id float64 1.55k 110k ⌀ | title stringlengths 1 256 ⌀ | template_id float64 0 6 ⌀ | doi stringlengths 39 49 ⌀ | url stringlengths 40 92 ⌀ | authors stringlengths 1 933 ⌀ | protocol_text stringlengths 34 1.08M | steps_list stringlengths 2 269k |
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null | null | null | dx.doi.org/10.17504/protocols.io.ng4dbyw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Este protocolo describe los pasos para propagar <em>in vitro</em> hongos tipo <strong>sombrero</strong> (Ver <a href=" https://www.protocols.io/private/be76339cd7204260002c2492d08d30cf" target="_blank">este</a> protocolo para hongos tipo <strong>terraza</strong>). Este protoc... | [] |
61,381 | A Complete Guide to Tardigrade Isolation and Phylogenetic Characterization for Undergraduate Students | 4 | dx.doi.org/10.17504/protocols.io.81wgb64qqlpk/v1 | https://www.protocols.io/view/a-complete-guide-to-tardigrade-isolation-and-phylo-b77drri6 | Tom D'Elia, Megan Carroll, Martin Almberg, Kyle Bartow | TITLE: A Complete Guide to Tardigrade Isolation and Phylogenetic Characterization for Undergraduate Students
AUTHORS: Tom D'Elia, Megan Carroll, Martin Almberg, Kyle Bartow
[DESCRIPTION]
Here we present a complete guide for the isolation and phylogenetic characterizations of tardigrades suitable for the undergraduate... | ["[Collecting Lichens and Moss for Tardigrade Isolation] Gather materials required to collect Tardigrades from environmental samples.\nLab notebook\nPetri dish or shallow clear container\nRazor blade or pocket knife\nPen or marker\nGPS enabled device", "[Collecting Lichens and Moss for Tardigrade Isolation] Find a lich... |
49,735 | NGS Protocol Automation | 5 | null | https://www.protocols.io/view/ngs-protocol-automation-butfnwjn | erick.rios. | TITLE: NGS Protocol Automation
AUTHORS: erick.rios.
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Automation_v1_2.sh</div><div class = "text-block"> Written by Erick (02/05/2021)</div><div class = "text-block">--------------------------------------------</div><div class = "text-block">Hello to "v... | ["ENTIRE=n\n ALIGNMENTS=n\n REGIONS=n\n MUTATIONS=n\n INDEX=n\n echo -n \"Perform ENTIRE Protocol? (Y/n): \"read ENTIREif [[ “$ENTIRE” == Y ]]; then\n echo “WILL perform ENTIRE protocol.”\n fiif [ $ENTIRE != n -a $ENTIRE != Y ]; then\n echo “You said $ENTIRE, assuming ‘NO’”\n ENTIRE=n\n fi\n ###########################... |
86,383 | CAMbank: CPT Field Processing v1 | 4 | null | https://www.protocols.io/view/cambank-cpt-field-processing-v1-cykpxuvn | Eliah G Overbey, Krista A Ryon, jak, chm2042 | TITLE: CAMbank: CPT Field Processing v1
AUTHORS: Eliah G Overbey, Krista A Ryon, jak, chm2042
[DESCRIPTION]
Field processing of CPT vacutainers for the Cornell Aerospace Medicine Biobank (CAMbank).
Instructions for preserving: Plasma, PBMCs, and RBC Pellets.
[STEPS]
SECTION: Perform Venipuncture
1. After venipunctur... | ["[Perform Venipuncture] After venipuncture, invert the tubes 8 to 10 times to fully mix in the sodium heparin anticoagulant.\n\nStore the tube upright at room temperature until centrifugation.\n\nTo ensure proper barrier formation, blood samples should be centrifuged within 2 hours of blood collection. Centrifugation ... |
null | null | null | dx.doi.org/10.17504/protocols.io.ke8cthw | null | null | TITLE: No Title
AUTHORS:
[STEPS] | [] |
36,617 | SPARC Cat - Sham Control Chronic Cat 1, Day 14 | 1 | dx.doi.org/10.17504/protocols.io.bfzhjp36 | https://www.protocols.io/view/sparc-cat-sham-control-chronic-cat-1-day-14-bfzhjp36 | Brett Hanzlicek, Anna Rietsch, Margot Damaser | TITLE: SPARC Cat - Sham Control Chronic Cat 1, Day 14
AUTHORS: Brett Hanzlicek, Anna Rietsch, Margot Damaser
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a procedure for a sham control chronic cat experiment (Day 14) for cystotomy (bladder surgery). The cystotomy is performed without U... | ["[Transport Cat]\nTransport cat from housing site to surgery site.", "[Animal Prep and catheter placement]\nAnimal is anesthetized and abdomen is shaved by the vet team. The cat is then moved into the surgery room and attached to monitors by the vet team.", "[Animal Prep and catheter placement]\nDrape animal and perf... |
49,194 | iPSC Image Analysis: From raw pics to .csv file | 5 | null | https://www.protocols.io/view/ipsc-image-analysis-from-raw-pics-to-csv-file-buainsce | Jesse Cohn | TITLE: iPSC Image Analysis: From raw pics to .csv file
AUTHORS: Jesse Cohn
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the pipeline I've been using to analyze images from the InCell of the Kampmann i3N-CRISPRi cell lines. The broad overall steps are:</div><div class = "te... | ["[Installing needed software]\nThis protocol utilizes a Python package called \"StarDist\" to identify nuclei and make \"label images\", which are then subsequently analyzed in CellProfiler. For StarDist, see this website for instructions on how to install the package (and for information about the package in general)... |
20,492 | Antidepressant for Symptoms Remission of Gastroesophageal Reflux Disease: A Network Meta-Analysis (protocol) | null | dx.doi.org/10.17504/protocols.io.x9kfr4w | null | Xiaobei Si, Linyu Huo, Shuai Wang, Yu Lan, Shuo Zhang, Xumin Zhang | TITLE: Antidepressant for Symptoms Remission of Gastroesophageal Reflux Disease: A Network Meta-Analysis (protocol)
AUTHORS: Xiaobei Si, Linyu Huo, Shuai Wang, Yu Lan, Shuo Zhang, Xumin Zhang
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Objective</span><span> To ... | [] |
28,877 | Induction of Type 1 Diabetes, Myocardial Infarction, Echocardiography, Measurement of Blood Glucose and Tissue Weights | null | dx.doi.org/10.17504/protocols.io.8fmhtk6 | null | Michael Hill | TITLE: Induction of Type 1 Diabetes, Myocardial Infarction, Echocardiography, Measurement of Blood Glucose and Tissue Weights
AUTHORS: Michael Hill
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span></div><div class = "text-block"><span>This protocol pre... | ["Induction of Type 1 DM Type 1 DM was induced in male Sprague–Dawley rats by administering a single intraperitoneal (i.p.) injection of streptozotocin (STZ) (65 mg/kg body wt) (Sigma) prepared daily in citrate buffer pH 4.5 for maximal stability. The control group was injected with the vehicle only. Development of DM ... |
78,207 | Single-cell Epi2-Seq | 1 | null | https://www.protocols.io/view/single-cell-epi2-seq-cqk7vuzn | Christoph Geisenberger, Jeroen van den Berg, Vincent van Batenburg, Buys De Barbanson, Jeroen de Ridder, Alexander van Oudenaarden | TITLE: Single-cell Epi2-Seq
AUTHORS: Christoph Geisenberger, Jeroen van den Berg, Vincent van Batenburg, Buys De Barbanson, Jeroen de Ridder, Alexander van Oudenaarden
[DESCRIPTION]
Here we describe the full protocol for single-cell Epi2-Seq which enables joint readout of histone modifications and DNA methylation in ... | ["[Preparation of Tet1 Reaction Buffer and Fe2+ solution] Assemble TET1 reaction buffer (volumes are suggestions and can be scaled up or down)", "[Chromatin Immuno-Cleavage (ChIC)] Fixation and permeabilization\nHarvest cells and wash twice with PBS at room temperature (centrifuge 3 min, 500 g to pellet)\nResuspend cel... |
48,623 | NFIA is a gliogenic switch enabling rapid derivation of functional human astrocytes from pluripotent stem cells | 4 | dx.doi.org/10.17504/protocols.io.btqpnmvn | https://www.protocols.io/view/nfia-is-a-gliogenic-switch-enabling-rapid-derivati-btqpnmvn | Jason Tchieu, Elizabeth L. Calder, Sudha R. Guttikonda, Eveline M. Gutzwiller, Kelly A. Aromolaran, Julius A. Steinbeck, Peter A. Goldstein, Lorenz Studer | TITLE: NFIA is a gliogenic switch enabling rapid derivation of functional human astrocytes from pluripotent stem cells
AUTHORS: Jason Tchieu, Elizabeth L. Calder, Sudha R. Guttikonda, Eveline M. Gutzwiller, Kelly A. Aromolaran, Julius A. Steinbeck, Peter A. Goldstein, Lorenz Studer
[DESCRIPTION]
<div class = "text-blo... | ["[Cell culture]\nMaintain human pluripotent stem cells (both embryonic and induced) on vitronectin-coated dishes in Essential 8 (E8) medium (Thermo) as previously described.", "[Cell culture]\nPurchase induced PSCs.", "[Cell culture]\nCells were used for differentiation between passages 30–50 and passaged twice every ... |
20,411 | U Michigan - Glomerular Filtration Rate Determination with Minipump Inulin Clearance | null | dx.doi.org/10.17504/protocols.io.x63frgn | null | Jeff Hodgin | TITLE: U Michigan - Glomerular Filtration Rate Determination with Minipump Inulin Clearance
AUTHORS: Jeff Hodgin
[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">This is the prot... | ["Minipump preparation:\nThe micro-osmotic pumps are filled with approximately 100 μl of a 3 % FITC inulin solution.", "Procedures of surgery:\n2.1 Mice are anesthetized with isoflurane in gas anesthetic machine rented from Unit for Laboratory Animal Medicine (ULAM), University of Michigan.\n2.2 Two minipumps are inser... |
null | null | null | dx.doi.org/10.17504/protocols.io.gcrbsv6 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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17,570 | Single Cell and Single Nuclei Analysis Human Heart Tissue | null | dx.doi.org/10.17504/protocols.io.veae3ae | null | Monika Litvinukova, Eric Lindberg, Henrike Maatz, Hongbo Zhang, Michael Radke, Michael Gotthardt, Kourosh Saeb-Parsy, Sarah Teichmann, Norbert Hübner | TITLE: Single Cell and Single Nuclei Analysis Human Heart Tissue
AUTHORS: Monika Litvinukova, Eric Lindberg, Henrike Maatz, Hongbo Zhang, Michael Radke, Michael Gotthardt, Kourosh Saeb-Parsy, Sarah Teichmann, Norbert Hübner
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol provides a wal... | ["[Pre-processing ]\nTransfer the tissue into a petri dish with 1ml of the dPBS. Carefully clean off the fat without damaging the pericardium layer.", "[Pre-processing ]\nDetermine the orientation of the tissue for sectioning.In the ventricular tissue, the outer layer, pericardium, is very stiff, light-pink to white wi... |
