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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91,706 | Direct ELISA | 1 | dx.doi.org/10.17504/protocols.io.261ged83ov47/v1 | https://www.protocols.io/view/direct-elisa-c5s2y6ge | Michael X. Henderson | TITLE: Direct ELISA
AUTHORS: Michael X. Henderson
[DESCRIPTION]
This protocol details Direct ELISA.
[STEPS]
SECTION: Direct ELISA
1. Dilute 100 ng - 500 ng of protein of interest (e.g. α-synuclein) in Takeda buffer per well and add 30 µL total liquid per well to 384-well Nunc Maxisorp plate.
SECTION: Direct ELISA
2.... | ["[Direct ELISA] Dilute 100 ng - 500 ng of protein of interest (e.g. α-synuclein) in Takeda buffer per well and add 30 µL total liquid per well to 384-well Nunc Maxisorp plate.", "[Direct ELISA] Seal with removable clear adhesive cover.", "[Direct ELISA] Centrifuge the plate at 1000 x g for 1 min to pull down protein o... |
94,113 | Stereology-mediated cell count using StereoInvestigator | 4 | dx.doi.org/10.17504/protocols.io.dm6gp3kddvzp/v1 | https://www.protocols.io/view/stereology-mediated-cell-count-using-stereoinvesti-c759zq96 | mariangela.massarocenere | TITLE: Stereology-mediated cell count using StereoInvestigator
AUTHORS: mariangela.massarocenere
[DESCRIPTION]
Protocol for cell counting using StereoInvestigator software.
[STEPS]
1. Set slide properly on the microscope and set new reference point
2. Click on Probes → Optical Fractionator Workflow → Start a new su... | ["Set slide properly on the microscope and set new reference point", "Click on Probes → Optical Fractionator Workflow → Start a new subject →", "Enter cut thickness: 30 µm (cut with cryostat)", "Enter interval according to the thickness: 5 if SNpc, 6 if STR", "In Select Low Mag Lens, click 5X", "Click on Next Step", "... |
null | null | null | dx.doi.org/10.17504/protocols.io.ez4bf8w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This is a collection of BioLegend protocols for the Intracellular Flow Cytometry Staining, including the Activation and Intracellular Staining of Whole Blood.</p>
[STEPS]
?. | [] |
109,420 | ReViBE: protocol for Refit Visualisation of lithic reduction sequences using the Blender Engine | 1 | dx.doi.org/10.17504/protocols.io.kqdg32jrpv25/v1 | https://www.protocols.io/view/revibe-protocol-for-refit-visualisation-of-lithic-dn4k5guw | Javier Sánchez-Martínez, Katia Calmet, Jorge Martínez-Moreno, Xavier Roda Gilabert | TITLE: ReViBE: protocol for Refit Visualisation of lithic reduction sequences using the Blender Engine
AUTHORS: Javier Sánchez-Martínez, Katia Calmet, Jorge Martínez-Moreno, Xavier Roda Gilabert
[DESCRIPTION]
Here, we introduce ReViBE, a step-by-step protocol for visualising lithic refits through the utilisation of im... | ["[Part 1 - Initial remarks and set up preparation] Place the camera on a tripod (ideally with a zoom lens with a focal length between 35mm and 80mm). Do not use an autofocus lens.", "[Part 1 - Initial remarks and set up preparation] With 3 light sources, create diffused lighting from both sides and above. Try to avoid... |
29,885 | Protocols for Synthetic mRNAs Drive Highly Efficient iPS Cell Differentiation to Dopaminergic Neurons | 2 | null | https://www.protocols.io/view/protocols-for-synthetic-mrnas-drive-highly-efficie-9e5h3g6 | Yingchao Xue, Xiping Zhan, Shisheng Sun, Senthilkumar S. Karuppagounder, Shuli Xia, Valina L Dawson, Ted M Dawson, John Laterra, Jianmin Zhang, Mingyao Ying | TITLE: Protocols for Synthetic mRNAs Drive Highly Efficient iPS Cell Differentiation to Dopaminergic Neurons
AUTHORS: Yingchao Xue, Xiping Zhan, Shisheng Sun, Senthilkumar S. Karuppagounder, Shuli Xia, Valina L Dawson, Ted M Dawson, John Laterra, Jianmin Zhang, Mingyao Ying
[DESCRIPTION]
<div class = "text-blocks"><di... | [] |
24,423 | CGAP Human Oesophagus Epithelium Dissociation - Tissue Stability | null | dx.doi.org/10.17504/protocols.io.34fgqtn | null | Anna Wilbrey-Clark, Adam Hunter | TITLE: CGAP Human Oesophagus Epithelium Dissociation - Tissue Stability
AUTHORS: Anna Wilbrey-Clark, Adam Hunter
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. Receive oesophagus sample from mid-region in hypothermasol FRS solution (Sigma H4416).
?. Wash the samples with 10ml cold PBS to remove any residu... | ["Receive oesophagus sample from mid-region in hypothermasol FRS solution (Sigma H4416).", "Wash the samples with 10ml cold PBS to remove any residual contamination, stomach content and loose mucus.", "Pour oesophagus onto 100mm glass petri dish and add another 10ml fresh cold PBS.", "Open the samples longitudinally.",... |
74,083 | Welcome_to_UCSC_CSC_protocols | 3 | null | https://www.protocols.io/view/welcome-to-ucsc-csc-protocols-ckkbuusn | Beverley M Rabbitts | TITLE: Welcome_to_UCSC_CSC_protocols
AUTHORS: Beverley M Rabbitts
[DESCRIPTION]
Welcome!
You have reached the Protocols.io workspace for the University of California, Santa Cruz Chemical Screening Center.
Please refer to the CSC website for information on training, instrument specifications, rules, contact and visit... | [] |
46,766 | Culture media for human islets (based ont eh Edmonton protocol) | 4 | dx.doi.org/10.17504/protocols.io.brwnm7de | https://www.protocols.io/view/culture-media-for-human-islets-based-ont-eh-edmont-brwnm7de | Corentin Cras-Méneur | TITLE: Culture media for human islets (based ont eh Edmonton protocol)
AUTHORS: Corentin Cras-Méneur
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Culture media for human islets</div></div>
[STEPS]
?. [CMRL Media]
of of of of of
500 mL
8.5 mL
8.5 mL
5 mL
5 mL | ["[CMRL Media]\nof of of of of\n500 mL\n8.5 mL\n8.5 mL\n5 mL\n5 mL"] |
42,171 | BHI + v2 salts media | 4 | dx.doi.org/10.17504/protocols.io.bme3k3gn | https://www.protocols.io/view/bhi-v2-salts-media-bme3k3gn | Matthew Haines | TITLE: BHI + v2 salts media
AUTHORS: Matthew Haines
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-style:italic;">Vibrio natriegens </span><span>grows exceptionally well in BHI + v2 salts media (</span><a href="http://2018.igem.org/Team:Marburg/Results" style = "text-decoration... | ["[Prepare stock salt solutions]\nPrepare the following salt solutions at the given concentrations:\n[NaCl]\n[KCl]\n[MgCl2.6H2O]", "[Prepare BHI media]\nDissolve in ddH2O in a 1 L graduated bottle.\n[BHI dry medium]\n400 mL", "[Sterilise and combine]\nSterilise all solutions by autoclaving.", "[Sterilise and combin... |
null | null | null | dx.doi.org/10.17504/protocols.io.ddp25m | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Sequence for barcoded oligos for linker amplified libraries. Numbers 1 to 29 were developed at the Tucson Marine Phage Lab dervied from MID 1 to 14 recommended by Roche.
[GUIDELINES]
<strong>Rules for oligo creation:</strong> <br />- No duplicate nucleotides in a row, including... | [] |
19,932 | SYSB 3036 W02: Parsing FASTA files | null | dx.doi.org/10.17504/protocols.io.xp4fmqw | null | Frank Aylward | TITLE: SYSB 3036 W02: Parsing FASTA files
AUTHORS: Frank Aylward
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Week 1</div><div class = "text-block">Introduction to parsing FASTA files.</div><div class = "text-block">Commands to be entered into the command line are in bold. </div><div class = "tex... | ["Today we will be looking at the genome of Yersinia pestis, which can be found on NCBI at this locationftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/009/065/GCA_000009065.1_ASM906v1Copy this URL into your browser and take a look at the files. These are publicly-available files that are made available from the Nationa... |
null | null | null | dx.doi.org/10.17504/protocols.io.eusbewe | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Widely used protocol to extract DNA from plant leaves.<br />Many versions circulate on the web, this is the version as we use it.<br />It works well on maize, tomato and probably many other plants.
[BEFORE_START]
Prepare all reagents and materials.<br /><br />TE Buffer, pH 8.0 ... | [] |
103,092 | Purification of BNIP3-GFP | 0 | dx.doi.org/10.17504/protocols.io.kqdg328r7v25/v1 | https://www.protocols.io/view/purification-of-bnip3-gfp-dgwu3xew | Elias Adriaenssens | TITLE: Purification of BNIP3-GFP
AUTHORS: Elias Adriaenssens
[DESCRIPTION]
This protocol details the purification of BNIP3-GFP.
