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 |
|---|---|---|---|---|---|---|---|
47,177 | Cecret Workflow Protocol for SARS-CoV-2 Assembly and Lineage Classification | 5 | null | https://www.protocols.io/view/cecret-workflow-protocol-for-sars-cov-2-assembly-a-bsbhnaj6 | Erin Young, TOAST CDC Workgroup | TITLE: Cecret Workflow Protocol for SARS-CoV-2 Assembly and Lineage Classification
AUTHORS: Erin Young, TOAST CDC Workgroup
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol provides instructions on how to install the staphb_toolkit and run the Cecret workflow. Cecret produces SARS-C... | ["[Load Dependencies]\nLoad Software Dependencies\nThe staphb_toolkit requires either singularity or docker, Python 3.6 or greater, and Java version 8 or later. If you do not yet have these installed, do so at this time, and ensure they are in your PATH. Within the CDC high-performance computing cluster, these dependen... |
19,688 | Southern blotting probes for HBV genotype D | null | dx.doi.org/10.17504/protocols.io.xggfjtw | null | Fumihiko TAKEUCHI | TITLE: Southern blotting probes for HBV genotype D
AUTHORS: Fumihiko TAKEUCHI
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Southern blotting probes for HBV genotype D.</div><div class = "text-block">HBV cccDNA, rcDNA, and dslDNA can be detected by these probes.</div><div style = "text-align :; fl... | ["[PCR reaction]\nPrepare the 9 tubes (ccc1-9 probes) and mix the reagent (DO NOT mix other primer set.For example, ccc1 fwd and ccc3 rev. AB1Ex taq0.5 ul210 X buffer10 ul3dNTPmix8 ul4Template (Supernatant DNA)5 ul5Primer (3 uM)17 ul X 2 (Forward and Reverse)6DNase free water42.5 ul7Total100 ul\nAB1Ex taq0.5 ul210 X ... |
null | null | null | dx.doi.org/10.17504/protocols.io.taseiee | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>A quick Lowry.Assay for the extraction and determination of total protein from <em>Synechocystis.</em></p>
<p> </p>
<p> </p>
<p><em>Photo credit: Miriam Dreesbach, Institute for Synthetic Microbiology, HHU Düsseldorf</em></p>
[BEFORE_START]
<p>Remeber to prepare BSA standard... | [] |
66,873 | Total Health ACV Keto Gummies (Pros and Cons) Is It Scam Or Trusted? | 1 | dx.doi.org/10.17504/protocols.io.j8nlkkqedl5r/v1 | https://www.protocols.io/view/total-health-acv-keto-gummies-pros-and-cons-is-it-cdizs4f6 | andrewfilintof | TITLE: Total Health ACV Keto Gummies (Pros and Cons) Is It Scam Or Trusted?
AUTHORS: andrewfilintof
[DESCRIPTION]
Total Health ACV Keto Gummies
[STEPS]
1. You could take some time and constancy, to attempt investigate various food sources and diets to find the best weight reduction procedure. Anything weight reduct... | ["You could take some time and constancy, to attempt investigate various food sources and diets to find the best weight reduction procedure. Anything weight reduction strategy Total Health ACV Keto Gummies you use, it is important to remain propelled and keep away from common nourishing snares, like eating way an exces... |
36,790 | Telerehabilitation in patients with respiratory tract diseases: protocol for a scoping review | null | dx.doi.org/10.17504/protocols.io.bf6wjrfe | https://www.protocols.io/view/telerehabilitation-in-patients-with-respiratory-tr-bf6wjrfe | Shunsuke Taito, Kota Yamauchi, Yuki Kataoka | TITLE: Telerehabilitation in patients with respiratory tract diseases: protocol for a scoping review
AUTHORS: Shunsuke Taito, Kota Yamauchi, Yuki Kataoka
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:left"><span style = "font-weight:bold;">Background</spa... | [] |
60,899 | Immunofluorescence | 4 | dx.doi.org/10.17504/protocols.io.14egn741mv5d/v1 | https://www.protocols.io/view/immunofluorescence-b7qbrmsn | William Hancock-Cerutti, Pietro De Camilli | TITLE: Immunofluorescence
AUTHORS: William Hancock-Cerutti, Pietro De Camilli
[DESCRIPTION]
This protocol describes the fixation of cultured cells in paraformaldehyde solution and immunofluorescent labeling of mitochondria and DNA.
[STEPS] | [] |
15,161 | YEP Medium | null | dx.doi.org/10.17504/protocols.io.s2zegf6 | null | Roscoff Culture Collection | TITLE: YEP Medium
AUTHORS: Roscoff Culture Collection
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Use for </span><span style = "font-style:italic;">Schizochytrium</span></div></div>
[STEPS]
?. Filter 1L of aged seawater (at least two months) on prefilter and 0.2 µm filter
?. Heat seawater... | ["Filter 1L of aged seawater (at least two months) on prefilter and 0.2 µm filter", "Heat seawater during 20min at 100°C", "To 300 mL of seawater, add :1 g Difco bacto-peptone1 g Bacto yeast extract10 g D-glucose anhydrous", "Complete final volume to 500mL of seawater", "Autoclave the medium", "Under laminar flow hood,... |
75,779 | P6- PROCEDIMIENTO DE FORMACIÓN TRANSVERSAL | 1 | dx.doi.org/10.17504/protocols.io.q26g7y3w3gwz/v1 | https://www.protocols.io/view/p6-procedimiento-de-formaci-n-transversal-cm9bu92n | cgarcia | TITLE: P6- PROCEDIMIENTO DE FORMACIÓN TRANSVERSAL
AUTHORS: cgarcia
[DESCRIPTION]
La EIDUCAM planificará y desarrollará la formación transversal anualmente en cursos impartidos de forma intensiva a lo largo de todo el curso para facilitar la planificación temporal de su asistencia por parte de los alumnos. Estas activi... | ["[P6- PROCEDIMIENTO DE FORMACIÓN TRANSVERSAL] Anualmente, durante el mes de diciembre, la EIDUCAM abrirá una convocatoria al profesorado para que realicen propuestas de cursos para el programa de formación transversal del doctorado. Se dará un plazo de un mes.", "[P6- PROCEDIMIENTO DE FORMACIÓN TRANSVERSAL] Las propue... |
null | null | null | dx.doi.org/10.17504/protocols.io.gwwbxfe | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p style="text-align: center;"><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-Tr.png" /> </p>
<p... | [] |
82,172 | Tissue-specific in vivo transformation of plasmid DNA in Neotropical tadpoles using electroporation | 4 | dx.doi.org/10.17504/protocols.io.8epv5jjq4l1b/v1 | https://www.protocols.click/view/tissue-specific-in-vivo-transformation-of-plasmid-cug4wtyw | Jesse Delia, Maiah Gaines-Richardson, Sarah C. Ludington, Najva Akbari, Cooper Vasek, Daniel Shaykevich, Lauren A O'Connell | TITLE: Tissue-specific in vivo transformation of plasmid DNA in Neotropical tadpoles using electroporation
AUTHORS: Jesse Delia, Maiah Gaines-Richardson, Sarah C. Ludington, Najva Akbari, Cooper Vasek, Daniel Shaykevich, Lauren A O'Connell
[DESCRIPTION]
Electroporation is an increasingly common technique used for exog... | ["[Anesthesia Preparation] Mix 0.02g ethyl 3-aminobenzoate methanesulfonate (MS-222) and 0.08g sodium bicarbonate with 60 mL tadpole water", "[Anesthesia Preparation] Store at 4C for up to one week", "[Electrode Set-Up for Targeting Muscle Fibers] Remove the tips from two 5 mL serological pipettes using scissors", "[El... |
101,190 | Working in the eBSL-3 | 0 | null | https://www.protocols.io/view/working-in-the-ebsl-3-de3e3gje | Briana L McGovern | TITLE: Working in the eBSL-3
AUTHORS: Briana L McGovern
[DESCRIPTION]
This information has been recorded based on my experience with an eBSL-3. It is not an SOP but rather a guide/peak/reference into what goes into working in an enhanced facility. I did not have this sort of guide and want to provide it to others that... | ["[Regulatory Paperwork] The enhanced BSL-3 facility requires extensive documentation. This documentation can and will be inspected at random by the CDC, so it must be filled out properly every single time you enter the facility.\n\nYou will fill out the following information in blue or black ink:\nDate\nPressure readi... |
null | null | null | dx.doi.org/10.17504/protocols.io.inbcdan | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol provides an efficient DNA extraction and purification of historical museum hides, which potentially have been chemically tanned. </p>
<p> </p>
[BEFORE_START]
<p>Separate PCR-free facility</p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
... | [] |
43,623 | Artificial colonization of logs with ambrosia beetles | 3 | dx.doi.org/10.17504/protocols.io.bnufmetn | https://www.protocols.io/view/artificial-colonization-of-logs-with-ambrosia-beet-bnufmetn | Jiri Hulcr | TITLE: Artificial colonization of logs with ambrosia beetles
AUTHORS: Jiri Hulcr
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes how to artificially colonize logs with ambrosia beetles. </div><div class = "text-block"><span>This protocol is part of the Bark Beetle Mycobiome (... | [] |
56,443 | SciNote troubleshooting protocol | 1 | dx.doi.org/10.17504/protocols.io.b3c3qiyn | https://www.protocols.io/view/scinote-troubleshooting-protocol-b3c3qiyn | Audrey Apgar | TITLE: SciNote troubleshooting protocol
AUTHORS: Audrey Apgar
[DESCRIPTION]
This protocol was designed for testing out the SciNote integration with protocols.io - not to be used for actual scientific experiments.
[STEPS]
1. 60 min
allow vial to thaw
2. 5 mL
pull out 5mL and dispense into pH cup
3.
calibrate pH ... | ["60 min \nallow vial to thaw", "5 mL \npull out 5mL and dispense into pH cup", "calibrate pH meter", "measure pH sample and record in the results section"] |
62,968 | Oprah Winfrey Keto ACV Gummies: Scam Or Legit Gummy Bears? | 1 | dx.doi.org/10.17504/protocols.io.kqdg3pb21l25/v1 | https://www.protocols.io/view/oprah-winfrey-keto-acv-gummies-scam-or-legit-gummy-b9qyr5xw | oprahwinfreyscambears | TITLE: Oprah Winfrey Keto ACV Gummies: Scam Or Legit Gummy Bears?