31,715 | Comparative efficacy and safety of oral antihypertensive agents in pregnant women with chronic hypertension: a network meta-analysis | null | dx.doi.org/10.17504/protocols.io.ba8bihsn | null | Ioannis Bellos, Vasilios Pergialiotis, Georgios Daskalakis, Dimitrios Loutradis | TITLE: Comparative efficacy and safety of oral antihypertensive agents in pregnant women with chronic hypertension: a network meta-analysis
AUTHORS: Ioannis Bellos, Vasilios Pergialiotis, Georgios Daskalakis, Dimitrios Loutradis
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Chronic hypertension co... | ["Review title Comparative efficacy and safety of oral antihypertensive agents in pregnant women with chronic hypertension: a network meta-analysis", "Review question Population: Pregnant women with chronic/pre-existing hypertension Intervention: Oral antihypertensive treatment Comparator: Pregnant untreated women with... |
null | null | null | dx.doi.org/10.17504/protocols.io.gfabtie | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?. | [] |
26,750 | Emergency Contacts | null | dx.doi.org/10.17504/protocols.io.6c6haze | null | Steven Wilhelm, Gary LeCleir | TITLE: Emergency Contacts
AUTHORS: Steven Wilhelm, Gary LeCleir
[STEPS]
?. AB1Knoxville Fire Department9112Knoxville Police9113Ambulance Service91145UT Police974-3111 (call 911 first)67Environmental Health & Safety974-50848Radiation Safety Dept.974-55809BioSafety Dept. 974-19381011Steve Wilhelm (PRINCIPAL INVEST... | ["AB1Knoxville Fire Department9112Knoxville Police9113Ambulance Service91145UT Police974-3111 (call 911 first)67Environmental Health & Safety974-50848Radiation Safety Dept.974-55809BioSafety Dept. 974-19381011Steve Wilhelm (PRINCIPAL INVESTIGATOR)865-405-88171213Gary LeCleir865-368-1516\nAB1Knoxville Fire Departm... |
null | null | null | dx.doi.org/10.17504/protocols.io.crbv2m | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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35,297 | TissueCyte Image QC | null | dx.doi.org/10.17504/protocols.io.bep9jdr6 | null | Allen Institute for Brain Science | TITLE: TissueCyte Image QC
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the QC step that occurs after the week of TissueCyte runs, and prior to analysis.</div><div class = "text-block"><span style = "font-weight:bold;">Note</span>... | [] |
26,546 | UC Davis - Hematoxylin and Eosin (H&E) | null | dx.doi.org/10.17504/protocols.io.56sg9ee | null | Jennifer Rutkowsky | TITLE: UC Davis - Hematoxylin and Eosin (H&E)
AUTHORS: Jennifer Rutkowsky
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">Staining tissues on a slide with Heatoxylin and Eosin.</div><div class = "text-block"><span sty... | ["Heat slide to 37ºC for 20 min", "Move through the following solutions sequentially for the noted amount of time", "Mount tissue with a coverslip"] |
46,315 | isolating human malaria parasites for RNA-sequencing at ultra-low densities | 1 | dx.doi.org/10.17504/protocols.io.brgjm3un | https://www.protocols.io/view/isolating-human-malaria-parasites-for-rna-sequenci-brgjm3un | Kathryn Milne, Florian Bach, Wiebke Nahrendorf, J. Alexandra Rowe, Philip J Spence | TITLE: isolating human malaria parasites for RNA-sequencing at ultra-low densities
AUTHORS: Kathryn Milne, Florian Bach, Wiebke Nahrendorf, J. Alexandra Rowe, Philip J Spence
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The large subtelomeric multi-gene families encoded in the </span><span ... | ["[prepare in advance]\nsecurely insert the correct rotor into the centrifuges you will use", "[leukocyte depletion]\nRemoving virtually all white blood cells is essential for successful down-stream analysis of the parasite transcriptome. Each white cell contains at least 200 times the amount of RNA compared to a ring-... |
65,641 | Stem Cell Renew - Amazing Formula That Really Help You Faster! | 3 | dx.doi.org/10.17504/protocols.io.3byl4b8m2vo5/v1 | https://www.protocols.io/view/stem-cell-renew-amazing-formula-that-really-help-y-ccchsst6 | H A | TITLE: Stem Cell Renew - Amazing Formula That Really Help You Faster!
AUTHORS: H A
[DESCRIPTION]
We ought to explore how Stem Cell Renew capabilities and what makes the upgrade not equivalent to various recipes sold web based today.
[STEPS] | [] |
57,492 | A Survival Analysis based Volatility and Sparsity Modeling Network for Student Dropout Prediction | 1 | dx.doi.org/10.17504/protocols.io.b4duqs6w | https://www.protocols.io/view/a-survival-analysis-based-volatility-and-sparsity-b4duqs6w | Feng Pan, Bingyao Huang , Chunhong Zhang, Xinning Zhu, Zhenyu Wu, Moyu Zhang, Yang Ji, Zhanfei Ma, Zhengchen Li | TITLE: A Survival Analysis based Volatility and Sparsity Modeling Network for Student Dropout Prediction
AUTHORS: Feng Pan, Bingyao Huang , Chunhong Zhang, Xinning Zhu, Zhenyu Wu, Moyu Zhang, Yang Ji, Zhanfei Ma, Zhengchen Li
[DESCRIPTION]
Student Dropout Prediction (SDP) is of pivotal significance in mitigating wit... | ["Prepare the dataset:\nWe conduct experiments on two benchmark datasets to evaluate our proposed model. Both of them are drawn from the largest MOOC platform in China, XuetangX (see https://www.xuetangx.com/). The first dataset KDDCup 2015 is available at https://www.biendata.xyz/competition/kddcup2015/data/, which ha... |
30,359 | Marchantia Cryopreservation of Gemmae | null | dx.doi.org/10.17504/protocols.io.9vxh67n | null | Marius Rebmann, marta tomaselli, Linda Silvestri, Susana Sauret-Gueto, Michelle Lim | TITLE: Marchantia Cryopreservation of Gemmae
AUTHORS: Marius Rebmann, marta tomaselli, Linda Silvestri, Susana Sauret-Gueto, Michelle Lim
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Simplified cryopreservation protocol for </span><span style = "font-style:italic;">Marchantia polymorpha </s... | ["[Preculture]\nCollect fresh gemmae and plate on preculture plates, incubate 1-3 days under normal growth conditions (e.g. 21°C constant light)", "[Encapsulation]\nPlace small drops (approx. 40μL) of alginate solution on an empty 4.5cm petridish/multi-well plate to form beads.", "[Encapsulation]\nUse forceps to transf... |
49,060 | Human Islet Cryopreservation Version 2.0 | 1 | dx.doi.org/10.17504/protocols.io.bt6cnraw | https://www.protocols.io/view/human-islet-cryopreservation-version-2-0-bt6cnraw | James Lyon, Aliya Spigelman, Jocelyn E Manning Fox, Patrick Macdonald | TITLE: Human Islet Cryopreservation Version 2.0
AUTHORS: James Lyon, Aliya Spigelman, Jocelyn E Manning Fox, Patrick Macdonald
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol details the cryopreservation of human islets, as performed by the Alberta Diabetes Institute IsletCore. Human i... | ["[Preparation of Solutions]\nABCDE1M199 (10L)ConcentrationWeight/VolumeSupplierCatalogue #2M199 powder9.41g/L\n1 bottle\nMediatech-Corning90050PB 33NaHCO326 mM\n22.0g\nFisher ScientificS233-5004HEPES10 mM\n23.83g\nFisher ScientificBP310-15Penicillin/Streptomycin20,000 U/ml penicillin and 20,000 μg/ml streptomycin50ml\... |
null | null | null | dx.doi.org/10.17504/protocols.io.qxbdxin | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol describes how to use agarose with a low gelling point (27-30°C; often called low-melting agarose) to immobilize Aiptasia larvae for microscopy.</p>
<p>Larvae stay alive and in one place for prolonged periods of several hours but continue to mainly spin around th... | [] |
25,303 | A step-by-step beginner’s protocol for whole genome sequencing of human bacterial pathogens | null | dx.doi.org/10.17504/protocols.io.4xxgxpn | null | Sanjay Gautam, Rajendra KC, Kelvin WC Leong, Micheál Mac Aogáin, Ronan F. O’Toole | TITLE: A step-by-step beginner’s protocol for whole genome sequencing of human bacterial pathogens
AUTHORS: Sanjay Gautam, Rajendra KC, Kelvin WC Leong, Micheál Mac Aogáin, Ronan F. O’Toole
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Bacterial whole genome sequencing (WGS) is becoming a widely-u... | ["[Extraction of bacterial genomic DNA]\nPellet the liquid culture media () by centrifuging at for in a sterile microfuge tube.\n200 µl\nCRITICAL STEP: All bacterial cultures should be treated as potentially pathogenic to the laboratory worker and colleagues. Therefore, the use of appropriate aseptic techniques, and ... |
55,773 | Picking worms | 1 | dx.doi.org/10.17504/protocols.io.b2p5qdq6 | https://www.protocols.io/view/picking-worms-b2p5qdq6 | Bonnie Evans | TITLE: Picking worms
AUTHORS: Bonnie Evans
[DESCRIPTION]
Transferring worms using a platinum wire pick
[STEPS]
1. Light the ethanol burner. Take care that there is nothing directly above it, eg. papers attached to shelf.
2. Place the platinum wire part of the pick in the flame to sterilise it. Let it cool before to... | ["Light the ethanol burner. Take care that there is nothing directly above it, eg. papers attached to shelf.", "Place the platinum wire part of the pick in the flame to sterilise it. Let it cool before touching the plate.", "Pick up some bacteria from the plate with the platinum wire.", "Look down the microscope to ide... |
94,624 | Sinai SCENT TMC - Olink NPX manager for Olink Data Analysis | 4 | null | https://www.protocols.io/view/sinai-scent-tmc-olink-npx-manager-for-olink-data-a-c8m8zu9w | Hui Xie | TITLE: Sinai SCENT TMC - Olink NPX manager for Olink Data Analysis
AUTHORS: Hui Xie
[DESCRIPTION]
To describe the procedures for using Fluidigm “Real-Time PCR Analysis” software and “Olink NPX manager” software to analyze Olink Assay data and generate final result reports. Fluidigm Real-Time PCR Analysis software gene... | ["[Raw data Ct value analysis] Copy the Biomark File (entire Chip-run folder corresponding to the Olink assay) from the Biomark Computer to USB drive, the size (~1.3 GB). There should be always 2 sub-folders and 4 files in the Chip run folder.", "[Raw data Ct value analysis] Connect USB drive from above step with HIMC ... |
null | null | null | dx.doi.org/10.17504/protocols.io.cv7w9m | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This is the synthesis protocol for modified nucleotides using the HiScribe™ T7 Quick High Yield RNA Synthesis Kit (E2050). The kit is capable of synthesizing biotin- or dye-modified RNA.
