Lyso-IP).", "[Processing of polar metabolite samples] Resuspend the lysosomes attached to the magnetic beads an... |
44,955 | How to Assign CHARMM Parameters to Desmond-generated System with viparr4 | 5 | dx.doi.org/10.17504/protocols.io.bp53mq8n | https://www.protocols.io/view/how-to-assign-charmm-parameters-to-desmond-generat-bp53mq8n | Dmitry Lupyan | TITLE: How to Assign CHARMM Parameters to Desmond-generated System with viparr4
AUTHORS: Dmitry Lupyan
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">You can use the Schrödinger software suite to prepare systems for molecular dynamics simulations, however, only the OPLS _2005 and OPLS3e force field... | ["[Setting up a Schrödinger Python Environment]\nSet up a Python Virtual EnvironmentIn order to avoid compatibility issues with the Python modules, and ensure interoperability with Schrödinger's Python modules, use the Schrödinger software to create a new virtual environment.", "[Setting up a Schrödinger Python Environ... |
18,382 | Quantitative reverse transcriptase-PCR analysis | null | dx.doi.org/10.17504/protocols.io.v7ne9me | null | Kiichi Hirota, Yoshiyuki Matsuo | TITLE: Quantitative reverse transcriptase-PCR analysis
AUTHORS: Kiichi Hirota, Yoshiyuki Matsuo
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. Total RNA was purified using RNeasy™ (Qiagen, Valencia, CA, USA).
?. For cDNA synthesis, 1 µg of total RNA was reverse transcribed using QuantiTect Reverse Transcr... | ["Total RNA was purified using RNeasy™ (Qiagen, Valencia, CA, USA).", "For cDNA synthesis, 1 µg of total RNA was reverse transcribed using QuantiTect Reverse Transcription Kit (Qiagen).", "Real-time PCR was performed using QuantiTect SYBR green PCR kit (Qiagen). PCR primers were purchased from Qiagen.", "Amplification ... |
56,799 | Multivariate Analysis of Variegated Expression in Neurons | 4 | dx.doi.org/10.17504/protocols.io.14egn78jyv5d/v1 | https://www.protocols.io/view/multivariate-analysis-of-variegated-expression-in-b3p7qmrn | Hannah M Shoenhard, Michael Granato | TITLE: Multivariate Analysis of Variegated Expression in Neurons
AUTHORS: Hannah M Shoenhard, Michael Granato
[DESCRIPTION]
Behavioral screens in model organisms have greatly facilitated the identification of genes and genetic pathways that regulate defined behaviors. Identifying the neural circuitry via which specifi... | ["[Assay phenotype of interest] Fixation\n\nFix larvae in 4% PFA in PBS + 0.25% Triton (PBS-T), overnight (O/N) at 4⁰C. Note that with MAP-mapping, quick fixation is essential due to the rapid kinematics of ERK phosphorylation, whereas since this protocol only uses tERK, exact timing of fixation is not essential for su... |
null | null | null | dx.doi.org/10.17504/protocols.io.k8iczue | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?. | [] |
56,053 | Use of haemocytometer to quantify concentration of cells' suspensions | 1 | dx.doi.org/10.17504/protocols.io.b2yvqfw6 | https://www.protocols.io/view/use-of-haemocytometer-to-quantify-concentration-o-b2yvqfw6 | abotero | TITLE: Use of haemocytometer to quantify concentration of cells' suspensions
AUTHORS: abotero
[DESCRIPTION]
This protocol presents the procedures to estimate the concentration of cells' suspensions using an hemocytometer
[GUIDELINES]
