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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95,761 | PROTEIN INJECTION PROTOCOL | 0 | dx.doi.org/10.17504/protocols.io.dm6gp3738vzp/v1 | https://www.protocols.io/view/protein-injection-protocol-c9rrz556 | Scott Vermilyea | TITLE: PROTEIN INJECTION PROTOCOL
AUTHORS: Scott Vermilyea
[DESCRIPTION]
This protocol details the injection parameters of the protein.
[STEPS]
SECTION: Injection Parameters
1. Stereotaxic coordinates:
SECTION: Injection Parameters
1.1. Intracortical/Intrastriatal (IC/IS): 2.0 mm lateral from the midline, +0.2 mm rel... | ["[Injection Parameters] Stereotaxic coordinates:", "[Injection Parameters] Intracortical/Intrastriatal (IC/IS): 2.0 mm lateral from the midline, +0.2 mm relative to bregma, and 0.8 and 2.6 mm deep from the dura.", "[Injection Parameters] Brainstem: 0.2 mm lateral from the midline, -7.34 mm from bregma, 3.75 mm deep fr... |
19,843 | Preparing single-cell suspension from human embryo/fetus | null | dx.doi.org/10.17504/protocols.io.xmbfk2n | null | Sten Linnarsson, Emelie Braun | TITLE: Preparing single-cell suspension from human embryo/fetus
AUTHORS: Sten Linnarsson, Emelie Braun
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol for human embryo/fetal tissue handling and dissociation, suitable for subsequent single-cell RNA sequencing and in situ hybridization.</div>... | ["[Preparations]\nOxygenate Earl's Balanced Salt Solution (EBSS) by bubbling with 95% O2:5% CO2 on ice for 5-10 min (until appropriate pH is reached).", "[Preparations]\nAdd 5 mL EBSS to Papain vial, dissolve at , then move to room temperature (RT).\nFor embryonic/foetal heart dissociation, 5 mL of collagenase II is us... |
92,328 | OT-2 Modular Cloning Construct Assembly | 1 | dx.doi.org/10.17504/protocols.io.5jyl8p82rg2w/v1 | https://www.protocols.io/view/ot-2-modular-cloning-construct-assembly-c6egzbbw | Ana Mariya Anhel, Lorea Alejaldre, Ángel Goñi-Moreno | TITLE: OT-2 Modular Cloning Construct Assembly
AUTHORS: Ana Mariya Anhel, Lorea Alejaldre, Ángel Goñi-Moreno
[DESCRIPTION]
This protocol is meant to create modular cloning constructs from different parts into a final plate and, optionally, perform the temperature profile needed to the assembly of the constructs.
The ... | ["[Files Preparation] Preparing Customized Template\n\nPreparing the template (a .xlsx) with the specific variables for each experiment.\n\nHere there is attached a template of the variable file with several sheets and a PDF file explaining each variable:\nGeneralVariables: variables related mainly to the labware that ... |
32,766 | mrdA deletion strain | 1 | null | https://www.protocols.io/view/mrda-deletion-strain-bb86irze | Wolfram Moebius | TITLE: mrdA deletion strain
AUTHORS: Wolfram Moebius
[DESCRIPTION]
Making mrdA deletion DH5α strain
- Amplification of PCR product to replace mrdA sequence in the genome (Kan_VcmrdA fragment amplified from pWW308_VcmrdA plasmid). PCR product has homology with EcmrdA sequence at 5' and 3' ends for homologous recombin... | ["[Transform cells with pSIM5 construct] Streak DH5α cells onto LB agar plate and incubate at 37 °C \nInoculate LB with one colony from strain DH5α\nTransform chemically competent cells (Invitrogen) with pSIM5 plasmid\nAdd 1 µL to 100 µL in a 1.5ml eppendorf tube\non ice 30 min \nHeat shock at 42 °C (in a water bath) ... |
76,481 | Soil organic carbon stocks and change protocol | 1 | null | https://www.protocols.io/view/soil-organic-carbon-stocks-and-change-protocol-cnw9vfh6 | SCarolina Córdova, Curtis Dell, Mark Liebig, Michel A Cavigelli, Phil Robertson | TITLE: Soil organic carbon stocks and change protocol
AUTHORS: SCarolina Córdova, Curtis Dell, Mark Liebig, Michel A Cavigelli, Phil Robertson
[DESCRIPTION]
The change in soil organic carbon (SOC) over time serves as an integrated indicator of carbon (C) balance in cropping systems and as an integral metric of soil he... | ["[Sample Collection] Collect whole-profile soil samples at 1 m depth at decadal intervals (or for shallower soils to the depth of parent material) or for surface soils only, at 0-25 cm or 0-30 cm depth at shorter intervals. In cropping systems, take samples post-harvest (late fall or early winter) or pre-planting (ear... |
73,986 | Skin Biopsy Protocol (Mammals): Non-lethal Sampling | 1 | dx.doi.org/10.17504/protocols.io.n2bvj64nxlk5/v3 | https://www.protocols.io/view/skin-biopsy-protocol-mammals-non-lethal-sampling-ckhaut2e | sanaz.arenivas, justin_bohling, comizzolip, mhouck, racheljohnston, Jacquelyn Mountcastle, Budhan Pukazhenthi, phil.purdy, brian_small, seth_willey | TITLE: Skin Biopsy Protocol (Mammals): Non-lethal Sampling
AUTHORS: sanaz.arenivas, justin_bohling, comizzolip, mhouck, racheljohnston, Jacquelyn Mountcastle, Budhan Pukazhenthi, phil.purdy, brian_small, seth_willey
[DESCRIPTION]
Version date: January 2023
The following protocol illustrates how to collect and ship li... | ["[Preparation] Pre-chill icepacks in the freezer the day before planning to collect and ship samples.", "[Preparation] Record all information indicated in the biopsy form, including a picture of the animal for identification and GPS location where the animal was found.", "[Preparation] For general sedation, anesthetiz... |
57,187 | Bogus protocols: test access to process & material info | 1 | dx.doi.org/10.17504/protocols.io.b34bqqsn | https://www.protocols.io/view/bogus-protocols-test-access-to-process-amp-materia-b34bqqsn | Abby Moore | TITLE: Bogus protocols: test access to process & material info
AUTHORS: Abby Moore
[DESCRIPTION]
The purpose of this protocol is to test accessing the material and process components and icons.
[STEPS]
SECTION: This is the first section
1. In this step, I'll use the centrifugation component and icon.
37000 rcf... | ["[This is the first section] In this step, I'll use the centrifugation component and icon.\n\n37000 rcf, 2 min, -20 °C", "[This is the first section] In this step, I'll use the shaker component.", "[This is the first section] In this substep, I'll use the incubation icon.", "[This is the first section] In this step, I... |
41,943 | Learn Partial Correlation Disease-Specific Networks | 5 | dx.doi.org/10.17504/protocols.io.bk7xkzpn | https://www.protocols.io/view/learn-partial-correlation-disease-specific-network-bk7xkzpn | Lillian Thistlethwaite | TITLE: Learn Partial Correlation Disease-Specific Networks
AUTHORS: Lillian Thistlethwaite
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes how to construct disease-specific network structures as described in Thistlethwaite et al. (2020). </div><div class = "text-block">Thistl... | ["[Prepare dataset]", "[Prepare dataset]\nLearn disease-specific network folds for three different network learning paradigms for 5 disease states (citrullinemia, maple syrup urine disease, methylmalonic aciduria, propionic aciduria, phenylketonuria):i) latent embedding + network pruning (\"ind\")ii) latent embeddin... |
34,076 | SU transfer 2088 test | null | dx.doi.org/10.17504/protocols.io.bdh4i38w | null | Masha Test Acc | TITLE: SU transfer 2088 test
AUTHORS: Masha Test Acc
[STEPS]
?. transfer
?. test | ["transfer", "test"] |
81,480 | Refractive Index Matching - EasyIndex | 1 | dx.doi.org/10.17504/protocols.io.kxygx965kg8j/v1 | https://www.protocols.io/view/refractive-index-matching-easyindex-cttgwnjw | Holly Myers, Daphne Toglia | TITLE: Refractive Index Matching - EasyIndex
AUTHORS: Holly Myers, Daphne Toglia
[DESCRIPTION]
This protocol is modified from the Index Matching protocol found in the LifeCanvas Technologies Full Active Pipeline Protocol (see references). At the end of this process, the specimen should have the same refractive index a... | ["[LifeCanvas Index Matching] Shake bottle of LifeCanvas EasyIndex well to homogenize the solution. Let the bottle sit for 30 min to allow any bubbles to settle.", "[LifeCanvas Index Matching] Using a serological pipet, create 20mL of 50% EasyIndex by measuring 10mL of nuclease free water and 10mL of LifeCanvas EasyInd... |
62,528 | RMX MALE ENHANCEMENT IF YOU ARE STRUGGLING LOW DRIVE, MINIMAL ERECTION, POOR LIBIDO! Click Here!! | 3 | dx.doi.org/10.17504/protocols.io.5jyl896wdv2w/v1 | https://www.protocols.io/view/rmx-male-enhancement-if-you-are-struggling-low-dri-b9a8r2hw | jodynoory | TITLE: RMX MALE ENHANCEMENT IF YOU ARE STRUGGLING LOW DRIVE, MINIMAL ERECTION, POOR LIBIDO! Click Here!!
AUTHORS: jodynoory
[DESCRIPTION]
RMX Male Enhancement
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.erdbd26 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
For use in <a href="https://www.protocols.io/view/Polyacrylamide-Gel-System-For-Electrophoresis-Of-P-ep7bdrn" target="_blank">Polyacrylamide Gel System For Electrophoresis Of Proteins</a>.
[STEPS]
?.