[GUIDELINES]
We strongly recommend wearing gloves and using nuclease-free t... | [] |
51,882 | Extraction of bacterial DNA using ChargeSwitch gDNA Mini Bacteria kit on KingFisher Flex robot | 1 | dx.doi.org/10.17504/protocols.io.bwwipfce | https://www.protocols.io/view/extraction-of-bacterial-dna-using-chargeswitch-gdn-bwwipfce | Leyi Wang, Carol Maddox, Melanie Prarat, Yan Zhang, Lifang Yan, Akhilesh Ramachandran, Sai Sankara Narayanan, Girish Patil, Sarah Nemser, Mothomang Oyinloye, Olgica Ceric | TITLE: Extraction of bacterial DNA using ChargeSwitch gDNA Mini Bacteria kit on KingFisher Flex robot
AUTHORS: Leyi Wang, Carol Maddox, Melanie Prarat, Yan Zhang, Lifang Yan, Akhilesh Ramachandran, Sai Sankara Narayanan, Girish Patil, Sarah Nemser, Mothomang Oyinloye, Olgica Ceric
[DESCRIPTION]
This procedure is... | ["Bacterial Broth Culture\n\nIf using broth, pick single colony and grow in 5 ml Trypticase Soy Broth (TSB), overnight grow at 37 degree without shaking. Use 0.4 ml of the bacterial culture and centrifuge for 4min at 8000 rpm, discard supernatant and resuspend the cell pellet in 100 μL of Resuspension Buffer (R4) conta... |
85,948 | LRRK2 and LAMP1 immunofluorescence staining in various cell lines | 4 | dx.doi.org/10.17504/protocols.io.bp2l6x991lqe/v1 | https://www.protocols.io/view/lrrk2-and-lamp1-immunofluorescence-staining-in-va-cx64xrgw | Siyu Chen, eva karasmanis | TITLE: LRRK2 and LAMP1 immunofluorescence staining in various cell lines
AUTHORS: Siyu Chen, eva karasmanis
[DESCRIPTION]
This protocol is being used to test the antibody , as well as . Please note that after multiple rounds of optimization, anti-LRRK2 antibody generates significant non-specific signals in the LRR... | ["[Day 0: : Seed cells] Add 300 µL of 11 ug/mL fibronectin into each ibidi well. Incubate at RT for 60 min.", "[Day 0: : Seed cells] Rinse the wells with PBS for 3 times", "[Day 0: : Seed cells] Make GDB buffer if necessary", "[Day 0: : Seed cells] Seed adherent cells to 40-80% confluency in each well. Incubate at 37 ... |
79,760 | Human Bladder organoid culture Lee et al 2018 | 4 | null | https://www.protocols.click/view/human-bladder-organoid-culture-lee-et-al-2018-cr5qv85w | Gabriela Vallejo Flores | TITLE: Human Bladder organoid culture Lee et al 2018
AUTHORS: Gabriela Vallejo Flores
[DESCRIPTION]
HUMAN
[BEFORE_START]
Washing medium: Organoid culture media (hepatocyte media with 10 ng/ml EGF, 5% CS-FBS, 10 mM Y-27632 (STEMCELL Technologies), and 1X Glutamax (GIBCO)),supplemented with 100 mg/ml Primocin.
Orga... | ["[Tumor digestion] Tumor tissues were then incubated in 10 mL of the organoid culture media supplemented with 100 mg/ml Primocin and 1:10 dilution of collagenase/hyaluronidase (STEMCELL Technologies) at 37 C for 15 min. Dissociated tissues were spun down at 350 g for 5 min, resuspended in 10 mL of PBS, and spun down a... |
84,239 | Ambulatory Recordings of Wireless Bladder and Colon Devices in Pigs | 1 | dx.doi.org/10.17504/protocols.io.n2bvj3y85lk5/v1 | https://www.protocols.io/view/ambulatory-recordings-of-wireless-bladder-and-colo-cwhpxb5n | Brett Hanzlicek | TITLE: Ambulatory Recordings of Wireless Bladder and Colon Devices in Pigs
AUTHORS: Brett Hanzlicek
[DESCRIPTION]
This protocol is for collecting ambulatory, wireless data from a coloMOCA impantled into a pig colon.
[STEPS]
SECTION: Ambulatory Testing
1. Place BluMOCA receiver radio into pocket on the pig jacket.
SE... | ["[Ambulatory Testing] Place BluMOCA receiver radio into pocket on the pig jacket.", "[Ambulatory Testing] Wake the coloMOCA with the waker set between 9V-15V, 1.5A.", "[Ambulatory Testing] Plug the Bluetooth dongle into the computer.", "[Ambulatory Testing] Record from ColoMOCA using LabVIEW software; take notes about... |
72,425 | Extraction and ONT MinLibrary Preparation of uHMW gDNA | 4 | null | https://www.protocols.io/view/extraction-and-ont-minlibrary-preparation-of-uhmw-ciyhuft6 | Kaylee S. Herzog, jfauver | TITLE: Extraction and ONT MinLibrary Preparation of uHMW gDNA
AUTHORS: Kaylee S. Herzog, jfauver
[DESCRIPTION]
This custom protocol optimizes extraction, purification, and Oxford Nanopore Technologies (ONT) MinION library preparation for ultra-high molecular weight genomic DNA (uHMW gDNA) from parasitic nematodes. It ... | ["[Part 1: Ultra-HWM gDNA extraction | Zymo Quick-DNA HWM MagBead Plus Kit | ~3 hr] Set dry bath to 55 °C", "For each sample, add the following to a clean 1.5 mL microcentrifuge tube to create a master mix:\n 95 µL \n 95 µL \n 10 µL", "Using a new pipette tip or sterilized forceps, add one whole ... |
88,441 | SMARTerV4 (0.5x) Amplification for single-cell or single-nuclei RNASeq Protocol | 1 | dx.doi.org/10.17504/protocols.io.8epv517xdl1b/v3 | https://www.protocols.io/view/smarterv4-0-5x-amplification-for-single-cell-or-si-c2kzycx6 | Allen Institute | TITLE: SMARTerV4 (0.5x) Amplification for single-cell or single-nuclei RNASeq Protocol
AUTHORS: Allen Institute
[DESCRIPTION]
Protocol to generate full-length cDNA from single cells, or nuclei, using Takara SMARTer V4.
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.c5zy75 | null | null | TITLE: No Title
AUTHORS:
[BEFORE_START]
Determine number of samples <strong>and</strong> standards to test in 96 well plate format. Multiply by 2 if running everything in duplicate for total number of wells. <br /><br />Use a black-walled plate with black bottoms if possible. Black-sided wells with clear bottoms o... | [] |
87,288 | TaqMan Array Card (TAC) for enteropathogen detection | 1 | dx.doi.org/10.17504/protocols.io.5qpvo3k8xv4o/v1 | https://www.protocols.io/view/taqman-array-card-tac-for-enteropathogen-detection-czgyx3xw | Jie Liu, erhk | TITLE: TaqMan Array Card (TAC) for enteropathogen detection
AUTHORS: Jie Liu, erhk
[DESCRIPTION]
Enteric infections are caused by a wide variety of pathogens and simultaneous infection with multiple pathogens can be common, thus making comprehensive diagnostic testing challenging. The TaqMan Array Card (TAC) is a 384... | ["[Total nucleic acid extraction from stool samples.] Sample preparation. For fecal samples, weigh 180–220 mg stool or 200ul if liquid, into a 2 ml screw top tube that is compatible with the bead beater. For rectal swab sample, it is recommended to use low stopper, plastic applicator. After the shaft of the swab is sna... |
78,977 | Soluble and insoluble A-SYN fractionation | 1 | dx.doi.org/10.17504/protocols.io.8epv5j515l1b/v1 | https://www.protocols.io/view/soluble-and-insoluble-a-syn-fractionation-crc9v2z6 | michela.deleidi, María José Pérez J., Hariam Raji, Pascale Baden, Federico Bertoli | TITLE: Soluble and insoluble A-SYN fractionation
AUTHORS: michela.deleidi, María José Pérez J., Hariam Raji, Pascale Baden, Federico Bertoli
[DESCRIPTION]
Soluble/insoluble alpha-synuclein fractionation is a technique used to separate different forms of the alpha-synuclein protein based on their solubility propertie... | ["[Soluble and insoluble A-SYN fractionation] Perform extraction and detection of Triton-soluble (T-sol) and Triton-insoluble (T-insol) alpha-synuclein as described in Stojkovska and Mazzulli 53.", "[Soluble and insoluble A-SYN fractionation] Lyse individual organoids in 1% Triton X-100 extraction buffer supplemented w... |
40,172 | SARS-CoV-2 McGill Artic PCR Protocol, 2.5 ul RT and V3 only + LA1 | 1 | dx.doi.org/10.17504/protocols.io.bjgkkjuw | https://www.protocols.io/view/sars-cov-2-mcgill-artic-pcr-protocol-2-5-ul-rt-and-bjgkkjuw | Sarah Reiling, Josh Quick, Ioannis Ragoussis | TITLE: SARS-CoV-2 McGill Artic PCR Protocol, 2.5 ul RT and V3 only + LA1
AUTHORS: Sarah Reiling, Josh Quick, Ioannis Ragoussis
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>V3 only primers for this protocol were designed using </span><a href="http://primal.zibraproject.org" style = "text-dec... | ["[Primer pool preparation]\nPRIMER POOL PREPARATIONIf required resuspend lyophilised primers at a concentration of 100 µM each\nV3 only primers for this protocol were designed using Primal Scheme and generate overlapping 400 nt amplicons. Primer names and dilutions are listed in the table below. https://github.com/sar... |
52,371 | MPRA library preparation | 1 | null | https://www.protocols.io/view/mpra-library-preparation-bxdtpi6n | Gerald Raffl, Boyan Bonev | TITLE: MPRA library preparation
AUTHORS: Gerald Raffl, Boyan Bonev
[DESCRIPTION]
Protocol to generate both DNA and RNA MPRA libraries.