The lower limit for accurate counting of cells in a hemocytometer is usually ... | ["Wash the hemocytometer with a washer bottle and dry it using a paper towel", "Cover the hemocytometer with the coverslip and place it on a flat surface", "Vortex briefly the cell suspension whose concentration will be calculated", "Using a micropipette collect 10-100 µl of the previously agitated suspension", "Place ... |
32,592 | Novel coronavirus (2019-nCoV) real-time RT-PCR ORF1ab 2020 (Wuhan-ORF1ab; nCoV-specific test) | null | dx.doi.org/10.17504/protocols.io.bb3qiqmw | null | Judy A. Northill, Ian Mackay | TITLE: Novel coronavirus (2019-nCoV) real-time RT-PCR ORF1ab 2020 (Wuhan-ORF1ab; nCoV-specific test)
AUTHORS: Judy A. Northill, Ian Mackay
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><ul style = "list-style-type:disc;"><li style = "counter-reset:ol0;list-style-type:disc;"><span>A real-time RT-PC... | ["[Mix]\nOligonucleotides ABC1Oligo NameSequence 5'-3'Location based on NC_045512*2WuhanORF1ab-FAATCCACCTGCTCTACAAGATG5455-54763WuhanORF1ab-RCATCACCTAACTCACCTACTGTC5566-55444WuhanORF1ab-P6FAM-AGCTTCACCAGCCCTTGCTCT-BHQ15505-5485\nABC1Oligo NameSequence 5'-3'Location based on NC_045512*2WuhanORF1ab-FAATCCACCTGCTCTACAAGA... |
68,090 | Osmolality-controlled fixation and simple preparation of human red blood cells for scanning electron microscopy | 4 | dx.doi.org/10.17504/protocols.io.36wgq7xj5vk5/v1 | https://www.protocols.io/view/osmolality-controlled-fixation-and-simple-preparat-ceq2tdye | Heather N Colvin, Glen Marrs, Regina Joice Cordy | TITLE: Osmolality-controlled fixation and simple preparation of human red blood cells for scanning electron microscopy
AUTHORS: Heather N Colvin, Glen Marrs, Regina Joice Cordy
[DESCRIPTION]
Scanning electron microscopy (SEM) provides a way to visualize red blood cell (RBC) morphology. Previous methods for human RBC f... | ["Suspend human RBCs in osmolality-controlled buffer\n \n\n\n Add 25 µL of packed, washed RBCs to 500 µL osmolality-controlled buffer from Step #1\n\n Mix well with pipette, gently", "Dilute fixed, washed RBCs in dH2O \nMix RBC pellet well with pipette and add 5 µL of fixed RBC pellet to 995 µL dH2O to create at ... |
72,187 | Protocol 1: Electroporation of Agrobacterium tumefaciens with a plasmid of interest | 4 | dx.doi.org/10.17504/protocols.io.n2bvj88nwgk5/v1 | https://www.protocols.io/view/protocol-1-electroporation-of-agrobacterium-tumefa-ciq3udyn | Sarah M Prostak, Edgar M Medina, Erik Kalinka, Lillian Fritz-Laylin | TITLE: Protocol 1: Electroporation of Agrobacterium tumefaciens with a plasmid of interest
AUTHORS: Sarah M Prostak, Edgar M Medina, Erik Kalinka, Lillian Fritz-Laylin
[DESCRIPTION]
Electroporation is a widespread method of transforming competent Agrobacterium tumefaciens (Agro) cells with a plasmid containing a T-DNA... | ["[Steps] Cool the following materials on ice at least 20 min prior to starting:\n\nPlate with a lawn of wild-type Agrobacterium grown overnight at 28 °C. \nPurified plasmid(s) of interest.\nMolecular biology grade water, sterile.\n10% (v/v) glycerol, sterile.\n1.5 mL centrifuge tube(s), enough to hold the volume of Ag... |
68,877 | LRRK2 expression and purification | 1 | dx.doi.org/10.17504/protocols.io.8epv59wd4g1b/v1 | https://www.protocols.io/view/lrrk2-expression-and-purification-cfhmtj46 | Xinbo Wang, Pietro De Camilli | TITLE: LRRK2 expression and purification
AUTHORS: Xinbo Wang, Pietro De Camilli
[DESCRIPTION]
This protocol details methods for the expression of human LRRK2 in Expi293F cells and its in vitro purification.