AUTHORS: oprahwinfreyscambears
[DESCRIPTION]
Oprah Winfrey Keto ACV Gummies: Scam Or Legit Gummy Bears?
[STEPS]
1. Oprah Winfrey Keto ACV Gummies: Scam Or Legit Gummy Bears?
Oprah Winfrey Keto Reviews-If you have decided that the time has come to lo... | ["Oprah Winfrey Keto ACV Gummies: Scam Or Legit Gummy Bears?\nOprah Winfrey Keto Reviews-If you have decided that the time has come to lose a many redundant pounds, know that the path to take is neither easy nor short.\nStill, presumably, with the right provocation, If it were enough to suffer exhausting sessions in th... |
90,656 | Lentivirus preparation for neuronal transdifferentiation | 4 | dx.doi.org/10.17504/protocols.io.kxygx317wg8j/v1 | https://www.protocols.io/view/lentivirus-preparation-for-neuronal-transdifferent-c4r8yv9w | Ching-Chieh Chou, Judith Frydman | TITLE: Lentivirus preparation for neuronal transdifferentiation
AUTHORS: Ching-Chieh Chou, Judith Frydman
[DESCRIPTION]
This is a protocol for the preparation of Lentiviruses.
[STEPS]
SECTION: Preparation of culture medium and plasmids
1. 1. HEK293T medium @4C lasts for 1 month. A total of 500 mL:
435 ml DMEM (High g... | ["[Preparation of culture medium and plasmids] 1. HEK293T medium @4C lasts for 1 month. A total of 500 mL:\n435 ml DMEM (High glucose, GlutaMAX) (Thermo Fisher Scientific) \n50 ml Fetal bovine serum (FBS) (Thermo Fisher Scientific) \n5 ml Penicillin-Streptomycin (Thermo Fisher Scientific) \n5 ml HEPES (1M; Thermo Fishe... |
77,850 | 96-well plate OT-2 liquid handler integrated live-cell and endpoint viability drug activity screen | 4 | dx.doi.org/10.17504/protocols.io.rm7vzbq3rvx1/v1 | https://www.protocols.io/view/96-well-plate-ot-2-liquid-handler-integrated-live-cp92vr8e | Rolando DZ Lyles, M Julia Martinez, Benjamin Sherman, Kerry Burnstein | TITLE: 96-well plate OT-2 liquid handler integrated live-cell and endpoint viability drug activity screen
AUTHORS: Rolando DZ Lyles, M Julia Martinez, Benjamin Sherman, Kerry Burnstein
[DESCRIPTION]
This protocol details OT-2 liquid handler integrated live-cell and endpoint viability drug activity screening on a 96-we... | ["[Day 1: Prepare cell lines for seeding into 96-well plates via Opentrons OT-2 liquid handler] In a sterile tissue culture hood, aspirate media from t75-flask.", "[Day 1: Prepare cell lines for seeding into 96-well plates via Opentrons OT-2 liquid handler] Perform a wash with 5 mL Phosphate Buffered Saline (PBS) (Hycl... |
49,772 | Protocol: Investigating DOIs classes of errors | 5 | dx.doi.org/10.17504/protocols.io.buuknwuw | https://www.protocols.io/view/protocol-investigating-dois-classes-of-errors-buuknwuw | Ricarda Boente, Arcangelo Massari, Cristian Santini, Deniz Tural | TITLE: Protocol: Investigating DOIs classes of errors
AUTHORS: Ricarda Boente, Arcangelo Massari, Cristian Santini, Deniz Tural
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The purpose of this protocol is to provide an automated process to repair invalid DOIs that have been collected by the Ope... | ["[DATA IMPORT]\nWe import a CSV containing invalid DOI-to-DOI citations. The invalid DOIs were collected by Silvio Peroni while processing data provided by Crossref, and are provided on public licence in Citations to invalid DOI-identified entities obtained from processing DOI-to-DOI citations to add in COCI (Peroni, ... |
71,232 | Invertebrate bulk sample metabarcoding protocol collection | 2 | dx.doi.org/10.17504/protocols.io.j8nlkw4n6l5r/v2 | https://www.protocols.io/view/invertebrate-bulk-sample-metabarcoding-protocol-co-chs8t6hw | 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] | [] |
71,497 | Quick-Start Protocol for DNeasy® PowerSoil® Pro Kit | 1 | dx.doi.org/10.17504/protocols.io.j8nlkwk45l5r/v1 | https://www.protocols.io/view/quick-start-protocol-for-dneasy-powersoil-pro-kit-ch3ht8j6 | Carlos Goller | TITLE: Quick-Start Protocol for DNeasy® PowerSoil® Pro Kit
AUTHORS: Carlos Goller
[DESCRIPTION]
This protocol will allow users to operate the DNeasy® PowerSoil® Pro Kit.
[BEFORE_START]
Ensure that the PowerBead Pro Tubes rotate freely in the centrifuge without rubbing.
If Solution CD3 has precipitated, heat at 60°C... | ["[Using the DNeasy® PowerSoil® Pro Kit] Spin the PowerBead Pro Tube briefly to ensure that the beads have settled at the bottom. Add up to 250 mg of soil and 800 µL of Solution CD1. Vortex briefly to mix.", "[Using the DNeasy® PowerSoil® Pro Kit] Secure the PowerBead Pro Tube horizontally on a Vortex Adapter for 1.5... |
24,029 | Human RBM3 ELISA | null | dx.doi.org/10.17504/protocols.io.3p5gmq6 | null | Lisa-Maria Rosenthal, Giang Tong, Katharina Schmitt | TITLE: Human RBM3 ELISA
AUTHORS: Lisa-Maria Rosenthal, Giang Tong, Katharina Schmitt
[STEPS]
?. Prepare RBM3 standards in RBM3 Dilution Buffer: 0, 31.25, 62.5, 125, 250, 500, 1000 and 2000 pg/ml.
?. Dilute the serum samples 1:10 with RBM3-SAMPLE-BUF.
?. Pipette 50μl/well RBM3-Standards (0-2000 pg/ml) and 50μl/well dil... | ["Prepare RBM3 standards in RBM3 Dilution Buffer: 0, 31.25, 62.5, 125, 250, 500, 1000 and 2000 pg/ml.", "Dilute the serum samples 1:10 with RBM3-SAMPLE-BUF.", "Pipette 50μl/well RBM3-Standards (0-2000 pg/ml) and 50μl/well diluted samples in duplicates onto 96-well microplate.", "Pipette 50μl/well detection conjugate – ... |
61,967 | Enzymatically Cleavable Linkers | 6 | dx.doi.org/10.17504/protocols.io.4r3l2o3yxv1y/v1 | https://www.protocols.io/view/enzymatically-cleavable-linkers-b8rprv5n | BOC Sciences | TITLE: Enzymatically Cleavable Linkers
AUTHORS: BOC Sciences
[DESCRIPTION]
Enzyme-cleavable linkers have emerged as a particularly effective ADC linker type due to their ability to selectively release payloads in the lysosomes of target cells. BOC Sciencesis committed to providing flexible ADC enzymatically cleav... | [] |
93,035 | DAB Staining of Fixed Mouse Brain Tissue Sections | 1 | dx.doi.org/10.17504/protocols.io.n92ldm127l5b/v1 | https://www.protocols.io/view/dab-staining-of-fixed-mouse-brain-tissue-sections-c64jzgun | Katerina Rademacher, Ken Nakamura | TITLE: DAB Staining of Fixed Mouse Brain Tissue Sections
AUTHORS: Katerina Rademacher, Ken Nakamura
[DESCRIPTION]
This protocol describes steps for immunohistochemical 1 3,3’-Diaminobenzidine (DAB) staining of free floating fixed mouse brain tissue sections.
[STEPS]
SECTION: Day 1
1. Blocking and primary antibody inc... | ["[Day 1] Blocking and primary antibody incubation.", "[Day 1] Pull all sections into 1x dPBS in 24-well netwells.", "[Day 1] Wash 3 times with 1x dPBS, 10 mins each.", "[Day 1] Wash 3 times with 1x TBS, 10 mins each.", "[Day 1] Quench endogenous peroxidase activity with quenching buffer, 5 mins at RT. Just covering th... |
null | null | null | dx.doi.org/10.17504/protocols.io.u3ceyiw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Media for V. natriegens
LB2:
Standard LB media (10.0 g/L Tryptone, 5.0 g/L Yeast Extract, 10.0 g/L NaCl) with additional 1.5% NaCl
LBv2 Salts:
Standard LB media (10.0 g/L Tryptone, 5.0 g/L Yeast Extract, 10.0 g/L NaCl) with additional with additional v2 salts (204 mM NaCl, 4.... | [] |
90,822 | Pull-down Assays | 1 | dx.doi.org/10.17504/protocols.io.x54v9pw5pg3e/v1 | https://www.protocols.io/view/pull-down-assays-c4xeyxje | Leonardo A Parra-Rivas | TITLE: Pull-down Assays
AUTHORS: Leonardo A Parra-Rivas
[DESCRIPTION]
Pull-down Assays
[STEPS]
1. To pull down proteins from brain lysates and LP2(P4) fractions, 1-2 mg of the
sample was incubated with 25-50 μg of glutathione beads containing GST fusion
proteins for 12-16 hrs.