[STEPS]
SECTION: DNA & RNA extraction from fixed nuclei
2. Pellet sorted nuclei in a 1.5 mL tube at 2500 x g, 4°C for 3min.
Resuspend pellet in 1X ProtK digestion buffer (95 µL ... | ["[DNA & RNA extraction from fixed nuclei] Pellet sorted nuclei in a 1.5 mL tube at 2500 x g, 4°C for 3min.\nResuspend pellet in 1X ProtK digestion buffer (95 µL nuclease free water, 95 µL 2X digestion buffer, 10 µL Proteinase K)", "[DNA & RNA extraction from fixed nuclei] Preheat a ThermoMixer to 55°C.", "[DNA... |
41,576 | OnsiteGene 3 Protocol Nasal Extract | 4 | dx.doi.org/10.17504/protocols.io.bkugkwtw | https://www.protocols.io/view/onsitegene-3-protocol-nasal-extract-bkugkwtw | yliu | TITLE: OnsiteGene 3 Protocol Nasal Extract
AUTHORS: yliu
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This OnsiteGene protocol is designed for testing the nasal swab samples with a superfast nucleic acid extraction procedure and a superfast real-time PCR procedure. It uses the Star Array® ... | ["[Sample Collection Procedure]\nAnterior nasal swab should be collected with the assistance of a healthcare worker or technician.", "[Sample Collection Procedure]\nBefore collection, clean hands using alcohol-based sanitizer or soap and water (no fragrances) and wear appropriate PPE (at minimum, gloves and a mask).", ... |
null | null | null | dx.doi.org/10.17504/protocols.io.dxa7id | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocols is from:<br />Daniel J. Dickinson, et al. (2015) <a href="http://www.genetics.org/content/early/2015/06/03/genetics.115.178335" target="_blank">Streamlined genome engineering with a self-excising drug selection cassette</a>. <em>Genetics</em><span class="cit-sep c... | [] |
91,838 | Western blotting to detect ATP13A2 | 1 | dx.doi.org/10.17504/protocols.io.e6nvwdqz2lmk/v1 | https://www.protocols.io/view/western-blotting-to-detect-atp13a2-c5w6y7he | Stephanie Vrijsen, Marine Houdou, Peter Vangheluwe | TITLE: Western blotting to detect ATP13A2
AUTHORS: Stephanie Vrijsen, Marine Houdou, Peter Vangheluwe
[DESCRIPTION]
Protocol to detect ATP13A2 via Western Blotting.
[STEPS]
SECTION: Harvesting cells
1. Collect the cells by using TrypLE.
SECTION: Harvesting cells
2. Centrifuge cell suspensions at 450 xg, 4°C for 5 min... | ["[Harvesting cells] Collect the cells by using TrypLE.", "[Harvesting cells] Centrifuge cell suspensions at 450 xg, 4°C for 5 min.", "[Harvesting cells] Resuspend cell pellets with DPBS and centrifuge following the same indications as in 2. Repeat once.", "[Harvesting cells] Discard supernatants and keep cell pellets ... |
27,819 | Phenol/Chloroform Genomic DNA extraction from Tissue Culture cells | null | dx.doi.org/10.17504/protocols.io.7ejhjcn | null | John Tyson | TITLE: Phenol/Chloroform Genomic DNA extraction from Tissue Culture cells
AUTHORS: John Tyson
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Old-School Phenol/Chloroform Genomic HMW DNA Preparation</span></div><div class = "text-block">In order to mitigate damage/s... | ["Remove tissue culture media from two T25 flasks of cells ( ~ 1 x 107 cells / per flask, or 60 – 80 % confluency)", "Pour the viscous sample into a 50 ml tube after gently scrapping the surface of the two T25’s with a cell scrapper.", "Incubate for at .\n37 °C", "Add proteinase K (20mg/ml) to a final concentration of... |
48,822 | Lachat: NO3 Protocol | 1 | null | https://www.protocols.io/view/lachat-no3-protocol-btwwnpfe | USDA | TITLE: Lachat: NO3 Protocol
AUTHORS: USDA
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Lachat NO3 Protocol.</div></div>
[STEPS]
?. Assemble all reagents/standards and check all reagent/standard levels to ensure you have enough to complete your analysis.IF STANDARDS AND SAMPLE WERE REFRIGERATED A... | ["Assemble all reagents/standards and check all reagent/standard levels to ensure you have enough to complete your analysis.IF STANDARDS AND SAMPLE WERE REFRIGERATED ALLOW >30 MIN TO WARM2 Reagents, Marked NO3/NO2Sulfanilamide Color ReagentAmmonium Chloride Buffer1 Carrier. WILL ALWAYS MATCH YOUR EXTRACTANT. 2M KCl orD... |
67,391 | Single cell survival assay | 4 | dx.doi.org/10.17504/protocols.io.4r3l2okxxv1y/v1 | https://www.protocols.io/view/single-cell-survival-assay-cd27s8hn | Hanqin Li, Dirk Hockemeyer | TITLE: Single cell survival assay
AUTHORS: Hanqin Li, Dirk Hockemeyer
[DESCRIPTION]
This protocol describes the experimental procedure used to measure single cell survival rates post nucleofection of human pluripotent stem cells (hPSCs).
General Notes:
1. Throughout these protocols, the term hPSC is used to collecti... | ["hPSCs are cultured on MEFs as described in the collection \"Thawing, Passaging, and Freezing of hPSCs on MEFS\" dx.doi.org/10.17504/protocols.io.b4msqu6e", "0.5 million hPSCs are nucleofected as described in “Nucleofection of hPSCs\" dx.doi.org/10.17504/protocols.io.b4pcqviw", "Seed 1/100, 1/500 of cells post-nucleof... |
51,183 | CPMU | 1 | null | https://www.protocols.io/view/cpmu-bv8pn9vn | Bjorn Bartholdy, a.g.henry | TITLE: CPMU
AUTHORS: Bjorn Bartholdy, a.g.henry
[DESCRIPTION]
Mineralising solution for the oral biofilm. From Sissons et al. 1991.
[BEFORE_START]
This solution MUST be prepared in a sterile and starch-free environment.
[STEPS]
1. Add 300 mL distilled (or deionized) dH2O to a 1000 mL beaker, with stirring and hea... | ["Add 300 mL distilled (or deionized) dH2O to a 1000 mL beaker, with stirring and heat 60 °C", "Add:\n\n- 1.55 g \n- 1.44 g \n- 0.72 g \n- 0.08 g \n- 30 g", "Add the remaining 700 mL and keep stirring until precipitate has completely dissolved\nStore in fridge at 4 °C"] |
63,879 | Martha MacCallum CBD Gummies THE MOST POPULAR CBD GUMMY BEARS IN UNITED STATES READ HERE REVIEWS, BENEFITS, SIDE EFFECT, INGREDIENTS, DOES IT REALLY WORK? IS IT SAFE? BUY NOW GET INSTANTLY | 1 | dx.doi.org/10.17504/protocols.io.q26g74629gwz/v1 | https://www.protocols.io/view/martha-maccallum-cbd-gummies-the-most-popular-cbd-camfsc3n | kaurnikki | TITLE: Martha MacCallum CBD Gummies THE MOST POPULAR CBD GUMMY BEARS IN UNITED STATES READ HERE REVIEWS, BENEFITS, SIDE EFFECT, INGREDIENTS, DOES IT REALLY WORK? IS IT SAFE? BUY NOW GET INSTANTLY
AUTHORS: kaurnikki
[DESCRIPTION]
Martha MacCallum CBD Gummies
[STEPS]
1. Martha MacCallum CBD GummiesProduct Review: ... | ["Martha MacCallum CBD GummiesProduct Review: —Martha MacCallum CBD GummiesUsed For: — 🔶Pain Relief\n🔶Health Benefits\n🔶Burn excess fat\n🔶Better gut health & promote digestion\n🔶Improves heart health\n🔶Control your appetite\n➢ Where to Buy - 🔶Click Here to Rush Your Order from the Official Website\n➤ Price (for... |
49,148 | Direct oligonucleotide sequencing with nanopores | 4 | dx.doi.org/10.17504/protocols.io.bt84nryw | https://www.protocols.io/view/direct-oligonucleotide-sequencing-with-nanopores-bt84nryw | Sachin Chalapati, Conor Crosbie, dixita limbachiya, Nimesh Pinnamaneni | TITLE: Direct oligonucleotide sequencing with nanopores
AUTHORS: Sachin Chalapati, Conor Crosbie, dixita limbachiya, Nimesh Pinnamaneni
[DESCRIPTION]
Third-generation DNA sequencing has enabled users to sequence long, unamplified DNA fragments with minimal steps. Direct sequencing of ssDNA or RNA gives valuable insigh... | ["[Normalization] Normalize 3xr6 dried oligo-pool to 0.25 uM with TE buffer and verified with Qubit 4 using Qubit ssDNA Assay Kit", "[Normalization] INS3 and EINS3 are diluted from their stock concentrations to 0.5 uM with TE buffer and verified with Qubit 4 using Qubit ssDNA Assay Kit", "[Normalization] INS3 RC, EINS3... |
51,613 | Viral sequence identification SOP with VirSorter2 | 5 | dx.doi.org/10.17504/protocols.io.bwm5pc86 | https://www.protocols.io/view/viral-sequence-identification-sop-with-virsorter2-bwm5pc86 | Jiarong Guo, Dean Vik, Akbar Adjie Pratama, Simon Roux, Matthew Sullivan | TITLE: Viral sequence identification SOP with VirSorter2
AUTHORS: Jiarong Guo, Dean Vik, Akbar Adjie Pratama, Simon Roux, Matthew Sullivan
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol shows how to use VirSorter2, checkV, DRAMv and some manual curation criteria for viral sequence ide... | ["[Install dependencies and prep test data]\nInstall dependenciesWe need following three tools for this SOP:VirSorter2(version >=2.2.3)CheckV(version >=0.7.0)DRAMv(version >=1.2.0)First lets create new conda environment for this tutorial:# install VirSorter2, checkV and DRAMv conda create -n viral-id-sop virsorter=2 ch... |
62,896 | OMS Atlas FFPE Spatial Mapping | 1 | null | https://www.protocols.io/view/oms-atlas-ffpe-spatial-mapping-b9nqr5dw | Brett Johnson, Danielle Galipeau, George Thomas | TITLE: OMS Atlas FFPE Spatial Mapping
AUTHORS: Brett Johnson, Danielle Galipeau, George Thomas
[DESCRIPTION]
This protocol describes the procedure by which the OMS Atlas serially sections a FFPE block, prepares the resulting slides, and then distributes the specimens for downstream analysis.