[STEPS]
SECTION: LRRK2 expression and purification
1. Transfect the constructs encoding 3xFlag-LRRK2, 3xFlag-LR... | ["[LRRK2 expression and purification] Transfect the constructs encoding 3xFlag-LRRK2, 3xFlag-LRRK2(I2020T), 3xFlag-RCKW or 3xFlag-GFP-LRRK2 into Expi293F cells according to manufacturer instructions.", "[LRRK2 expression and purification] Express the proteins for 4320 min following induction according to manufacturer i... |
null | null | null | dx.doi.org/10.17504/protocols.io.rsyd6fw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The protocol aims explicitly to amplify RRV viruses and not other viruses.</p>
<p>Alyssa Pyke designed the original assay which was published in 2011 (see below). Subsequently, Alyssa Pyke modified the reverse primer, and it is this most recent, revised version, described her... | [] |
97,133 | ‘From women for women’: A citizen science approach engaging women in the isolation and application of the vaginal health-associated bacterium Lactobacillus crispatus | 0 | dx.doi.org/10.17504/protocols.io.81wgbzdkygpk/v1 | https://www.protocols.io/view/from-women-for-women-a-citizen-science-approach-e-da4m2gu6 | Shardelice Illidge, Remco Kort, Rosanne Hertzberger | TITLE: ‘From women for women’: A citizen science approach engaging women in the isolation and application of the vaginal health-associated bacterium Lactobacillus crispatus
AUTHORS: Shardelice Illidge, Remco Kort, Rosanne Hertzberger
[DESCRIPTION]
A vaginal microbiome rich in Lactobacillus crispatus is associated with... | ["[Practicals] Participants received an online questionnaire (Supplemental file 3: Appendix C. Participation in the crispatus Study - Questionnaire, that focused on hormonal aspects, and a sampling kit at their home address containing:", "[Practicals] Two sample collection tubes. One for metagenomic sampling (with DNA/... |
99,868 | Fresh 4% Paraformaldehyde in PBS | 1 | dx.doi.org/10.17504/protocols.io.x54v9mwnmg3e/v2 | https://www.protocols.io/view/fresh-4-paraformaldehyde-in-pbs-ddr4258w | Allen Institute for Brain Science | TITLE: Fresh 4% Paraformaldehyde in PBS
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
Freshly prepared 4% Paraformaldehyde in PBS is used to fix adult and developing mouse brains during the transcardial perfusion process, as well as for immersion fixation. This solution can be used for no more than one wee... | [] |
85,587 | Gavage - food supplementation for stalled weight gain in mice | 4 | dx.doi.org/10.17504/protocols.io.n2bvj36jxlk5/v1 | https://www.protocols.click/view/gavage-food-supplementation-for-stalled-weight-gai-cxttxnnn | taylor.panczyk | TITLE: Gavage - food supplementation for stalled weight gain in mice
AUTHORS: taylor.panczyk
[DESCRIPTION]
In mice, specifically in Ndufs2fl/fl mice, weight gain usually stops above 70 days post injecton with the TH-Cre AAV into SNc. From that point, food supplements should be provided once daily via a gavage of 0.4-0... | ["[Gavage] Provide light anesthesia with isoflurane.", "[Gavage] Once the animals are ready we look to put the feeding tube behind its tongue.", "[Gavage] Once there, we place the feeding tube parallel to the animal with a light hyperextension, in this manner the feeding tube will get into the stomach with no effort**\... |
21,283 | Yale - Beta hydroxybutyrate (Cobas) | null | dx.doi.org/10.17504/protocols.io.y2bfyan | null | Gary Cline, John Stack | TITLE: Yale - Beta hydroxybutyrate (Cobas)
AUTHORS: Gary Cline, John Stack
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">Procedure used to determine the concentration of β-Hydroxybutyrate in blood, serum, and plasma.... | ["Calibrate Cobas for β-Hydroxybutyrate by running a β-Hydroxybutyrate standard and three ß-Hydroxybutyrate controls.", "Sample handling as performed by the Cobas Mira Plus. a) Pipette 3 µL of sample into cuvette. b) Add 105µL of ß-Hydroxybutyrate Reagent. c) Mixture is incubated at 37˚C for 10 minutes. d) ... |
null | null | null | dx.doi.org/10.17504/protocols.io.q6cdzaw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol can be used to dissociate adult human kidney “on ice” - maintaining authentic gene expression profiles. It was designed using a mix of Collagenases (Type 4, and A) which provide broad proteolytic activity, but preferentially cleave extracellular bonds, largely l... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.cgwtxd | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Protocol for blunting ends by 3' overhang removal and fill-in of 3' recessed (5' overhang) ends using T4 DNA Polymerase.