2. The mixtures were washed t... | ["To pull down proteins from brain lysates and LP2(P4) fractions, 1-2 mg of the\nsample was incubated with 25-50 μg of glutathione beads containing GST fusion\nproteins for 12-16 hrs.", "The mixtures were washed three times with 1X PBS with\n0.15% Triton X-100, and then resuspended in 20 μl of 1X NuPAGE LDS sample\nbuf... |
52,004 | A streamlined protocol for high-throughput amplification-based analysis of DNA samples via nanopore sequencing (based on the 96-well PCR barcoding kit) | 4 | dx.doi.org/10.17504/protocols.io.bw2cpgaw | https://www.protocols.io/view/a-streamlined-protocol-for-high-throughput-amplifi-bw2cpgaw | Jordan P Cuff, Annalise S Hooper, Shrinivas Nivrutti Dighe, Angela Marchbank, Peter Kille | TITLE: A streamlined protocol for high-throughput amplification-based analysis of DNA samples via nanopore sequencing (based on the 96-well PCR barcoding kit)
AUTHORS: Jordan P Cuff, Annalise S Hooper, Shrinivas Nivrutti Dighe, Angela Marchbank, Peter Kille
[DESCRIPTION]
Nanopore sequencing facilitates the rapid and... | ["[Prepare DNA] Extract and purify your DNA in a manner appropriate for the sample type, the hypothesis being tested and this protocol. Consider the length of DNA that you are ideally interested in and how the tissue/sample type might best be lysed/extracted from. This protocol will be most successful when using sample... |
101,125 | Purification of FIP200 CTR-GFP | 0 | dx.doi.org/10.17504/protocols.io.j8nlk8866l5r/v1 | https://www.protocols.io/view/purification-of-fip200-ctr-gfp-dezd3f26 | Elias Adriaenssens, Eleonora Turco | TITLE: Purification of FIP200 CTR-GFP
AUTHORS: Elias Adriaenssens, Eleonora Turco
[DESCRIPTION]
This protocol details the purification GFP-FIP200 (CTR).
[STEPS]
SECTION: Purification procedure
1. To purify GFP-FIP200(CTR), as described previously (Turco et al. 2019 Mol Cell, PMID: 30853400), fuse the C-terminal domai... | ["[Purification procedure] To purify GFP-FIP200(CTR), as described previously (Turco et al. 2019 Mol Cell, PMID: 30853400), fuse the C-terminal domain of FIP200 (1458-1594aa) to a N-terminal 6xHis-TEV-GFP-tag through cloning into a pET-DUET1 vector (available on Addgene).", "[Purification procedure] After the transfor... |
64,837 | Via Keto Apple Gummies What are Customers Saying? Know the Truth! | 3 | dx.doi.org/10.17504/protocols.io.dm6gpbm55lzp/v1 | https://www.protocols.io/view/via-keto-apple-gummies-what-are-customers-saying-k-cbjdski6 | officials | TITLE: Via Keto Apple Gummies What are Customers Saying? Know the Truth!
AUTHORS: officials
[DESCRIPTION]
Click Here To BUY ViaKeto Apple Gummies From Official Website
ViaKeto Apple Gummies
[STEPS] | [] |
40,674 | Tissue Mapper | 1 | dx.doi.org/10.17504/protocols.io.bjyakpse | https://www.protocols.io/view/tissue-mapper-bjyakpse | Maci Heal | TITLE: Tissue Mapper
AUTHORS: Maci Heal
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the process of using the Tissue Mapper software to map single neurons of the intrinsic cardiac nervous system, annotate or "trace" key cardiac anatomy on select histological sections of an... | ["[Software installation setup]\nHave Tissue Mapper installed and licensed on your workstation of choice through an MBF Bioscience representative.", "[Software installation setup]\nAfter launching Tissue Mapper, set an API key to your profile to pull the ontology list from SciCrunch to annotate your organ of choice wit... |
67,943 | Single Cell RNA sequencing (scRNAseq) of fresh human lung cell suspension | 4 | dx.doi.org/10.17504/protocols.io.4r3l2owdxv1y/v1 | https://www.protocols.io/view/single-cell-rna-sequencing-scrnaseq-of-fresh-human-cekftctn | Julian Alonso Chamucero, Mauricio Rojas, Ana Mora | TITLE: Single Cell RNA sequencing (scRNAseq) of fresh human lung cell suspension
AUTHORS: Julian Alonso Chamucero, Mauricio Rojas, Ana Mora
[DESCRIPTION]
Gene expression analysis is a molecular biology approach that allows, among other things, to evaluate the differential expression of genes involved in the developmen... | ["[Tissue Dissociation] Soak the lung pieces in PBS (3x) to remove red blood cells.", "[Tissue Dissociation] Compress with a sterile gauze pad to remove excess liquid.", "[Tissue Dissociation] Carefully remove the parietal pleura.", "[Tissue Dissociation] Dissect the tissue into 1-cm3 pieces and transfer to a 50 ml con... |
57,602 | Consulting firms in the public management of epidemics. A scoping-review protocol | 1 | dx.doi.org/10.17504/protocols.io.b4haqt2e | https://www.protocols.io/view/consulting-firms-in-the-public-management-of-epide-b4haqt2e | Lucille Gallardo , Lara Gautier, Fanny Chabrol, Lola Traverson, Sydia Oliveira, Valery Ridde | TITLE: Consulting firms in the public management of epidemics. A scoping-review protocol
AUTHORS: Lucille Gallardo , Lara Gautier, Fanny Chabrol, Lola Traverson, Sydia Oliveira, Valery Ridde
[DESCRIPTION]
The aim of this scoping review is to produce a state of knowledge about the role of private consulting firms... | ["Context\n\nSocial sciences research evidences about private consulting firm’s role in public policy is large (Saint-Martin 2006; Empson et al. 2015; Hurl et Vogelpohl 2021a). Studies in sociology, political science, economy, or international relations, reveal that the involvement of these firms with public organizati... |
14,800 | Murine CD8 T cell restimulation in vitro | 1 | dx.doi.org/10.17504/protocols.io.spqedmw | https://www.protocols.io/view/murine-cd8-t-cell-restimulation-in-vitro-spqedmw | Kristin Anderson | TITLE: Murine CD8 T cell restimulation in vitro
AUTHORS: Kristin Anderson
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol outlines the steps for re-stimulating engineered murine CD8 T cells in vitro.</div><div class = "text-block"><span>In brief: Transduced T cells were re-stimulated w... | ["[Day 0: Prepare peptide-pulsed antigen-presenting cells]\n1. Obtain spleens to pulse with peptide. Record pertinent information regarding donor mice (mouse background, number of spleens, gender, date of birth).2. Harvest T cells by smashing spleens through a 40um filter. Rinse with 10-20 mL of T cell media and transf... |
null | null | null | dx.doi.org/10.17504/protocols.io.dbt2nm | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
<strong>Notes:</strong><br /><br />Goal initially is to screen several seawater samples on several roseobacter hosts to determine breadth of rosephage present at each location and then to focus on a single site.<br /><br />Nomenclature for viruses should include a designation for... | [] |
71,688 | MEDPC2XL application use to transfer/convert medpc4 data file info into an excel file, AJA,6-27-2022 | 1 | dx.doi.org/10.17504/protocols.io.5qpvorbqxv4o/v1 | https://www.protocols.io/view/medpc2xl-application-use-to-transfer-convert-medpc-ch9gt93w | Alicia Avelar | TITLE: MEDPC2XL application use to transfer/convert medpc4 data file info into an excel file, AJA,6-27-2022
AUTHORS: Alicia Avelar
[DESCRIPTION]
Protocol for transferring data from MedPC 4 program to Excel files.
[BEFORE_START]
Must use PC, the medpc2xl application will not work on macs.
Make sure theinternet is w... | ["Find data files that you want to transfer in dropbox", "Find medpc templates folder in dropbox.You will need these to use with the medpc2xl app in order for it to extract the data from the medpc file and transfer it to excel.", "Make sure the computer you are working on has fully licensed and updated excel software."... |
107,371 | Spray inoculation of peach trees or leaves with the plant pathogen Xanthomonas arboricola pv. pruni. | 0 | dx.doi.org/10.17504/protocols.io.eq2lywbxrvx9/v1 | https://www.protocols.io/view/spray-inoculation-of-peach-trees-or-leaves-with-th-dk4j4yun | Daniela Negrete-Moreno, Annabel Miller, Elizabeth Cieniewicz | TITLE: Spray inoculation of peach trees or leaves with the plant pathogen Xanthomonas arboricola pv. pruni.
AUTHORS: Daniela Negrete-Moreno, Annabel Miller, Elizabeth Cieniewicz
[DESCRIPTION]
Description:
Potted tree experiments and detached leaf assays are used for many purposes, including:
observing the effect... | [] |
87,048 | Deprescribing criteria for older people | 1 | dx.doi.org/10.17504/protocols.io.bp2l6x2bklqe/v1 | https://www.protocols.io/view/deprescribing-criteria-for-older-people-cy9gxz3w | rdelassalas | TITLE: Deprescribing criteria for older people
AUTHORS: rdelassalas
[DESCRIPTION]
Introduction/Objective: To propose deprescribing criteria in older people with non-communicable disease (NCD).
Methods: This project was carried out following four stages.
1. A systematic review of the literature was conducted to identi... | [] |
37,391 | Treatment of coagulopathy in COVID-19 patients: protocol for a scoping review | null | dx.doi.org/10.17504/protocols.io.bgrpjv5n | https://www.protocols.io/view/treatment-of-coagulopathy-in-covid-19-patients-pro-bgrpjv5n | Hirotaka Mori, Hiroshi Ohkawara, Takayuki Ikezoe, Ryuichi Togawa, Mami Rikimaru, Yoko Shibata | TITLE: Treatment of coagulopathy in COVID-19 patients: protocol for a scoping review
AUTHORS: Hirotaka Mori, Hiroshi Ohkawara, Takayuki Ikezoe, Ryuichi Togawa, Mami Rikimaru, Yoko Shibata
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Background</div><div class = "text-block">Coronavirus infection ... | [] |
47,152 | CUT&RUN for nuclei using the CUTANA™ ChIC/CUT&RUN Kit | 4 | dx.doi.org/10.17504/protocols.io.5jyl85e78l2w/v1 | https://www.protocols.io/view/cut-amp-run-for-nuclei-using-the-cutana-chic-cut-a-bsaqnadw | Eric RA Pederson | TITLE: CUT&RUN for nuclei using the CUTANA™ ChIC/CUT&RUN Kit
AUTHORS: Eric RA Pederson
[DESCRIPTION]
Modified CUTANA™ ChIC/CUT&RUN Kit protocol using nuclei from brain tissue.