[BEFORE_START]
Transf... | ["[Preparation] Verify the identity of the FFPE block to be cut against written request for sectioning.", "[Preparation] Label each Tanner slide with a unique BEMS ID and slide number, corresponding to the written request and FFPE spatial map (below).", "[Sectioning] Align block on microtome to minimize tissue loss.", ... |
20,051 | U Mass - C-Peptide | null | dx.doi.org/10.17504/protocols.io.xttfnnn | null | Jason Kim | TITLE: U Mass - C-Peptide
AUTHORS: Jason Kim
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span></div><div class = "text-block">This experiment provides the quantification of multiple hormones using multiplexed-Luminex technology based on beads containin... | ["Add 200 µL of Assay Buffer into each well of the plate. Seal and mix on a plate shaker for 10 minutes at room temperature (20-25°C).", "Decant Assay Buffer and remove the residual amount from all wells by inverting the plate and tapping it smartly onto absorbent towels several times.", "Add 10 µL of appropriate matr... |
71,465 | Tissue Cyclic Immunofluorescence (t-CyCIF) version 3 | 1 | dx.doi.org/10.17504/protocols.io.5qpvorbndv4o/v2 | https://www.protocols.io/view/tissue-cyclic-immunofluorescence-t-cycif-version-3-ch2ht8b6 | Jia Ren Lin, Benjamin Izar, Zoltan Maliga, Yu-An Chen, Giorgio Gaglia, Ziming Du, Clarence Yapp, Shaolin Mei, Sandro Santagata, Peter Sorger | TITLE: Tissue Cyclic Immunofluorescence (t-CyCIF) version 3
AUTHORS: Jia Ren Lin, Benjamin Izar, Zoltan Maliga, Yu-An Chen, Giorgio Gaglia, Ziming Du, Clarence Yapp, Shaolin Mei, Sandro Santagata, Peter Sorger
[DESCRIPTION]
The architecture of normal and diseased tissues strongly influences the development and progres... | ["[Pre-Staining and Background Determination] Pre-staining and Background Determination takes approximately 16-24 hours.\n\nMake fluorophore bleaching solution. Combine 25 mL 1X PBS, 4.5 mL 30% (wt/vol) H2O2, and 0.8 mL 1 Molarity (M) NaOH in a 50-ml centrifuge tube. The final working concentration is 4.5% (wt/vol) H2O... |
null | null | null | dx.doi.org/10.17504/protocols.io.gztbx6n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Protocol for induction of protein production using the GAL1 promoter in yeast.</p>
[STEPS]
?.
?.
?.
?.
?.
?. | [] |
63,380 | Stamena 10RX | 3 | dx.doi.org/10.17504/protocols.io.kxygxz2kdv8j/v1 | https://www.protocols.io/view/stamena-10rx-b95ur86w | G Tsueng | TITLE: Stamena 10RX
AUTHORS: G Tsueng
[DESCRIPTION]
Once the blood spouts down to the penis, the penile district stands erect to satisfy the sex craving among women.
[STEPS] | [] |
48,768 | The impact of sleep on quality of life outcomes for prostate cancer patients and caregivers: A systematic review protocol | 1 | null | https://www.protocols.io/view/the-impact-of-sleep-on-quality-of-life-outcomes-fo-btu8nnzw | Rebecca Robbins, Chidera Ejikeme, Stephanie Orstad, Simona Porten, Carolyn Salter, Tatiana Sanchez-Nolasco, Dorice Viera, Stacy Loeb | TITLE: The impact of sleep on quality of life outcomes for prostate cancer patients and caregivers: A systematic review protocol
AUTHORS: Rebecca Robbins, Chidera Ejikeme, Stephanie Orstad, Simona Porten, Carolyn Salter, Tatiana Sanchez-Nolasco, Dorice Viera, Stacy Loeb
[DESCRIPTION]
<div class = "text-blocks"><d... | ["[Before Starting]\nBackground Prostate cancer treatment introduces potential barriers to sleep health, such as nighttime bladder irritation, night sweats and anxiety. Another major issue is sleep apnea, which has high global prevalence [1] and is associated with a greater risk of nocturia [3] and erectile dysfun... |
86,722 | IgG sequencing of rat hybridoma | 4 | dx.doi.org/10.17504/protocols.io.x54v9ppw1g3e/v1 | https://www.protocols.io/view/igg-sequencing-of-rat-hybridoma-cyxaxxie | Tamer B Shabaneh | TITLE: IgG sequencing of rat hybridoma
AUTHORS: Tamer B Shabaneh
[DESCRIPTION]
The purpose of this protocol is to amplify IgG antibody variable regions derived from rat hybridoma RNA, using RT-PCR and Sanger sequencing.
Materials needed:
- RNA extraction: Qiagen RNEasy mini kit (74104)
- Reverse Transcr... | ["[Primers] TS pF is ordered as RNA oligo; the remainder as DNA oligo\n\nuniversal TS pF\tAAGCAGTGGTATCAACGCAGAGTACATrGrGrG\n\nISPCR pF\t aagcagtggtatcaacgcagag\n\nrat IGHG RT pR\tGGACAGGGCTCCAGAGTTCC\n\nrat IGHG PCR pR\tGACTGGCTCAGGGAAATAGCC\n\nrat IGKC RT pR\tCTGATCAGTAACACTGTCCAGGAC\n\nrat IGKC PCR pR\tCACTGA... |
93,475 | Anatomical Verification (Mendonça et al 2024) | 1 | dx.doi.org/10.17504/protocols.io.14egn3o3ql5d/v1 | https://www.protocols.io/view/anatomical-verification-mendon-a-et-al-2024-c7ibzkan | Marcelo D Mendonça | TITLE: Anatomical Verification (Mendonça et al 2024)
AUTHORS: Marcelo D Mendonça
[DESCRIPTION]
Protocol for anatomical verification (sample prep, immunostaining and imaging) in Mendonça et al 2024.
[BEFORE_START]
Animals were euthanized after completion of the behavioural tests.
[STEPS]
SECTION: Sample Preparation... | ["[Sample Preparation] Anaesthetize mice with isoflurane, followed by intraperitoneal injection of ketamine-xylazine (5 mg/kg xylazine; 100 mg/kg ketamine).", "[Sample Preparation] Perfuse transcardially in 1% phosphate buffered saline (PBS) and then 4% paraformaldehyde (PFA) in PBS.", "[Sample Preparation] Dissect br... |
34,271 | nCoV-2019 sequencing protocol v2 | null | dx.doi.org/10.17504/protocols.io.bdp7i5rn | null | Josh Quick | TITLE: nCoV-2019 sequencing protocol v2
AUTHORS: Josh Quick
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">ARTIC amplicon sequencing protocol for MinION for nCoV-2019</div><div class = "text-block">This one-pot native barcoding protocol was developed in conjunction with Oxford Nanopore Technologies... | ["[cDNA preparation]\nMix the following components in an 0.2mL 8-strip tube;Component Volume50µM random hexamers 10mM dNTPs mix (10mM each) Template RNA Total\n1 µl\n1 µl\n11 µl\n13 µl\nViral RNA input from a clinical sample sho... |
91,300 | Perfusion and fixation of brain tissue for fresh frozen sections followed by immunofluorescence staining | 4 | dx.doi.org/10.17504/protocols.io.bp2l6xpr1lqe/v1 | https://www.protocols.io/view/perfusion-and-fixation-of-brain-tissue-for-fresh-f-c5ecy3aw | Martin T. Henrich, Fanni F. Geibl | TITLE: Perfusion and fixation of brain tissue for fresh frozen sections followed by immunofluorescence staining
AUTHORS: Martin T. Henrich, Fanni F. Geibl
[DESCRIPTION]
This protocol describes the generation of fresh frozen sections from mouse brain, and subsequent immunofluorescence staining.
[STEPS]
SECTION: Per... | ["[Perfusion and fixation-Before the Procedure] Set up equipment and Solutions: \n- PBS can be prepared from 10X concentrated solution\n\n- 4% PFA solution is prepared by diluting the concentrated PFA stock and PBS 10X stock.\nFor better results, it is recommended to prepare a fresh 4% PFA solution in PBS right before ... |
85,898 | CRISPR/Cas9 genome editing | 4 | dx.doi.org/10.17504/protocols.io.rm7vzxb38gx1/v1 | https://www.protocols.io/view/crispr-cas9-genome-editing-cx5ixq4e | wusj, schekman | TITLE: CRISPR/Cas9 genome editing
AUTHORS: wusj, schekman
[DESCRIPTION]
This protocol describes the generation of DNAJC5 KO using CRISPR/Cas9 edition
[STEPS]
SECTION: CRISPR/Cas9 genome editing
1. gRNA targeting exon 4 of DNAJC5 ( CACC GGAG GCCG CAGA AGAC AAAC A) was inserted into a
pX330-based plasmid expressing Ven... | ["[CRISPR/Cas9 genome editing] gRNA targeting exon 4 of DNAJC5 ( CACC GGAG GCCG CAGA AGAC AAAC A) was inserted into a\npX330-based plasmid expressing Venus fluorescent protein", "[CRISPR/Cas9 genome editing] HEK293T cells were transfected with pX330-pX330-Venus-DNAJC5-Exon4-gRNA by Lipofectamine 2000 followed the comme... |
91,759 | Tetraspeck Bead Imaging | 1 | dx.doi.org/10.17504/protocols.io.4r3l22br4l1y/v2 | https://www.protocols.io/view/tetraspeck-bead-imaging-c5upy6vn | Joseph S Beckwith | TITLE: Tetraspeck Bead Imaging
AUTHORS: Joseph S Beckwith
[DESCRIPTION]
Protocol for imaging tetraspeck beads on glass coverslips.