[GUIDELINES]
CAUTION: Elevated temperatures, excessive amounts of enzyme, failure to supplement with dNTPs or long reaction times will result in recessed end... | [] |
51,280 | Processamento de actígrafos para armazenamento - ActTrust | 5 | dx.doi.org/10.17504/protocols.io.bwbqpamw | https://www.protocols.io/view/processamento-de-act-grafos-para-armazenamento-act-bwbqpamw | Daniel Vartanian | TITLE: Processamento de actígrafos para armazenamento - ActTrust
AUTHORS: Daniel Vartanian
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Este protocolo faz parte do processo de coleta de dados actigráficos do Grupo Interdisciplinar de Pesquisa em Sono (GIPSO). Ele foi desenhado para os actí... | ["[Kanban]\nAdicione o cartão da tarefa no quadro de trabalho do seu projeto (somente para projetos que usam Kanban)\nAbra o quadro de trabalho de seu projeto e adicione um cartão chamado Realizar o processamento de actígrafos para armazenamento na lista Em andamento.No cartão, adicione uma etiqueta chamada Processamen... |
69,898 | Stone Tools Illustrations with Vector Art: The 'STIVA' Method | 1 | dx.doi.org/10.17504/protocols.io.cghitt4e | https://www.protocols.io/view/stone-tools-illustrations-with-vector-art-the-39-s-cghitt4e | Jacopo Niccolo Cerasoni | TITLE: Stone Tools Illustrations with Vector Art: The 'STIVA' Method
AUTHORS: Jacopo Niccolo Cerasoni
[DESCRIPTION]
Lithic illustrations are often used in scientific publications to efficiently communicate the technological and morphological characteristics of stone tools. They offer invaluable information and... | ["[Photograph Artefact] Lock camera on a tripod (ideally use a macro lens with a focal length of between 90mm to 105mm) and place in light box (if available).", "[Photograph Artefact] Place artefact flat onto the workspace.", "[Photograph Artefact] If the artefact does not sit flat due to its irregular shape, use an ap... |
null | null | null | dx.doi.org/10.17504/protocols.io.s4hegt6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Since 2012, numerous single-cell RNA sequencing (scRNA-seq) technologies have been introduced. Most involve either significant startup cost, an expert operator, or expensive library preparation. We developed a plate-based library prep that incorporates pre-amplification pooli... | [] |
69,610 | MTT assay on 96 well plate | 4 | dx.doi.org/10.17504/protocols.io.6qpvr4x5pgmk/v1 | https://www.protocols.io/view/mtt-assay-on-96-well-plate-cf8itrue | Adita Ayu Permanasari | TITLE: MTT assay on 96 well plate
AUTHORS: Adita Ayu Permanasari
[DESCRIPTION]
MTT assay to measure viability cells
[STEPS]
1. Prepare sample in DMSO
2. Observe cell on the plate, make a note about cells condition
3. Experiment by make a serial dilution sample in U-Type, suspend 40 times
4. Remove old medium from cel... | ["Prepare sample in DMSO", "Observe cell on the plate, make a note about cells condition", "Experiment by make a serial dilution sample in U-Type, suspend 40 times", "Remove old medium from cells", "Put 100 μl/well sample and DMSO, incubate 48 h, 37 oC", "Observe condition cells after 48 h incubation", "Checked toxicit... |
53,258 | Virus Concentration from Wastewater Using PEG Precipitation and Ultracentrifugation | 4 | dx.doi.org/10.17504/protocols.io.bx9ipr4e | https://www.protocols.io/view/virus-concentration-from-wastewater-using-peg-prec-bx9ipr4e | Jacquelina.Woods , rachel.rodriguez | TITLE: Virus Concentration from Wastewater Using PEG Precipitation and Ultracentrifugation
AUTHORS: Jacquelina.Woods , rachel.rodriguez
[DESCRIPTION]
This method was developed at the FDA’s Center for Food Safety and Applied Nutrition for GenomeTrakr’s pandemic response project, monitoring SARS-CoV-2 variants in was... | ["[Virus concentration] Place 800 mLof wastewater into an 1L centrifuge bottle.", "[Virus concentration] Add 200 µL of extraction control (concentration of 102 per mL), as described here: Preparation of Murine Norovirus for Use as an Extraction Control for Concentration of Viruses from Wastewater (protocols.io).", "[Vi... |
95,286 | LUHMES (lund human mesencephalic) culturing and differentiation protocol | 4 | dx.doi.org/10.17504/protocols.io.kxygx36ykg8j/v3 | https://www.protocols.io/view/luhmes-lund-human-mesencephalic-culturing-and-diff-c9awz2fe | Mallory Wright, William J Buchser, ckremitz, jwaligor, bachman@wustl.edu, serenaelia@wustl.edu | TITLE: LUHMES (lund human mesencephalic) culturing and differentiation protocol
AUTHORS: Mallory Wright, William J Buchser, ckremitz, jwaligor, bachman@wustl.edu, serenaelia@wustl.edu
[STEPS]
SECTION: LUHMES coating protocol
1.