[BEFORE_START]
The pre-experimentation steps are important
Also it is important that all the primers have been ordered and reconstitu... | ["[pre-experimentation] All steps should be performed on ice or at 4 °C.", "[pre-experimentation] Pre-chill all Dounces and pestles to 4 °C in a fridge. Or just leave on ice for a while.", "[pre-experimentation] Prepare buffers. \ni) Homogenization buffer\nii) 25X protease inhibitor\niii) wash buffer (see step 5)\niv) ... |
45,827 | Mitochondrial genome assembly | 5 | dx.doi.org/10.17504/protocols.io.bqzbmx2n | https://www.protocols.io/view/mitochondrial-genome-assembly-bqzbmx2n | Graham Etherington | TITLE: Mitochondrial genome assembly
AUTHORS: Graham Etherington
[DESCRIPTION]
De novo assembly of 49 mustelid whole mitochondrial genomes
[STEPS]
1. Calculate read length of fastq files for each sample and run MitoZ
2. Genome alignment. Concatenate the genomes and use ClustalW to align them.
2.1. Rename both t... | ["Calculate read length of fastq files for each sample and run MitoZ", "Genome alignment. Concatenate the genomes and use ClustalW to align them.", "Rename both the accession name and file name of the genome assemblies, as they'll all have the same name (work71.mitogenome.fa.reorder)", "Concatenate all of the assemblie... |
105,125 | UDA-multiome-protocol | 0 | dx.doi.org/10.17504/protocols.io.j8nlk82nwl5r/v1 | https://www.protocols.io/view/uda-multiome-protocol-diwd4fa6 | Yun Li | TITLE: UDA-multiome-protocol
AUTHORS: Yun Li
[DESCRIPTION]
Droplet microfluidics-based single-cell combinatorial indexing sequencing represents an attractive way to balance cost, scalability,
robustness, and accessibility. However, current methods need a tailored protocol for specific modality respectively, which may ... | ["[Transposition] Prepare Transposition Mix (7ul ATAC Buffer B (2000193); 3ul ATAC Buffer B (2000193) each sample) on ice. Pipette mix 10x and centrifuge briefly.", "[Transposition] Add 10 µl Transposition Mix to a tube of a PCR 8-tube strip for each sample.", "[Transposition] Refer to Nuclei Concentration Guidelines... |
26,641 | HyPR Protocol | 3 | null | https://www.protocols.io/view/hypr-protocol-59rg956 | Jamie Marshall, Benjamin R. Doughty, Vidya Subramanian, Philine Guckelberger, Qingbo Wang, Linlin M. Chen, Samuel G. Rodriques, Kaite Zhang, Charles P. Fulco, Joseph Nasser, Elizabeth J. Grinkevich, Teia Noel, Sarah Mangiameli, Anna Greka, Eric S. Lander, Fei Chen, Jesse Engreitz | TITLE: HyPR Protocol
AUTHORS: Jamie Marshall, Benjamin R. Doughty, Vidya Subramanian, Philine Guckelberger, Qingbo Wang, Linlin M. Chen, Samuel G. Rodriques, Kaite Zhang, Charles P. Fulco, Joseph Nasser, Elizabeth J. Grinkevich, Teia Noel, Sarah Mangiameli, Anna Greka, Eric S. Lander, Fei Chen, Jesse Engreitz
[DESCRIP... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.g77bzrn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div title="Page 5">
<div title="Page 4">
<p>This protocol explains how to use serial dilutions of sample protein to determine the linear ranges of detection for a target and internal loading control, and choose an appropriate amount of sample to load for QWB analysis.</p>
<p> <... | [] |
82,922 | Image processing and 3D reconstruction | 5 | dx.doi.org/10.17504/protocols.io.x54v9d99mg3e/v1 | https://www.protocols.io/view/image-processing-and-3d-reconstruction-cu8iwzue | Minghao Chen | TITLE: Image processing and 3D reconstruction
AUTHORS: Minghao Chen
[DESCRIPTION]
Image processing and 3D reconstruction
[STEPS]
SECTION: Image processing
1. Use cryoSPARC for the following steps except those particularly mentioned.
SECTION: Image processing
2. Do motion correction by [Patch Motion Correction]
Bin 2... | ["[Image processing] Use cryoSPARC for the following steps except those particularly mentioned.", "[Image processing] Do motion correction by [Patch Motion Correction]\nBin 2x in fourier cropping for super-resolution video stacks\nBin 1x in fourier cropping for regular video stacks", "[Image processing] Do contrast tra... |
62,817 | Regulation of mitophagy by the NSL complex underlies genetic risk for Parkinson’s disease: Bioinformatic Prioritisation and Hit Validation | 4 | dx.doi.org/10.17504/protocols.io.3byl4br2zvo5/v1 | https://www.protocols.io/view/regulation-of-mitophagy-by-the-nsl-complex-underli-b9j9r4r6 | Karishma D’Sa, Sebastian Guelfi, David Zhang, Alan Pittman, Daniah Trabzuni, Demis A. Kia, Nicholas W Wood, John Hardy, Claudia Manzoni, Mina Ryten | TITLE: Regulation of mitophagy by the NSL complex underlies genetic risk for Parkinson’s disease: Bioinformatic Prioritisation and Hit Validation
AUTHORS: Karishma D’Sa, Sebastian Guelfi, David Zhang, Alan Pittman, Daniah Trabzuni, Demis A. Kia, Nicholas W Wood, John Hardy, Claudia Manzoni, Mina Ryten
[DESCRIPTION]
Th... | ["[Selection of genes for High Content Screening]", "[Selection of genes for High Content Screening] Apply the same pipeline to the 2017 PD GWAS reported by Chang et al., 2017, to update the list of candidate genes.", "[Selection of genes for High Content Screening] Evaluate these processes with Gene Ontology Biologica... |
97,770 | DNA extraction and detection of Mansonella perstans from Dry Blood Spots (DBS) | 0 | dx.doi.org/10.17504/protocols.io.x54v928b4l3e/v1 | https://www.protocols.io/view/dna-extraction-and-detection-of-mansonella-perstan-dbqi2mue | Millicent Opoku, Dziedzom De Souza | TITLE: DNA extraction and detection of Mansonella perstans from Dry Blood Spots (DBS)
AUTHORS: Millicent Opoku, Dziedzom De Souza
[DESCRIPTION]
Mansonella perstans is a filarial parasite that causes mansonellosis in humans. Unlike other filarial parasitic diseases, mansonellosis is rarely symptomatic and hence poorly ... | [] |
69,917 | Title: Ultrasound-Guided Dry Needling versus Traditional Dry Needling for patients with Knee Osteoarthritis: A Double-blind Randomized Controlled Trial | 1 | dx.doi.org/10.17504/protocols.io.3byl4j2zjlo5/v1 | https://www.protocols.io/view/title-ultrasound-guided-dry-needling-versus-tradit-cgh5tt86 | Johnson C.Y. Pang, Professor Amy S.N. FU, Dr. Stanley K.H. LAM, Dr. B. PENG, Dr. Allan C.L. FU | TITLE: Title: Ultrasound-Guided Dry Needling versus Traditional Dry Needling for patients with Knee Osteoarthritis: A Double-blind Randomized Controlled Trial
AUTHORS: Johnson C.Y. Pang, Professor Amy S.N. FU, Dr. Stanley K.H. LAM, Dr. B. PENG, Dr. Allan C.L. FU
[DESCRIPTION]
Abstract
OBJECTIVE: To compare the effect ... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.vcke2uw | null | null | TITLE: No Title
AUTHORS:
[STEPS]
SECTION: Algal culture
?.
SECTION: Antibiotic treatment
?.
SECTION: Cell monitoring
?. | ["[Algal culture] Seven dinoflagellate species (Amphidinium carterae, Glenodinium foliaceum, Heterocapsa triquetra, Karlodinium veneficum, Prorocentrum minimum, Symbiodinium minutum, and Togula britannica) and Chromera velia were grown in 75 mL plastic flasks with Daigo IMK (Nihon Pharmaceutical Co., Ltd.), f/2, or ESM... |
null | null | null | dx.doi.org/10.17504/protocols.io.q9edz3e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>A protocol for quantification of circulating microRNA using TaqMan assays.</p>
<p>MicroRNAs are purified from platelet-poor plasma using Nucleospin columns</p>
<p>During the purification step samples are spiked with cel-miR-39 as a mean of technical normalization</p>
<p>Norma... | [] |
62,417 | Preparation of 2% Agarose Gel for Electrophoresis | 1 | null | https://www.protocols.io/view/preparation-of-2-agarose-gel-for-electrophoresis-b87rrzm6 | Stephane Fadanka, Shalo Minette, Nadine Mowoh | TITLE: Preparation of 2% Agarose Gel for Electrophoresis
AUTHORS: Stephane Fadanka, Shalo Minette, Nadine Mowoh
[DESCRIPTION]
The agarose gel consists of microscopic pores that act as a molecular sieve which separates molecules based upon the charge, size and shape.Agarose gel electrophoresis can also be used to ... | ["[Measuring Agarose powder] Accurately weigh 0.5 g of Agarose- electrophoresis grade (Cas 9012-36-6) into a weighing boat using a clean spatula and transfer the powder into a 50ml or 100ml beaker.", "[Measuring Agarose powder] Measure 25 mL of 1xTBE (diluted from a 10x stock as described in the citation below )and d... |
104,292 | Immunohistochemistry against p62 and LBP110 | 0 | dx.doi.org/10.17504/protocols.io.kqdg32b47v25/v1 | https://www.protocols.io/view/immunohistochemistry-against-p62-and-lbp110-dh4c38sw | Dennis de Bakker | TITLE: Immunohistochemistry against p62 and LBP110
AUTHORS: Dennis de Bakker
[DESCRIPTION]
Immunohistochemistry staining co-labeling LBP110 and p62/SQSTM1 and DAPI.