[STEPS]
SECTION: Purification - BNIP3-GFP
1. To purify GFP-tagged
BNIP3-GFP (available from Addgene) or BNIP3(W18A/L21A)-GFP (ΔLIR) (available from Addgene),
we purchase the gene-synthes... | ["[Purification - BNIP3-GFP] To purify GFP-tagged \n\nBNIP3-GFP (available from Addgene) or BNIP3(W18A/L21A)-GFP (ΔLIR) (available from Addgene), \n\nwe purchase the gene-synthesized codon-optimized cytosol-exposed domain of BNIP3 (1-158aa) fused to a C-terminal GFP-tag in a pFastBac-Dual vector from Genscript (availab... |
69,813 | Effect of supplementation of Iron and Enterobactin on C. elegans behaviour on Keio E. coli mutants (6-well plates) | 1 | dx.doi.org/10.17504/protocols.io.dm6gpj8bpgzp/v1 | https://www.protocols.io/view/effect-of-supplementation-of-iron-and-enterobactin-cgevtte6 | Saul Moore | TITLE: Effect of supplementation of Iron and Enterobactin on C. elegans behaviour on Keio E. coli mutants (6-well plates)
AUTHORS: Saul Moore
[DESCRIPTION]
Protocol for screening candidate behaviour-modifying E. coli BW25113 single-gene deletion mutants from the 'Keio Collection', to investigate their differential e... | ["[Preparing NGM agar + pouring plates] Prior to screening, prepare the materials needed for screening C. elegans on selected Keio E. coli mutants:\n\n- 6-well plates (aka. 'imaging plates')\n- 15 mL Falcon tubes\n- 50 mL Erlenmeyer flasks\n- 90 mm Petri plates (aka. 'maintenance plates')\n- 150 mm Petri plates (aka. '... |
79,710 | PDI Staff Roles | 3 | dx.doi.org/10.17504/protocols.io.6qpvr4zk3gmk/v1 | https://www.protocols.io/view/pdi-staff-roles-cr36v8re | Katie Wolf, samayita.bandyopadhyay | TITLE: PDI Staff Roles
AUTHORS: Katie Wolf, samayita.bandyopadhyay
[DESCRIPTION]
This is a description of PDI Staff, their roles and responsibilities as of March 2023. This is subject to evolution as everything else.
[STEPS] | [] |
80,341 | BAF_Protocol_002 On-Bead Digestion (Magnetic Beads) of Proteins in Solution or Provided Already on Beads | 1 | dx.doi.org/10.17504/protocols.io.3byl4j43rlo5/v1 | https://www.protocols.io/view/baf-protocol-002-on-bead-digestion-magnetic-beads-cspvwdn6 | nesf | TITLE: BAF_Protocol_002 On-Bead Digestion (Magnetic Beads) of Proteins in Solution or Provided Already on Beads
AUTHORS: nesf
[DESCRIPTION]
This protocol is used to more easily digest a tissue or cell protein lysate (after precipitation and reconstitution) on a magnetic bead for easier manipulation and washing. The p... | ["[On-bead Digestion (Start Step #13 if Beads were Affinity Capture)] Place the tubes on a magnetic rack for 2 minutes. Remove and discard supernatant.", "[On-bead Digestion (Start Step #13 if Beads were Affinity Capture)] Add 200 uL of ACN (100% stock) to reach a final concentration of 50% (v/v). Incubate for 8 minute... |
72,080 | Kraus et al., 2022 FBXO7 /Park15 | 2 | dx.doi.org/10.17504/protocols.io.kxygx99pwg8j/v1 | https://www.protocols.io/view/kraus-et-al-2022-fbxo7-park15-cimquc5w | Felix Kraus | TITLE: Kraus et al., 2022 FBXO7 /Park15
AUTHORS: Felix Kraus
[DESCRIPTION]
The protein kinase PINK1 and ubiquitin ligase Parkin promote removal of damaged mitochondria via a feed-forward mechanism involving ubiquitin (Ub) phosphorylation, Parkin activation, and ubiquitylation of mitochondrial outer membrane proteins... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.t3aeqie | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol can be used to prepare nuclear suspensions from fresh or frozen tissue for single cell DNA or RNA sequencing experiments. For RNA analysis it is recommended to use fresh tissue samples, due to RNA degradation that occurs during freeze- thaw cycles, however for DNA ... | ["[Tissue preparation] {\"blocks\":[{\"key\":\"28rb7\",\"text\":\"Cut fresh or frozen tissue (about 1x1x1cm) and mince it with a scalpel in a 10-cm Petri dish with for (10-15 min) until tissue chunks are no longer visible.\",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[],\"entityRanges\":[{\"offset\":98,... |
61,942 | Biotin Labeled Nucleotides | 1 | null | https://www.protocols.io/view/biotin-labeled-nucleotides-b8qwrvxe | BOC Sciences | TITLE: Biotin Labeled Nucleotides
AUTHORS: BOC Sciences
[DESCRIPTION]
Biotin labelled nucleotides, which is a compound linked to nucleotides by the carboxyl site of biotin. If the nucleic acid can be labeled with biotin by enzymatic reaction, the biotin-avidin protein system can be used for tracer detection. Biot... | [] |
35,609 | Opentrons COVID-19 testing: Station A, Zymo kit, 24 or 48 samples | null | dx.doi.org/10.17504/protocols.io.bezzjf76 | https://www.protocols.io/view/opentrons-covid-19-testing-station-a-zymo-kit-24-o-bezzjf76 | Max Marrone | TITLE: Opentrons COVID-19 testing: Station A, Zymo kit, 24 or 48 samples
AUTHORS: Max Marrone
[STEPS]
?. [Reagent preparation]
?. [Initial OT-2 setup]
Clean the OT-2.
?. [Reagent preparation]
Pipette Proteinase K from the Zymo kit into a 1.5 mL snap cap tube.For 24 samples, pipette . For 48 samples, pipette .Place th... | ["[Reagent preparation]", "[Initial OT-2 setup]\nClean the OT-2.", "[Reagent preparation]\nPipette Proteinase K from the Zymo kit into a 1.5 mL snap cap tube.For 24 samples, pipette . For 48 samples, pipette .Place the Proteinase K tube into slot D1 of the reagent tube rack.Prepare the reagent tube rack, an Opentrons ... |
null | null | null | dx.doi.org/10.17504/protocols.io.c3yypv | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?. | [] |
24,112 | TRAP Assay | null | dx.doi.org/10.17504/protocols.io.3sqgndw | null | Eva Feldman | TITLE: TRAP Assay
AUTHORS: Eva Feldman
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span></div><div class = "text-block">The use of total radical-trapping antioxidant parameter (TRAP) has recently been proposed to explore the antioxidant property of a p... | ["[Sample Preparation - DRG:]\n1. Remove 2 DRG from vial, cut in half and weigh. Do in duplicate. 2. Add 30 µL 30mM PB and sonicate on 4 on ice. 3. Spin at maximum g’s for 10 min at 4ºC. 4. Remove sup and store on ice.", "[Performing the Assay:]\n1. Using a White Solid Bottom plate, prepare plate by loading buffer for ... |
87,480 | LRRK2 thermal shift assay | 4 | dx.doi.org/10.17504/protocols.io.kxygx3y6kg8j/v2 | https://www.protocols.io/view/lrrk2-thermal-shift-assay-cznyx5fw | Verena Dederer, chatterjeedeep, Sebastian Mathea, Stefan Knapp | TITLE: LRRK2 thermal shift assay
AUTHORS: Verena Dederer, chatterjeedeep, Sebastian Mathea, Stefan Knapp
[DESCRIPTION]
Thermal shift assay or differential scanning fluorimetry analyzes the effect of small molecules on the thermostability of a protein by gradual heat denaturation and monitoring absorption of the fluore... | ["[Fluorescent-based thermal shift assay] Prepare 4 µM master mix of protein in buffer (20 mM Hepes pH 7.4, 150 mM NaCl, 5% glycerol) and add 1:1000 dilution of SYPR Orange.", "[Fluorescent-based thermal shift assay] Aliquot 20 µL of the master mix into a white 96 well plate.", "[Fluorescent-based thermal shift assay] ... |
87,060 | Transfection and validation of BK channel expressing HEK-293 cells for the study of Mir-9 regulation. | 4 | dx.doi.org/10.17504/protocols.io.yxmvm3ek5l3p/v1 | https://www.protocols.io/view/transfection-and-validation-of-bk-channel-expressi-cy9uxz6w | Katherine Cordero Padilla, Gerardo L. Alvarado Monefledt, Adriel Guevarez-Galan, Hector G Marrero Hernandez, Mario E. Lloret-Torres, Cristina Velazquez Marrero | TITLE: Transfection and validation of BK channel expressing HEK-293 cells for the study of Mir-9 regulation.
AUTHORS: Katherine Cordero Padilla, Gerardo L. Alvarado Monefledt, Adriel Guevarez-Galan, Hector G Marrero Hernandez, Mario E. Lloret-Torres, Cristina Velazquez Marrero
[DESCRIPTION]
Research has identified the... | ["[Cell Culture] Thaw and plate the cells as follows:", "[Cell Culture] Resuspend in modified DMEM media composed of Dulbecco’s modified Eagle’s medium with 10% fetal bovine serum (FBS), 2.52 mM; 10 units and 10µg/mL of Penicillin/Streptomycin (Pen/Strep), and 1mM Na-pyruvate.", "[Cell Culture] Pipette 20µL of the resu... |
35,984 | Assessing IL-15 bioavailability ("the bioassay") | 1 | dx.doi.org/10.17504/protocols.io.yxmvmxqw9l3p/v1 | https://www.protocols.io/view/assessing-il-15-bioavailability-34-the-bioassay-34-bfdqji5w | Philippa R Kennedy, Joshua T Walker, Todd Lenvik | TITLE: Assessing IL-15 bioavailability ("the bioassay")
AUTHORS: Philippa R Kennedy, Joshua T Walker, Todd Lenvik
[DESCRIPTION]
Assessing the capacity of IL-15 analogs (e.g. within TriKE molecules) to stimulate proliferation of NK-92 cells. NK-92 are deprived of cytokines overnight, then cultured with IL-15 an... | ["[NK-92 culture] Defrost NK-92 (malignant non-Hodgkin's lymphoma; see Cell Line Information) and culture for at least one week prior to initiation of the assay.", "[NK-92 culture] NK-92 media\nAlpha Minimum Essential Medium plus ribonucleosides and deoxyribonucleosides \n(Gibco Cat. No. 12571) \n0.1 mM 2-mercaptoethan... |
64,293 | Measuring tension, pellet transit, and calcium imaging within cell subtypes in response to pelvic nerve stimulation | 4 | dx.doi.org/10.17504/protocols.io.ewov1nmxpgr2/v1 | https://www.protocols.io/view/measuring-tension-pellet-transit-and-calcium-imagi-ca2dsga6 | Thomas Gould, Dante Heredia | TITLE: Measuring tension, pellet transit, and calcium imaging within cell subtypes in response to pelvic nerve stimulation
AUTHORS: Thomas Gould, Dante Heredia
[DESCRIPTION]
A protocol to measure the effects of pelvic nerve stimulation on colonic motility
[GUIDELINES]
Nothing beyond steps
[STEPS]
1. After sacrific... | ["After sacrifice, the caudal half of the animal is pinned out. A ventral midline incision is made and the colon is cut at the cecum and separated from the small intestine, which is removed. Then the pelvic nerve is dissected by slowly removing all of the muscle bone and cartilage surrounding the distal colon. Leave ... |
31,176 | Table 2. Multilocus genotyping results of the 24 Giardia-positive samples successfully genotyped at least at one of the three loci investigated. Shushtar County (Iran), 2017‒2018. | null | dx.doi.org/10.17504/protocols.io.bapgidjw | null | Abdollah Rafiei, Raheleh Baghlaninezhad, Pamela C. Köster, Begoña Bailo, Marta Hernández de Mingo, David Carmena, Esmat Panabad, Molouk Beiromvand | TITLE: Table 2. Multilocus genotyping results of the 24 Giardia-positive samples successfully genotyped at least at one of the three loci investigated. Shushtar County (Iran), 2017‒2018.