0.1 mg/mL
50 µg/µL
Thaw an aliquot of Poly-L-Ornithine solution at room temperature.
SECT... | ["[LUHMES coating protocol] 0.1 mg/mL\n50 µg/µL\nThaw an aliquot of Poly-L-Ornithine solution at room temperature.", "[LUHMES Passaging (~ every 2-3 days)] use a 5mL pipette to Triturate cells only 1 or 2 times before seeding.", "[LUHMES Passaging (~ every 2-3 days)] Discard the supernatant and resuspend in 1mL LUHMES ... |
null | null | null | dx.doi.org/10.17504/protocols.io.dsg6bv | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Hybridized Chain Reaction Fluroescent <em>In Situ</em> Hybridization for squid tissue and colonized <em>V. fischeri</em>.
[STEPS]
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null | null | null | dx.doi.org/10.17504/protocols.io.khfct3n | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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null | null | null | dx.doi.org/10.17504/protocols.io.hntb5en | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Describes novel low conductivity media and multipulse electroporation protocol using a NEPA21 Type II pulse generator with settings optimized to balance transfection efficiency with cell viability for this marine diatom. </p>
[BEFORE_START]
<p>Pseudo nitzschia multiseries cu... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.inzcdf6 | null | null | TITLE: No Title
AUTHORS:
[BEFORE_START]
<p>You will need to make the 20 mL of Lysis Buffer prior to running this protocol.</p>
[STEPS]
?.
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?.
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?.
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?.
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null | null | null | dx.doi.org/10.17504/protocols.io.qx7dxrn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol is kit-free and can be used to isolate high quality genomic DNA of predominantly Aiptasia from symbiotic anemones which can be used e.g. as PCR template for genotyping.</p>
<p> </p>
<p>It is based on the method described in Coffroth et al., 1992.</p>
[BEFORE_ST... | [] |
86,385 | Image processing of full-length monomeric LRRK2 | 5 | dx.doi.org/10.17504/protocols.io.dm6gp3j4dvzp/v1 | https://www.protocols.io/view/image-processing-of-full-length-monomeric-lrrk2-cykrxuv6 | Jaime Alegrio Louro, Amalia Villagran Suarez, Marta Sanz Murillo, Andres Leschziner | TITLE: Image processing of full-length monomeric LRRK2
AUTHORS: Jaime Alegrio Louro, Amalia Villagran Suarez, Marta Sanz Murillo, Andres Leschziner
[DESCRIPTION]
This protocol assumes that 2000 to 4000 movies of full-length LRRK2 embedded on vitreous ice are collected with an electron microscope equipped with a direct... | ["After movie alignment and CTF estimation (Patch Motion Correction and Patch CTF Estimation jobs in CryoSPARC), discard the micrographs with an estimated resolution worse than 4.5-5 Å.", "We often perform these image pre-processing steps while the movies are being recorded, using CryoSPARC Live.", "Initially pick your... |
null | null | null | dx.doi.org/10.17504/protocols.io.h3rb8m6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><span class="" lang="en"><span class="">This three-way holding dilution offers some advantages such as preserving the quality of the initial product, preventing waste with contamination and rationalizing the use.</span></span></p>
[STEPS]
?.
?.