[STEPS]
SECTION: Tissue preparation
1. Day 1: Whole mouse brain (2 years old, male) was fixed overnight in 4%PFA.
SECTION: Tissue preparation
2. Day 2:... | ["[Tissue preparation] Day 1: Whole mouse brain (2 years old, male) was fixed overnight in 4%PFA.", "[Tissue preparation] Day 2: Brain was washed 3x 5' in PBS + 4% Sucrose", "[Tissue preparation] Day2: Brain was incubated overnight in PBS + 30% Sucrose", "[Tissue preparation] Day3: Brain was embedded into optimal cutti... |
45,544 | 1. Sample_prep_WB | 4 | null | https://www.protocols.io/view/1-sample-prep-wb-bqqgmvtw | Elizabeth Fozo | TITLE: 1. Sample_prep_WB
AUTHORS: Elizabeth Fozo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Sample preparation for Western bolt assay</div></div>
[STEPS]
?. [Sample preparation for Western bolt assay]
Grow cells, harvest, wash with DI water, and store cell pellet at -800C
?. [Sample preparatio... | ["[Sample preparation for Western bolt assay]\nGrow cells, harvest, wash with DI water, and store cell pellet at -800C", "[Sample preparation for Western bolt assay]\nLysis buffer(50 mM Tris HCl pH 7.5, 200 mM NaCl, 5% Glycerol)- we don’t add DTT or PMSF(https://www.embl.de/pepcore/pepcore_services/protein_purification... |
46,894 | Homemade Gibson Mastermix | 1 | dx.doi.org/10.17504/protocols.io.br2nm8de | https://www.protocols.io/view/homemade-gibson-mastermix-br2nm8de | Anna Behle, Tatsuya Sakaguchi | TITLE: Homemade Gibson Mastermix
AUTHORS: Anna Behle, Tatsuya Sakaguchi
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Recipe for homemade 2 x Gibson Mastermix. </div></div>
[STEPS]
?. [Preparation of 5x isothermal reaction buffer]
Recipe for 4 mL: ABCD1ComponentMolarity / ConcentrationAmountFina... | ["[Preparation of 5x isothermal reaction buffer]\nRecipe for 4 mL: ABCD1ComponentMolarity / ConcentrationAmountFinal concentration2Tris-HCl, pH 7.51 M2 mL500 mM3MgCl21 M200 µL50 mM4dATP100 mM40 µL1 mM5dCTP100 mM40 µL1 mM6dGTP100 mM40 µL1 mM7dTTP100 mM40 µL1 mM8DTT1 M200 µL50 mM9PEG-8000-1 g25 %10NAD+100 mM200 µL5 mM11... |
44,798 | Quantification of 16S rRNA Gene Copies Using ddPCR (EvaGreen-based assay: 338F-805R) | 1 | dx.doi.org/10.17504/protocols.io.bpy6mpze | https://www.protocols.io/view/quantification-of-16s-rrna-gene-copies-using-ddpcr-bpy6mpze | Roey Angel, Eva Petrova | TITLE: Quantification of 16S rRNA Gene Copies Using ddPCR (EvaGreen-based assay: 338F-805R)
AUTHORS: Roey Angel, Eva Petrova
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol describes how to quantify 16S rRNA bacterial gene or transcript copy numbers using </span><a href="https://... | ["[Primers]\nThe assay uses the following universal 16S bacteria primers: ABCD1NameDirectionSequenceTarget region12BAC338FFACT CCT ACG GGA GGC AG338-3543BAC805RRGAC TAC CAG GGT ATC TAA TC785-805 1. Relative to E. coli SSU rRNA gene\nABCD1NameDirectionSequenceTarget region12BAC338FFACT CCT ACG GGA GGC AG338-3543BAC... |
50,801 | Designing an EpiTYPER bisulfite sequencing assay for age estimation in Acinonyx jubatus based on human orthologues | 5 | dx.doi.org/10.17504/protocols.io.j8nlk4yk1g5r/v1 | https://www.protocols.io/view/designing-an-epityper-bisulfite-sequencing-assay-f-bvurn6v6 | Louis-Stéphane Le Clercq, Desire Dalton, Antoinette Kotze, Paul Grobler | TITLE: Designing an EpiTYPER bisulfite sequencing assay for age estimation in Acinonyx jubatus based on human orthologues
AUTHORS: Louis-Stéphane Le Clercq, Desire Dalton, Antoinette Kotze, Paul Grobler
[DESCRIPTION]
Age is key factor in animal ecology as it can be used to assign animals to important age classes, rang... | ["[Retrieving CpG from human sequencing] Most research papers on humans give a \"CG\" value which corresponds to a CpG site in the human genome based on Illumina sequencing. The following steps were used to retrieve the human sequence for reported CG values using the University of California Santa Cruz (UCSC) Genome Br... |
51,746 | Preparation of Single Cell Suspension from Human Lymph Node Tissue | 1 | dx.doi.org/10.17504/protocols.io.bwsapeae | https://www.protocols.io/view/preparation-of-single-cell-suspension-from-human-l-bwsapeae | Steven B. Wells, Peter A. Szabo, Nora Lam, Maya M.L. Poon | TITLE: Preparation of Single Cell Suspension from Human Lymph Node Tissue
AUTHORS: Steven B. Wells, Peter A. Szabo, Nora Lam, Maya M.L. Poon
[DESCRIPTION]
This protocol describes a method for the isolation of pan-lymphocytes, pan-myeloid cells, and progenitors from human lymph node tissue. By providing defined media f... | ["[Preparing Mediums and Buffers] Create the following IMDM-FBS-PSQ Media in a 500 mL bottle of IMDM by using the table below:\n \n Component Volume (mL) Starting Conc. Final Conc.* IMDM 500 - - Penicillin-Streptomycin-Glutamine 5 100X 1X FBS 50 100% 10%", "[Preparing Mediums and Buffers] Cre... |
null | null | null | dx.doi.org/10.17504/protocols.io.h56b89e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Protocol for Immunohistochemistry free-floating sections with anti-NeuN antibody for avian tissue.</p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
102,387 | αS PFF Clearance Assay Protocol | 0 | dx.doi.org/10.17504/protocols.io.n2bvjndmxgk5/v1 | https://www.protocols.io/view/s-pff-clearance-assay-protocol-df8t3rwn | Scott Vermilyea | TITLE: αS PFF Clearance Assay Protocol
AUTHORS: Scott Vermilyea
[DESCRIPTION]
This protocol details the clearance of αS PFF assay.
[STEPS]
SECTION: αS PFF Clearance Assay Protocol
1. Prepare S PFF working solution as above (for 4 1527 final concentration).
SECTION: αS PFF Clearance Assay Protocol
2. Treat for 120 m... | ["[αS PFF Clearance Assay Protocol] Prepare S PFF working solution as above (for 4 1527 final concentration).", "[αS PFF Clearance Assay Protocol] Treat for 120 min.", "[αS PFF Clearance Assay Protocol] Wash cells with PBS followed by trypsin (000.5%) for 1 min to remove excess PFF bound on the extracellular surface."... |
87,799 | In vivo tissue-specific chromatin profiling in Drosophila | 4 | dx.doi.org/10.17504/protocols.io.kxygxp1d4l8j/v2 | https://www.protocols.io/view/in-vivo-tissue-specific-chromatin-profiling-in-dro-czyxx7xn | Vikki M. Weake, Juan P P Jauregui-Lozano, Sarah E McGovern | TITLE: In vivo tissue-specific chromatin profiling in Drosophila
AUTHORS: Vikki M. Weake, Juan P P Jauregui-Lozano, Sarah E McGovern
[DESCRIPTION]
Chromatin regulation plays an essential role in many nuclear processes, and genome-wide chromatin profiling approaches contribute to understanding how chromatin regulates c... | ["[Recipes] Homogenization/wash buffer\n40 mM HEPES, pH 7.5\n120 mM KCl\n0.4% NP40 (IGEPAL)\n\nDilution buffer [cold]\n40 mM HEPES, pH 7.5\n120 mM KCl\n\nBead washing buffer [cold]\n1X Phosphate Buffer Saline (PBS) buffer, pH 7.4\n2.5 mM MgCl2\n0.02% Tween-20\n\n## Omni-ATAC\n Omni-ATAC tagmentation mix\n25 µL 2X buffe... |
57,789 | Expansion of mouse embryonic fibroblasts (MEFs) for hPSC cultures | 4 | dx.doi.org/10.17504/protocols.io.b4n5qvg6 | https://www.protocols.io/view/expansion-of-mouse-embryonic-fibroblasts-mefs-for-b4n5qvg6 | Hanqin Li, Oriol Busquets, Steven Poser, Dirk Hockemeyer, Frank Soldner | TITLE: Expansion of mouse embryonic fibroblasts (MEFs) for hPSC cultures
AUTHORS: Hanqin Li, Oriol Busquets, Steven Poser, Dirk Hockemeyer, Frank Soldner
[DESCRIPTION]
This protocol describes the expansion of mouse embryonic fibroblasts (MEFs) as feeder cells for human pluripotent stem cell (hPSC) culture.