AUTHORS: Abdollah Rafiei, Raheleh Baghlaninezhad, Pamela C. Köster, Begoña Bailo, Marta Hernández de Mingo, David Carmena, Esmat Pana... | [] |
87,573 | Behavioral Research of Environment and Air pollution Through Education (BREATHE) Study | 4 | dx.doi.org/10.17504/protocols.io.j8nlko9bxv5r/v1 | https://www.protocols.io/view/behavioral-research-of-environment-and-air-polluti-czrvx566 | Yorusaliem Abrham, Mehrdad Arjomandi | TITLE: Behavioral Research of Environment and Air pollution Through Education (BREATHE) Study
AUTHORS: Yorusaliem Abrham, Mehrdad Arjomandi
[DESCRIPTION]
This protocol details behavioral research of environment and air pollution through education (BREATHE) study.
Background-Despite the wealth of scientific informat... | ["[Clinical Assessments] Demographics:\nDemographic information (date of birth, gender, race, family income) will be recorded at Visit 1.", "[Clinical Assessments] Clinical Laboratory Measurements:\nNot applicable.", "[Evaluations by visit] Participants will be asked to complete a total of three in-person visits and on... |
null | null | null | dx.doi.org/10.17504/protocols.io.t3neqme | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol is designed for use with food-safe materials. It may be used to illustrate principles of gel electrophoresis for children, or as a party novelty for scientifically-minded adults. It is currently a work in progress and will be updated as necessary. Currently differ... | ["[Gelatin Preparation] Prepare gelatin in heat-safe bowl by adding only the quantity of hot water recommended on the packet to the gelatin. This should be approximately half of the required water depending on gelatin brand. Stir until dissolved.", "Pour gelatin into takeaway container until 1.5cm/0.5 inches deep.", "P... |
22,759 | Transfection of V5 labelled plasmid derived from regulatory sequences of Blastocrithidia sp. p57 | null | dx.doi.org/10.17504/protocols.io.2gfgbtn | null | Binnypreet Kaur | TITLE: Transfection of V5 labelled plasmid derived from regulatory sequences of Blastocrithidia sp. p57
AUTHORS: Binnypreet Kaur
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The plasmid named as p57-V5+G418 was cloned in the backbone pBluescript II SK(+).</div><div class = "text-block"><span>The ... | [] |
97,094 | USDA LTAR Common Experiment measurement: Discharge from artificial subsurface drains | 0 | dx.doi.org/10.17504/protocols.io.x54v92ewzl3e/v1 | https://www.protocols.io/view/usda-ltar-common-experiment-measurement-discharge-da3e2gje | Gary W. Feyereisen, Kevin W. King, Kevin J. Cole, Mark R. Williams, Rob W. Malone, David D. Bosch, Claire Baffaut | TITLE: USDA LTAR Common Experiment measurement: Discharge from artificial subsurface drains
AUTHORS: Gary W. Feyereisen, Kevin W. King, Kevin J. Cole, Mark R. Williams, Rob W. Malone, David D. Bosch, Claire Baffaut
[DESCRIPTION]
Subsurface drain discharge, sometimes simply referred to as drainage, is a process by whi... | ["[Data collection] Measurement\n\nSubsurface drain discharge can increase rapidly in response to precipitation events, so the stage is recorded at short time intervals (seconds to hours). \nMost often, discharge measurement devices are connected to an electronic data logger, which records stage in the device as well a... |
108,569 | Use of resources and cost in the management of gastrointestinal hemorrhage caused by oral anticoagulants | 0 | dx.doi.org/10.17504/protocols.io.ewov1963klr2/v1 | https://www.protocols.io/view/use-of-resources-and-cost-in-the-management-of-gas-dm9z4976 | Jorge Machado Alba | TITLE: Use of resources and cost in the management of gastrointestinal hemorrhage caused by oral anticoagulants
AUTHORS: Jorge Machado Alba
[DESCRIPTION]
Introduction: Oral anticoagulants (OACs) used to treat
nonvalvular atrial fibrillation (NVAF) are frequently associated with
complications, especially gastrointestin... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.knwcvfe | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Protocol for amplification of the mitochondrial gene "Citocrome Oxidase I" and the nuclear genes "subunit a from the Histone 3" and "Internal Transcribed Spacer 2" from <em>Nephila clavipes</em> (Araneae: Araneidae).</p>
[GUIDELINES]
<p><strong>Mitochondrial gene Citochrome ... | [] |
64,388 | An analysis of Relative Telomere Length (RTL) during peri-operative chemotherapy in patients with operable gastric or gastro-oesophageal junction adenocarcinoma | 1 | dx.doi.org/10.17504/protocols.io.ca5csg2w | https://www.protocols.io/view/an-analysis-of-relative-telomere-length-rtl-during-ca5csg2w | Jeff Evans, Nicol Keith | TITLE: An analysis of Relative Telomere Length (RTL) during peri-operative chemotherapy in patients with operable gastric or gastro-oesophageal junction adenocarcinoma
AUTHORS: Jeff Evans, Nicol Keith
[DESCRIPTION]
OBJECTIVES
The primary objective of this study is:
(a) to analyse Relative Telomere Length (RTL) in bloo... | [] |
69,860 | Step A: Culturing | 4 | dx.doi.org/10.17504/protocols.io.yxmvm2736g3p/v1 | https://www.protocols.io/view/step-a-culturing-cggcttsw | k.z.cooper | TITLE: Step A: Culturing
AUTHORS: k.z.cooper
[DESCRIPTION]
Culturing step for bacterial genome resequencing project
[STEPS]
SECTION: Preparation
2. Ensure agar plates are pre-poured
SECTION: Preparation
3. Pre-label the plates using only the numbers provided on the spreadsheet under heading ‘Sample_Label’
SECTION: Pr... | ["[Preparation] Ensure agar plates are pre-poured", "[Preparation] Pre-label the plates using only the numbers provided on the spreadsheet under heading ‘Sample_Label’", "[Preparation] Get required glycerol stocks and keep on dry ice", "[Creating streak plate] Create streak plate inoculum using inoculation loop from gl... |
18,394 | Single Nucleus RNAseq Sample Prep from Nodose Ganglia | 1 | dx.doi.org/10.17504/protocols.io.v72e9qe | https://www.protocols.io/view/single-nucleus-rnaseq-sample-prep-from-nodose-gang-v72e9qe | Sebastian Preissl, Jamie Verheyden, Xin Sun | TITLE: Single Nucleus RNAseq Sample Prep from Nodose Ganglia
AUTHORS: Sebastian Preissl, Jamie Verheyden, Xin Sun
[DESCRIPTION]
How to isolate single nucei from nodose vagal ganglia neurons in preparation for 10XGenomics sequencing.
[STEPS]
1. Nodose ganglia are dissected and flash frozen in liquid nitrogen.Store ... | ["Nodose ganglia are dissected and flash frozen in liquid nitrogen.Store at -80C until ready to isolate nuclei.Grind up the sample with liquid nitrogen using the 1.5mL centrifuge tube and fitting pestle.", "Add 500 ul Lysis Buffer to pulverized tissue, pipette 10x up and down and place on ice\nIncubate 5 min with the o... |
78,330 | Synaptic immunohistochemistry - wholemount via acetone permeabilization | 4 | dx.doi.org/10.17504/protocols.io.261ge38q7l47/v1 | https://www.protocols.io/view/synaptic-immunohistochemistry-wholemount-via-aceto-cqq2vvye | Anya Suppermpool, FishFloorUCL | TITLE: Synaptic immunohistochemistry - wholemount via acetone permeabilization
AUTHORS: Anya Suppermpool, FishFloorUCL
[DESCRIPTION]
Whole-mount Immunohistochemistry – acetone permeabilization
Works with anti-MAGUK ab.
Modified from M Westerfield protocol.