?.
?. | [] |
95,823 | MINECRAFTseq V1 | 0 | null | https://www.protocols.io/view/minecraftseq-v1-c9tpz6mn | Yuriy Baglaenko | TITLE: MINECRAFTseq V1
AUTHORS: Yuriy Baglaenko
[DESCRIPTION]
Genetic studies have identified thousands of individual disease-associated non-coding alleles, but identification of the causal alleles and their functions remain critical bottlenecks. Even though CRISPR-Cas editing has enabled targeted modification of DNA,... | ["[Lysis plate generation] In a PCR clean hood, prepare a lysis mix containing the following reagents: \n \n\n \n\nSeal the plates with an aluminum PCR seal and spin down for 1 minute at 1000g, 4°C.\n\nProceed immediately to the next step or store the plate on ice to avoid denaturing of Recombinant RNase Inhibitor.\nFo... |
null | null | null | dx.doi.org/10.17504/protocols.io.gwibxce | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div class="page" title="Page 1">
<div class="layoutArea">
<div class="column">
<p>This is a complete apoptosis assay example. It details the seeding, induction, and detection of the HeLa cellular response to Anisomycin treatment.</p>
<p> </p>
<p><strong>Developed for:</strong><... | [] |
68,152 | DNA extraction using the Qiagen 67563 MagAttract HMW DNA Kit (48) | 4 | dx.doi.org/10.17504/protocols.io.5jyl89428v2w/v1 | https://www.protocols.io/view/dna-extraction-using-the-qiagen-67563-magattract-h-cesytefw | Murray Grant, Shannon Greer, Joana Vicente | TITLE: DNA extraction using the Qiagen 67563 MagAttract HMW DNA Kit (48)
AUTHORS: Murray Grant, Shannon Greer, Joana Vicente
[DESCRIPTION]
This protocol is for extraction of genomic DNA from Xanthomonas culture for DNA sequencing.
[STEPS]
1. Heat the mixer (e.g., Eppendorf Thermomixer or an equivalent mixer) to 56°C ... | ["Heat the mixer (e.g., Eppendorf Thermomixer or an equivalent mixer) to 56°C for the lysis step.", "If precipitate has formed in Buffer ATL, dissolve by incubating at 37°C with occasional shaking.", "Ensure that 96 - 100 % ethanol is added to buffers MW1 and PE.", "Before proceeding to next step, ensure that the magne... |
109,185 | Sinai SCENT TMC - 5x5 Project Mouse Harvesting | 0 | dx.doi.org/10.17504/protocols.io.dm6gpzp5dlzp/v1 | https://www.protocols.io/view/sinai-scent-tmc-5x5-project-mouse-harvesting-dnu95ez6 | Sojin Kim | TITLE: Sinai SCENT TMC - 5x5 Project Mouse Harvesting
AUTHORS: Sojin Kim
[DESCRIPTION]
We propose a total of 10 C57BL/6 mice (5 males and 5 females) to be studied for each study group or cellular senescence inducer intervention.
[STEPS]
SECTION: Experimental Design
1. Males and females are grouped and housed in stand... | ["[Experimental Design] Males and females are grouped and housed in standard cages, provided LabDiet 5K0G and acidified water ad libitum. Euthanasia is performed by cervical dislocation (CMQ93-26).\n\nControl: Tissues collected at 32 weeks.\nDoxorubicin: IP injection (5 mg/kg) at 26 weeks on days 0 and 10, with tissue ... |
null | null | null | dx.doi.org/10.17504/protocols.io.f8qbrvw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol provides a procedure to generate taxonomic data from assembled contigs using centrifuge. </p>
[GUIDELINES]
<p><a href="http://www.ccb.jhu.edu/software/centrifuge/manual.shtml" target="_blank">Centrifuge documentation</a></p>
[STEPS]
?.
?.
?.
?.
?.
?.
?. ... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.d2i8cd | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Isobaric peptide termini labeling (IPTL) is a quantification method which permits relative quantification using quantification points distributed throughout the whole tandem mass spectrometry (MS/MS) spectrum. It is based on the complementary derivatization of peptide termini wi... | [] |
91,976 | HyDrop-RNA v1.0 | 1 | dx.doi.org/10.17504/protocols.io.dm6gpwqjjlzp/v5 | https://www.protocols.io/view/hydrop-rna-v1-0-c53gy8jw | Florian De Rop, Suresh Poovathingal, Stein Aerts | TITLE: HyDrop-RNA v1.0
AUTHORS: Florian De Rop, Suresh Poovathingal, Stein Aerts
[DESCRIPTION]
Step-by-step protocol for performing HyDrop-RNA. The duration of each step assumes an experienced protocol user. For a first-time user, we recommend doubling the expected time for each step.
[STEPS]
SECTION: Microfluidics P... | ["[Microfluidics Preparation] Setting up the Microfluidic Framework\nThese steps need to happen in advance before the run can be started, as time between the preparation of the cell resuspension in RT mix and actual encapsulation needs to be minimised to preserve cell viability.", "[Microfluidics Preparation] Boot up ... |
29,302 | CasX GFP-Targeting gRNA IVT | null | dx.doi.org/10.17504/protocols.io.8uwhwxe | null | Connor Tsuchida, Liz O'Brien | TITLE: CasX GFP-Targeting gRNA IVT
AUTHORS: Connor Tsuchida, Liz O'Brien
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol explains how to transcribe gRNA in vitro. </div></div>
[STEPS]
?. [DNase Treatment]
Take 10μL sample pre-DNase, mixed with for analytical gel.
[2x formamide dye]
2... | ["[DNase Treatment]\nTake 10μL sample pre-DNase, mixed with for analytical gel.\n[2x formamide dye]\n2x Formamide Dye can be made as follows: 20mL formamide2.2mL of 100mM (10mM final concentration) EDTAA spatula tip-ful of powdered xylenecyanolA spatula tip-ful of powderedbromophenol blue", "[DNase Treatment]\nAdd to ... |
13,409 | Quantification of foliar polyphenolic concentration using a 96-well microtitre method | 1 | dx.doi.org/10.17504/protocols.io.81wgbmxovpko/v1 | https://www.protocols.io/view/quantification-of-foliar-polyphenolic-concentratio-rb9d2r6 | Megan Nickerson, Jana M U'Ren | TITLE: Quantification of foliar polyphenolic concentration using a 96-well microtitre method
AUTHORS: Megan Nickerson, Jana M U'Ren
[DESCRIPTION]
Phenolics are secondary metabolites found in various fruits and vegetables. To estimate polyphenol concentrations, the Folin-Ciocalteu (F-C) reagent can be used to react wit... | ["[Grinding Samples] Clean the tissue grinding cabinet (or other work space) with 10% bleach and 70% ethanol. Spray with 95% ethanol and allow to evaporate before using the cabinet.", "[Grinding Samples] Spray with EtOH and place your metal 1/8 tsp. scoops and any racks to be used in the cabinet. Let EtOH evaporate.", ... |
null | null | null | dx.doi.org/10.17504/protocols.io.ekzbcx6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Stellaris RNA FISH protocol for sequential labeling with IF and RNA FISH in adherent cells.
[BEFORE_START]
<p align="LEFT">Reagents and Equipment</p>
<p align="LEFT">Reagents and Consumables:</p>
<p align="LEFT">a) TE buffer (10 mM Tris-HCl, 1 mM EDTA, pH 8.0)</p>
<p align="LEF... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.ek2bcye | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
For <a href="https://www.protocols.io/view/Transcriptomics-During-One-Step-Growth-Curves-for-dem3c5" target="_blank">Transcriptomics During One-Step Growth Curves for Cellulophaga Phages protocol</a>.
[STEPS]
?.
?.
?.
?. | [] |
100,754 | Vector Digestion and Purification | 0 | dx.doi.org/10.17504/protocols.io.261ge5dyog47/v1 | https://www.protocols.io/view/vector-digestion-and-purification-dems3c6e | Carolina Lopez | TITLE: Vector Digestion and Purification
AUTHORS: Carolina Lopez
[DESCRIPTION]
Protocol for plasmid digestion and purification
[STEPS]
SECTION: Isolate Digested Vector:
2. 1. Digest Vector with New England Biolabs Restriction Enzymes:
2. Incubate for 120 min at 37 °C.
3. Add 10 µL of 6x loading buffer to reaction a... | ["[Isolate Digested Vector:] 1. Digest Vector with New England Biolabs Restriction Enzymes:\n \n2. Incubate for 120 min at 37 °C.\n3. Add 10 µL of 6x loading buffer to reaction and vortex briefly to mix.\n4. Make 1% low melt-agarose gel.\n a) Mix 1 g of Agar with 100 mL of TAE Buffer.\n b) Microwave to bo... |
95,379 | Preparation of mouse and human α-synuclein fibrils | 4 | dx.doi.org/10.17504/protocols.io.q26g7p268gwz/v1 | https://www.protocols.io/view/preparation-of-mouse-and-human-synuclein-fibrils-c9dtz26n | Arpine Sokratian, andrew.west west | TITLE: Preparation of mouse and human α-synuclein fibrils
AUTHORS: Arpine Sokratian, andrew.west west
[DESCRIPTION]
This protocol describes the preparation of homogeneous a-synuclein fibrils. The primary objective is to generate alpha-synuclein fibrils with high homogeneity in size, devoid of other protein species suc... | ["[Generation of α-synuclein fibrils via shaking cycles] Thaw down an aliquot of α-synuclein monomer stock (track down a batch number with identified EU number, concentration, A260/280 ratio) on iceon ice /quick water bath incubation at 42 °C with shaking", "[Generation of α-synuclein fibrils via shaking cycles] Spin d... |
72,689 | UMN SenNet Liver Collection Protocol | 1 | dx.doi.org/10.17504/protocols.io.3byl4jqb8lo5/v1 | https://www.protocols.io/view/umn-sennet-liver-collection-protocol-ci8ruhv6 | Steve Johnson | TITLE: UMN SenNet Liver Collection Protocol
AUTHORS: Steve Johnson
[DESCRIPTION]
UMN CTSI Biorepository and Laboratory Services (BLS)
BioNet Specimen Procurement Agreement
Project Title: SenNet Liver Collection Protocol
[STEPS]
1.