General n... | ["Wash the plates twice with DPBS", "Add Trypsin and incubate for 5 min (37°C; 5% CO2)", "Add MEF medium to neutralize the Trypsin and collect the solution into a conical tube.", "Centrifuge at 250 x g, 5 min", "Remove the supernatant. Re-suspend the cell pellet in fresh MEF medium to plate on gelatin-coated plates (Di... |
105,273 | The design and manufacture of massively scalable inertial focusing prototype microfluidic devices | 0 | dx.doi.org/10.17504/protocols.io.n2bvjnrmpgk5/v3 | https://www.protocols.io/view/the-design-and-manufacture-of-massively-scalable-i-di2z4gf6 | Thomas Carvell | TITLE: The design and manufacture of massively scalable inertial focusing prototype microfluidic devices
AUTHORS: Thomas Carvell
[DESCRIPTION]
Microfluidics is a rapidly expanding field and microfluidic devices have been used in a variety of biomedical applications such as cell sorting, disease diagnostics and various... | ["[Design of exemplar parts] Open computer-aided design software and ensure 3D-modelling format is\nselected and units are set to millimetres.", "[Design of exemplar parts] Select the rectangle tool and enter x-y coordinates for origin (0, 0). The width is 35 and the height is 70. This generates the ‘device rectangle’.... |
99,024 | Tumor Dissociation to Single Cell Suspension | 0 | dx.doi.org/10.17504/protocols.io.bp2l62bjkgqe/v1 | https://www.protocols.io/view/tumor-dissociation-to-single-cell-suspension-dcxq2xmw | Liliana Berube, Loren Lopez Rivera, Randall J Kimple | TITLE: Tumor Dissociation to Single Cell Suspension
AUTHORS: Liliana Berube, Loren Lopez Rivera, Randall J Kimple
[DESCRIPTION]
This protocol has been used to generate a single cell suspension from tumor tissue for use in single cell analysis. It has been optimized to eliminate dead cells that may be present after can... | ["[Materials] Tumor Dissociation Kit, human (Miltenyi Biotec, 130-095-929)\nRPMI 1640 or DMEM media\nMACS SmartStrainers (70 µm, 30 µm) (Miltenyi Biotec, 130-098-462, 130-098-458)\ngentleMACS Octo Dissociator with Heaters (Miltenyi Biotec, 130-096-427)\ngentleMACS C Tubes (Miltenyi Biotec, 130-093-237, 130-096-334)\nRe... |
105,003 | Vaciado Estados Financieros Auditados | 0 | null | https://www.protocols.io/view/vaciado-estados-financieros-auditados-disj4ecn | Maria de los Rios | TITLE: Vaciado Estados Financieros Auditados
AUTHORS: Maria de los Rios
[DESCRIPTION]
Este protocolo de codificación de datos para estados financieros auditados está diseñado para garantizar precisión, consistencia y replicabilidad en la creación de conjuntos de datos financieros. Incluye directrices detalladas para ... | ["[Objetivo y Alcance] - Objetivo: Crear un conjunto de datos riguroso y estandarizado a\npartir de los estados financieros auditados para análisis financiero avanzado,\nmodelado predictivo e investigación.\n- Alcance: Cubrir todos los indicadores financieros significativos,\nincluyendo elementos del balance general, d... |
26,943 | Library preparation protocol to sequence V3-V4 region of 16S rRNA to run in Illumina MiSeq platform | null | dx.doi.org/10.17504/protocols.io.6i7hchn | null | Somasundhari Shanmuganandam, Benjamin Schwessinger, Robyn Hall | TITLE: Library preparation protocol to sequence V3-V4 region of 16S rRNA to run in Illumina MiSeq platform
AUTHORS: Somasundhari Shanmuganandam, Benjamin Schwessinger, Robyn Hall
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is an optimised protocol for 16S library preparation of V3-V4 region... | ["[Stage 1 PCR amplification]\nThe PCR reaction setup is given below AB1ReagentsVolume (µl) for 25µl reaction22X Platinum™ SuperFi™ PCR Master Mix12.5 µL3Water, nuclease-free Upto 25 µl410 µM forward primer 1.25 µL510 µM reverse primer 1.25 µL6Template DNA4.6 ng Add reagents and DNA in a sterilised PCR tube in the ord... |
40,901 | ELISA for quantification of CXC motif chemokine ligand 2 (CXCL2) in human serum or plasma. | 6 | dx.doi.org/10.17504/protocols.io.bj7dkri6 | https://www.protocols.io/view/elisa-for-quantification-of-cxc-motif-chemokine-l-bj7dkri6 | Angel Justiz-Vaillant, Belkis Ferrer-Cosme | TITLE: ELISA for quantification of CXC motif chemokine ligand 2 (CXCL2) in human serum or plasma.
AUTHORS: Angel Justiz-Vaillant, Belkis Ferrer-Cosme
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. An anti-human CXCL2 coating antibody is adsorbed onto the microwells by incubation overnight at 4°C... | ["An anti-human CXCL2 coating antibody is adsorbed onto the microwells by incubation overnight at 4°C with carbonate-bicarbonate buffer.", "Add 50 µl of human serum or plasma. Human CXCL2 present in the serum or plasma binds to antibodies adsorbed into the microwells.", "The microplate is blocked with 3% non-fat milk-P... |
24,082 | CTAB DNA Extraction for high quality/molecular weight DNA | null | dx.doi.org/10.17504/protocols.io.3rsgm6e | null | Yaowu Yuan | TITLE: CTAB DNA Extraction for high quality/molecular weight DNA
AUTHORS: Yaowu Yuan
[STEPS]
?. Grind plant tissue in a mortar cooled with liquid nitrogen.
?. Add .
[CTAB DNA Extraction buffer]
?. Wait until it warms up and becomes a green paste, then transfer to an eppie tube.
?. Incubate the CTAB/plant extract mixtu... | ["Grind plant tissue in a mortar cooled with liquid nitrogen.", "Add .\n[CTAB DNA Extraction buffer]", "Wait until it warms up and becomes a green paste, then transfer to an eppie tube.", "Incubate the CTAB/plant extract mixture for at in the heat block and invert to mix throughout the 15 minutes.", "Add : IsoAmyl Al... |
94,173 | Mouse Habituation - Head Fixation on Disk | 4 | dx.doi.org/10.17504/protocols.io.j8nlkojmxv5r/v1 | https://www.protocols.io/view/mouse-habituation-head-fixation-on-disk-c775zrq6 | Avalon Amaya, Jackie Swapp | TITLE: Mouse Habituation - Head Fixation on Disk
AUTHORS: Avalon Amaya, Jackie Swapp
[DESCRIPTION]
This protocol describes a customized mouse habituation protocol for mice within experiments involving head fixation onto disks.
Mouse habituation is a common technique utilized for mice undergoing behavioral experiment... | ["[Habituating a Mouse on a Disk] Day 1: \nHandle mouse for 2-5 min.", "[Habituating a Mouse on a Disk] Day 4: \nHandle mouse for 1-2 min, secure mouse to head fixation stage, and place mouse within designated behavioral training box for 10 minutes.", "[Habituating a Mouse on a Disk] Day 5 (Passive Behavior): \nHandle ... |
103,898 | Construction of individuals ddRADseq libraries for micro-algae (Kelp) V.1 | 0 | dx.doi.org/10.17504/protocols.io.rm7vzjo68lx1/v1 | https://www.protocols.io/view/construction-of-individuals-ddradseq-libraries-for-dhp235qe | Stéphane Mauger, Komlan Avia | TITLE: Construction of individuals ddRADseq libraries for micro-algae (Kelp) V.1
AUTHORS: Stéphane Mauger, Komlan Avia
[DESCRIPTION]
This protocol describes a double digested restriction-site associated DNA (ddRADseq) procedure, that is a variation on the original RAD sequencing method (Davey & Blaxter 2011), which is... | ["[Solutions and buffers preparations] Annealing buffer stock (10x)\nAnnealing buffer composed 100 mM Tris-HCl, pH8; 500 mM NaCl and 10 mM EDTA \n5 mL\n5 mL\n1 mL \n39 mL \n \nHomogenize and autoclave.\n\nStore at Room temperature", "[Solutions and buffers preparations] 5 M sodium chloride solution (NaCl)\n29.2 g \nDis... |
87,160 | Photorepair Fluence Response Protocol | 1 | dx.doi.org/10.17504/protocols.io.6qpvr671bvmk/v2 | https://www.protocols.io/view/photorepair-fluence-response-protocol-czcyx2xw | Daniel Ma, David McDonald, NATALIE HULL | TITLE: Photorepair Fluence Response Protocol
AUTHORS: Daniel Ma, David McDonald, NATALIE HULL
[DESCRIPTION]
Photorepair light exposures are performed on microorganism samples following UV light exposure (i.e. UV disinfection) to determine microorganism regrowth and repair kinetics. Photorepair is a light-dependent, en... | ["[Introduction and Pre-Experiment] The photorepair fluence response protocol is based on Bohrerova and Linden (2007).\n \nTo perform the photorepair fluence response experiment, you will first need to perform a UV fluence response experiment after the references below. Photorepair experiments and sample handling must ... |
68,611 | Snap-Frozen Tissue Preparation | 4 | dx.doi.org/10.17504/protocols.io.n92ldzoyxv5b/v1 | https://www.protocols.io/view/snap-frozen-tissue-preparation-ce9bth2n | Stephen Fisher, Marielena Grijalva, Rong Guo, sarahjoh, Hieu Nguyen, John Renz, Jean G Rosario, Steven Rudich, Brian Gregory, Junhyong Kim, Kate O'Neill | TITLE: Snap-Frozen Tissue Preparation
AUTHORS: Stephen Fisher, Marielena Grijalva, Rong Guo, sarahjoh, Hieu Nguyen, John Renz, Jean G Rosario, Steven Rudich, Brian Gregory, Junhyong Kim, Kate O'Neill
[DESCRIPTION]
This protocol describes preservation of tissue by snap-freezing. Biospecimens preserved with this protoc... | ["Place pre-weighed piece of tissue in either a 1.5mL Eppendorf tube or 1.5mL cryo tube.", "Quick freeze by immediately placing tube on dry ice.", "Transfer tube to a -80℃ ultra-low freezer for Biobanking or until ready for downstream processing."] |
83,801 | Biomek 96 well plating | 1 | dx.doi.org/10.17504/protocols.io.j8nlko5m1v5r/v1 | https://www.protocols.io/view/biomek-96-well-plating-cv3zw8p6 | William J Buchser, jwaligor | TITLE: Biomek 96 well plating
AUTHORS: William J Buchser, jwaligor
[DESCRIPTION]
Randomized plating of cells using Biomek.
[STEPS]