Lavinia Sheets: T. Nicolson Lab September, 2010
Revised A... | ["[Day 1] Tricaine, Dechorionated beforehand (2dpf)", "[Day 1] Fix 1.5-2h in BT fix (*use bought fix) at 4C", "[Day 1] Replace fixative with PO4 buffer.\n(Optional) Store at 4C overnight (shaking not necessary)", "[Day 1] (less fix time higher SNR but mushy) 5h fixation works for 5dpf – 9dpf larvae, time may need to be... |
64,798 | Non-destructively barcoding hundreds of freshwater macroinvertebrates with a MinION | 4 | dx.doi.org/10.17504/protocols.io.rm7vzy974lx1/v1 | https://www.protocols.io/view/non-destructively-barcoding-hundreds-of-freshwater-cbh6sj9e | Elise C. Knobloch, Ray C Schmidt | TITLE: Non-destructively barcoding hundreds of freshwater macroinvertebrates with a MinION
AUTHORS: Elise C. Knobloch, Ray C Schmidt
[DESCRIPTION]
This project aimed to optimize protocols needed to produce CO1 barcodes for 1000s of African freshwater macroinvertebrates, from many different orders, in the most cost-... | ["[Specimen preparation and DNA extraction]", "[Specimen preparation and DNA extraction]", "[Specimen preparation and DNA extraction]", "[Specimen preparation and DNA extraction]", "Cover with TempPlate sealing foil or reusable TempPlate pressure-fit sealing mat", "[DNA extraction] Place one rinsed and dried specimen i... |
null | null | null | null | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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24,087 | HLA genotyping using SS-SBT methods | null | dx.doi.org/10.17504/protocols.io.3rxgm7n | null | Ryosuke Tashiro, Hidetoshi Inoko, Kuniyasu Niizuma, Teiji Tominaga | TITLE: HLA genotyping using SS-SBT methods
AUTHORS: Ryosuke Tashiro, Hidetoshi Inoko, Kuniyasu Niizuma, Teiji Tominaga
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Genomic DNA was obtained from the patients’ 2ml of whole blood using the QIAamp DNA Mini Kit for genomic DNA purification (Qiag... | ["DNA extraction", "Long-ranged PCR", "Sequencing", "Data analysis", "Construction of barcoded library", "Fisrts denature\n94 °C", "Denature\n98 °C", "Annealing (30 cycles)\n[HLA-A, B,C]\n[HLA-DRB1]\n[HLA-DQB1]\n[HLA-DQB1]\n[HLA-A, B, C]\n[HLA-DRB1]", "Output of NGS read data", "Homology search using Blat", "Selection ... |
50,653 | HPAP Processing Protocol | 4 | dx.doi.org/10.17504/protocols.io.bvp5n5q6 | https://www.protocols.io/view/hpap-processing-protocol-bvp5n5q6 | Michael Betts, Gregory Golden | TITLE: HPAP Processing Protocol
AUTHORS: Michael Betts, Gregory Golden
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Early in life, a combination of environmental insults and genetic pre-disposition results in an autoimmune reaction to pancreatic b-cells in the Islets of Langerhans, leading to b-c... | ["BLOOD1. Spin down vials at 2000rpm for 15min at room temperature2. Aliquot plasma into cryovials and freeze and store at ; toss remaining plasma3. Measure volume of spun down blood and transfer to a new conical tube4. Using a 1:1 ratio of spun blood to R10 media, wash vials and transfer to the conical with the spun... |
50,139 | Confocal imaging power settings – protocol and discussion | 1 | dx.doi.org/10.17504/protocols.io.bu73nzqn | https://www.protocols.io/view/confocal-imaging-power-settings-protocol-and-discu-bu73nzqn | Marco Polin, Antoine Allard, Kelsey Cremin, Emily Skates, Orkun S Soyer | TITLE: Confocal imaging power settings – protocol and discussion
AUTHORS: Marco Polin, Antoine Allard, Kelsey Cremin, Emily Skates, Orkun S Soyer
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Confocal microscopy is a commonly used microscopy technique involving a point laser scanned across a sampl... | ["[Confocal imaging power settings-step-by-step protocol]\nPrepare sample.", "[Confocal imaging power settings-step-by-step protocol]\nUse sample to set your microscope up for correct laser and scanning settings.", "[Confocal imaging power settings-step-by-step protocol]\nMake sure you use a calibrated power-meter and ... |
76,683 | High Spatial Resolution MALDI Imaging Mass Spectrometry Data Acquisition | 1 | dx.doi.org/10.17504/protocols.io.n92ldpq99l5b/v1 | https://www.protocols.io/view/high-spatial-resolution-maldi-imaging-mass-spectro-cn5jvg4n | Katerina V Djambazova, Martin Dufresne, Angela R.S. Kruse, Jamie Allen, allison.b.esselman, Madeline E. Colley, David Anderson, ali.zahraei, Olof Isberg, Melissa Farrow, Jeff Spraggins | TITLE: High Spatial Resolution MALDI Imaging Mass Spectrometry Data Acquisition
AUTHORS: Katerina V Djambazova, Martin Dufresne, Angela R.S. Kruse, Jamie Allen, allison.b.esselman, Madeline E. Colley, David Anderson, ali.zahraei, Olof Isberg, Melissa Farrow, Jeff Spraggins
[DESCRIPTION]
This protocol provides ... | ["Place slides in a MTP 2-slide holder. Scan slides using flatbed scanner, allowing for sufficient contrast to visualize the tissue boundary. Ensure the slides have fiducials.", "Use the FlexImaging software to load the optical image of the slides. Teach the target position with three teaching points. Check the accurac... |
null | null | null | dx.doi.org/10.17504/protocols.io.p5adq2e | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
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?. | [] |
49,535 | In vitro transcription of crRNA and tracrRNA from DNA oligos for cas9 enrichment and nanopore sequencing (for Bac - PULCE) | 1 | dx.doi.org/10.17504/protocols.io.buk7nuzn | https://www.protocols.io/view/in-vitro-transcription-of-crrna-and-tracrrna-from-buk7nuzn | Olin Silander | TITLE: In vitro transcription of crRNA and tracrRNA from DNA oligos for cas9 enrichment and nanopore sequencing (for Bac - PULCE)
AUTHORS: Olin Silander
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">In this protocol we describe the steps for the design and production of dual guide RNAs (dgRNAs... | ["[Preparation ]\nRNAse Zap equipment, gloves and bench prior to starting protocol. Turn on heat block to reach a temperature of .\n95 °C", "[Annealing T7 to crRNA and tracrRNA template]\nPool your crRNA DNA oligo sequences in equimolar amounts. For small numbers of crRNAs we order templates from IDT with oligos dilut... |
null | null | null | dx.doi.org/10.17504/protocols.io.gwvbxe6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p style="text-align: center;"><img class="s-mce-img" style="display: block; margin-left: auto; margin-right: auto;" src="https://s3.amazonaws.com/pr-journal/hnnfjtn.png" width="100" height="90" data-src="https://s3.amazonaws.com/pr-journal/hnnfjtn.png" data-ofn="nehirarma-üst-T... | [] |
67,544 | mFISH3D | 4 | dx.doi.org/10.17504/protocols.io.kqdg3pjxql25/v1 | https://www.protocols.io/view/mfish3d-cd7ys9pw | Tatsuya Murakami | TITLE: mFISH3D
AUTHORS: Tatsuya Murakami
[DESCRIPTION]
The protocol is for the multiplexed in situ hybridization in 3D (mFISH3D) in an adult mouse brain / a block of a human brain.
[BEFORE_START]
If you worry about the contamination of RNAse, use RNAse-free water to make all the reagents.
[GUIDELINES]
See safety da... | ["[Tissue sample preparation: a whole-mouse brain, blocks of a fresh frozen human brain] Incubate tissue in 4% paraformaldehyde (pH 6.5~7.0) overnight at 4°C.", "[Tissue sample preparation: a whole-mouse brain, blocks of a fresh frozen human brain] (optional) Subdissect the tissue. The dissected volume will be the fi... |
50,682 | Lithium Acetate / SDS Extraction of Genomic DNA from Saccharomyces cerevisiae | 1 | null | https://www.protocols.io/view/lithium-acetate-sds-extraction-of-genomic-dna-from-bvq2n5ye | Clark Fritsch | TITLE: Lithium Acetate / SDS Extraction of Genomic DNA from Saccharomyces cerevisiae
AUTHORS: Clark Fritsch
[DESCRIPTION]
This protocol is just a quick description of the protocol provided by Looke et al., 2011 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3182553/). The purpose of this protocol is simply to provide a... | ["Pick one yeast colony from the plate or spin down 100-200 μl of liquid yeast culture (OD600=0.4). Suspend cells in 100 μl of 200mM LiOAc, 1 % SDS solution. Alternatively, you can spin down 100 - 500 uL of liquid culture at 3,000 rcf for 4 minutes and then resuspend the pelleted cells in 100 uL of 200 mM LiOAc, 1% SDS... |
43,298 | FCMPASS - Cataloguing light scatter reference materials | 5 | dx.doi.org/10.17504/protocols.io.bniamcae | https://www.protocols.io/view/fcmpass-cataloguing-light-scatter-reference-materi-bniamcae | Joshua Welsh, Sean Cook, Jennifer Jones | TITLE: FCMPASS - Cataloguing light scatter reference materials
AUTHORS: Joshua Welsh, Sean Cook, Jennifer Jones
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol outlines the steps required to catalogue light scatter reference materials using the FCMPASS software. This is one of a number... | ["[Opening the Bead Catalogue]\nOpen FCMPASS.", "[Opening the Bead Catalogue]\nClick ‘Catalogue’ in the top menu bar", "[Bead Catalogue Basic Protocol]\nUnder the ‘Light Scatter’ tab entry fields exist for each of the pertinent metadata for reporting with light scatter calibration.", "[Bead Catalogue Basic Protocol]\nD... |
null | null | null | dx.doi.org/10.17504/protocols.io.eifbcbn | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?. | [] |
90,728 | Pulldowns | 1 | dx.doi.org/10.17504/protocols.io.5jyl8pw6dg2w/v1 | https://www.protocols.io/view/pulldowns-c4ugywtw | Dan Tudorica | TITLE: Pulldowns
AUTHORS: Dan Tudorica
[DESCRIPTION]
Traditional in vitro pulldown
[STEPS]
SECTION: Pulldown
1. In a final volume of 30 μL, 20 μg of purified MBP-Rubicon RH domain was mixed with 20 μg of RAB7A in 50 mM HEPES 7.5, 150 mM NaCl, 2 mM MgCl2, 10 mM TCEP buffer.
Include a negative control consisting of o... | ["[Pulldown] In a final volume of 30 μL, 20 μg of purified MBP-Rubicon RH domain was mixed with 20 μg of RAB7A in 50 mM HEPES 7.5, 150 mM NaCl, 2 mM MgCl2, 10 mM TCEP buffer.\n\nInclude a negative control consisting of only soluble Rab7, with no MBP-Rubicon, in order to test your washing efficacy.", "[Pulldown] Incubat... |
19,567 | Setting up a liquid culture and harvesting C.elegans | null | dx.doi.org/10.17504/protocols.io.xcpfivn | null | Vidur Sabharwal | TITLE: Setting up a liquid culture and harvesting C.elegans
AUTHORS: Vidur Sabharwal
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. Add 30ml S Medium to a sterilized 250 ml flask.