Process:
Patient Identification: As soon as a patient is scheduled, the research tea... | ["Process:\nPatient Identification: As soon as a patient is scheduled, the research team will email bionet@umn.edu a completed Specimen Procurement Request Form.\nPatient Consent: Researcher consents. The original signed consent form will be placed in the patient\n chart and scanned into Epic. BioNet will verify consen... |
102,616 | Device Fabrication Using Soft Lithography Technique | 0 | dx.doi.org/10.17504/protocols.io.5qpvokpydl4o/v1 | https://www.protocols.io/view/device-fabrication-using-soft-lithography-techniqu-dgfy3tpw | Jann Gamboa | TITLE: Device Fabrication Using Soft Lithography Technique
AUTHORS: Jann Gamboa
[DESCRIPTION]
Standard Operating Procedure
Institute of Biomedical Engineering
University of Toronto
Name of the procedures: Device Fabrication using Soft Lithography Technique
Location: MB308A
PI: Dr. Freeman Lan
Instructor: Jann Gamboa
... | ["[Equipment Preparation] Hot Plates and Oven", "[Equipment Preparation] The first step consists of turning one hot plate to 95 °C and another hot plate to ~200 °C", "[Potential Hazards] is a reproductive toxin and goes through gloves!\n\n2. Wear cut resistant gloves when using the razor!\n\n3. Always put the lid on wh... |
88,721 | OSU TriState SenNet Normal Donor Lung Acceptance Criteria | 1 | dx.doi.org/10.17504/protocols.io.ewov1qzjkgr2/v1 | https://www.protocols.io/view/osu-tristate-sennet-normal-donor-lung-acceptance-c-c2vrye56 | Sean D. Stacey, Brenda F. Reader, Lorena Rosas, Victor Peters, Ana L. Mora, mauricio.rojas | TITLE: OSU TriState SenNet Normal Donor Lung Acceptance Criteria
AUTHORS: Sean D. Stacey, Brenda F. Reader, Lorena Rosas, Victor Peters, Ana L. Mora, mauricio.rojas
[DESCRIPTION]
This protocol describes the criteria required for inclusion of human lung specimen from healthy “normal” organ donors in the Comprehensive T... | ["[Inclusion Criteria] Donor is consented for research by Lifeline of Ohio or registered organ donor, 18-80 years of age, negative for HCV, HBV, HIV, and no history of latent tuberculosis or active COVID-19\ninfection. Depending on the investigators’ request we remove specimens from upper, lower, or both lobes of a sin... |
30,649 | Deep Dye Drop Protocol | 1 | null | https://www.protocols.io/view/deep-dye-drop-protocol-96zh9f6 | Chiara Victor, Ben Gaudio, Mirra Chung, Mario Niepel, Marc Hafner, Luca Gerosa, Clarence Yapp, Kartik Subramanian, Peter Sorger, Caitlin Mills, Ajit Johnson Nirmal, Nicholas Clark | TITLE: Deep Dye Drop Protocol
AUTHORS: Chiara Victor, Ben Gaudio, Mirra Chung, Mario Niepel, Marc Hafner, Luca Gerosa, Clarence Yapp, Kartik Subramanian, Peter Sorger, Caitlin Mills, Ajit Johnson Nirmal, Nicholas Clark
[DESCRIPTION]
High-throughput measurement of cells perturbed using libraries of small molecule... | ["Pulse cells with EdU+ stain dead cells with LDR\n\nFor 10 ml:\n1 mL optiprep (10% final)\n9 mL PBS\n5 µL LDR (1:2000 final)\n10 µL EdU (10 µM final)\n\n384-well plate: Add 15 µL per well along the edge of the wells using a multi-channel pipette and incubate for 60 min (or desired pulse duration) @ 37 °C \n96-well ... |
80,840 | Wnt-3a and R-spo1 conditioned media reporter assay | 4 | null | https://www.protocols.io/view/wnt-3a-and-r-spo1-conditioned-media-reporter-assay-cs7gwhjw | Natalia Martagón, Gurdrun Kliem | TITLE: Wnt-3a and R-spo1 conditioned media reporter assay
AUTHORS: Natalia Martagón, Gurdrun Kliem
[DESCRIPTION]
Protocol designed to measure the activity of Wnt-3a or R-spondin-1 (Rspo1) conditioned media.
A reporter HEK cell line expressing luciferase under Wnt-3a stimulation is cultured with conditioned media follo... | ["[Day 2: cell stimulation] Add 250 µL of conditioned medium (CM) to test in the desired concentration\nR-spondin: 12.5 % volume Wnt-3a CM + 2.5 % volume Rspo1 CM (3)\nWnt3a CM .50 % volume 250 µL Sample + 250 µL HEK medium", "[Day 1: Seeding of Hek 293 STF cells] Start with one almost confluent T75 culture bottle ... |
null | null | null | dx.doi.org/10.17504/protocols.io.mehc3b6 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
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20,773 | UC Davis - Electrocardiography | null | dx.doi.org/10.17504/protocols.io.yidfua6 | null | Anil Singapuri | TITLE: UC Davis - Electrocardiography
AUTHORS: Anil Singapuri
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">Cardiac hypertrophy is one of the most common causes of heart failure. The development of cardiac hypertroph... | ["Mice will be anesthetized with intraperitoneal ketamine 100 mg/kg and xylazine 5 mg/kg, intubated and mechanically ventilated with supplemental oxygen at a respiratory rate of 100 breaths/min and tidal volume of 0.2 ml.", "The fur will be removed from the surgical incision sites (Nair) and the skin cleaned with Betad... |
80,053 | Library preparation (dsDNA double indexing, full-UDG, 2x split) | 1 | dx.doi.org/10.17504/protocols.io.8epv5jpwdl1b/v1 | https://www.protocols.io/view/library-preparation-dsdna-double-indexing-full-udg-csevwbe6 | Marcel Keller, Christiana L Scheib | TITLE: Library preparation (dsDNA double indexing, full-UDG, 2x split)
AUTHORS: Marcel Keller, Christiana L Scheib
[DESCRIPTION]
Protocol for the preparation of double indexed double-stranded DNA libraries for Illumina sequencing, optimized for ultra-short ancient DNA molecules, modified from Meyer & Kircher (2010) Co... | ["[Blunt End Repair 1] Use 1.5 ml ER tube to set up the Blunt End Repair Master Mix on ice .", "[Blunt End Repair 1] Add 20 µl Master Mix to each tube of the ER strip.", "[Blunt End Repair 1] Vortex and spin down DNA extracts, add 25 µl of template DNA or water to each tube.", "[Blunt End Repair 1] Mix carefully by res... |
91,224 | Assay for the Enzymatic Degradation of PET Beads | 4 | dx.doi.org/10.17504/protocols.io.bp2l6xp8klqe/v1 | https://www.protocols.io/view/assay-for-the-enzymatic-degradation-of-pet-beads-c5byy2pw | Joao Vitor Molino | TITLE: Assay for the Enzymatic Degradation of PET Beads
AUTHORS: Joao Vitor Molino
[DESCRIPTION]
This assay focuses on assessing the enzymatic degradation of PET beads through absorbance measurements at 240nm. The primary goal is to quantify the enzymatic activity on PET beads by monitoring the release of BHET. This i... | ["[Reaction Setup] In each PCR tube, add 30mg of PET plastic beads.", "[Reaction Setup] Add 100 µL of 1 Molarity (M) potassium phosphate buffer to the tubes", "[Reaction Setup] Add 100 µL of the enzyme solution to the tubes with PET beads to initiate the reaction. These constitute the test samples.", "[Reaction Setup] ... |
31,413 | Generating Stable Cell Lines with Lentivirus | null | dx.doi.org/10.17504/protocols.io.bawvife6 | null | Addgene the Nonprofit Plasmid Repository | TITLE: Generating Stable Cell Lines with Lentivirus
AUTHORS: Addgene the Nonprofit Plasmid Repository
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol is for generating stable cell lines with lentivirus. To see the full abstract and additional resources, please visit the </span><a... | ["[Transduction]\nPrepare a batch of DMEM complete + 10 µg/mL polybrene by diluting of 10 mg/mL polybrene into media.\n20 µl\n20 ml", "[Transduction]\nRapidly thaw the lentiviral aliquot at .\n37 °C", "[Transduction]\nPrepare a range of dilutions of the lentivirus in DMEM complete + 10 µg/mL polybrene. ABC1Dilution... |
47,514 | RT-PCR multiplex en Tiempo Real para la detección de virus SARS-CoV-2 | 4 | dx.doi.org/10.17504/protocols.io.bsm2nc8e | https://www.protocols.io/view/rt-pcr-multiplex-en-tiempo-real-para-la-detecci-n-bsm2nc8e | Priscila Nayu Lope Pari, Maribel Huaringa Nunes, Carlos Padilla Rojas, Nancy Rojas Serrano, Janett Protilla Romero, Gloria Arotinco Garayar, Lely Solari Serpa | TITLE: RT-PCR multiplex en Tiempo Real para la detección de virus SARS-CoV-2
AUTHORS: Priscila Nayu Lope Pari, Maribel Huaringa Nunes, Carlos Padilla Rojas, Nancy Rojas Serrano, Janett Protilla Romero, Gloria Arotinco Garayar, Lely Solari Serpa
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>V... | [] |
25,945 | Introduction to Soil Science Lab Manual | null | dx.doi.org/10.17504/protocols.io.5jzg4p6 | null | Savanah St. Clair, Maryam Saraylou, Elnura Maine | TITLE: Introduction to Soil Science Lab Manual
AUTHORS: Savanah St. Clair, Maryam Saraylou, Elnura Maine
[STEPS] | [] |
81,368 | Miltenyi Biotec: Adipose Tissue Dissociation -- University of Minnesota TMCs | 1 | dx.doi.org/10.17504/protocols.io.kqdg39jxqg25/v1 | https://www.protocols.io/view/miltenyi-biotec-adipose-tissue-dissociation-univer-ctpywmpw | Miltenyi Biotec, Laura J Niedernhofer, David A Bernlohr | TITLE: Miltenyi Biotec: Adipose Tissue Dissociation -- University of Minnesota TMCs
AUTHORS: Miltenyi Biotec, Laura J Niedernhofer, David A Bernlohr
[DESCRIPTION]
Dissociation of human adipose tissue using Miltenyi dissociation kit Catalog #130-105-808 and Protocol #140-004-708.02
[STEPS]
1.