?. | [] |
41,521 | Recombinant protein expression and purification of codon-optimized Bst-LF polymerase | 4 | dx.doi.org/10.17504/protocols.io.bksrkwd6 | https://www.protocols.io/view/recombinant-protein-expression-and-purification-of-bksrkwd6 | Maira Rivera, Severine Cazaux, Ariel Cerda, Anibal Arce Medina, Isaac Núñez, Tamara Matute, Alex Brown, Javier Gasulla, Fernan Federici, Cesar A Ramirez-Sarmiento | TITLE: Recombinant protein expression and purification of codon-optimized Bst-LF polymerase
AUTHORS: Maira Rivera, Severine Cazaux, Ariel Cerda, Anibal Arce Medina, Isaac Núñez, Tamara Matute, Alex Brown, Javier Gasulla, Fernan Federici, Cesar A Ramirez-Sarmiento
[DESCRIPTION]
<div class = "text-blocks"><div class = "... | ["[DAY 1 – Plasmid transformation]\nTransform of pET15b plasmid containing codon-optimized Bst-LF polymerase into E. coli C41 competent cells using either heat shock or electroporation.\n100 ng", "[DAY 1 – Plasmid transformation]\nSpread transformed cells in LB Agar plates supplemented with Amp. Grow plate overnight at... |
86,212 | Reverse-phase high pH fractionation (using Thermo Fisher, Cat# 84868) | 4 | dx.doi.org/10.17504/protocols.io.yxmvm32bnl3p/v1 | https://www.protocols.io/view/reverse-phase-high-ph-fractionation-using-thermo-f-cyfcxtiw | Louise Uoselis | TITLE: Reverse-phase high pH fractionation (using Thermo Fisher, Cat# 84868)
AUTHORS: Louise Uoselis
[DESCRIPTION]
This protocol uses the Pierce™ High pH Reversed-Phase Peptide Fractionation Kit (Thermo Fisher, Cat# 84868)
[STEPS]
SECTION: Conditioning the columns
1. Remove the white cap on the end of the column and ... | ["[Conditioning the columns] Remove the white cap on the end of the column and place the column in a 2 mL collection tube.", "[Conditioning the columns] Centrifuge at 5000 rcf, 2 min at Room temperature, discard the liquid.", "[Conditioning the columns] Remove the screw cap and add 300 µL acetonitrile (ACN) to the colu... |
82,947 | TIANprep Mini Plasmid Kit Protocol | 4 | dx.doi.org/10.17504/protocols.io.dm6gpj4n5gzp/v2 | https://www.protocols.click/view/tianprep-mini-plasmid-kit-protocol-cu9bwz2n | TIANGEN Biotech | TITLE: TIANprep Mini Plasmid Kit Protocol
AUTHORS: TIANGEN Biotech
[DESCRIPTION]
TIANprep Mini Plasmid Kit is based on alkaline lysis technology followed by adsorption of DNA onto silica membrane in the presence of high salt. Plasmid DNA purified with TIANprep Mini Plasmid Kit is immediately readyfor use. Phenol extra... | ["[Preparation of Bacterial Cells] Centrifiguation of 1-5 mL of bacterial cells in a microcentrifuge tube at 12000 rpm, 1 min", "[Preparation of Bacterial Cells] Direct drainage of supernatant by opening and inverting the tube.", "[Preparation of Bacterial Cells] Complete resuspension of the bacteria pellet in 250 µL... |
68,476 | Transforming E. coli (Instructor protocol) | 4 | null | https://www.protocols.io/view/transforming-e-coli-instructor-protocol-ce44tgyw | Brian Teague | TITLE: Transforming E. coli (Instructor protocol)
AUTHORS: Brian Teague
[DESCRIPTION]
This is the instructor protocol for
Setup for this lab can be pretty intensive if you're starting from scratch. It requires:
Competent E. coli
LB-agar + kanamycin plates
SOC outgrowth media
Notably, commercial competent E. col... | ["[Prepare kanamycin stock solution] Weigh 0.5 g of into a 15 ml conical centrifuge tube.", "[Pour LB-agar + kanamycin plates] Fill a 1 liter screw-cap bottle with approximately 900 mL of deionized water.", "[Pour LB-agar + kanamycin plates] Add water to a total volume of 1 L (eyeballing is OK, no need to dirty a gra... |
80,711 | Total Starch Enzymatic Digestion | 1 | null | https://www.protocols.io/view/total-starch-enzymatic-digestion-cs3fwgjn | Lynn Doran, Amanda P. De Souza | TITLE: Total Starch Enzymatic Digestion
AUTHORS: Lynn Doran, Amanda P. De Souza
[DESCRIPTION]
Enzymatic digestion of total soluble starch to glucose in plant tissue extracts for preparation for quantification via the GOD-POD Method (NZYtech).