[STEPS]
SECTION: Slide Preparation
1. Glass coverslips (Fisher Scientific, 12373128, #1 thickness 22 mm x 50 mm) were plasma cleaned for 30 min (Ar plasma cleaner, PDC-002, Harrick Plasm... | ["[Slide Preparation] Glass coverslips (Fisher Scientific, 12373128, #1 thickness 22 mm x 50 mm) were plasma cleaned for 30 min (Ar plasma cleaner, PDC-002, Harrick Plasma).", "[Slide Preparation] Stick a frame-seal slide chamber (9 mm x 9 mm, SLF0201, Biorad) on the cover glass. Use some blunt tweezers to press down t... |
77,171 | BG11_and_inducer_preparation | 4 | dx.doi.org/10.17504/protocols.io.eq2ly71melx9/v1 | https://www.protocols.io/view/bg11-and-inducer-preparation-cpktvkwn | maurice.mager1808 | TITLE: BG11_and_inducer_preparation
AUTHORS: maurice.mager1808
[DESCRIPTION]
Protocol for the preparation of media and inducers used during the interlaboratory study published by Mager et al. 2023.
[STEPS]
SECTION: HEPES buffer preparation
2.
Buffer solutiong/LHEPES, NaOH (pH 8)240
SECTION: Stock solution 1 prepa... | ["[HEPES buffer preparation] Buffer solutiong/LHEPES, NaOH (pH 8)240", "[Stock solution 1 preparation] Stock 1g/LNaNO3600CaCl2 * 2H2O14.4", "[Stock solution 2 preparation] Stock 2g/LMgSO4 * 7H2O30FeCl3 * 6H2O1.62Na2EDTA * 2 H2O2.24Micronutrients400 mL", "[Stock solution 3 preparation] Stock 3g/LKH2PO416Na2EDTA * 2 H2O5... |
71,149 | Invertebrate bulk sample metabarcoding protocol collection | 2 | dx.doi.org/10.17504/protocols.io.j8nlkw4n6l5r/v1 | https://www.protocols.io/view/invertebrate-bulk-sample-metabarcoding-protocol-co-chqmt5u6 | Dominik Buchner | TITLE: Invertebrate bulk sample metabarcoding protocol collection
AUTHORS: Dominik Buchner
[DESCRIPTION]
This is a collection of protocols currently used in the LeeseLab to perform invertebrate bulk sample metabarcoding. Feel free to contact us if any questions arise.
[STEPS] | [] |
58,412 | RT-QuIC Assay for the Detection of Chronic Wasting Disease in Rectal Mucosa of White-Tailed Deer | 4 | dx.doi.org/10.17504/protocols.io.yxmvmn2y6g3p/v1 | https://www.protocols.io/view/rt-quic-assay-for-the-detection-of-chronic-wasting-b5akq2cw | Robert B. Piel, David A. Schneider, Aaron Lomax, Daniel Walsh, Eric M. Nicholson, Tracy A. Nichols, Susan E. Veneziano | TITLE: RT-QuIC Assay for the Detection of Chronic Wasting Disease in Rectal Mucosa of White-Tailed Deer
AUTHORS: Robert B. Piel, David A. Schneider, Aaron Lomax, Daniel Walsh, Eric M. Nicholson, Tracy A. Nichols, Susan E. Veneziano
[DESCRIPTION]
This protocol details a Real-Time Quaking-Induced Conversion (RT-QuIC) as... | ["[Sample Preparation: Rectal Mucosa Homogenization – 10% w/v] For each sample, prepare a 2-mL screw cap tube containing 1 g of 0.7 mm Zirconia beads (BioSpec 11079107zx) and label with sample/animal ID.", "[Sample Preparation: Rectal Mucosa Homogenization – 10% w/v] Weigh and add biopsy sample (up to 150 mg*) to each ... |
26,356 | Long Read Viromics Amplification Library Preparation (VirION 2) | 1 | null | https://www.protocols.io/view/long-read-viromics-amplification-library-preparati-5yug7ww | Marie Burris, Natalie Solonenko, Olivier Zablocki, Ben Temperton | TITLE: Long Read Viromics Amplification Library Preparation (VirION 2)
AUTHORS: Marie Burris, Natalie Solonenko, Olivier Zablocki, Ben Temperton
[STEPS]
?. [Sample Concentration ]
Prepare 48 ul of sample to use as input for the next step. Sample should have between 1ng - 100 ng of DNA for reliable library success. See... | ["[Sample Concentration ]\nPrepare 48 ul of sample to use as input for the next step. Sample should have between 1ng - 100 ng of DNA for reliable library success. See \"Preparation of extracted DNA for long-read library prep\" concerning preparation of DNA for this protocol.", "[DNA repair, End repair and dA tailing]\n... |
35,279 | Artificial Cerebrospinal Fluid IX (ACSF.IX) | null | dx.doi.org/10.17504/protocols.io.beppjdmn | null | Allen Institute for Brain Science | TITLE: Artificial Cerebrospinal Fluid IX (ACSF.IX)
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Artificial Cerebrospinal Fluid IX (ACSF.IX) is used for applications including tissue bath solution during electrophysiological recording for probing synaptic... | [] |
32,363 | MojoSort™ Whole Blood Human CD8 Nanobeads Whole Blood Column Protocol | null | dx.doi.org/10.17504/protocols.io.bbujinun | null | Sam Li | TITLE: MojoSort™ Whole Blood Human CD8 Nanobeads Whole Blood Column Protocol
AUTHORS: Sam Li
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>BioLegend MojoSort™ nanobeads work in commonly used separation columns, based on our internal research as well as validation by external testing by acade... | ["Collect whole blood in collection tube that has anticoagulant, preferably EDTA. Note: Keep MojoSort™ Buffer on ice throughout the procedure.", "Add 1mL of whole blood into a new tube.", "Resuspend the beads by vortexing, maximum speed, 5 touches. Add 50 µL of pre-diluted conjugated Nanobeads. Mix well and incubate on... |
43,580 | Hybridization of RNA Probes | 4 | dx.doi.org/10.17504/protocols.io.bns4megw | https://www.protocols.io/view/hybridization-of-rna-probes-bns4megw | Jonathan Houseley, Cristina Cruz | TITLE: Hybridization of RNA Probes
AUTHORS: Jonathan Houseley, Cristina Cruz
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Over the past decade a plethora of noncoding RNAs (ncRNAs) have been identified, initiating an explosion in RNA research. Although RNA sequencing methods provide unsurpassed i... | ["[Hybridization of RNA Probes]\nIMPORTANT: Make sure you have appropriate training to work with radioactivity under the local rules and legislation for your institution, and perform all radioactive work in the designated area.", "[Hybridization of RNA Probes]\nEnsure that the hybridization bottles and internal seals a... |
26,069 | CRISPR-Cas9 episome conjugation into Phaeodactylum tricornutum | null | dx.doi.org/10.17504/protocols.io.5pvg5n6 | null | Mark Moosburner, Andrew Allen | TITLE: CRISPR-Cas9 episome conjugation into Phaeodactylum tricornutum
AUTHORS: Mark Moosburner, Andrew Allen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Bacterial-conjugation methodology used to introduce the CRISPR-Cas9 episome generated using the GG2 assembly protocol.</div><div class = "text-... | ["[Prepare conjugation transformation plate]\nPrepare conjugation plate", "[Prepare conjugation transformation plate]\nAutoclave of 1.6% agarose solution (in MQ-H2O)Incubate autoclaved bottle/flask in waterbath\n45 ml\n50 °C", "[Prepare conjugation transformation plate]\nPipette mL of N-free ASW (Artificial Sea Wat... |
86,037 | CD3 Cell Density in Substantia Nigra and Cerebral Peduncle Image Analysis | 1 | dx.doi.org/10.17504/protocols.io.dm6gp3j9pvzp/v1 | https://www.protocols.io/view/cd3-cell-density-in-substantia-nigra-and-cerebral-cx9vxr66 | Hemanth Ramesh Nelvagal, Toby J Curless, Zane Jaunmuktane | TITLE: CD3 Cell Density in Substantia Nigra and Cerebral Peduncle Image Analysis
AUTHORS: Hemanth Ramesh Nelvagal, Toby J Curless, Zane Jaunmuktane
[DESCRIPTION]
QuPath is a bioimage analysis software designed for digital pathology and whole slide image analysis. This protocol describes how to measure CD3 density in t... | ["[Annotation] Manually annotate the substantia nigra and cerebral peduncle on NZConnect (Hamamatsu), a web-based whole-slide image (WSI) viewer.", "[Annotation] Download the annotations using a Python script then import into QuPath [1] using a Groovy script.", "[QuPath Deconvolution and CD3 Density Measurement] In QuP... |
4,608 | Genomic DNA extraction and PCR | null | dx.doi.org/10.17504/protocols.io.gq8bvzw | null | Mark Dewitt & Julia Wong | TITLE: Genomic DNA extraction and PCR
AUTHORS: Mark Dewitt & Julia Wong
[STEPS]
?. [Extraction]
Count cells
The amount of cells per µL of QuickExtract is flexible, depending on desired application. For assessment of editing outcomes (e.g. from pools of cells edited with the Cas9 RNP using our other protocols), use suf... | ["[Extraction]\nCount cells\nThe amount of cells per µL of QuickExtract is flexible, depending on desired application. For assessment of editing outcomes (e.g. from pools of cells edited with the Cas9 RNP using our other protocols), use sufficient cells to paint in accurate picture from a single PCR (>1000 cells per PC... |
39,607 | SOLUTION- 06 - Lysis Buffer | 3 | dx.doi.org/10.17504/protocols.io.biwxkffn | https://www.protocols.io/view/solution-06-lysis-buffer-biwxkffn | Marco Cosentino, Elisa Storelli, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Marco Ferrari, Franca Marino | TITLE: SOLUTION- 06 - Lysis Buffer
AUTHORS: Marco Cosentino, Elisa Storelli, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Marco Ferrari, Franca Marino
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This recipe is used in the following protocols:</div><div class = "text-block"><span styl... | [] |
89,477 | Brimblecombe, K.R. et al. (2023) Inhibition of striatal dopamine release by the L-type calcium channel inhibitor isradipine, co-varies with risk factors for Parkinson’s. | 2 | dx.doi.org/10.17504/protocols.io.4r3l27dxxg1y/v2 | https://www.protocols.io/view/brimblecombe-k-r-et-al-2023-inhibition-of-striatal-c3mdyk26 | Katherine Brimblecombe, Stephanie J Cragg | TITLE: Brimblecombe, K.R. et al. (2023) Inhibition of striatal dopamine release by the L-type calcium channel inhibitor isradipine, co-varies with risk factors for Parkinson’s.