https://www.miltenyib... | ["https://www.miltenyibiotec.com/US-en/products/adipose-tissue-dissociation-kit-mouse-and-rat.html#130-105-808"] |
28,189 | Protocol for Lambda Exonuclease (NEB #M0262) | 1 | null | https://www.protocols.io/view/protocol-for-lambda-exonuclease-neb-m0262-7r5hm86 | New England Biolabs | TITLE: Protocol for Lambda Exonuclease (NEB #M0262)
AUTHORS: New England Biolabs
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Lambda Exonuclease efficiently degrades 5' phosphorylated linear dsDNA from 5' to 3' direction, leaving supercoiled dsDNA intact.*</div><div class = "text-block"><span sty... | ["Set-up the reaction as follows: AB1Components50 μl REACTION2 DNA up to 5 μg3 Lambda Exonuclease Reaction Buffer (10X) 5 μl (1X)4 Lambda Exonuclease 1 μl (5 units)5 Nuclease-free H2O up to 50 μl\nAB1Components50 μl REACTION2 DNA up to 5 μg3 Lambda Exonu... |
null | null | null | dx.doi.org/10.17504/protocols.io.crjv4m | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This transformation protocol is for the C2527I cells. (For the C2527H protocol, see <a href="https://www.protocols.io/view/Transformation-Protocol-C2527H-imsv4d" target="_blank">here</a>.)
[GUIDELINES]
<strong>Transformation Protocol Variables<br /></strong><br /><strong>Thawin... | [] |
97,004 | Populating NCBI template for submissions using BioNumerics v7.6 | 1 | dx.doi.org/10.17504/protocols.io.81wgbp5bovpk/v4 | https://www.protocols.io/view/populating-ncbi-template-for-submissions-using-bio-dayk2fuw | Ruth Timme, Maria Balkey, Julie Haendiges | TITLE: Populating NCBI template for submissions using BioNumerics v7.6
AUTHORS: Ruth Timme, Maria Balkey, Julie Haendiges
[DESCRIPTION]
PURPOSE: to define the standard operating procedure for collecting isolate metadata using BioNumerics for submission of food/environmental isolates to NCBI.
SCOPE: to provide a stan... | ["[New Version for this protocol] Visit the new version of this protocol by clicking the following link: https://www.protocols.io/view/populating-ncbi-template-for-submissions-using-bio-3byl4qn4ovo5/v1"] |
null | null | null | dx.doi.org/10.17504/protocols.io.ke5ctg6 | null | null | TITLE: No Title
AUTHORS:
[STEPS] | [] |
68,398 | Pre-Extraction and Matrix Application via a HTX M5 Sprayer for Intact Proteoform MALDI Imaging | 1 | null | https://www.protocols.io/view/pre-extraction-and-matrix-application-via-a-htx-m5-ce2ntgde | Kevin J. Zemaitis, Dusan Velickovic, Ljiljana.PasaTolic | TITLE: Pre-Extraction and Matrix Application via a HTX M5 Sprayer for Intact Proteoform MALDI Imaging
AUTHORS: Kevin J. Zemaitis, Dusan Velickovic, Ljiljana.PasaTolic
[DESCRIPTION]
Scope:
Using an HTX M5 sprayer this protocol outlines a pre-extraction step for increased sensitivity for intact proteoform analyses, thi... | ["[Preparing the HTX sprayer] The preparation of the HTX M5 sprayer employed is similar to other protocols, it has an external pump and 5 mL sample loop which must be purged prior to analyses.", "[Preparing the HTX sprayer] House nitrogen gas flow is regulated to 10 PSI prior to turning on the pump power supply and ini... |
null | null | null | dx.doi.org/10.17504/protocols.io.dwi7cd | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Protocol for transforming XL-10 Gold Ultracompetent cells from Stratagene (now Agilent). Protocol adopted from manufacturer's instructions and simplified to remove use of special media and beta-mercaptoethanol
[GUIDELINES]
<strong>Use of 14-ml BD Falcon polypropylene round-bott... | [] |
46,357 | Semi-Automated and Miniaturized SARS-CoV-2 Detection using TaqPath COVID-19 Multiplex Real-Time RT-PCR Assay | 4 | dx.doi.org/10.17504/protocols.io.brhvm366 | https://www.protocols.io/view/semi-automated-and-miniaturized-sars-cov-2-detecti-brhvm366 | Peter De Hoff, Sydney Morgan, Louise C Laurent | TITLE: Semi-Automated and Miniaturized SARS-CoV-2 Detection using TaqPath COVID-19 Multiplex Real-Time RT-PCR Assay
AUTHORS: Peter De Hoff, Sydney Morgan, Louise C Laurent
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The purpose of this procedure is to describe the setup of a semi-automated and ... | ["[Workstation Preparation]\nSet up:Turn on equipment (Mosquito HV, Mosquito X1, QuantStudio 7, Centrifuge) and ensure all equipment and programs start up correctly. Ensure the centrifuge is set to Decontaminate workspace, pipettes, and equipment using RNASEZap or equivalent.Fill two (2) ice trays with crushed ice... |
89,598 | Intracellular neuromelanin quantification | 4 | dx.doi.org/10.17504/protocols.io.rm7vzx71xgx1/v1 | https://www.protocols.io/view/intracellular-neuromelanin-quantification-c3q6ymze | Núria Peñuelas | TITLE: Intracellular neuromelanin quantification
AUTHORS: Núria Peñuelas
[DESCRIPTION]
Protocol for quantifying intracellular neuromelanin in coronal sections of the rodent brain, in HE stained sections (NM-occupied area) and unstained sections (NM OD).
[STEPS]
SECTION: H&E-stained sections (NM-occupied neuronal ... | ["[H&E-stained sections (NM-occupied neuronal area)] Scan H&E sections using the Pannoramic Midi II FL, HQ SCIENTIFIC 60x and section images were acquired with CaseViewer software at an objective magnification of 63x.", "[H&E-stained sections (NM-occupied neuronal area)] Acquire SNpc images at 63x with CaseView... |
52,136 | Patch-Seq Recording and Extraction Detailed Protocol | 1 | dx.doi.org/10.17504/protocols.io.bw6gphbw | https://www.protocols.io/view/patch-seq-recording-and-extraction-detailed-protoc-bw6gphbw | Brian Lee, Kristen Hadley, Allen Institute for Brain Science | TITLE: Patch-Seq Recording and Extraction Detailed Protocol
AUTHORS: Brian Lee, Kristen Hadley, Allen Institute for Brain Science
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is a detailed version of the Allen Institute's Patch-Seq Recording and Extraction protocol, which describes ... | [] |
97,062 | Cryo-ET data acquisition, tomogram reconstruction, and analysis | 0 | dx.doi.org/10.17504/protocols.io.e6nvw1podlmk/v1 | https://www.protocols.io/view/cryo-et-data-acquisition-tomogram-reconstruction-a-da2e2gbe | Dorothy zhao | TITLE: Cryo-ET data acquisition, tomogram reconstruction, and analysis
AUTHORS: Dorothy zhao
[DESCRIPTION]
Aggregation of proteins containing expanded polyglutamine (polyQ) repeats is the cytopathologic hallmark of a group of dominantly inherited neurodegenerative diseases, including Huntington's disease (HD). Hunting... | ["[Cryo-ET data acquisition] Lamellas were imaged in a FEI G2 Polara or Titan Krios cryo-TEM equipped with a field emission gun\noperating at 300 kV, a post-column energy filter (Gatan, Pleasanton, CA, USA) operating at zero-loss, and a 4k x 4k K2 Summit direct electron detector (Gatan). The energy filter was used to i... |
58,784 | Predation selection trial protocol | 3 | null | https://www.protocols.io/view/predation-selection-trial-protocol-b5m8q49w | Laura Lopez, Meghan Duffy | TITLE: Predation selection trial protocol
AUTHORS: Laura Lopez, Meghan Duffy
[DESCRIPTION]
This is a protocol to determine if Chaoborus preferentially feed on infected or uninfected Daphnia.