[BEFORE_START]
Extract and dry total starch pellet from plant tissue per... | ["Prepare fresh daily 120 U/mL α-amylase (Bacillus licheniformis) in MOPS buffer. 1 mL per sample will be needed. Initial concentration of α-amylase is 3000 U/mL. Use C1V1 = C2V2 to calculate the volume of α-amylase and MOPS buffer to use.", "Prepare fresh daily 30 U/mL amyloglucosidase (Aspergillus niger) in acetate... |
22,831 | High resolution labeling of vagal afferent fibers using Dextran-Biotin with counterstaining | null | dx.doi.org/10.17504/protocols.io.2ipgcdn | null | Terry Powley, Jennifer McAdams, Robert Phillips | TITLE: High resolution labeling of vagal afferent fibers using Dextran-Biotin with counterstaining
AUTHORS: Terry Powley, Jennifer McAdams, Robert Phillips
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the methods used to trace and enable morphometric quantification of vaga... | ["[Animals]\nTwo- to four-month-old malerats in the weight range of 180g to 360g at the time of tracer injection were housed individually in wire hanging cages or in vented rack plastic cages in an Association for Assessment and Accreditation of Laboratory Animal Care-approved temperature (22–24 °C) and humidity (40–60... |
61,105 | Ringer's Solution | 6 | dx.doi.org/10.17504/protocols.io.8epv59e16g1b/v1 | https://www.protocols.click/view/ringer-39-s-solution-b7wrrpd6 | Mark Ellisman, Mason Mackey, Eric Bushong, Marianne Martone, Thomas Deerinck | TITLE: Ringer's Solution
AUTHORS: Mark Ellisman, Mason Mackey, Eric Bushong, Marianne Martone, Thomas Deerinck
[DESCRIPTION]
Standard protocol for preparing 100mL of Ringer's Solution for mice and rat perfusions.
[GUIDELINES]
Make sure you bubble for at least 5 minutes before adding calcium chloride to Ringer's ... | ["1.0 mL (Na2HPO4, 18 g/L, at room temperature)", "9.9 mL (NaCl, 79.8 g/L, 4 ºC fridge)", "1.0 mL (KCl, 37.5 g/L, 4 ºC fridge)", "1.0 mL (MgCl2• 6H2O, 20 g/L, 4 ºC fridge)", "2.5 mL (NaHCO3, 50 g/L, 4 ºC fridge)", "0.200g of Dextrose", "1.0 ml Lidocaine hydrochloride", "1.0 ml heparin (prevents blood clotting) \n —b... |
99,771 | Mouse perfusion | 0 | dx.doi.org/10.17504/protocols.io.eq2lyw77pvx9/v1 | https://www.protocols.io/view/mouse-perfusion-ddn325gn | Bryan Killinger | TITLE: Mouse perfusion
AUTHORS: Bryan Killinger
[DESCRIPTION]
General protocol for mouse perfusion fixation.
[STEPS]
1. Anesthetize mouse using mixture of ketamine and xylazine. (Ketamine = 100mg ketamine / kg bodyweight, 10mg xylazine / kg bodyweight)
2. Ensure deep anesthesia with paw pinch. Mouse should not respo... | ["Anesthetize mouse using mixture of ketamine and xylazine. (Ketamine = 100mg ketamine / kg bodyweight, 10mg xylazine / kg bodyweight)", "Ensure deep anesthesia with paw pinch. Mouse should not respond.", "Using four 26g needles, secure mouse paws to corkboard.", "Make an incision along the abdomen, extending up to the... |
90,789 | Stereotaxic Injection by Nanoject Protocol | 1 | dx.doi.org/10.17504/protocols.io.bp2l6nr7kgqe/v4 | https://www.protocols.io/view/stereotaxic-injection-by-nanoject-protocol-c4wdyxa6 | Allen Institute for Brain Science | TITLE: Stereotaxic Injection by Nanoject Protocol
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
This protocol describes the delivery of a neuronal tracer using the Nanoject II. The surgery uses a stereotaxic system to target specific brain coordinates in the mouse.
Note: Research reported in this publicat... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.iaecabe | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol provides an efficient DNA extraction and purification of ancient sorft tissue. </p>
[BEFORE_START]
<p>Clean</p>
[STEPS]
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?.
?.
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?. | [] |
101,276 | Immunoprecipitation | 0 | dx.doi.org/10.17504/protocols.io.5jyl822z7l2w/v1 | https://www.protocols.io/view/immunoprecipitation-de543g8w | Agnes Roczniak-Ferguson, Shawn M. Ferguson | TITLE: Immunoprecipitation
AUTHORS: Agnes Roczniak-Ferguson, Shawn M. Ferguson
[DESCRIPTION]
This protocol details the immunoprecipitation of Hela cells.
