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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22,576 | Dot blot to verify microinjection efficacy in Euplotes crassus | null | dx.doi.org/10.17504/protocols.io.2aqgadw | null | RACHELE CESARONI, Rachele Cesaroni | TITLE: Dot blot to verify microinjection efficacy in Euplotes crassus
AUTHORS: RACHELE CESARONI, Rachele Cesaroni
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. Grow cells up to a density of 1000 cells/ml, and transfer 400 μl of each culture to an Eppendorf tube.
?. Pellet the cells at max speed for 5 min... | ["Grow cells up to a density of 1000 cells/ml, and transfer 400 μl of each culture to an Eppendorf tube.", "Pellet the cells at max speed for 5 minutes, and resuspend them in 400 μl of ddH2O.", "Add 50 μl of 0.5 M EDTA, pH 8.0 and 50 μl of 4 M NaOH to the cells.", "Lyse the cells at 68°C for 30 minutes, and centrifuge ... |
49,621 | Genomic DNA extraction from Mycobacterium avium | 1 | dx.doi.org/10.17504/protocols.io.bupvnvn6 | https://www.protocols.io/view/genomic-dna-extraction-from-mycobacterium-avium-bupvnvn6 | Tetsuya Komatsu, Kenji Ohya, Justice Opare Odoi, Shota Suganuma, Kotaro Sawai, Takayuki Wada, Tomotada Iwamoto, Fumito Maruyama | TITLE: Genomic DNA extraction from Mycobacterium avium
AUTHORS: Tetsuya Komatsu, Kenji Ohya, Justice Opare Odoi, Shota Suganuma, Kotaro Sawai, Takayuki Wada, Tomotada Iwamoto, Fumito Maruyama
[DESCRIPTION]
Mycobacterium avium subsp. hominissuis (MAH) is one of the most important agents causing non-tuberculosis mycob... | ["Suspend colonies on 7H11 agar into 300 µl of TE.", "Centrifuge at 5,000 g for 10 min.", "Discard supernatant, followed by suspension in 300 µl of acetone.", "Centrifuge at 5,000 g for 10 min.", "Discard acetone, followed by suspension in 200 µl of TE.", "Add lysozyme at the final concentration of 100 µg/ml.", "Incuba... |
66,335 | Via Keto Gummies Reviews - [Scam Alert 2022] Shark Tank Price | 1 | dx.doi.org/10.17504/protocols.io.n92ldzx9ov5b/v1 | https://www.protocols.io/view/via-keto-gummies-reviews-scam-alert-2022-shark-tan-ccz7sx9n | Via Keto Gummies | TITLE: Via Keto Gummies Reviews - [Scam Alert 2022] Shark Tank Price
AUTHORS: Via Keto Gummies
[DESCRIPTION]
Weight Loss
[STEPS]
1. ➢ Product Name — Via Keto Gummies
➢ Composition — Natural Organic Compound
➢ Side-Effects — NA
➢ Availability — Online
➢ Rating — 4.5/5
➢ Official Website - Click Here!
Most people atte... | ["➢ Product Name — Via Keto Gummies\n➢ Composition — Natural Organic Compound\n➢ Side-Effects — NA\n➢ Availability — Online\n➢ Rating — 4.5/5\n➢ Official Website - Click Here!\n\nMost people attempt to carry on with a superior way of life by removing handled food varieties and other unwanted feasts. Weight reduction ha... |
37,742 | Dextran | 3 | null | https://www.protocols.io/view/dextran-bg4njyve | Marco Cosentino, Elisa Storelli, Alessandra Luini, Emanuela Rasini, Massimiliano Legnaro, Marco Ferrari, Franca Marino | TITLE: Dextran
AUTHORS: Marco Cosentino, Elisa Storelli, Alessandra Luini, Emanuela Rasini, Massimiliano Legnaro, Marco Ferrari, Franca Marino
[STEPS] | [] |
24,188 | CZ Biohub RNA Library Prep Protocol on Echo 550 | null | dx.doi.org/10.17504/protocols.io.3u4gnyw | null | Saharai Caldera, Madeline Mayday, Lillian Khan, Eric D. Chow, Matt S. Zinter, Joseph L. DeRisi | TITLE: CZ Biohub RNA Library Prep Protocol on Echo 550
AUTHORS: Saharai Caldera, Madeline Mayday, Lillian Khan, Eric D. Chow, Matt S. Zinter, Joseph L. DeRisi
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = ":justify;">Preparation of high-quality sequencing libraries is a costly and ti... | ["Spin plate of sample RNA in vacuum evaporator at the appropriate temperature and time settings to dry completely (approximately 40ºC for 25-30 minutes, depending on number of samples and machine used).", "[PREPARE INITIAL RNA SAMPLE PLATE]\nLoad 5uL of sample RNA into a 384-well PCR plate. Repeat with all desired sam... |
101,378 | Montagem de genomas de fungos (short reads) | 0 | dx.doi.org/10.17504/protocols.io.261ge5rpog47/v1 | https://www.protocols.io/view/montagem-de-genomas-de-fungos-short-reads-de9a3h2e | Thiago Mafra Batista | TITLE: Montagem de genomas de fungos (short reads)
AUTHORS: Thiago Mafra Batista
[DESCRIPTION]
This protocol provides step-by-step instructions for students and researchers to assemble fungal nuclear genomes using Illumina short reads with SPAdes software. Before assembling the genome, we will align the short reads ag... | ["[Avaliação da qualidade do sequenciamento] Para avaliarmos os parâmetros de qualidade, sobretudo o phred score, utilizaremos dois softwares: FastQC e MultiQC.\n\n \nO fastqc gera um arquivo .html e um arquivo .zip para cada read. Os arquivos .html podem ser abertos em qualquer navegador de internet. Já o multiqc util... |