[STEPS] | [] |
25,056 | Seminavis robusta protocol collection | null | dx.doi.org/10.17504/protocols.io.4p8gvrw | null | Lev Tsypin, Aaron Turkewitz | TITLE: Seminavis robusta protocol collection
AUTHORS: Lev Tsypin, Aaron Turkewitz
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This is a collection of media, reagents, and protocols for the cultivation and manipulation of the diatom </span><span style = "font-style:italic;">Seminavis robust... | [] |
109,177 | Nanopore Transcriptomic Sequencing with C. elegans | 0 | dx.doi.org/10.17504/protocols.io.8epv5r4d6g1b/v1 | https://www.protocols.io/view/nanopore-transcriptomic-sequencing-with-c-elegans-dnuz5ex6 | Victoria Yarmey | TITLE: Nanopore Transcriptomic Sequencing with C. elegans
AUTHORS: Victoria Yarmey
[DESCRIPTION]
This protocol entails sequencing native RNA of young adult C. elegans using NanoPore sequencing (Oxford NanoPore Technologies, ONT). RNA extraction will be conducted using modified versions of Zymo’s “Direct-zol‱ RNA Minip... | ["[Nematode Culture & Synchronization (Day 0)] Culture C. elegans on plates (NGM agar plates) until adulthood and/or they have begun laying eggs onto the E. coli lawn.", "[Nematode Culture & Synchronization (Day 0)] Prepare fresh bleaching solution in a sterile 1.5mL microcentrifuge tube:\n\n \n \n Vo... |
87,113 | FLIM-FRET analyses with mCitrine / mScarlet-I -tagged chitin receptors stably expressed in A. thaliana | 4 | dx.doi.org/10.17504/protocols.io.dm6gp3zj1vzp/v1 | https://www.protocols.io/view/flim-fret-analyses-with-mcitrine-mscarlet-i-tagged-czbhx2j6 | Elena-Kristin.Petutschnig, leon.pierdzig, Josephine Mittendorf, Jule Meret Niebisch, Volker Lipka | TITLE: FLIM-FRET analyses with mCitrine / mScarlet-I -tagged chitin receptors stably expressed in A. thaliana
AUTHORS: Elena-Kristin.Petutschnig, leon.pierdzig, Josephine Mittendorf, Jule Meret Niebisch, Volker Lipka
[DESCRIPTION]
Elucidating protein-protein interactions is crucial for our understanding of molecular p... | ["[Generation of transgenic lines expressing mCitrine- and mScarlet-I-tagged proteins] Clone the two proteins of interest you wish to test for interaction in frame with mCitrine and mScarlet-I. A tested vector for this purpose is pGreenII-0229 (Hellens et al., 2000). Transform constructs into Arabidopsis thaliana (for ... |
26,867 | 15 Determination of Enzyme Activity | null | dx.doi.org/10.17504/protocols.io.6gthbwn | null | TJUSLS China | TITLE: 15 Determination of Enzyme Activity
AUTHORS: TJUSLS China
[STEPS]
?. [System setup – protein concentration]
Soak the 96-well plates in 75% ethanol and put the container in ultrasonic cleaner for 30min to 1 hour, then use ddH2O to wash these plates several times. Put these clean plates in drying oven at 55°C. ~
... | ["[System setup – protein concentration]\nSoak the 96-well plates in 75% ethanol and put the container in ultrasonic cleaner for 30min to 1 hour, then use ddH2O to wash these plates several times. Put these clean plates in drying oven at 55°C. ~\n55 °C", "[System setup – protein concentration]\nDilute the enzyme using ... |
null | null | null | dx.doi.org/10.17504/protocols.io.r9jd94n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Exploring the different ways to run an iMicrobe app on data in iMicrobe</p>
[BEFORE_START]
<p>Create an iMicrobe account.</p>
[STEPS]
?.
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.gp6bvre | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>GreenGlo ™, 20,000X in Water, is a non-carcinogenic and non-toxic alternative to Ethidium bromide used for the detection of nucleic acids in agarose gels. It is as sensitive as Ethidium bromide. There is no toxic DMSO as GreenGlo ™ is supplied in water. <br /> <br />GreenGlo ... | [] |
79,525 | Expansion microscopy | 1 | dx.doi.org/10.17504/protocols.io.j8nlkwp56l5r/v1 | https://www.protocols.io/view/expansion-microscopy-crwdv7a6 | michela.deleidi, María José Pérez J., Hariam Raji | TITLE: Expansion microscopy
AUTHORS: michela.deleidi, María José Pérez J., Hariam Raji
[DESCRIPTION]
Expansion microscopy is a technique to visualize biological structures with higher spatial resolution than traditional microscopy methods.
[STEPS]
SECTION: Expansion microscopy
1.
Block cells with 10% (v/v) normal ... | ["[Expansion microscopy] Block cells with 10% (v/v) normal goat serum (NGS) in 0.1% (v/v) Triton X-100 in PBS and incubate it with primary antibodies in blocking solution .", "[Expansion microscopy] After a 3-h incubation with the corresponding secondary antibody (Alexa Fluor, Invitrogen), wash the samples and treat w... |
34,144 | Supplemented M9 media | 1 | null | https://www.protocols.io/view/supplemented-m9-media-bdj8i4rw | Wolfram Moebius | TITLE: Supplemented M9 media
AUTHORS: Wolfram Moebius
[DESCRIPTION]
Supplemented M9 media
[STEPS]
1.
For 500 mL need:
Dissolve 56.4 g M9 salts (5X) in MilliQ water, make up to 1L and autoclave
Dissolve 10 g of casamino acids in MilliQ water, make up to 10 mL and filter with a filter
5 mL 40% w/v glucose, autocl... | ["For 500 mL need:\n\nDissolve 56.4 g M9 salts (5X) in MilliQ water, make up to 1L and autoclave\nDissolve 10 g of casamino acids in MilliQ water, make up to 10 mL and filter with a filter \n5 mL 40% w/v glucose, autoclaved\n1 mL 1M MgSO4, filter sterilised\n50 uL 1M CaCl2, filter sterilised\n50 uL 1% w/v thiamine h... |
57,725 | Adapting hPSCs cultured on MEFs to feeder-free system | 4 | dx.doi.org/10.17504/protocols.io.b4k5quy6 | https://www.protocols.io/view/adapting-hpscs-cultured-on-mefs-to-feeder-free-sys-b4k5quy6 | Hanqin Li, Oriol Busquets, Steven Poser, Dirk Hockemeyer, Frank Soldner | TITLE: Adapting hPSCs cultured on MEFs to feeder-free system
AUTHORS: Hanqin Li, Oriol Busquets, Steven Poser, Dirk Hockemeyer, Frank Soldner
[DESCRIPTION]
This protocol describes the procedure of adapting human pluripotent stem cells (hPSCs) to feeder-free culturing conditions using mTeSR-plus or StemFlex
General ... | ["When MEFs-cultured hPSCs reach 50% confluency, change medium to hPSCs medium + Rock inhibitor, preparing for the feeder-free adaptation on the next day.", "Coat three wells of a 6-well plate with either VTN/Matrigel/Geltrex for each cell line. \n\nFor a detailed protocol, refer to \"Coating plates,\" which can be fou... |
null | null | null | dx.doi.org/10.17504/protocols.io.cq4vyv | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This is the suggested protocol for use with λ DNA-Mono Cut Mix (<a href="https://www.neb.com/products/n3019-dna-mono-cut-mix" target="_blank">N3019</a>), фX174 DNA-HaeIII Digest (<a href="https://www.neb.com/products/n3026-x174-dna-haeiii-digest" target="_blank">N302... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.j7ncrme | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Invitrogen's <a href="https://www.thermofisher.com/antibody/product/HA-Tag-Antibody-clone-2-2-2-14-Monoclonal/26183" target="_blank">HA tag monoclonal antibody</a> in combination with <a href="https://www.thermofisher.com/order/catalog/product/WB7104" target="_blank">Western ... | [] |
74,350 | General Guidelines for Culture of Multiple Myeloma Cell Lines | 1 | dx.doi.org/10.17504/protocols.io.rm7vzb6n4vx1/v1 | https://www.protocols.io/view/general-guidelines-for-culture-of-multiple-myeloma-ckunuwve | Dennis Juarez, dfruman | TITLE: General Guidelines for Culture of Multiple Myeloma Cell Lines
AUTHORS: Dennis Juarez, dfruman
[DESCRIPTION]
General guidelines for culture and use of myeloma cell lines in the Fruman Lab.