?. Inoculate the S Medium with a concentrated E. coli OP50 pellet to a final concentration of 30g/L
?. Wash each of 5 large pl... | ["Add 30ml S Medium to a sterilized 250 ml flask.", "Inoculate the S Medium with a concentrated E. coli OP50 pellet to a final concentration of 30g/L", "Wash each of 5 large plates (90cm) of C. elegans (just cleared of bacteria) with 5 ml S Medium and add to the 30 ml flask.", "Put the flask on a shaker at 200rpm\n20 °... |
53,731 | Use of cholera toxin subunit B to label neural projections to lower urinary tract organs | 1 | dx.doi.org/10.17504/protocols.io.byqbpvsn | https://www.protocols.io/view/use-of-cholera-toxin-subunit-b-to-label-neural-pro-byqbpvsn | Janet R Keast, Peregrine B Osborne, John-Paul Fuller-Jackson | TITLE: Use of cholera toxin subunit B to label neural projections to lower urinary tract organs
AUTHORS: Janet R Keast, Peregrine B Osborne, John-Paul Fuller-Jackson
[DESCRIPTION]
This protocol is used to visualise sensory and autonomic neurons innervating organs of the lower urinary tract in an experimental adult ma... | ["[Preparation for surgery] Prepare cholera toxin subunit B solutions: low salt formulation with 0.05% Evans Blue.", "[Preparation for surgery] Anesthetise animal (2.5% isoflurane in oxygen, or as required for maintenance)", "[Preparation for surgery] Apply eye lubricant and place animal on heated pad.", "[Preparation ... |
39,459 | SARS-CoV-2 McGill Nextera Flex sequencing protocol_SS_V3_LA1_5uLRT | 1 | dx.doi.org/10.17504/protocols.io.bisbkean | https://www.protocols.io/view/sars-cov-2-mcgill-nextera-flex-sequencing-protocol-bisbkean | Sarah Reiling, Marie-Michelle Simon, Anne-Marie Roy, Shu-Huang Chen, Josh Quick, Ioannis Ragoussis | TITLE: SARS-CoV-2 McGill Nextera Flex sequencing protocol_SS_V3_LA1_5uLRT
AUTHORS: Sarah Reiling, Marie-Michelle Simon, Anne-Marie Roy, Shu-Huang Chen, Josh Quick, Ioannis Ragoussis
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">How the Nextera DNA Flex Assay Works... | ["[cDNA preparation]\ncDNA PREPARATIONMix the following components in an 0.2mL 8-strip tube;Component Volume50 µM random hexamers 10 mM dNTPs mix (10 mM each) Template RNA Total\n1 µl\n1 µl\n11 µl\n13 µl\nViral RNA input from a ... |
24,555 | Sequencing Protocols for the One Thousand Plant Transcriptomes Initiative | null | dx.doi.org/10.17504/protocols.io.38jgrun | null | Eric J. Carpenter, Naim Matasci, Shuangxiu Wu, Jing Sun, Jun Yu, Fabio Rocha Jimenez Vieira, Chris Bowler, Richard G. Dorrell, Matt Gitzendanner, Ling Li, Wensi Du, Kristian Ullrich, Michael S. Barker, James H. Leebens-Mack, Gane Ka-Shu Wong | TITLE: Sequencing Protocols for the One Thousand Plant Transcriptomes Initiative
AUTHORS: Eric J. Carpenter, Naim Matasci, Shuangxiu Wu, Jing Sun, Jun Yu, Fabio Rocha Jimenez Vieira, Chris Bowler, Richard G. Dorrell, Matt Gitzendanner, Ling Li, Wensi Du, Kristian Ullrich, Michael S. Barker, James H. Leebens-Mack, Gane ... | [] |
51,685 | Low-Pass WGS Sequencing Library Preparation | 4 | dx.doi.org/10.17504/protocols.io.bwqdpds6 | https://www.protocols.io/view/low-pass-wgs-sequencing-library-preparation-bwqdpds6 | Christopher T Boniface | TITLE: Low-Pass WGS Sequencing Library Preparation
AUTHORS: Christopher T Boniface
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Simple protocol for generating WGS libraries using KAPA HyperPrep library preparation reagents.</div></div>
[STEPS]
?. [DNA extraction ]
Extract 10-50ng of tumor DNA fr... | ["[DNA extraction ]\nExtract 10-50ng of tumor DNA from FFPE needle-core biopsy or resection using QIAamp DNA FFPE Tissue Kit", "[DNA extraction ]\nCheck sonicated DNA size distribution using Agilent Bioanalyzer 2100 system or similar electrophoresis", "[DNA extraction ]\nQuantify extracted DNA and then sonicate 10-50ng... |
106,527 | Food intake behavior protocol | 0 | dx.doi.org/10.17504/protocols.io.14egn6r5yl5d/v1 | https://www.protocols.io/view/food-intake-behavior-protocol-dj974r9n | Santiago Unda, Michael G. Kaplitt | TITLE: Food intake behavior protocol
AUTHORS: Santiago Unda, Michael G. Kaplitt
[DESCRIPTION]
This protocol describes the behavioral test to measure food intake in mice.
[STEPS]
1. Habituate mice in single cages 2 days prior the test day.
2. Fast the mice for 18 hours with access to water.
3. Using a small weight sca... | ["Habituate mice in single cages 2 days prior the test day.", "Fast the mice for 18 hours with access to water.", "Using a small weight scale measure food chow and allow ad libitum food intake.", "Record food chow weight at 1, 2-, 4-, 6-, and 24-hours post-food chow access."] |
30,207 | Salmonella blood culture surveillance: Salmonella serotyping | null | dx.doi.org/10.17504/protocols.io.9q7h5zn | null | Jan Jacobs | TITLE: Salmonella blood culture surveillance: Salmonella serotyping
AUTHORS: Jan Jacobs
[STEPS] | [] |
64,433 | Fluxactive Complete (NEW 2022!) Does It Work Or Just Scam? | 3 | dx.doi.org/10.17504/protocols.io.81wgb6kbolpk/v1 | https://www.protocols.io/view/fluxactive-complete-new-2022-does-it-work-or-just-ca6rshd6 | Fluxactive Complete | TITLE: Fluxactive Complete (NEW 2022!) Does It Work Or Just Scam?
AUTHORS: Fluxactive Complete
[DESCRIPTION]
Fluxactive Complete – Official Website Link – Click Here
[STEPS] | [] |
67,407 | https://www.facebook.com/DiaetoxilAvisFrance/ | 1 | dx.doi.org/10.17504/protocols.io.q26g742z9gwz/v1 | https://www.protocols.io/view/https-www-facebook-com-diaetoxilavisfrance-cd3ps8mn | Alexcartersz | TITLE: https://www.facebook.com/DiaetoxilAvisFrance/
AUTHORS: Alexcartersz
[DESCRIPTION]
Diaetoxil Avis: ne personne a besoin d'avoir un corps sain. Peu importe votre richesse financière ou toutes les ressources dont vous disposez, si votre santé est mauvaise, vous attirerez de nombreux problèmes de santé dans votre... | ["[https://www.facebook.com/DiaetoxilAvisFrance/]"] |
96,397 | Rapid transposas based total DNA library preparation and sequencing using MinION | 0 | null | https://www.protocols.io/view/rapid-transposas-based-total-dna-library-preparati-dadm2a46 | Lavi Singh, Ashley Jones, Benjamin Schwessinger | TITLE: Rapid transposas based total DNA library preparation and sequencing using MinION
AUTHORS: Lavi Singh, Ashley Jones, Benjamin Schwessinger
[DESCRIPTION]
This protocols is part of the ANU Biosecurity mini-research project #1 "Plant Pathogen Diagnostics: Visuals, subcultures, and genomics".