[STEPS]
1. Seed Hela cells into 150 mm dishes at a density of 1.9 million cells. The cells will be near confluent in 2 days. Otherwise seeding 4x106 of cells/150 ... | ["Seed Hela cells into 150 mm dishes at a density of 1.9 million cells. The cells will be near confluent in 2 days. Otherwise seeding 4x106 of cells/150 mm dish will be near confluent the next day. Expect to get 3-5 mg of protein per dish. These numbers will be different for other cell lines and will have to be det... |
26,543 | UC Davis - Immunohistochemistry IBA1 | null | dx.doi.org/10.17504/protocols.io.56pg9dn | null | Jennifer Rutkowsky | TITLE: UC Davis - Immunohistochemistry IBA1
AUTHORS: Jennifer Rutkowsky
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">Ionized calcium-binding adapter molecule 1 (IBA1) is specifically expressed in macrophages / micr... | ["Immunohistochemistry was performed on four-micron thick, formalin-fixed, paraffin-embedded tissue sections, mounted on charged slides, and air-dried overnight at 37ºC.", "Sections were deparaffinized through xylene to 100% reagent alcohol, and then treated with 0.3% hydrogen peroxide in 100% methanol for 30 minutes."... |
92,134 | Preparation of fresh paraformaldehyde for mouse perfusion and tissue fixation | 4 | dx.doi.org/10.17504/protocols.io.6qpvr3qbbvmk/v1 | https://www.protocols.io/view/preparation-of-fresh-paraformaldehyde-for-mouse-pe-c58ey9te | thnasko | TITLE: Preparation of fresh paraformaldehyde for mouse perfusion and tissue fixation
AUTHORS: thnasko
[DESCRIPTION]
Hnasko lab - preparation of fresh PFA for ms perfusion and tissue fixation
[STEPS]
1. 1. For 1 Lof 4% paraformaldehyde, warm up 700 mLof ddH2O in a glass beaker using microwave until 40-60 °C.
2. 2. Pl... | ["1.\tFor 1 Lof 4% paraformaldehyde, warm up 700 mLof ddH2O in a glass beaker using microwave until 40-60 °C.", "2.\tPlace on heated stir plate in a chemical fume hood, add a magnetic stir bar and start stirring and insert thermometer into solution.", "3.\tWeigh 40 g of granular paraformaldehyde (PFA, EMS, cat# 19210).... |
61,985 | PBMCs isolation from CPT™ tube | 1 | dx.doi.org/10.17504/protocols.io.kxygxeqr4v8j/v2 | https://www.protocols.io/view/pbmcs-isolation-from-cpt-tube-b8r9rv96 | Woong-Yang Park, Jay Shin, Shyam Prabhakar | TITLE: PBMCs isolation from CPT™ tube
AUTHORS: Woong-Yang Park, Jay Shin, Shyam Prabhakar
[DESCRIPTION]
This protocol details the procedure for collection and isolation of blood samples using CPT tubes.
[BEFORE_START]
The BD Vacutainer® CPT™ Tube (Cat. no.362753) should be at Room temperature (18-25ºC) and prope... | ["[PBMCs isolation from CPT™ tube] Mix the blood sample immediately prior to centrifugation by gently inverting the tube 8 to 10 times.", "[PBMCs isolation from CPT™ tube] Centrifuge the CPT tube at 1500 rcf (Relative Centrifugal Force) in a horizontal rotor (swing-out head) for 30 min at 20 °C (Speed change of accel/d... |
36,579 | Glycine-HCl Buffer | null | dx.doi.org/10.17504/protocols.io.bfybjpsn | https://www.protocols.io/view/glycine-hcl-buffer-bfybjpsn | Neilier Junior | TITLE: Glycine-HCl 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 for enzymati... | ["[Glycine-HCl Buffer]\nMix and indicated volume of hydrochloric acid. ABCDEFGHI1mL of HCl44.032.424.216.811.48.26.43.62pH2.22.42.62.83.03.23.43.6\npH range: to (a) 0.1 M Glycine: 7.5 g L-1 (M.W.: 75.0 g mol-1)(b) 0.1 M Hydrochloric acid\n[glycine]\nABCDEFGHI1mL of HCl44.032.424.216.811.48.26.43.62pH2.22.42.62.83... |
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