SECTION: Creating Plate Layouts in FIVTools
1. Open FIVTools and click "Layouts."
SECTION: Creating Plate Layouts in FIVTools
2. Edit "Exp Name" to the correct FIV Number (make sure to ... | ["[Creating Plate Layouts in FIVTools] Open FIVTools and click \"Layouts.\"", "[Creating Plate Layouts in FIVTools] Edit \"Exp Name\" to the correct FIV Number (make sure to keep \"FIV\" in the name)\n1. Click once on the “Export Folder” bar so it updates the location", "[Creating Plate Layouts in FIVTools] Choose the ... |
null | null | null | dx.doi.org/10.17504/protocols.io.q6rdzd6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This is a protocol for the detection of phosphorylated antigens via flow cytometry without the use of commercially available kits. It is adapted from the publication linked after the description</p>
[BEFORE_START]
<p>Prepare IMDM (complete):</p>
<p> </p>
<p>Add to the 500 ml... | [] |
79,515 | A sequencing and subtyping protocol for Influenza A and B viruses using Illumina® COVIDSeq™ Assay Kit | 4 | dx.doi.org/10.17504/protocols.io.n2bvj8mrxgk5/v1 | https://www.protocols.io/view/a-sequencing-and-subtyping-protocol-for-influenza-crv3v68n | Ying Lin, Jeffrey Koble, Priyanka Prashar, Anita Pottekat, Christina Middle, Scott Kuersten, Michael Oberholzer, Robert Brazas, Darcy Whitlock, Robert Schlaberg, Gary P. Schroth | TITLE: A sequencing and subtyping protocol for Influenza A and B viruses using Illumina® COVIDSeq™ Assay Kit
AUTHORS: Ying Lin, Jeffrey Koble, Priyanka Prashar, Anita Pottekat, Christina Middle, Scott Kuersten, Michael Oberholzer, Robert Brazas, Darcy Whitlock, Robert Schlaberg, Gary P. Schroth
[DESCRIPTION]
Summary
... | ["[Tagment PCR Amplicons] Place on the preprogrammed thermal cycler and run the TAG program (Table 7).\n \n Step Temperature Time 1 55°C 5 min 2 10°C Hold", "[Tagment PCR Amplicons] Seal and shake at 1600 rpm for 1 minute.\nIf there is liquid on the sealing film, centrif... |
null | null | null | dx.doi.org/10.17504/protocols.io.rffd3jn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Endothelin is the most powerful vasoconstrictor. It exists not only in the vascular endothelium, but also in various tissues and cells. It is an important factor in regulating cardiovascular function and maintains basal vascular tone and heart, and plays an important role in ... | [] |
36,613 | SPARC Cat - Sham Control Chronic Cat 3, Day 0 | 1 | dx.doi.org/10.17504/protocols.io.bfzdjp26 | https://www.protocols.io/view/sparc-cat-sham-control-chronic-cat-3-day-0-bfzdjp26 | Brett Hanzlicek, Margot Damaser | TITLE: SPARC Cat - Sham Control Chronic Cat 3, Day 0
AUTHORS: Brett Hanzlicek, Margot Damaser
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a procedure for a sham control chronic cat experiment (Day 0) for cystotomy (bladder surgery). The cystotomy is performed without UroMOCA impla... | ["[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... |
61,644 | RNAscope spatial transcript imaging in fresh-frozen mouse and human liver tissue | 1 | dx.doi.org/10.17504/protocols.io.kqdg3p3e7l25/v1 | https://www.protocols.io/view/rnascope-spatial-transcript-imaging-in-fresh-froze-b8fkrtkw | Aubrianna Decker, Brent Stockwell | TITLE: RNAscope spatial transcript imaging in fresh-frozen mouse and human liver tissue
AUTHORS: Aubrianna Decker, Brent Stockwell
[DESCRIPTION]
We captured transcript distributions of select liver cell marker genes via in situ hybridization of specific targeting probes with the RNAscope Multiplex Fluorescent v2 Assa... | ["[Tissue pretreatment] Tissue sections (8-10 µm thickness) were first post-fixed with 4% paraformaldehyde (PFA) in phosphate buffered saline (PBS) and dehydrated in Ethanol (EtOH) immediately after fixation, immersed for 5 minutes at a time in 50% EtOH, 70% EtOH, 100% EtOH, and 100% EtOH an additional time.", "[Tissue... |
63,900 | Synogut Reviews - Is it Safe and Effective For Gut Health? | 1 | dx.doi.org/10.17504/protocols.io.bp2l61pjrvqe/v1 | https://www.protocols.io/view/synogut-reviews-is-it-safe-and-effective-for-gut-h-cam4sc8w | Synogut Reviews | TITLE: Synogut Reviews - Is it Safe and Effective For Gut Health?
AUTHORS: Synogut Reviews
[DESCRIPTION]
Nourishment is vital to an individual's wellbeing and prosperity. It is fundamental for be sure that your eating routine is serving your body and mind well and assisting you with feeling your best. Continue to per... | [] |
60,965 | Human Pregnant Uterine Myometrium Tissue Collection and Preservation Methods - UCSD Female Reproductive TMC | 1 | dx.doi.org/10.17504/protocols.io.3byl4bznjvo5/v1 | https://www.protocols.io/view/human-pregnant-uterine-myometrium-tissue-collectio-b7sdrna6 | Valentina Stanley, Scott Lindsay-Hewett, Mana Parast, Louise Laurent | TITLE: Human Pregnant Uterine Myometrium Tissue Collection and Preservation Methods - UCSD Female Reproductive TMC
AUTHORS: Valentina Stanley, Scott Lindsay-Hewett, Mana Parast, Louise Laurent
[DESCRIPTION]
Human pregnant uterine myometrium tissue collection and storage protocol for HuBMAP's UCSD Female Reproduc... | ["[Preparation] At the time of c-section, obtain a full-thickness uterine myometrial biopsy from the superior edge of the incision site, prior to closure (about 2.0cm x 1.0cmx 0.5cm). Collect the tissue into an empty sterile cup.", "[Preparation] Wash the tissue in cold PBS.", "[Preparation] Place tissue on the guaze p... |
12,289 | E. coli protein expression and purification | null | dx.doi.org/10.17504/protocols.io.p89drz6 | null | Diep R. Ganguly, Timothy Rhodes, Nay Chi Khin, Estee E Tee, Kai Xun Chan | TITLE: E. coli protein expression and purification
AUTHORS: Diep R. Ganguly, Timothy Rhodes, Nay Chi Khin, Estee E Tee, Kai Xun Chan
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol for recombinant protein expression in E. coli for enzyme assays, protein crystallography etc.</div></div>
[ST... | ["[Transformation]\nTransform desired E. coli cell strain with plasmid to be expressed using desired method (e.g. heat shock or electroporation depending on type of competency).", "[Protein expression]\nInnoculate bacterial colony from selective media into LB + antibiotic of choice. Use p100-200 pipette tip to scrape c... |
100,500 | Axon tracing and node segmentation of myelinated bladder afferents in the pelvic nerve | 0 | dx.doi.org/10.17504/protocols.io.bp2l62x3rgqe/v1 | https://www.protocols.io/view/axon-tracing-and-node-segmentation-of-myelinated-b-dedu3a6w | John-Paul Fuller-Jackson, Peregrine B Osborne, Janet R Keast | TITLE: Axon tracing and node segmentation of myelinated bladder afferents in the pelvic nerve
AUTHORS: John-Paul Fuller-Jackson, Peregrine B Osborne, Janet R Keast
[DESCRIPTION]
This protocol describes method for tracing myelinated axons labelled with the adeno-associated virus, AAV-PHP.S and neurofascin immunohistoch... | ["[Image acquisition] On a confocal microscope, scan the nerve fascicle with sufficient magnification and resolution to achieve a voxel size of at least 0.099 x 0.099 x 1 μm (XYZ). This will require multiple tiles acquired with 10% overlap.", "[Image pre-processing] Stitch together the tiled image stack dataset into a ... |
45,294 | Citrate sampling and 2D imaging from rhizotron grown roots with ZrOH DGT gels | 1 | dx.doi.org/10.17504/protocols.io.bqgnmtve | https://www.protocols.io/view/citrate-sampling-and-2d-imaging-from-rhizotron-gro-bqgnmtve | raphael.tiziani , Markus Puschenreiter, Erik Smolders, Tanja Mimmo, José Carlos Herrera, Stefano Cesco, Jakob Santner | TITLE: Citrate sampling and 2D imaging from rhizotron grown roots with ZrOH DGT gels
AUTHORS: raphael.tiziani , Markus Puschenreiter, Erik Smolders, Tanja Mimmo, José Carlos Herrera, Stefano Cesco, Jakob Santner
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The reliable sampling of root exudates i... | ["[Gel application ]\nThe gel size to use depends on the root which has to be sampled. Also entire sheets to sample whole root systems are possible. If imaging is the objective we highly recommend to cut the gel in a shape which allows to remember the orientation of the gel in order to prevent confusion later. Moreover... |
null | null | null | dx.doi.org/10.17504/protocols.io.f7abrie | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.pnedmbe | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The growing of microbrewerys in Brazil has imposing an increase in the production of different supplies for brewing, iincluding yeast biomass for beer fermentation. In Brazil,only four companies produce and sell yeasts for microbreweries, and only two companies are able to at... | [] |
55,503 | DNA extraction with CTAB and chloroform:isoamyl alcohol | 4 | null | https://www.protocols.io/view/dna-extraction-with-ctab-and-chloroform-isoamyl-al-b2fpqbmn | Molly A Moynihan | TITLE: DNA extraction with CTAB and chloroform:isoamyl alcohol
AUTHORS: Molly A Moynihan
[DESCRIPTION]
This protocol is based off of Zhou et al. 1996, Kellogg et al. 2019, and Crump et al. 2003.
Zhou, Jizhong, Mary Ann Bruns, and James M. Tiedje. "DNA recovery from soils of diverse composition." Applied and environm... | ["[Prepare Reagents] Prepare DNA extraction buffer:\n100mM Tris-HCl (pH 8), 100mM EDTA (pH 8), 100mM sodium phosphate buffer (pH 8), 1.5M NaCl, 1% CTAB", "[Prepare Reagents] For a 1000mL (1L) solution of DNA extraction buffer combine: \n 100mL 1M Tris-HCl (pH 8)\n 200mL 0.5 M EDTA (pH 8)\n 100mL 10x sodium pho... |
63,757 | Mitochondrial Respiratory Chain Complex Determination | 4 | dx.doi.org/10.17504/protocols.io.81wgb69wqlpk/v1 | https://www.protocols.io/view/mitochondrial-respiratory-chain-complex-determinat-cahmsb46 | mitsjoecohen | TITLE: Mitochondrial Respiratory Chain Complex Determination
AUTHORS: mitsjoecohen
[DESCRIPTION]
Mitochondrial respiratory chain complex I (NADH oxidase) and mitochondrial respiratory chain complex II (succinate dehydrogenase) are the main elements of the electron transport chain (ETC). Complex I catalyzes the oxida... | [] |
108,232 | FUNDIS Setting up PCR for rDNA ITS Barcoding of Fungi using ONT Nanopore | 0 | null | https://www.protocols.io/view/fundis-setting-up-pcr-for-rdna-its-barcoding-of-fu-dmxg47jw | Harte Singer | TITLE: FUNDIS Setting up PCR for rDNA ITS Barcoding of Fungi using ONT Nanopore
AUTHORS: Harte Singer
[DESCRIPTION]
This protocol involves using pre-made dual-indexed master mix 96 well plates to run PCR on fungal specimens that have already had their DNA extracted, diluted and in PCR 8 strip tubes. Quality check incl... | ["[Setting up PCR] Remove DNA extracts from the freezer and allow to thaw before beginning. Note the plate number in your notebook (i.e. FDS-CA TB05)", "[Setting up PCR] Once thawed, spin DNA extracts down for 2 s in a benchtop PCR tube centrifuge.", "[Setting up PCR] Remove 96 well plate of forward indexed primers (IT... |
null | null | null | dx.doi.org/10.17504/protocols.io.rc3d2yn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>In this paper, we apply statistics and network analysis methods to explore the dynamic characteristics of three transaction networks. We download transaction data from the respective blockchain explorers. To the best of our knowledge, these are the largest datasets adopted in... | [] |
32,850 | Determination of infectious lentiviral titers with GFP-encoding lentivirus | null | dx.doi.org/10.17504/protocols.io.bcbsisne | null | Susanna C. Concilio | TITLE: Determination of infectious lentiviral titers with GFP-encoding lentivirus
AUTHORS: Susanna C. Concilio
[STEPS] | [] |
63,382 | Total Carbless Keto Gummies [100% EFFECTIVE] Is This Unique Formula For Weight Loss? | 3 | dx.doi.org/10.17504/protocols.io.6qpvr62xbvmk/v1 | https://www.protocols.io/view/total-carbless-keto-gummies-100-effective-is-this-b95wr87e | H Douglas Morris | TITLE: Total Carbless Keto Gummies [100% EFFECTIVE] Is This Unique Formula For Weight Loss?