You will be provided... | ["[Preparation of input DNA] This first series of steps will be performed by the three groups we selected in week 5. We will use their total native DNA samples for sequencing. We selected these samples bases on DNA concentrations and DNA integrity. We assessed the former using Qubit and the latter perform agarose gel e... |
53,232 | Analysis of Lysophagic Flux in Cultured Cells using Lyso-Keima | 1 | dx.doi.org/10.17504/protocols.io.bx8qprvw | https://www.protocols.io/view/analysis-of-lysophagic-flux-in-cultured-cells-usin-bx8qprvw | Vinay V. Eapen, Sharan Swarup, Melisa Hoyer, Harper JW | TITLE: Analysis of Lysophagic Flux in Cultured Cells using Lyso-Keima
AUTHORS: Vinay V. Eapen, Sharan Swarup, Melisa Hoyer, Harper JW
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Lysophagy-the selective elimination of damaged lysosomes by the autophagy pathway-is a critical housekeeping mechanis... | ["[Generation of Stable Cell line expressing mKeima-Galectin-3]\nPack mKeima tagged Galectin 3 Lentiviral vector in HEK293T by cotransfection of pPAX2, pMD2 and the vector of interest in a 4:2:1 ratio using polyethelenimine (PEI).", "[Generation of Stable Cell line expressing mKeima-Galectin-3]\nCollect virus containin... |
49,560 | 3'-DGE High Throughput RNA Library Preparation | 1 | dx.doi.org/10.17504/protocols.io.bumynu7w | https://www.protocols.io/view/3-39-dge-high-throughput-rna-library-preparation-bumynu7w | Sarah Boswell, Caitlin Mills, Feodor Price, Stewart Rudnicki | TITLE: 3'-DGE High Throughput RNA Library Preparation
AUTHORS: Sarah Boswell, Caitlin Mills, Feodor Price, Stewart Rudnicki
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is for the high-throughput transcriptome screening method called, 3’ Digital Gene Expression (3’-DGE). In this... | ["[Cell Plating]\nCell plating conditions will vary depending on your experiment and cell type. Usually 2,000-10,000 cells per well.For best compatibility with ICCB-L robotics please use GREINER MICROPLATE, 384 WELL, PS, F-BOTTOM, µCLEAR now sold as Perkin Elmer CellCarrier ULTRA\nThis protocol has only been tested wit... |
null | null | null | dx.doi.org/10.17504/protocols.io.e8fbhtn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol is for processing 20x10<sup>6</sup> cells (or ~100µl wet cell pellet). It can be scaled up and down accordingly.</p>
<p> </p>
<p>It is part of the FOCUS™ Mitochondria Kit <a href="https://www.protocols.io/view/Collection-of-FOCUS-Mitochondria-Kit-protocols-e8tbh... | [] |
45,789 | qPCR: Bacterial SSU rRNA 338F-516P-805R | 1 | dx.doi.org/10.17504/protocols.io.bqx5mxq6 | https://www.protocols.io/view/qpcr-bacterial-ssu-rrna-338f-516p-805r-bqx5mxq6 | Roey Angel, Eva Petrova, Ana Lara | TITLE: qPCR: Bacterial SSU rRNA 338F-516P-805R
AUTHORS: Roey Angel, Eva Petrova, Ana Lara
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Universal 16S rRNA probe-based-qPCR assay for bacteria.</div><div class = "text-block"><span>The primers and probe are taken from </span><a href="http://dx.doi.or... | ["[Primers and probe]\nABCD1NameTypeSequenceTarget region12BAC338FForwardACT CCT ACG GGA GGC AG338-3543BAC516P2ProbeTGC CAG CAG CCG CGG TAA TA516-5364BAC805RReverseGAC TAC CAG GGT ATC TAA TC 785-8051. Relative to E. coli SSU rRNA gene2. The probe must be dual-labelled either with 5’-6-FAM, 3’-BHQ1 or any other valid co... |
45,909 | Methods of investigation and assessment of ecological water resources | 6 | dx.doi.org/10.17504/protocols.io.bq3vmyn6 | https://www.protocols.io/view/methods-of-investigation-and-assessment-of-ecologi-bq3vmyn6 | 1141969519 , Xiao Wang | TITLE: Methods of investigation and assessment of ecological water resources
AUTHORS: 1141969519 , Xiao Wang
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Methods of investigation and assessment of ecological water resources</span></div></div>
[STEPS]
?. [methods... | ["[methods]\nSampling and data collectionThe sampling and field investigation were carried out in the downstream salt marsh area within 50 km of the West Taijinar Lake in April 2019. Random sampling of water was conducted at 5–10 km intervals in the accessible parts of the salt marsh area.Thirteen surface water samples... |
null | null | null | dx.doi.org/10.17504/protocols.io.dtq6mv | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Tris-Acetate-Phosphate medium (TAP) is among the most common for Chlamydomonas reinhardtii. This protocol uses premade TAP from <a href="https://www.thermofisher.com/order/catalog/product/A1379801" target="_blank">ThermoFisher</a>. Alternative and significantly cheaper TAP mediu... | [] |
21,009 | UC Davis - Macrovascular Permeability and Lipoprotein Flux | null | dx.doi.org/10.17504/protocols.io.yrrfv56 | null | John Rutledge | TITLE: UC Davis - Macrovascular Permeability and Lipoprotein Flux
AUTHORS: John Rutledge
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">One of the three indices of arterial function that are compromised to a varying ... | ["Mice are anesthetized with an intraperitoneal injection with 50 mg pentobarbital/kg weight.", "Blood was collected from each animal through the right atrium using a 22-gauge needle and a heparinized syringe. Blood was transferred to sterile Vacutainers and centrifuged at 2800 rpm for 10 min. Plasma samples were separ... |
79,529 | Differentiation NPCs to Dopaminergic/Midbrain Neurons | 4 | dx.doi.org/10.17504/protocols.io.8epv5jp65l1b/v1 | https://www.protocols.io/view/differentiation-npcs-to-dopaminergic-midbrain-neur-crwhv7b6 | michela.deleidi | TITLE: Differentiation NPCs to Dopaminergic/Midbrain Neurons
AUTHORS: michela.deleidi
[DESCRIPTION]
This protocol details methods for differentiation of NPCs to Dopaminergic/Midbrain Neurons.
[STEPS]
SECTION: Day -2: split NPCs
1. Coat numbers of wells you need on a well-plate with Matrigel:
SECTION: Day -2: spl... | ["[Day\t-2: split NPCs] Coat numbers of wells you need on\ta well-plate with Matrigel:", "[Day\t-2: split NPCs] Dilute thawed Matrigel out of 4 °C 1/10 in DMEM/F12 without HEPES.", "[Day\t-2: split NPCs] Incubate 30 min 37 °C in incubator.", "[Day\t-2: split NPCs] Remove\told medium and add 500 µL (Sigma Aldrich, #A696... |
14,818 | Mouse Pancreatic Islet Isolation | null | dx.doi.org/10.17504/protocols.io.sqaedse | https://www.protocols.io/view/mouse-pancreatic-islet-isolation-sqaedse | Nancy Smith, Aliya Spigelman, Haopeng Lin, Patrick Macdonald | TITLE: Mouse Pancreatic Islet Isolation
AUTHORS: Nancy Smith, Aliya Spigelman, Haopeng Lin, Patrick Macdonald
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol details islet isolation from mouse pancreas. The protocol is divided into 3 main parts; </span><span style = "font-style:i... | ["[Solution Prep- Hanks’ Balanced Salts (HBSS) - Sigma H6136]\nMeasure out 900ml of room temperature H2O.", "[Solution Prep- Hanks’ Balanced Salts (HBSS) - Sigma H6136]\nWhile gently stirring the water, add the powdered medium. Stir until dissolved. DO NOT HEAT.", "[Solution Prep- Hanks’ Balanced Salts (HBSS) - Sigma H... |
85,597 | Mouse Olfactory Horizontal Basal Cell Culture | 4 | dx.doi.org/10.17504/protocols.io.j8nlkok26v5r/v1 | https://www.protocols.io/view/mouse-olfactory-horizontal-basal-cell-culture-cxt5xnq6 | Alp Ozgun, Priya Suman, Josée Coulombe, Julianna Tomlinson, Earl G. Brown, John M. Woulfe, Michael G. Schlossmacher | TITLE: Mouse Olfactory Horizontal Basal Cell Culture
AUTHORS: Alp Ozgun, Priya Suman, Josée Coulombe, Julianna Tomlinson, Earl G. Brown, John M. Woulfe, Michael G. Schlossmacher
[DESCRIPTION]
This protocol describes isolation and culture of basal cells from the olfactory epithelium of mice. The process involves serial... | ["Dissect olfactory mucosa from nasal septum on ice .\nInduce anesthesia via intraperitoneal injection of 0.15 mL euthanyl, followed by\ndecapitation. Peel off skin and excise the eyes and the jaw. Disinfect the skull with 70% ethanol and carefully bisect along the sagittal plane, maintaining a 1 mm distance from the i... |
104,713 | Long Amplicon Nanopore Sequencing for Dual-Typing RdRp and VP1 Genes of Norovirus Genogroups I and II in Wastewater | 1 | dx.doi.org/10.17504/protocols.io.8epv5xpmjg1b/v2 | https://www.protocols.io/view/long-amplicon-nanopore-sequencing-for-dual-typing-dihh4b36 | George Scott, David Ryder, Mary Buckley, Richard Hill, Samantha Treagus, Tina Stapleton, David Walker, James Lowther, Frederico Batista | TITLE: Long Amplicon Nanopore Sequencing for Dual-Typing RdRp and VP1 Genes of Norovirus Genogroups I and II in Wastewater
AUTHORS: George Scott, David Ryder, Mary Buckley, Richard Hill, Samantha Treagus, Tina Stapleton, David Walker, James Lowther, Frederico Batista
[DESCRIPTION]
This protocol outlines the procedures... | ["[First-Round PCR]", "[PCR Product Quantification]", "[GI and GII PCR Product Pooling]", "[Native Barcoding and Sequencing] Perform end-prep and barcoding following the manufacturer’s instructions for ligation sequencing of amplicons in the Native Barcoding Kit 96 V14 by Oxford Nanopore Technologies", "[Native Barcodi... |
33,040 | New chemiphotobleaching protocol for Raman spectroscopy | null | dx.doi.org/10.17504/protocols.io.bchqit5w | null | Elena Yakubovskaya, Tatiana Zaliznyak, Joaquin Martinez Martinez, Gordon Taylor | TITLE: New chemiphotobleaching protocol for Raman spectroscopy
AUTHORS: Elena Yakubovskaya, Tatiana Zaliznyak, Joaquin Martinez Martinez, Gordon Taylor
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">We present a new and simple chemiphotobleaching method to irreversibly suppress background fluoresce... | ["Concentrate cells from fixed suspension onto GTTP 0.2 um membranes by filtering appropriate volume. (depend on cells density)", "Fix cells suspension with 2% final concentration of formaldehyde for 15 min.", "Put the filter in a small petri dish and fill in with 2 ml of 3 % Hydrogen Peroxide.", "Put the petri dish wi... |
null | null | null | dx.doi.org/10.17504/protocols.io.pxndpme | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
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20,473 | iPSC Freezing | null | dx.doi.org/10.17504/protocols.io.x8zfrx6 | null | Celeste Karch, Rita Martinez, Jacob Marsh | TITLE: iPSC Freezing
AUTHORS: Celeste Karch, Rita Martinez, Jacob Marsh
[STEPS]
?. Aspirate media
?. Gently wash cells with 1x PBS.
Use 2-3 mL per well in 6 well plate.
?. Add Accutase (Gibco A11105-01) directly to the cells and incubate at for 3-4 minutes.