[STEPS]
1. Incubator Settings: 37 degrees Celsius, 5% CO2
2. Medium: 88% RPMI 1640, 10% FBS, 1% Pen/Strep/Glutamine, 1% (Fi... | ["Incubator Settings: 37 degrees Celsius, 5% CO2", "Medium: 88% RPMI 1640, 10% FBS, 1% Pen/Strep/Glutamine, 1% (Final: 10 mM) of 1M HEPES", "Cryopreservation: Freeze medium: 90% FBS, 10% DMSO. 5 million cells are resuspended in 500uL of freeze media, transferred to cryotubes, and frozen slowly in Mr. Frosty™ Freezing C... |
64,712 | Crude Membrane Fractionation of Cultured Cells | 1 | dx.doi.org/10.17504/protocols.io.yxmvmnb99g3p/v1 | https://www.protocols.io/view/crude-membrane-fractionation-of-cultured-cells-cbfgsjjw | Asad Malik, Dario R Alessi, Suzanne R Pfeffer | TITLE: Crude Membrane Fractionation of Cultured Cells
AUTHORS: Asad Malik, Dario R Alessi, Suzanne R Pfeffer
[DESCRIPTION]
We present here a protocol for fractionating crude cellular extracts to prepare membrane and cytosol-enriched fractions and a nuclei-containing insoluble fraction from cultured cells. We dep... | ["[Crude Membrane Fractionation] Pour off media from the culture dish and aspirate completely by holding plate on edge. Wash cells twice with 5 mL of ice-cold PBS.", "[Crude Membrane Fractionation] Immediately transfer the dishes to ice--this is best accomplished using wet paper towel-covered steel blocks resting on ic... |
48,716 | Untargeted Top-down Proteomics by LC-MS/MS on Eclipse | 1 | dx.doi.org/10.17504/protocols.io.bttknnkw | https://www.protocols.io/view/untargeted-top-down-proteomics-by-lc-ms-ms-on-ecli-bttknnkw | Bryon Drown, Jeannie Camarillo, Rafael Melani, Neil Kelleher | TITLE: Untargeted Top-down Proteomics by LC-MS/MS on Eclipse
AUTHORS: Bryon Drown, Jeannie Camarillo, Rafael Melani, Neil Kelleher
[DESCRIPTION]
Describes the LC-MS/MS data acquisition procedure for top-down proteomics samples using the Thermo Scientific Orbitrap Eclipse Tribrid mass spectrometer
[STEPS]
1. Sample... | ["Samples were analyzed on a Thermo Scientific Orbitrap Eclipse Tribrid mass spectrometer in line with a Dionex Ultimate 3000 RSLCnano system", "Samples (6 µL ) were injected via the autosampler and loaded onto a self-packed trap column (150 μm i.d. x 2 cm length packed with PLRP-S 5-μm particles 1,000-Å pore size) for... |
54,869 | Microplate-based DNA Quantification with EzFluoroStain DNA reagent | 4 | dx.doi.org/10.17504/protocols.io.bztvp6n6 | https://www.protocols.io/view/microplate-based-dna-quantification-with-ezfluoros-bztvp6n6 | Maho Saita, Kyoko Aikawa, Kenji Ohgane | TITLE: Microplate-based DNA Quantification with EzFluoroStain DNA reagent
AUTHORS: Maho Saita, Kyoko Aikawa, Kenji Ohgane
[DESCRIPTION]
This protocol offers an safer alternative to the ethidium bromide-based DNA quantification protocol, utilizing an DNA-selective dye EzFluoroStain DNA (WSE-7130, ATTO corporation, Tok... | ["[Sample preparation] Prepare dilution series of standard DNA solution, depending on the concentration of your sample.", "[Sample preparation] Prepare EzFluoroStain DNA working solution.", "[Sample preparation] Mix 5 µL of the DNA samples with 95 µL of the EzFluoroStain DNA working solution on a black 96-well micropla... |
69,773 | Protocol for 6mA labeling and HMW DNA extraction from fresh frozen human brain samples | 1 | dx.doi.org/10.17504/protocols.io.j8nlkw54wl5r/v1 | https://www.protocols.io/view/protocol-for-6ma-labeling-and-hmw-dna-extraction-f-cgdmts46 | Jonas Demeulemeester , Koen Theunis | TITLE: Protocol for 6mA labeling and HMW DNA extraction from fresh frozen human brain samples
AUTHORS: Jonas Demeulemeester , Koen Theunis
[DESCRIPTION]
This protocol details the procedure of 6mA labeling and HMW DNA extraction of fresh frozen brain tissue. The protocol is inspired by Fiber-seq.
[STEPS]
SECTION: ... | ["[6mA labeling and HMW DNA extraction] Place the Dounce homogenizer and pestles on ice, chill the centrifuge to 4 °C and preheat the ThermoMixer to 37 °C.", "[6mA labeling and HMW DNA extraction] Carefully transfer 3-4 ( diameter) tissue punch biopsies (~25 mg) to the chilled Dounce homogenizer.", "[6mA labeling and ... |
40,884 | Antigen-specific staining of EV markers with fluorochrome-conjugated antibodies | 1 | dx.doi.org/10.17504/protocols.io.bj6ukrew | https://www.protocols.io/view/antigen-specific-staining-of-ev-markers-with-fluor-bj6ukrew | Aizea Morales-Kastresana, Joshua Welsh, Jennifer Jones | TITLE: Antigen-specific staining of EV markers with fluorochrome-conjugated antibodies
AUTHORS: Aizea Morales-Kastresana, Joshua Welsh, Jennifer Jones
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The use of antibodies for EV staining and analysis using flow cytometry poses challenges due to the r... | ["Wash one qEV column per EV preparation with 20 mL of DPBS. Never allow the columns to become dry.", "Pipette 1x109EVs in a 10 µL volume of DPBS and add 2 µg of Fc Block reagent to block Fc receptors. Incubate with no agitation for 10 minutes at room temperature.\nNote: The presence of Fc receptors on EVs is not well ... |
106,358 | High-Capacity cDNA Reverse Transcription | 0 | dx.doi.org/10.17504/protocols.io.6qpvr8wq2lmk/v1 | https://www.protocols.io/view/high-capacity-cdna-reverse-transcription-dj4w4qxe | Hector Martell Martinez | TITLE: High-Capacity cDNA Reverse Transcription
AUTHORS: Hector Martell Martinez
[DESCRIPTION]
This protocol details the high-capacity cDNA reverse transcription.
[STEPS]
SECTION: Nanodrop
1. Nanodrop each isolated sample of RNA.
SECTION: Nanodrop
1.1. A good concentration of RNA is between 200 3172- 2000 3172 .
If ... | ["[Nanodrop] Nanodrop each isolated sample of RNA.", "[Nanodrop] A good concentration of RNA is between 200 3172- 2000 3172 .\n\nIf the concentration is above 2000 3172 then dilute the sample with water for a final concentration below2000 3172 .", "[Nanodrop] A good 260/280 value is ~2.0.", "[Nanodrop] A good 260/230 v... |
null | null | null | dx.doi.org/10.17504/protocols.io.repd3dn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol describes the study of a computational model of urban growth, including real data processing, model exploration and calibration. See github repository for code and paper for real and simulation datasets.</p>
[STEPS]
?.
?.
?.
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.r2dd8a6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
The protocol provides an inexpensive, rapid (30 min) and reliable technique for obtaining counts of viruses and prokaryotes simultaneously. The method is from:<br />Patel A, Noble RT, Steele JA, Schwalbach MS, Hewson I, Fuhrman JA.<a href="http://www.nature.com/nprot/journal/v2/... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.d7j9km | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<span style="color: #000339; font-family: Raleway, sans-serif; font-size: 14px; background-color: #f6f6f4;">This tutorial demonstrates the use of VIROME for comparing viral metagenome libraries analyzed with the VIROME pipeline as well as comparative analysis of viral communitie... | [] |
24,049 | Biochemical Measures of Neuropathy - Glutathione Peroxidase | null | dx.doi.org/10.17504/protocols.io.3qrgmv6 | null | Eva Feldman | TITLE: Biochemical Measures of Neuropathy - Glutathione Peroxidase
AUTHORS: Eva Feldman
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span></div><div class = "text-block">Oxidative stress is highly correlated with the metabolic changes caused by hypergly... | ["[Sample Preparation — Tissue:]\n1. Homogenize the tissue in 5–10 mL of cold buffer (i.e., 50 mM Tris-HCl, pH 7.5, 5 mM EDTA, and 1 mM DTT) per gram of tissue. General Equation: μL Buffer = mg Tissue X 10\n2. Centrifuge at 10,000 x g for 15 minutes at 4°C.\n3. Remove supernatant for assay and store on i... |
null | null | null | dx.doi.org/10.17504/protocols.io.jwpcpdn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Best practices for preparation of phytoplankton samples for quantitative immunoblotting in the Campbell Lab.</p>
[STEPS] | [] |
19,869 | U Mass - Acute lipid infusion | null | dx.doi.org/10.17504/protocols.io.xm5fk86 | null | Jason Kim | TITLE: U Mass - Acute lipid infusion
AUTHORS: Jason Kim
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span><span style = "font-weight:bold;"> </span></div><div class = "text-block">Triglyceride emulsion and heparin will be intravenously infused for 5 hou... | ["Survival surgery is performed to establish a chronic indwelling catheter at 5~6 days prior to experiment for intravenous infusion. (refer to M1023: Surgery-jugular vein cannulation)", "Mice are fasted overnight (~15 hours) or for 5 hours prior to the start of experiment.", "Place a mouse in a rat-size restrainer wit... |
55,479 | Perfusion Live Microscopy Using Zeiss LSM 780 and Ibidi Perfusion Sets | 1 | null | https://www.protocols.io/view/perfusion-live-microscopy-using-zeiss-lsm-780-and-b2exqbfn | Emir Bora Akmeriç | TITLE: Perfusion Live Microscopy Using Zeiss LSM 780 and Ibidi Perfusion Sets
AUTHORS: Emir Bora Akmeriç
[DESCRIPTION]
Step by step protocol for setting up live microscopy experiments with Ibidi perfusion sets
[STEPS]
SECTION: Cell Seeding
1. Check whether HUVECs in T25/T75 are confluent
SECTION: Cell Seeding
3.... | ["[Cell Seeding] Check whether HUVECs in T25/T75 are confluent", "[Cell Seeding] Bring trypsin, PBS, media and FBS to to 37C inside cell culture incubator", "[Cell Seeding] Gelatinize 2 or 3 Ibidi 0.4 luer u-slides with 0.2% gelatin in water", "[Cell Seeding] Trypsinize dish and count cells. A minimum of 500k cells are... |
95,773 | A Comprehensive Guide to Quality Assessment and Data Submission for Genomic Surveillance of Enteric Pathogens | 2 | dx.doi.org/10.17504/protocols.io.eq2lyprkplx9/v4 | https://www.protocols.io/view/a-comprehensive-guide-to-quality-assessment-and-da-c9r5z586 | Ruth Timme, Marc Allard, Errol Strain, Tina Lusk Pfefer, Candace Hope Bias, Maria Sanchez | TITLE: A Comprehensive Guide to Quality Assessment and Data Submission for Genomic Surveillance of Enteric Pathogens
AUTHORS: Ruth Timme, Marc Allard, Errol Strain, Tina Lusk Pfefer, Candace Hope Bias, Maria Sanchez