AUTHORS: H Douglas Morris
[DESCRIPTION]
These pills additionally help to enhance the body’s immune system as well as also make your metabolic rate quick.
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.qvddw26 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Siamese fighting fish Betta splendens are notorious for their aggressiveness and accordingly have been widely used to study aggression. However, the lack of a reference genome has so far limited the understanding of the genetic basis of aggression in this species. Here we pre... | [] |
97,147 | Murine Source Protocol -- University of Minnesota TMC | 0 | dx.doi.org/10.17504/protocols.io.eq2lywzqrvx9/v1 | https://www.protocols.io/view/murine-source-protocol-university-of-minnesota-tmc-da432gyn | David A Bernlohr | TITLE: Murine Source Protocol -- University of Minnesota TMC
AUTHORS: David A Bernlohr
[DESCRIPTION]
The following protocol includes murine source information regarding mice used at the University of Minnesota TMC.
[STEPS]
SECTION: Mouse Euthanasia
1. Mice are euthanized primarily with CO2 asphyxiation and secondari... | ["[Mouse Euthanasia] Mice are euthanized primarily with CO2 asphyxiation and secondarily with cervical dislocation.", "[Adipose Tissue Collection] Subcutaneous adipose: \nWithout cutting into the peritoneal cavity, make an incision longitudinal\nacross the cavity and down the leg. Pull back the skin to expose subcutane... |
35,954 | Proliferation assay | 1 | dx.doi.org/10.17504/protocols.io.261geojwol47/v1 | https://www.protocols.io/view/proliferation-assay-bfcsjiwe | Philippa R Kennedy | TITLE: Proliferation assay
AUTHORS: Philippa R Kennedy
[DESCRIPTION]
Assessing the impact of drugs and treatments on natural killer (NK) cell viability and expansion.
[STEPS]
1. PBMCs or enriched NK cells (see Isolating NK cells from human blood products) are labeled with a permanent amine-reactive dye (CellTrace Vi... | ["PBMCs or enriched NK cells (see Isolating NK cells from human blood products) are labeled with a permanent amine-reactive dye (CellTrace Violet Proliferation Kit, Cat. No:C34557, Thermo Fisher) according to the manufacturer's instructions.", "Cells are exposed to various experimental conditions, then harvested after ... |
35,281 | Artificial Cerebrospinal Fluid VIII (ACSF.VIII) | null | dx.doi.org/10.17504/protocols.io.beprjdm6 | null | Allen Institute for Brain Science | TITLE: Artificial Cerebrospinal Fluid VIII (ACSF.VIII)
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes how to make Artificial Cerebrospinal Fluid VIII (ACSF.VIII). ACSF.VIII is used for multiple applications including incubation of ... | [] |
45,470 | SEM materials checklist | 4 | null | https://www.protocols.io/view/sem-materials-checklist-bqm6mu9e | Elizabeth Fozo | TITLE: SEM materials checklist
AUTHORS: Elizabeth Fozo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">SEM materials checklist</div></div>
[STEPS]
?. [Bing from Fozo lab]
Poly-L-lysineSmall weight boats5 – 15mL conical tubesAnhydrous ethanol40mL 95% Ethanol25mL MethanolSterile WaterP1000 pipetteP20... | ["[Bing from Fozo lab]\nPoly-L-lysineSmall weight boats5 – 15mL conical tubesAnhydrous ethanol40mL 95% Ethanol25mL MethanolSterile WaterP1000 pipetteP200 pipetteP20 pipetteP200 compatible tipsP1000 compatible tips3–10mL serological pipet3 – 5mL serological pipetPipet aidSmall tweezersPermanent MarkerGlovesTimer", "[Col... |
42,488 | BSCI:414--Lab 4 Plate Setup for COVID RT-qPCR | 1 | null | https://www.protocols.io/view/bsci-414-lab-4-plate-setup-for-covid-rt-qpcr-bmqyk5xw | Harley King | TITLE: BSCI:414--Lab 4 Plate Setup for COVID RT-qPCR
AUTHORS: Harley King
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The purpose of this experiment is to show where saliva samples and positive and negative controls will be placed on a 96-well plate by an OpenTrons robot.</div></div>
[STEPS]
?.... | ["[Discuss Sample Types]\nReview SalivaDirect for sample processing protocol: https://www.protocols.io/view/salivadirect-rna-extraction-free-sars-cov-2-diagno-bkjgkujw?step=11", "[Inset Well Plate in Benchling Lab Notebook]\nOpen your Benchling Lab Notebook and insert \"Lab 4\" with heading \"H1\". Add pertinent links ... |
90,818 | Immunoprecipitations and Western blots analysis | 1 | dx.doi.org/10.17504/protocols.io.36wgq3ep5lk5/v1 | https://www.protocols.io/view/immunoprecipitations-and-western-blots-analysis-c4xayxie | Leonardo A Parra-Rivas | TITLE: Immunoprecipitations and Western blots analysis
AUTHORS: Leonardo A Parra-Rivas
[DESCRIPTION]
Immunoprecipitations and Western blots analysis
[STEPS]
1. Immunoprecipitations were performed using
1-2 mg of total protein. Samples were incubated overnight with the indicated
antibody at 4° C, followed by the addit... | ["Immunoprecipitations were performed using\n1-2 mg of total protein. Samples were incubated overnight with the indicated\nantibody at 4° C, followed by the addition of 50 μl of protein G-agarose beads\n(Thermo Scientific, Cat#20397).", "Immunoprecipitated proteins were recovered by centrifugation at 2,500× rpm for 2 m... |
15,826 | Reverse-transcriptase PCR | null | dx.doi.org/10.17504/protocols.io.tpsemne | null | Cynthia L. Blanco | TITLE: Reverse-transcriptase PCR
AUTHORS: Cynthia L. Blanco
[STEPS] | [] |
106,414 | Annotation for Fungi | 0 | null | https://www.protocols.io/view/annotation-for-fungi-dj6n4rde | Sebastian Bassi, Claudia V. Gonzalez, Tristan Yang | TITLE: Annotation for Fungi
AUTHORS: Sebastian Bassi, Claudia V. Gonzalez, Tristan Yang
[DESCRIPTION]
Protocol to annotate a fungi genome
[STEPS]
SECTION: Setup
1. Install Docker
If you don't have Docker already, install it. There are two versions, Docker Engine (also known as CE) and Docker Desktop. The Desktop ver... | ["[Setup] Install Docker\n\nIf you don't have Docker already, install it. There are two versions, Docker Engine (also known as CE) and Docker Desktop. The Desktop version is more user friendly but since may require commercial license for large enterprise, this tutorial is based on the Docker engine. Both version will w... |
null | null | null | dx.doi.org/10.17504/protocols.io.f7dbri6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><strong>CZV8-proto agar </strong></p>
<p> <strong><u>500 mL</u></strong> <strong><u>300 mL</u></strong></p>
<p>Czapek-Dox broth 22.7 g 13.62 g</... | [] |
51,977 | Simple electroporation for efficient CRISPR/Cas9 genome editing in murine zygotes | 1 | dx.doi.org/10.17504/protocols.io.bwzhpf36 | https://www.protocols.io/view/simple-electroporation-for-efficient-crispr-cas9-g-bwzhpf36 | Simon E. Tröder, Branko Zevnik | TITLE: Simple electroporation for efficient CRISPR/Cas9 genome editing in murine zygotes
AUTHORS: Simon E. Tröder, Branko Zevnik
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Electroporation of zygotes represents a rapid alternative to the elaborate pronuclear injection procedure for CRISPR/Cas9-m... | ["[guide RNA annealing]\nResuspend lyophilized crRNA, tracrRNA and ssODN in T10E0.1 buffer to 100 µM (e.g. 5 nmol in 50 µl)(Store at -80 °C until use)", "[guide RNA annealing]\nCombine 5 µl crRNA (100 µM) and 5 µl tracrRNA (100 µM) in a nuclease-free PCR tube to yield an equimolar crRNA:tracrRNA duplex solution of 50 µ... |
21,519 | STAGE (STop And Go Extraction) C18 tips for Desalting and Clean Up | null | dx.doi.org/10.17504/protocols.io.y9pfz5n | null | Teesha C. Luehr | TITLE: STAGE (STop And Go Extraction) C18 tips for Desalting and Clean Up
AUTHORS: Teesha C. Luehr
[STEPS]
?. [Preparing Solutions]
Abbreviations:ACN: acetonitrileTFA: trifluoroacetic acidFA: Formic AcidMeOH: Methanol
?. [Preparing Solutions]
1% TFA
?. [Preparing Solutions]
2-propanol
?. [Preparing Solutions]
Buffer A... | ["[Preparing Solutions]\nAbbreviations:ACN: acetonitrileTFA: trifluoroacetic acidFA: Formic AcidMeOH: Methanol", "[Preparing Solutions]\n1% TFA", "[Preparing Solutions]\n2-propanol", "[Preparing Solutions]\nBuffer A: 2% ACN with 0.1% TFATo make\n100 ml\n[1% TFA]\n[ACN]\n[Milli-Q water]", "[Preparing Solutions]\nBuffer ... |
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