AUTHORS: Katherine Brimblecombe, Stephanie J Cragg
[DESCRIPTION]
This collection contains three protocols detailing methods used in Brimbleco... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.f3xbqpn | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.qu2dwye | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
54,946 | RT-qPCR for detection of SARS-CoV-2 in wastewater | 4 | dx.doi.org/10.17504/protocols.io.bzwap7ae | https://www.protocols.io/view/rt-qpcr-for-detection-of-sars-cov-2-in-wastewater-bzwap7ae | David Findlay, Julie Bolland, Brindusa Cerghizan, Kirsty Campbell, David Thomson, Alexander Corbishley, David Gally, Stephen Fitzgerald, Alison Tidswell, Sean McAteer, Livia C T Scorza | TITLE: RT-qPCR for detection of SARS-CoV-2 in wastewater
AUTHORS: David Findlay, Julie Bolland, Brindusa Cerghizan, Kirsty Campbell, David Thomson, Alexander Corbishley, David Gally, Stephen Fitzgerald, Alison Tidswell, Sean McAteer, Livia C T Scorza
[DESCRIPTION]
As part of the global response to the 2019 novel Coro... | ["[Sample and equipment setup] At start of day, clean all surfaces with RNase away or 10% v/v bleach solution.", "[Sample and equipment setup] Turn on UV lamps in the Master Mix preparation cabinet and Template addition cabinet for 20 minutes.", "[Sample and equipment setup] Prior to analysis; ensure there are sufficie... |
20,410 | Nucleofection of iPSC | null | dx.doi.org/10.17504/protocols.io.x62frge | null | Celeste Karch, Rita Martinez, Jacob Marsh | TITLE: Nucleofection of iPSC
AUTHORS: Celeste Karch, Rita Martinez, Jacob Marsh
[STEPS]
?. [Nucleofection - Expand iPSCs]
Split 1 well from a 6 well plate into 3 wells in a 6 well plate.
Cells should be passaged as single cells prior to nucleofection. Split cells into 3 wells of a 6 well plate 48 hours prior to nucleo... | ["[Nucleofection - Expand iPSCs]\nSplit 1 well from a 6 well plate into 3 wells in a 6 well plate.\nCells should be passaged as single cells prior to nucleofection. Split cells into 3 wells of a 6 well plate 48 hours prior to nucleofection (plan for cells to be confluent in 48 hours). You will need 3 million cells per ... |
75,383 | The Health Impacts of Extreme Weather Events in Africa: A scoping review protocol | 1 | dx.doi.org/10.17504/protocols.io.n92ldpwdol5b/v1 | https://www.protocols.io/view/the-health-impacts-of-extreme-weather-events-in-af-cmuxu6xn | Galateia Terti, Sarah Louart, Sandrine Anquetin, Kouamé Kouadio, Valéry Ridde, Isabelle Ruin, Véronique Yoboué, Emmanuel Bonnet | TITLE: The Health Impacts of Extreme Weather Events in Africa: A scoping review protocol
AUTHORS: Galateia Terti, Sarah Louart, Sandrine Anquetin, Kouamé Kouadio, Valéry Ridde, Isabelle Ruin, Véronique Yoboué, Emmanuel Bonnet
[DESCRIPTION]
Background
In the last 20 years, 12,000 extreme weather events worldwide led to... | ["[INTRODUCTION] Rationale\nThe devastating effects of extreme weather and climate events on human health are evident, and they expect to increase in number and frequency due to changes in climatic conditions and urbanization in Africa and worldwide. Recent studies indicate the impact of extreme rainfall and heat waves... |
57,740 | Subcloning of genotype-confirmed hPSCs clones | 4 | dx.doi.org/10.17504/protocols.io.b4mkqu4w | https://www.protocols.io/view/subcloning-of-genotype-confirmed-hpscs-clones-b4mkqu4w | Hanqin Li, Yogendra Verma, Dirk Hockemeyer, Frank Soldner | TITLE: Subcloning of genotype-confirmed hPSCs clones
AUTHORS: Hanqin Li, Yogendra Verma, Dirk Hockemeyer, Frank Soldner
[DESCRIPTION]
This protocol describes a standard procedure for subcloning of genotype-confirmed human pluripotent stem cells (hPSCs).
General notes:
1. Throughout this protocol, the term hPSC is us... | ["Change medium to hPSCs medium + Rock inhibitor one day before subcloning", "Wash the genotype-confirmed wells with DPBS", "Add 25 µl Trypsin to those wells", "Incubate 5 min 37 °C", "Add 75 µl hPSCs medium + Rock inhibitor, mix well by pipetting", "Transfer dissociated cells to a 15 conical tube", "Prepare three MEF... |
44,832 | E_faecalis_conjugation_HR | 4 | null | https://www.protocols.io/view/e-faecalis-conjugation-hr-bpz8mp9w | Elizabeth Fozo | TITLE: E_faecalis_conjugation_HR
AUTHORS: Elizabeth Fozo
[STEPS]
?. [+Enterococcus faecalis conjugation and homologous recombination]
Inoculate 5 to 10 mL BHI (add antibiotics if necessary) with donor and recipient strains and incubate overnight at 37°C
?. [+Enterococcus faecalis conjugation and homologous recombinati... | ["[+Enterococcus faecalis conjugation and homologous recombination]\nInoculate 5 to 10 mL BHI (add antibiotics if necessary) with donor and recipient strains and incubate overnight at 37°C", "[+Enterococcus faecalis conjugation and homologous recombination]\nIn the morning, wash cultures 2x with BHI, then resuspend cel... |
37,356 | Mission, vision, and principles of the protocols.io company | 1 | dx.doi.org/10.17504/protocols.io.bgqkjvuw | https://www.protocols.io/view/mission-vision-and-principles-of-the-protocols-io-bgqkjvuw | Lenny Teytelman | TITLE: Mission, vision, and principles of the protocols.io company
AUTHORS: Lenny Teytelman
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is an internal document outlining our company culture and expectations for everyone who joins the team.</div></div>
[STEPS]
?. [Mission]
The broad mission... | ["[Mission]\nThe broad mission of protocols.io is to accelerate research by:increasing collaboration and sharing among researchersimproving efficiency of researchers by reducing mistakes and re-discovery", "[Mission]\nThe protocol-specific mission is to make it easy to share method details before, during and after publ... |
91,888 | Microsomal membrane isolation | 1 | dx.doi.org/10.17504/protocols.io.5qpvo3w7dv4o/v1 | https://www.protocols.io/view/microsomal-membrane-isolation-c5yqy7vw | Rania Abou El Asrar, Peter Vangheluwe | TITLE: Microsomal membrane isolation
AUTHORS: Rania Abou El Asrar, Peter Vangheluwe
[DESCRIPTION]
Microsomal membrane isolation
[STEPS]
SECTION: Harvest cells
1. Harvest cells by detachment with phosphate buffered saline (PBS, Sigma, D8537-500ml) + 0.2% EDTA.
SECTION: Harvest cells
2. Pellet cells by centrifugation... | ["[Harvest cells] Harvest cells by detachment with phosphate buffered saline (PBS, Sigma, D8537-500ml) + 0.2% EDTA.", "[Harvest cells] Pellet cells by centrifugation (5 min, 400 gavg, 4°C).", "[Harvest cells] Wash cell pellet in phosphate buffered saline (PBS, Sigma, D8537-500ml). Repeat 2 times.", "[Harvest cells] Pel... |
107,317 | Welcome & Onboarding | 0 | dx.doi.org/10.17504/protocols.io.14egn6m6zl5d/v2 | https://www.protocols.io/view/welcome-amp-onboarding-dk2v4ye6 | Andy Alexander, Emma Cimino | TITLE: Welcome & Onboarding
AUTHORS: Andy Alexander, Emma Cimino
[DESCRIPTION]
Must knows for onboarding at UCSB and in the Alexander laboratory.
[STEPS]
SECTION: Welcome to the Alexander lab!🙂 Below you will find useful information to help you get started working with us.
1. ABOUT YOUR ADVISOR.
I prefer if you ... | ["[Welcome to the Alexander lab!🙂 Below you will find useful information to help you get started working with us.] ABOUT YOUR ADVISOR.\nI prefer if you call me Andy. I am from a mountain town called Jamul outside of San Diego, California. I completed both my bachelors and PhD at UC San Diego and a postdoctoral fellow ... |
49,072 | Group B Streptococcus (Streptococcus agalactiae) Isolation, Identification and Antimicrobial Susceptibility Testing | 4 | dx.doi.org/10.17504/protocols.io.bt6qnrdw | https://www.protocols.io/view/group-b-streptococcus-streptococcus-agalactiae-iso-bt6qnrdw | Wisnu Tafroji, Maria da Gloria Carvalho, Fabiana C Pimenta, Miftahuddin majid khoeri, Dodi Safari | TITLE: Group B Streptococcus (Streptococcus agalactiae) Isolation, Identification and Antimicrobial Susceptibility Testing
AUTHORS: Wisnu Tafroji, Maria da Gloria Carvalho, Fabiana C Pimenta, Miftahuddin majid khoeri, Dodi Safari
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol p... | ["[Broth enrichment V/R swab culture for enhanced GBS growth]\nThaw the Vaginal/Rectal (V/R)-STGG specimens at room temperature (25oC) and vortex for approximately 10-20 seconds. Re-freeze the specimen (i.e., the STGG) as soon as possible and keep it cool in an ice bath during processing.Avoid multiple freeze-thaw cycl... |
null | null | null | dx.doi.org/10.17504/protocols.io.c9hz35 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Reference: <br />JB Waterbury & JM Willey. Isolation and growth of marine planktonic cyanobacteria. 1988. Methods in Enzymology 167: 100-105.