[DESCRIPTION]
This document outlines the steps necessary to assemble and submit the standard data packa... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.fm7bk9n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This describes setting up ssh keys and configuration to avoid having to use your NetID+ 2-factor authentication every time you log into the HPC. Windows users are encouraged to install Cygwin (http://www.cygwin.com), a free Unix-like environment that provides a terminal so a... | [] |
47,259 | Protocol_Impact of a telephone triage service for non-critical emergencies in Switzerland: a cross-sectional study | 1 | dx.doi.org/10.17504/protocols.io.bsd3na8n | https://www.protocols.io/view/protocol-impact-of-a-telephone-triage-service-for-bsd3na8n | Chloé Thierrin, Aurélie Augsburger, Fabrice Dami, Christophe Monney, Philippe Staeger, Carole Clair | TITLE: Protocol_Impact of a telephone triage service for non-critical emergencies in Switzerland: a cross-sectional study
AUTHORS: Chloé Thierrin, Aurélie Augsburger, Fabrice Dami, Christophe Monney, Philippe Staeger, Carole Clair
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify... | ["[Time table]\nStudy materials", "[Time table]\nStudy materials", "[Time table]\nEthical review", "[Time table]\nData collection", "[Time table]\nCoding/Analyzing data", "[Time table]\nWriting the manuscript", "[Time table]\nEthical review", "[Time table]\nData collection", "[Time table]\nCoding/Analyzing data", "[Tim... |
102,741 | Purification of germination-competent E. intestinalis spores | 0 | dx.doi.org/10.17504/protocols.io.3byl495wogo5/v1 | https://www.protocols.io/view/purification-of-germination-competent-e-intestinal-dgjv3un6 | Noelle V. Antao, Mahrukh Usmani, Frederick Rubino, Harshita Ramchandani, Pattana Jaroenlak, Kacie L. McCarty, Damian C. Ekiert, Gira Bhabha | TITLE: Purification of germination-competent E. intestinalis spores
AUTHORS: Noelle V. Antao, Mahrukh Usmani, Frederick Rubino, Harshita Ramchandani, Pattana Jaroenlak, Kacie L. McCarty, Damian C. Ekiert, Gira Bhabha
[DESCRIPTION]
Encephalitozoon intestinalis is a human-infecting microsporidian species, which can caus... | ["[Section 1: Parasite propagation and host cell lysis] Seed 2.1 × 106 Vero cells in a T-75 tissue culture flask with DMEM:HG supplemented with 10% FBS and 1X Non Essential Amino Acids.", "[Section 1: Parasite propagation and host cell lysis] After 48 hours, change media to DMEM: HG supplemented with 3% FBS and 1X Non ... |
39,576 | 4% Formaldehyde in .1M PB (FOR IMMUNO BRAINS) (1L) | 1 | null | https://www.protocols.io/view/4-formaldehyde-in-1m-pb-for-immuno-brains-1l-bivyke7w | Molly Brennan, Olivier George | TITLE: 4% Formaldehyde in .1M PB (FOR IMMUNO BRAINS) (1L)
AUTHORS: Molly Brennan, Olivier George
[STEPS]
?. .4M Phosphate buffer pH 7.4 (250mls)21.7 g Na2 HPO4 (sodium phosphate dibasic-heptahydrous) [86.8 g]~Make sure dibasic completely dissolves before adding monobasic! 2.6 g Na... | [".4M Phosphate buffer pH 7.4 (250mls)21.7 g Na2 HPO4 (sodium phosphate dibasic-heptahydrous) [86.8 g]~Make sure dibasic completely dissolves before adding monobasic! 2.6 g Na H2 PO4 (sodium phosphate monobasic-monohydrous) [10.4 g]Dissolve in 200 ml of d... |
null | null | null | dx.doi.org/10.17504/protocols.io.feubjew | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
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?.
?.
?.
?.
?.
?. | [] |
14,627 | Human Islet Purification - COBE setup | null | dx.doi.org/10.17504/protocols.io.sibecan | null | James Lyon, Patrick MacDonald, Jocelyn Manning Fox | TITLE: Human Islet Purification - COBE setup
AUTHORS: James Lyon, Patrick MacDonald, Jocelyn Manning Fox
[STEPS]
?. [Purge]
Turn on COBE 2991 processors and purge as follows:Set dials; centrifuge speed to 3000 rpm, super out rate to 450 mL/min and super out volume to 600 mL.Install foam ring and plastic shim in to COB... | ["[Purge]\nTurn on COBE 2991 processors and purge as follows:Set dials; centrifuge speed to 3000 rpm, super out rate to 450 mL/min and super out volume to 600 mL.Install foam ring and plastic shim in to COBE.Press START/SPIN, when rpm are at 3000, press SUPER OUT.Once alarm sounds press STOP/RESET.Allow COBE 2991 bowl ... |
66,891 | Où acheter Diaetoxil Avis, Diaetoxil Avis France Et Prix Detoxil En France Sur Le Site Officiel Achetez Maintenant ! | 1 | dx.doi.org/10.17504/protocols.io.4r3l2ok44v1y/v1 | https://www.protocols.io/view/o-acheter-diaetoxil-avis-diaetoxil-avis-france-et-cdjjs4kn | typcarter | TITLE: Où acheter Diaetoxil Avis, Diaetoxil Avis France Et Prix Detoxil En France Sur Le Site Officiel Achetez Maintenant !
AUTHORS: typcarter
[DESCRIPTION]
➢ Nom du produit - Detoxil Avis
➢Bénéfices clés - Améliorer la santé
➢ Structure - Composé Organique Naturel
➢ Effets secondaires - NA
➢ Note - ★★★★★
➢ Typ... | ["[Où acheter Diaetoxil Avis, Diaetoxil Avis France Et Prix Detoxil En France Sur Le Site Officiel Achetez Maintenant !]"] |
49,363 | Nuclei isolation from frozen gonad tissue | 1 | dx.doi.org/10.17504/protocols.io.n2bvjxqewlk5/v1 | https://www.protocols.io/view/nuclei-isolation-from-frozen-gonad-tissue-buftntnn | Maria del Carmen Sancho Serra or Carmen Sancho Serra | TITLE: Nuclei isolation from frozen gonad tissue
AUTHORS: Maria del Carmen Sancho Serra or Carmen Sancho Serra
[DESCRIPTION]
This protocol describes how to perform nuclei isolation from frozen gonad tissues using Dounce homogenizers. It can be used as well for ovary strips frozen in OCT
[GUIDELINES]
Human tissue and... | ["[Buffer preparation] Nuclei Isolation Buffer 1 (NIM1)\n\nCan be made, filtered and stored at 4°C for up to 6 months\n\n \nNuclei Isolation Buffer 2 (NIM2)\n\nTo be made and used on the day of experiment, keep on ice.\nPre-dilute 1M DTT: 5 ml 1 M DTT in 4.995 ml water.\nFor 100x Protease inhibitor stock, dissolve 1 ta... |
108,275 | SHARE-seq protocol v2.2 | 4 | null | https://www.protocols.io/view/share-seq-protocol-v2-2-dmyt47wn | Amelia Hall | TITLE: SHARE-seq protocol v2.2
AUTHORS: Amelia Hall
[DESCRIPTION]
An updated version of the protocol SHARE-seq, as used by the Epigenomics Platform and Gene Regulation Observatory at the Broad Institute in the service of data production for the IGVF project. Link to the original paper and protocol here: https://www.s... | ["[1.1 Ordering Oligo Plates and oligos for plate production] One of the more involved aspects of SHARE-seq (and SPLiT-seq) is properly making the oligo hybridization 96 well plates - this section covers that in detail before moving into any of the day to day aspects of this protocol (those start at step 24, in section... |
77,276 | Change Release Protocol | 1 | dx.doi.org/10.17504/protocols.io.5jyl8jk57g2w/v1 | https://www.protocols.io/view/change-release-protocol-cpp4vmqw | Abhishek Srivastava | TITLE: Change Release Protocol
AUTHORS: Abhishek Srivastava
[DESCRIPTION]
This is a set of protocols for releasing the changes or new feature to staging and production. This in being introduced so as the developer does not skip any critical step required during the whole release process. Any critical step if is missed... | ["[Merge checklist Staging] Merge checklist Staging", "[Merge checklist Staging] Regen pb.go from shared-proto master branch", "[Merge checklist Staging] Test in local", "[Merge checklist Staging] Test in feature env: <name of the feature environment>", "[Merge checklist Staging] Test Party", "[Merge checklist Staging]... |
103,219 | Wastewater grab sample processing with PEG-8000 precipitation | 0 | dx.doi.org/10.17504/protocols.io.4r3l2q3ojl1y/v1 | https://www.protocols.io/view/wastewater-grab-sample-processing-with-peg-8000-pr-dg2t3yen | Dilip Abraham, Nirmal kumar, Vinoth kumar, Ganesh Rajamanickam, Venkata Raghava Mohan | TITLE: Wastewater grab sample processing with PEG-8000 precipitation
AUTHORS: Dilip Abraham, Nirmal kumar, Vinoth kumar, Ganesh Rajamanickam, Venkata Raghava Mohan
[DESCRIPTION]
PEG (Polyethylene Glycol) is a chemically inert, nontoxic, water-soluble synthetic polymer and has been used in aqueous polymer two-phase sy... | ["[Sample] Wastewater grab samples", "[Procedural steps - PEG 8000 concentration method:] Collect 350 mL of sewage samples in a sterile Whirl-Pak bag and disinfect the sampling bag with ethanol to avoid contamination.", "[Procedural steps - PEG 8000 concentration method:] Transfer the bag to the laboratory in a cold... |
null | null | null | dx.doi.org/10.17504/protocols.io.e8sbhwe | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Protocol for Transfection Mouse Embryonic Stem Cells. </p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.cp3vqm | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
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36,751 | Growing overnight culture of OP50 as worm food | null | dx.doi.org/10.17504/protocols.io.bf5pjq5n | https://www.protocols.io/view/growing-overnight-culture-of-op50-as-worm-food-bf5pjq5n | Priota Islam | TITLE: Growing overnight culture of OP50 as worm food
AUTHORS: Priota Islam
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Luria broth (LB) is a nutrient-rich media commonly used to culture bacteria in the lab. LB agar plates are frequently used to isolate individual (clonal) colonies of bacteria c... | ["Obtain LB Broth from the Media kitchen- Make sure to make at least 500ml in volume for standardisation purposesLB Broth contents: 4gNaCl4 g Tryptone2 g Yeast Extract dH2O to 400 mL", "Obtain sterile Erlenmeyer flask from the media kitchen", "Wipe the work area with 70% ethanol and create a relatively sterile environm... |
53,809 | Polymerase chain reaction (PCR) | 4 | dx.doi.org/10.17504/protocols.io.bysrpwd6 | https://www.protocols.io/view/polymerase-chain-reaction-pcr-bysrpwd6 | Shuning Guo | TITLE: Polymerase chain reaction (PCR)
AUTHORS: Shuning Guo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is used to amplify target DNA fragment for plasmid construction or other use.</div></div>
[STEPS]
?. Choose one case from the cases below.