Individual donor cell lines exhibit variable sensitivity to a... | ["Aspirate media", "Gently wash cells with 1x PBS.\nUse 2-3 mL per well in 6 well plate.", "Add Accutase (Gibco A11105-01) directly to the cells and incubate at for 3-4 minutes.\nIndividual donor cell lines exhibit variable sensitivity to accutase-mediated dissociation. Thus, monitor cells closely to determine when sin... |
36,103 | Pseudorabies Virus Injection (PRV) into Spleen and Mesenteric Lymph Nodes (MLN) | null | dx.doi.org/10.17504/protocols.io.bfhfjj3n | https://www.protocols.io/view/pseudorabies-virus-injection-prv-into-spleen-and-m-bfhfjj3n | Kavi Rude, Jessica Sladek, Colin Reardon | TITLE: Pseudorabies Virus Injection (PRV) into Spleen and Mesenteric Lymph Nodes (MLN)
AUTHORS: Kavi Rude, Jessica Sladek, Colin Reardon
[STEPS]
?. [PRV Injection and Surgery]
Place the mouse into the induction chamber chamber and slide the lid all the way closed. Turn the appropriate stopcock valves to deliver the ap... | ["[PRV Injection and Surgery]\nPlace the mouse into the induction chamber chamber and slide the lid all the way closed. Turn the appropriate stopcock valves to deliver the appropriate amount of isoflurane and O2.", "[PRV Injection and Surgery]\nAs the mouse transitions from a state of awakeness to anesthetized, you sho... |
64,408 | Ikaria Lean Belly Juice Australia | 1 | dx.doi.org/10.17504/protocols.io.kxygxzqb4v8j/v1 | https://www.protocols.io/view/ikaria-lean-belly-juice-australia-ca5ysg7w | it makes weight reduction simpler by empowering thermogenesis What are the Benefits of Ikaria Lean B, it is smarter to comprehend the outcomes might be slow. Where To Buy Ikaria Lean Belly Juice in Aus, eBay, or Walmart.Silymarin: It is known for helping digestion. Otherwise called milk thorn, it is a characteristic l... | TITLE: Ikaria Lean Belly Juice Australia
AUTHORS: it makes weight reduction simpler by empowering thermogenesis What are the Benefits of Ikaria Lean B, it is smarter to comprehend the outcomes might be slow. Where To Buy Ikaria Lean Belly Juice in Aus, eBay, or Walmart.Silymarin: It is known for helping digestion. Oth... | ["Ikaria Lean Belly Juice Australia\nhttp://www.bestsupplement24x7.com/supplemet/ikaria-lean-belly-juice-australia/\nhttps://tomy-zonmy.jimdosite.com/\nhttps://the-dots.com/projects/ikaria-lean-belly-juice-australia-777369\nhttps://medium.com/@monticarlon/ikaria-lean-belly-juice-australia-3fe9d84abd25\nhttps://tomyzonm... |
50,910 | PCR Amplification of Clock and Adcyap1 genes with EmeraldAmp® GT PCR Master Mix in Avian species for polymorphism elucidation | 4 | dx.doi.org/10.17504/protocols.io.6qpvrdwk3gmk/v1 | https://www.protocols.io/view/pcr-amplification-of-clock-and-adcyap1-genes-with-bvx6n7re | Louis-Stéphane Le Clercq, Desiré Lee Dalton, Antoinette Kotzé, Paul Grobler | TITLE: PCR Amplification of Clock and Adcyap1 genes with EmeraldAmp® GT PCR Master Mix in Avian species for polymorphism elucidation
AUTHORS: Louis-Stéphane Le Clercq, Desiré Lee Dalton, Antoinette Kotzé, Paul Grobler
[DESCRIPTION]
This PCR protocol is used to amplify Clock and Adcyap1 gene regions in avian species wh... | ["[Master Mix set-up] Prepare Master Mix and Samples* for PCR.\n\n*Sample information has been deposited to BioSample and associated to the BioProject (PRJNA737185) which used this protocol.\n\n(An experiment template is included in excel format.)", "[Thermal cycling] Program and run the following thermal cycling profi... |
53,453 | tets protocol | 1 | dx.doi.org/10.17504/protocols.io.byfmptk6 | https://www.protocols.io/view/tets-protocol-byfmptk6 | Test Test | TITLE: tets protocol
AUTHORS: Test Test
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">this is a tets protocol</div></div>
[STEPS]
?. this is a test protocol to see the behavior when published | ["this is a test protocol to see the behavior when published"] |
60,353 | Automation Protocol for High-Efficiency and High-Quality Genomic DNA Extraction from Saccharomyces Cerevisiae | 4 | dx.doi.org/10.17504/protocols.io.8epv592p5g1b/v1 | https://www.protocols.io/view/automation-protocol-for-high-efficiency-and-high-q-b669rhh6 | Nina Alperovich, Benjamin M. Scott, David Ross | TITLE: Automation Protocol for High-Efficiency and High-Quality Genomic DNA Extraction from Saccharomyces Cerevisiae
AUTHORS: Nina Alperovich, Benjamin M. Scott, David Ross
[DESCRIPTION]
Here, we describe a protocol for automated extraction of genomic DNA (gDNA) from yeast liquid culture and colonies. The protocol use... | ["[Preparation of Zymolyase Stock] Prepare stock of Zymolyase 20T by dissolving to a concentration of 1 U/µL in 1x PBS.", "[Preparation of Zymolyase Stock] Divide Zymolyase solution into 800 µL aliquots and store at -20 °C until use.", "[Preparation of 2-Mercaptoethanol Stock] Prepare 0.001 % stock of 2-Mercaptoethanol... |
null | null | null | dx.doi.org/10.17504/protocols.io.mr6c59e | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
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22,593 | Transfection by Electroporation in Euplotes crassus | null | dx.doi.org/10.17504/protocols.io.2a9gah6 | null | Angela Piersanti | TITLE: Transfection by Electroporation in Euplotes crassus
AUTHORS: Angela Piersanti
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. 2x104 Euplotes crassus cells were collected and resuspended in 0.3 M glucose solution (7% sea water and 93% of 0.3 M glucose solution).
?. Each round of transfection 250 µl o... | ["2x104 Euplotes crassus cells were collected and resuspended in 0.3 M glucose solution (7% sea water and 93% of 0.3 M glucose solution).", "Each round of transfection 250 µl of cells were used. 0.25 µg of Label IT® Plasmid Delivery Control Cy®3 (Mirus) were added alone or mixed with 2.5 µl of Lipofectamine® 2000 Trans... |
null | null | null | dx.doi.org/10.17504/protocols.io.kzycx7w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>RNA extraction from E. coli cells based on the method described by Chomczynski and Sacchi, 1987</p>
[BEFORE_START]
<p>Always keep your samples on ice!</p>
[GUIDELINES]
<p>RNA is sensitive to degradation! Wear gloves, keep samples on ice when possible, use filter-tips<br />a... | [] |
64,612 | Eagle Hemp CBD Gummies Reviews, Side-Effects, Health Benefits, Pros & Cons | 1 | dx.doi.org/10.17504/protocols.io.yxmvmnbnng3p/v1 | https://www.protocols.io/view/eagle-hemp-cbd-gummies-reviews-side-effects-health-cbccsisw | viaketohack | TITLE: Eagle Hemp CBD Gummies Reviews, Side-Effects, Health Benefits, Pros & Cons
AUTHORS: viaketohack
[DESCRIPTION]
To address the aggravation, stress, nervousness, and Insomnia really, you want to get your hands on Eagle Hemp CBD Gummies. The all-normal unadulterated Cannabidiol gives strong help normally. The... | [] |
49,501 | Exploring tissue morphodynamics using the photoconvertible Kaede protein in amphioxus embryos | 4 | dx.doi.org/10.17504/protocols.io.j8nlk46z6g5r/v1 | https://www.protocols.io/view/exploring-tissue-morphodynamics-using-the-photocon-buj5nuq6 | Lydvina Meister, Hector Escriva, Stephanie Bertrand | TITLE: Exploring tissue morphodynamics using the photoconvertible Kaede protein in amphioxus embryos
AUTHORS: Lydvina Meister, Hector Escriva, Stephanie Bertrand
[DESCRIPTION]
Photoconvertible proteins are powerful tools widely used in cellular biology to study cell dynamics and organelles. Over the past decade, phot... | ["Preparation of the Kaede mRNA", "Gametes obtaining", "Oocytes injection\n\nMicroinjection is undertaken following the protocol published previously in:", "Photoconversion", "mRNA synthesis\n\nUse the and follow the manufacturer's instructions.\n1. Thaw the frozen reagents.\n2. Mix together:\n10 µL of 2X NTP/CAP\n2 ... |
79,542 | Single cell analysis of iPSC-derived midbrain organoids | 4 | dx.doi.org/10.17504/protocols.io.36wgqjk53vk5/v1 | https://www.protocols.io/view/single-cell-analysis-of-ipsc-derived-midbrain-orga-crwwv7fe | María José Pérez J., michela.deleidi | TITLE: Single cell analysis of iPSC-derived midbrain organoids
AUTHORS: María José Pérez J., michela.deleidi
[DESCRIPTION]
The following script was used for analysis of gene corrected (GC) versus GBA1 mutant (MUT) midbrain organoids. The purpose was to combine, filter, integrate, and identify clusters and differential... | ["[Part 1. Data preparation]", "[Part 2. Quality control]", "[Part 3. Data preparation and normalization]", "[Part 4. Data integration and visualization (directly after Part 3)]", "[Part 5. Obtain information from the datasets]", "[Part 6. Merge and analyse subclusters]", "[Part 7. Create a subset of cells from a selec... |
null | null | null | dx.doi.org/10.17504/protocols.io.mrac52e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The current protocol is a bleeding-resuscitation model intended to imitate the effects of severe blood loss and subsequent fluid resuscitation. The experimental subjects were Vietnamese pot-bellied pigs of both sexes weighing 33±4 kg. The animals underwent a 12-hours fasting ... | [] |
92,768 | Sequencing 10x Single Cell Libraries (UMGC Workflow) | 4 | dx.doi.org/10.17504/protocols.io.kqdg3xn4qg25/v1 | https://www.protocols.io/view/sequencing-10x-single-cell-libraries-umgc-workflow-c6t8zerw | Ksenija Sabic | TITLE: Sequencing 10x Single Cell Libraries (UMGC Workflow)
AUTHORS: Ksenija Sabic
[DESCRIPTION]
This protocol explains how to coordinate and send samples for sequencing to the University of Minnesota Genomics Center.