[GUIDELINES]
<strong>Reference: </strong><br />JB Waterbury & JM Willey. Isolation and growth of marine plankton... | [] |
83,655 | A protocol of density measurement of cholinergic innervation in 3D Images of the pig colon with Imaris 9.7 for neuroscientist | 5 | dx.doi.org/10.17504/protocols.io.q26g7pry9gwz/v1 | https://www.protocols.click/view/a-protocol-of-density-measurement-of-cholinergic-i-cvxfw7jn | Tao Li, Pu-Qing Yuan, Yvette Taché | TITLE: A protocol of density measurement of cholinergic innervation in 3D Images of the pig colon with Imaris 9.7 for neuroscientist
AUTHORS: Tao Li, Pu-Qing Yuan, Yvette Taché
[DESCRIPTION]
This protocol describes a step-by-step computational workflow for the density measurement of cholinergic innervation in three-di... | ["Open Imaris 9.7, click Arena<Observe Folder to find the image files.", "In the Observe Folder, double click the images that you wanted to analyze. Imaris automatically transfers the original .lsm format to .ims format.", "Open the image with .ims format.", "Create first surface (Surfaces 1) to contour the ganglion by... |
85,530 | WU sn-prep Protocol for solid tumors- joint snRNA+ATAC v2.9 | 1 | dx.doi.org/10.17504/protocols.io.261gednx7v47/v1 | https://www.protocols.click/view/wu-sn-prep-protocol-for-solid-tumors-joint-snrna-a-cxr2xm8e | Reyka Jayasinghe, Wagma Caravan, Andrew Houston, Nataly Naser Al Deen | TITLE: WU sn-prep Protocol for solid tumors- joint snRNA+ATAC v2.9
AUTHORS: Reyka Jayasinghe, Wagma Caravan, Andrew Houston, Nataly Naser Al Deen
[DESCRIPTION]
Nuclei dissociation protocol adapted from WU sn-prep Protocol for Solid Tumors - snRNA protocol v2.8 for simultaneous profiling of genetic expression (snRNA) a... | ["[Reagents and Tools] 1x Lysis buffer (2mL):\n10mM Tris-HCl (pH 7.4) (Thermo; 15567027), 20μL\n10mM NaCl (Thermo; AM9759), 4μL\n3 mM MgCl2 (Thermo; AM9530G), 6μL\nNP-40 substitute (Sigma, 74385-1L), 2μL\n1 M DTT (Sigma, 646563), 2μL\nNuclease Free Water (Invitrogen, AM9937), 1.966mL", "[Reagents and Tools] 0.1x Lysis ... |
64,696 | Small scale Lentivirus Production and Infection | 1 | dx.doi.org/10.17504/protocols.io.bp2l61z2zvqe/v1 | https://www.protocols.io/view/small-scale-lentivirus-production-and-infection-cbeysjfw | Herschel Dhekne, Suzanne R R R Pfeffer | TITLE: Small scale Lentivirus Production and Infection
AUTHORS: Herschel Dhekne, Suzanne R R R Pfeffer
[DESCRIPTION]
This protocol can be used for production and transduction of lentiviral sgRNA, shRNA and protein overexpression in conjunction with generation 2 and generation 3 lentivirus plasmids.
[STEPS]
SECTION:... | ["[Make lentivirus] Plate 293T cells at 40% confluency in a 6 well tissue plate submerged under 2 mL medium per well.", "[Make lentivirus] After 360 min, most cells will have attached.", "[Day 0] Prepare DNA mix for transfection:", "[Day 0] Add the following to 100 µL Optimem per well for transfection:\n \n 1µg ... |
null | null | null | dx.doi.org/10.17504/protocols.io.fgnbjve | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This is adapted from Benjy Neymotin's implementation of the SP6 in vitro transcription protocol for the purposes of doing 4tU labeled transcripts.</p>
[GUIDELINES]
<p>Currently, the polyA pSP64 plasmids in Gresham lab are DGP 104,105,106,229. These are the 700,900,1200, and ... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.d7k9kv | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<span style="color: #333333; font-family: helvetica, sans-serif; font-size: 14px; line-height: 21px;">Contrary to single-genome assemblers (e.g., Velvet and SOAPdenovo), MetaVelvet assumes metagenomics settings. Accordingly, </span><em style="color: #333333; font-family: helveti... | [] |
61,629 | Endoglycosidase H digestion of GCase | 4 | dx.doi.org/10.17504/protocols.io.8epv59ew4g1b/v1 | https://www.protocols.io/view/endoglycosidase-h-digestion-of-gcase-b8e5rtg6 | Laura Smith | TITLE: Endoglycosidase H digestion of GCase
AUTHORS: Laura Smith
[DESCRIPTION]
The N-linked glycoprotein profile of GCase trapped in the ER makes it susceptible to digestion by the glycosidase EndoH. Western blotting of GCase following EndoH digestion will yield an additional lower molecular weight band that corres... | ["[Principle] To study the subcellular localisation and transport of GCase mutants, the processing of its N-linked glycans was monitored by performing Endo H F digestions. Endo H cleaves only high mannose structures and hybrid structures.\n\nThe N-linked glycoprotein profile of GCase trapped in the ER makes it suscepti... |
31,027 | qPCR assay for detecting Batrachochytrium dendrobatidis | null | dx.doi.org/10.17504/protocols.io.baiticen | null | Omneya Ahmed Osman, Johan Andersson, Alexander Eiler, Mats Töpel, Tomas Larsson, Tomas Larsson | TITLE: qPCR assay for detecting Batrachochytrium dendrobatidis
AUTHORS: Omneya Ahmed Osman, Johan Andersson, Alexander Eiler, Mats Töpel, Tomas Larsson, Tomas Larsson
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The fungus </span><span style = "font-style:italic;">Batrachochytrium dendrobat... | ["[DNA extraction]\nDNA extraction was performed using Qiagen DNeasy power water sterivex kit. The quality of the extracted DNA was estimated using Nanodrop. \n\nQiagen DNeasy power water sterivex kit: https://www.qiagen.com/se/resources/resourcedetail?id=c5fe7d5f-070a-4ebe-ac04-4bbf05a13e91&lang=en", "[DNA extraction]... |
null | null | null | dx.doi.org/10.17504/protocols.io.er2bd8e | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
<p><strong>Supplemental notes:</strong> <br /><br />1) Concentration (A<sub>260</sub>/mL) is determined on a UV spectrophotometer (not for iodixanol-purified isolates). </p>
<p>2) Titer (PFU/mL) is determined by plaque assay. </p>
<p>3) 1 A<sub>260</sub> unit of PBCV-1 routinely ... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.q6gdzbw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Here we introduce Protein-indexed Assay of Transposase Accessible Chromatin with sequencing (Pi-ATAC) that combines single-cell chromatin and proteomic profiling. In conjunction with DNA transposition, the levels of multiple cell surface or intracellular protein epitopes are ... | ["[Then make a single cell suspension] Remove PBS from dish, but keep on ice.", "[Single cell suspension] Add single cell dissociation solution to dish (for most tissues: 200 U/ml Collagenase in HBSS-FBS (1%)).", "[Single cell suspension] Try to pipet with 10 ml pipet, fill into 15ml tube.", "[Single cell suspension] {... |
24,121 | Mammalian Cell Culture: Freezing | null | dx.doi.org/10.17504/protocols.io.3szgnf6 | null | Kenneth Schackart | TITLE: Mammalian Cell Culture: Freezing
AUTHORS: Kenneth Schackart
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes how to freeze cells that are being cultured in a tissue culture flask (T-75 or T-25).</div></div>
[STEPS]
?. [Wash Cells]
Remove media from flask.
?. [Wash Cell... | ["[Wash Cells]\nRemove media from flask.", "[Wash Cells]\nUsing serological pipet, add DPBS to flask [ for T-25].\n4 ml\n1 ml", "[Wash Cells]\nUsing serological pipet, remove DPBS and dispose into waste beaker.", "[Wash Cells]\nRepeat the above 2 steps, for a total of 2 washes.", "[Trypsinize]\nAdd warmed Trypsin-EDT... |
45,521 | Measurement of heat production (thermogenesis) in cells using ERthermAC dye_microplate method | 4 | dx.doi.org/10.17504/protocols.io.bqprmvm6 | https://www.protocols.io/view/measurement-of-heat-production-thermogenesis-in-ce-bqprmvm6 | Chih-Hao Wang, Yu-Hua Tseng, Yu-Hua Tseng | TITLE: Measurement of heat production (thermogenesis) in cells using ERthermAC dye_microplate method
AUTHORS: Chih-Hao Wang, Yu-Hua Tseng, Yu-Hua Tseng
[STEPS]
?. Wash differentiated adipocytes with PBS twice
?. Add 100 μL of staining solution per well of a 96-well plate
?. Incubate 37oC for 30~45 min
?. Wash with PBS... | ["Wash differentiated adipocytes with PBS twice", "Add 100 μL of staining solution per well of a 96-well plate", "Incubate 37oC for 30~45 min", "Wash with PBS twice", "Add 90 ul of DMEM-H serum-free and phenol red-free medium each well", "Equilibrate plate at 25 oC for 15 min", "Measure 2-3 points of basal red fluoresc... |
87,966 | SciPlex-ATAC (2-Level) | 1 | null | https://www.protocols.io/view/sciplex-atac-2-level-cz56x89e | Gregory T Booth | TITLE: SciPlex-ATAC (2-Level)
AUTHORS: Gregory T Booth
[DESCRIPTION]
Single-cell chromatin accessibility has emerged as a powerful means of understanding the epigenetic landscape of diverse tissues and cell types, but profiling cells from many independent specimens is challenging and costly. Here we describe a novel a... | ["[Indexted tagmentation] prepare mixture 12uL 2xTD buffer per well (freshly added 20% DMF).\nCombine 12uL 2XTD with 6 uL of 4xCLB (per well).\nAdd 18uL of mixture (TD+CLB) to each wells of plate and mix well (final well vol = 24 uL, with 1x CLB buffer).\nAdd 1 uL indexed Tn5 to each well.\n\nNote: Each well of the 96 ... |
36,535 | Implantation of a pelvic nerve array in rats_original from SP | 1 | dx.doi.org/10.17504/protocols.io.bfwxjpfn | https://www.protocols.io/view/implantation-of-a-pelvic-nerve-array-in-rats-origi-bfwxjpfn | James Fallon, Sophie Payne, Janet Keast, Peregrine Osborne | TITLE: Implantation of a pelvic nerve array in rats_original from SP
AUTHORS: James Fallon, Sophie Payne, Janet Keast, Peregrine Osborne
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">A pelvic nerve array is custom designed for implantation onto the pelvic nerve of male rats. This device is used fo... | ["[Surgical Preparation]\nPrior to surgery, pelvic nerve arrays are sterilised through a sonication process and autoclaving.", "[Surgical Preparation]\nSonication cycles: 15 mins in 5% Pyroneg, 5 mins distilled water, 5 mins in distilled water, 10 mins in 96% ethanol, 5 mins in distilled water, 5 mins in distilled wate... |
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