?. Add the following reagent to a PC... | ["Choose one case from the cases below.", "Add the following reagent to a PCR tube.(50 μl).2×High Fidelity Master Mix (MCLAB)25 μlTemplate1 μlForward Primer (10 μM)1 μlReverse Primer (10 μM)1 μlddH2O22 μl\n2×High Fidelity Master Mix (MCLAB)25 μlTemplate1 μlForward Primer (10 μM)1 μlReverse Primer (10 μM)1 μlddH2O22 μl"... |
42,307 | Chapter 4: Broken bones and dislocations | 4 | null | https://www.protocols.io/view/chapter-4-broken-bones-and-dislocations-bmjbk4in | Kerri Wolter | TITLE: Chapter 4: Broken bones and dislocations
AUTHORS: Kerri Wolter
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes how to treat broken bones and dislocations in vultures.</div></div>
[STEPS]
?. [Wing wraps]
When deciding which wrap to use, consider the location of the fra... | ["[Wing wraps]\nWhen deciding which wrap to use, consider the location of the fracture. The function of wing wraps is to stabilize the joints on either side of the fracture. Therefore, if a fracture occurs in the upper part of the wing (humerus, shoulder, or pectoral girdle: scapula, clavicle and coracoid) the wing wil... |
39,848 | Yoga compared to non-exercise or physical therapy exercise on pain, disability, and quality of life for patients with chronic low back pain: A systematic review and meta-analysis of randomized controlled trials | 1 | dx.doi.org/10.17504/protocols.io.bi6gkhbw | https://www.protocols.io/view/yoga-compared-to-non-exercise-or-physical-therapy-bi6gkhbw | 301910411478 | TITLE: Yoga compared to non-exercise or physical therapy exercise on pain, disability, and quality of life for patients with chronic low back pain: A systematic review and meta-analysis of randomized controlled trials
AUTHORS: 301910411478
[STEPS]
?. Paste List
?. Click Preview button | ["Paste List", "Click Preview button"] |
44,568 | Multiplexed snRNA-seq from frozen human brain samples | 4 | dx.doi.org/10.17504/protocols.io.kqdg369keg25/v1 | https://www.protocols.io/view/multiplexed-snrna-seq-from-frozen-human-brain-samp-bprymm7w | Marcos Nascimento | TITLE: Multiplexed snRNA-seq from frozen human brain samples
AUTHORS: Marcos Nascimento
[STEPS]
SECTION: CellPlex Barcoding
19. Add 1.9 mL of cold WRB supplemented with RNAse inhibitor. Gently pipette mix
SECTION: Preparation
2. Clean bench and pipettes with RNAse Zap.
SECTION: Nuclei Isolation
5. Use glass dounce ... | ["[CellPlex Barcoding] Add 1.9 mL of cold WRB supplemented with RNAse inhibitor. Gently pipette mix", "[Preparation] Clean bench and pipettes with RNAse Zap.", "[Nuclei Isolation] Use glass dounce homogenizer (Thomas Scientific; Catalog # 3431D76; size A). Put douncer on ice, pipette 1mL of lysis in the douncer. Transf... |
49,417 | Downloading Viral Metagenome Data | 5 | dx.doi.org/10.17504/protocols.io.buhhnt36 | https://www.protocols.io/view/downloading-viral-metagenome-data-buhhnt36 | Benjamin Bolduc | TITLE: Downloading Viral Metagenome Data
AUTHORS: Benjamin Bolduc
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Downloading reads from the </span><a href="https://github.com/MicroB3-IS/osd-analysis" style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;">Ocean Sampl... | ["[Download from SRA]\nOpen FASTQ-dump", "[Download from SRA]\nSpecify the SRA accession", "[Getting Started]\nThis is the very first step in downloading reads from Ocean Sampling Day (2014). If you navigate through their wiki and other documentation, you can find the SRA associated with this dataset: ERR771003.There a... |
104,646 | CDPH modified Artic v3 primers for SARS-CoV-2 sequencing | 0 | dx.doi.org/10.17504/protocols.io.x54v92w5pl3e/v1 | https://www.protocols.io/view/cdph-modified-artic-v3-primers-for-sars-cov-2-sequ-dife4bje | John Bell | TITLE: CDPH modified Artic v3 primers for SARS-CoV-2 sequencing
AUTHORS: John Bell
[DESCRIPTION]
This protocol lists the primer bed file for a modified Artic v3 set for SARS-CoV-2 sequencing. Two primers have been added to reduce dropouts.
[STEPS]
1. The attached bed file is a modified Artic v3 primer location list... | ["The attached bed file is a modified Artic v3 primer location list for SARS-CoV-2, used for sequencing by California Dept. of Public Health Viral and Rickettsial Disease Laboratory during the COVID-19 pandemic."] |
65,674 | Preparation of acute midbrain slices containing the superior colliculus and periaqueductal gray for patch-clamp recordings | 4 | dx.doi.org/10.17504/protocols.io.8epv51pz5l1b/v6 | https://www.protocols.io/view/preparation-of-acute-midbrain-slices-containing-th-ccdiss4e | Oriol Pavon Arocas, Tiago Branco | TITLE: Preparation of acute midbrain slices containing the superior colliculus and periaqueductal gray for patch-clamp recordings
AUTHORS: Oriol Pavon Arocas, Tiago Branco
[DESCRIPTION]
This protocol is a practical guide for preparing acute coronal slices from the midbrain of young adult mice for electrophysiology exp... | ["[General considerations]", "[General considerations] Abbreviations\n\n ACSF, artificial cerebrospinal fluid\n AgCl, silver chloride\n CaCl2, calcium chloride\n cm, centimetre\n CO2, carbon dioxide\n ddH2O , double distilled water\n g, gram\n HCl, hydrochloric ac... |
null | null | null | dx.doi.org/10.17504/protocols.io.izxcf7n | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
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?.
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80,902 | Inhibitor removal from DNA extracts | 1 | dx.doi.org/10.17504/protocols.io.rm7vzbp54vx1/v1 | https://www.protocols.io/view/inhibitor-removal-from-dna-extracts-cs9ewh3e | Dominik Buchner, Marie Borowski | TITLE: Inhibitor removal from DNA extracts
AUTHORS: Dominik Buchner, Marie Borowski
[DESCRIPTION]
This protocol describes how to remove inihibitory substances such as humic substances from DNA that has already been extracted. The protocol is formulated for an initial input of 100 µL of extracted DNA however it can be ... | ["[Inhibitor removal from DNA extracts] Prepare 100 µL of sample in 2 mL tubes.", "[Inhibitor removal from DNA extracts] Add 345 µL and 60 µL .\nVortex shortly.", "[Inhibitor removal from DNA extracts] 10000 x g, 20 °C . Transfer all of the supernatant to a new tube.", "[Inhibitor removal from DNA extracts] Add125 µL ,... |
null | null | null | dx.doi.org/10.17504/protocols.io.nkxdcxn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol is for dephosphorylation of 5´-ends of DNA using rSAP in restriction enzyme reaction (M0371)
[STEPS]
?.
?.
?.
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?. | [] |
95,577 | Efficient transfection protocol of rainbow trout gills epithelial (RTgill-W1) cell line through nucleofection system. | 0 | dx.doi.org/10.17504/protocols.io.8epv5x4yng1b/v1 | https://www.protocols.io/view/efficient-transfection-protocol-of-rainbow-trout-g-c9jzz4p6 | Sebastián Escobar-Aguirre, Amanda Escorza, Matias Escobar-Aguirre | TITLE: Efficient transfection protocol of rainbow trout gills epithelial (RTgill-W1) cell line through nucleofection system.
AUTHORS: Sebastián Escobar-Aguirre, Amanda Escorza, Matias Escobar-Aguirre
[DESCRIPTION]
In this protocol, we optimize the experimental condition to express plasmid DNA in salmonid fish rainbow ... | ["[Cell preparation] Before electroporation, cells should be between about 70 - 90% confluent (i.e 6x10e6 cells/ml in a 175 cm2 flask).", "[Cell preparation] Neutralize cells with growth medium 9 mL into the flask.", "[Cell preparation] Wash cells monolayer 2 times with 5 mLand 1 mL", "[Electroporation] Apply 1600 vo... |
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