[STEPS] | [] |
55,226 | Tissue extraction from whole caterpillars | 4 | dx.doi.org/10.17504/protocols.io.bz62p9ge | https://www.protocols.io/view/tissue-extraction-from-whole-caterpillars-bz62p9ge | James JN Kitson | TITLE: Tissue extraction from whole caterpillars
AUTHORS: James JN Kitson
[DESCRIPTION]
This protocol is designed for extracting DNA from Lepidopteran larvae but it will work on most animal tissue with some modifications to tube volumes and homogenisation settings.
[STEPS]
SECTION: Initial digestion of OPM larvae
8.... | ["[Initial digestion of OPM larvae] The next steps depend on the intended throughput: either single sample spin-columns or 96-well spin-column plates.", "[Initial digestion of OPM larvae] Incubate at 37 °C overnight (12-16 hours)\n\n37 °C", "[Initial digestion of OPM larvae] Centrifuge at 4,000 x g for 2 min.", "[DNA e... |
36,421 | SINGLE CELL HIGH-THROUGHPUT QRT-PCR PROTOCOL | null | dx.doi.org/10.17504/protocols.io.bftdjni6 | https://www.protocols.io/view/single-cell-high-throughput-qrt-pcr-protocol-bftdjni6 | Sirisha Achanta | TITLE: SINGLE CELL HIGH-THROUGHPUT QRT-PCR PROTOCOL
AUTHORS: Sirisha Achanta
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Single cell high-throughput qRT-PCR protocol combines high sensitivity technique of single cell qPCR with high-throughput qPCR technology that can generate data from 96 sample... | ["[Reagent Preparation]\nLysis Buffer: Combine Lysis enhancer and Resuspension buffer (CellsDirect Kit) as detailed in Table 1 (below) ABC1 Volume\n for one sample (μl) Volumes\n for 96 samples with overage ( for 110 samples) (μl) 2 Lysis enhancer\n (CellDirect kit) 0.5 55 3 Resuspension\n buf... |
48,022 | Extraction of flagellum basal body complexes from Buchnera aphidicola, an endosymbiont of aphids | 4 | dx.doi.org/10.17504/protocols.io.bs5wng7e | https://www.protocols.io/view/extraction-of-flagellum-basal-body-complexes-from-bs5wng7e | mschepers | TITLE: Extraction of flagellum basal body complexes from Buchnera aphidicola, an endosymbiont of aphids
AUTHORS: mschepers
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:justify"><span style = "font-style:italic;">Buchnera aphidicola</span><span> is an in... | ["[Liberating Buchnera from Aphids]\nGrow aphids from birth to fourth instar (10 days) and harvest from plants. For this protocol, we used 3-5g live aphids.", "[Liberating Buchnera from Aphids]\nLoad aphids into sterile fine mesh tea infuser or other sterile straining device.", "[Liberating Buchnera from Aphids]\nSubme... |
34,686 | Genetic network and data analysis | null | dx.doi.org/10.17504/protocols.io.bd46i8ze | https://www.protocols.io/view/genetic-network-and-data-analysis-bd46i8ze | Joachim Nwezeobi, Onyeyirichi Onyegbule, Chukwuemeka Nkere, Joseph Onyeka, Sharon van Brunschot, Susan Seal, John Colvin | TITLE: Genetic network and data analysis
AUTHORS: Joachim Nwezeobi, Onyeyirichi Onyegbule, Chukwuemeka Nkere, Joseph Onyeka, Sharon van Brunschot, Susan Seal, John Colvin
[STEPS]
?. The alignment file (.nex) obtained from Geneious was used to build the minimum spanning tree using Phyloviz [51], to identify the relatio... | ["The alignment file (.nex) obtained from Geneious was used to build the minimum spanning tree using Phyloviz [51], to identify the relationships and mutational distances between the different haplotypes.", "After the random selection and testing of two whitefly samples per field, a two-sided Fisher test and the chi-sq... |
77,154 | Selecting a Region of Interest for Hidden Markov Modeling using ebFRET | 1 | dx.doi.org/10.17504/protocols.io.rm7vzbb75vx1/v2 | https://www.protocols.io/view/selecting-a-region-of-interest-for-hidden-markov-m-cpkavkse | Clark Fritsch | TITLE: Selecting a Region of Interest for Hidden Markov Modeling using ebFRET
AUTHORS: Clark Fritsch
[DESCRIPTION]
This protocol follows from the "Basic Analysis Protocol" and is the first step towards analyzing your data using Hidden Markov Modeling. In this protocol, you select traces containing features that you wi... | ["After generating a catalog of traces that you consider worthy of further analysis and saving these traces to your \"GoodOnes.txt\" file for a given directory (as described in the \"Basic Analysis Protocol\") you will have the opportunity to measure specific parameters in your traces by manually selecting regions of i... |
68,573 | Targeted NGS feline respiratory panel including SARS-CoV-2 for Ion Torrent platform | 1 | dx.doi.org/10.17504/protocols.io.j8nlkk75wl5r/v1 | https://www.protocols.io/view/targeted-ngs-feline-respiratory-panel-including-sa-ce75thq6 | Jobin J Kattoor, Rebecca P Wilkes | TITLE: Targeted NGS feline respiratory panel including SARS-CoV-2 for Ion Torrent platform
AUTHORS: Jobin J Kattoor, Rebecca P Wilkes
[DESCRIPTION]
The current procedure is for NGS of feline respiratory pathogen panel including SARS-CoV-2 for Ion Torrent platform. Note, sensitivity of the method greatly depends on ty... | ["[Nucleic acid extraction]", "[Nucleic acid extraction] KingFisher Flex MagMAX Core extraction protocol\nIn the extraction room, prepare the sample as follows.", "[Nucleic acid extraction] Add 2 mL of DMEM to 5 mL tube.", "[Nucleic acid extraction] Swirl the anterior nasal or throat swab and break off the swab tip.", ... |
null | null | null | dx.doi.org/10.17504/protocols.io.hvhb636 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Luminex Milliplex Cytokine/Chemokine 9-plex MAG manufacturer's protocol</p>
[STEPS]
?.
?.
?.
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62,945 | P1 20/05 | 1 | dx.doi.org/10.17504/protocols.io.ewov1n7qkgr2/v1 | https://www.protocols.io/view/p1-20-05-b9p9r5r6 | Maria Gul | TITLE: P1 20/05
AUTHORS: Maria Gul
[DESCRIPTION]
qa
[STEPS]
1. test
Lorem ipsum dolor sit amet, consectetuer adipiscing elit. Lorem ipsum dolor sit amet, consectetuer adipiscing elit. Nam libero tempore, cum soluta nobis est eligendi optio cumque nihil impedit quo minus id quod maxime placeat facere possimus, omni... | ["test \n\nLorem ipsum dolor sit amet, consectetuer adipiscing elit. Lorem ipsum dolor sit amet, consectetuer adipiscing elit. Nam libero tempore, cum soluta nobis est eligendi optio cumque nihil impedit quo minus id quod maxime placeat facere possimus, omnis voluptas assumenda est, omnis dolor repellendus. Morbi imper... |
98,553 | A Free Analysis Pipeline to Coregister 3D Lightsheet or Serial Sectioned Mouse Brains to the Allen Brain Atlas Using ABBA and Obtain Region Specific Cell Density Quantifications for 800+ Regions | 0 | dx.doi.org/10.17504/protocols.io.8epv5rz1ng1b/v1 | https://www.protocols.io/view/a-free-analysis-pipeline-to-coregister-3d-lightshe-dcgz2tx6 | Liam McLaughlin | TITLE: A Free Analysis Pipeline to Coregister 3D Lightsheet or Serial Sectioned Mouse Brains to the Allen Brain Atlas Using ABBA and Obtain Region Specific Cell Density Quantifications for 800+ Regions
AUTHORS: Liam McLaughlin
[DESCRIPTION]
Coregistration of data from imaged brains unto a brain atlas is one step to es... | ["[Installation] The first step is to install ABBA1 and other necessary tools. Detailed instructions for ABBA installation can be found at https://biop.github.io/ijp-imagetoatlas/installation.html. Using Windows, installation of all ABBA dependencies can be easily accomplished by running an installer, but otherwise, ea... |
null | null | null | dx.doi.org/10.17504/protocols.io.drr555 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This is a protocol for <em>in vitro</em> transposon mutagenesis for introduction of internal epitope tags. It is from:<br />Zordan RE, Beliveau BJ, Trow JA, Craig NL, and Cormack BP (2015) <a href="http://www.genetics.org/content/200/1/47.long" target="_blank">Avoiding the Ends:... | [] |
39,100 | Retro-orbital Bleeding for Rats | 1 | null | https://www.protocols.io/view/retro-orbital-bleeding-for-rats-bie4kbgw | Sharona Sedighim, Olivier George | TITLE: Retro-orbital Bleeding for Rats
AUTHORS: Sharona Sedighim, Olivier George
[STEPS]
?. [Eye Bleeds Procedure]
Take a microcapillary tube (broken in half) and place it behind the eye.
?. [Eye Bleeds Procedure]
Twist it until you hear/feel a little pop, and blood should start coming out.
?. [Eye Bleeds Procedure]
L... | ["[Eye Bleeds Procedure]\nTake a microcapillary tube (broken in half) and place it behind the eye.", "[Eye Bleeds Procedure]\nTwist it until you hear/feel a little pop, and blood should start coming out.", "[Eye Bleeds Procedure]\nLet blood drip into the purple collection tube (try to fill it to the top line).", "[Eye ... |
null | null | null | dx.doi.org/10.17504/protocols.io.dke4td | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Concentrate phytoplankton samples about 100-fold typically from 5L down to 20 mL. Takes about 1 hour per sample. Samples can be used for flow cytometry sorting or for cultures. Enrichment by TFF usually keep growing for a longer time than unconcentrate sam... | [] |
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