70,099 | Handling and behavioral training protocol for in vivo electrophysiological and optogenetic manipulation of basal ganglia neurons in awake head-fixed mice | 4 | dx.doi.org/10.17504/protocols.io.14egn2xrqg5d/v1 | https://www.protocols.io/view/handling-and-behavioral-training-protocol-for-in-v-cgpttvnn | Mark Bevan | TITLE: Handling and behavioral training protocol for in vivo electrophysiological and optogenetic manipulation of basal ganglia neurons in awake head-fixed mice
AUTHORS: Mark Bevan
[DESCRIPTION]
This protocol details habituation of animals and behavioral training of animals for in vivo electrophysiology or optogenetic... | ["[Habituation] 1 week prior to in vivo electrophysiological recording, mice should be habituated to the experimental environment and the treadmill apparatus.", "[Habituation] It is recommended that all behavioral experiments be conducted during the dark phase of the light-dark cycle.", "[Habituation] Habituation proce... |
55,572 | Genotyping Arabidopsis T-DNA lines | 1 | dx.doi.org/10.17504/protocols.io.b2huqb6w | https://www.protocols.io/view/genotyping-arabidopsis-t-dna-lines-b2huqb6w | Steven J Burgess | TITLE: Genotyping Arabidopsis T-DNA lines
AUTHORS: Steven J Burgess
[DESCRIPTION]
This protocol is used for genotyping Arabidopsis seedlings to test for the presence of a transfer DNA (T-DNA) insertion. By using two primer sets it is possible to determine whether a seedling is homozygous, heterozygous or azygous for a... | ["[Prepare primer working solution] Re-suspend lyophilized primers in dH2O to a stock concentration of 100 mM. Note: primer sequences can be obtained from SALK T-DNA express if you have the T-DNA accession number (http://signal.salk.edu/tdnaprimers.2.html)", "[Prepare primer working solution] Create a 10 mM working sol... |
null | null | null | dx.doi.org/10.17504/protocols.io.c54y8v | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol describes how to concentrate viruses in liquid samples using an Amicon or Nanosep centrifugal ultrafiltration device. We use Amicons to concentrate medium volumes of samples (10s to 100s of mls) down to a final volume of ~4 ml. We use Nanoseps to concentrate smalle... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.qe4dtgw | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?. | [] |
68,272 | Removal of the Female Reproductive System En Bloc | 4 | dx.doi.org/10.17504/protocols.io.bp2l61jrzvqe/v1 | https://www.protocols.io/view/removal-of-the-female-reproductive-system-en-bloc-cewqtfdw | Stephen Fisher, Marielena Grijalva, Rong Guo, sarahjoh, Hieu Nguyen, John Renz, Jean G Rosario, Steven Rudich, Brian Gregory, Junhyong Kim, Kate O'Neill | TITLE: Removal of the Female Reproductive System En Bloc
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 removal of the ovaries, Fallopian tubes, and uterus as a whole... | ["Identify right round ligament and suture ligate laterally with 2-0 vicryl (Figure 1a).", "Divide right round ligament and continue dividing broad ligament cephalad toward the vesicouterine peritoneal reflection using Metzebaum scissors.", "Similarly identify, ligate, and divide left round ligament and incise broad li... |
81,348 | SUPERCAPACITOR | 5 | dx.doi.org/10.17504/protocols.io.bp2l69q9rlqe/v1 | https://www.protocols.io/view/supercapacitor-ctpcwmiw | a | TITLE: SUPERCAPACITOR
AUTHORS: a
[DESCRIPTION]
en este experimento utilizamos los componentes para crear un circuito rc, posteriormente lo conectamos a un osciloscopio para obtener los resultados
[BEFORE_START]
estar preparados para realizar el experimento con las medidas de seguridad adecuadas
[GUIDELINES]
seguir p... | ["Primero analizamos el ejemplo puesto por el profesor de como es un circuito equivalente a un supercapacitor.", "Tomamos los componentes y aparatos necesarios:\nProtoboard\n1 capacitor de 10 microFaradios\n1 capacitor de 100 microFaradios\n2 resistencias de 100 Ohms\n1 resistencia de 1000 Ohms\n5 cables de cobre\nOsci... |
null | null | null | dx.doi.org/10.17504/protocols.io.ex4bfqw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol describes how to attach biotin to Bovine Serum Mucin (BSM). The procedure uses a botin-NHS molecule to attach biotin to amines in the mucin proteins.
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?. | [] |
58,955 | Overall protocol for top-down LC-MS/MS of human heart tissue | 1 | dx.doi.org/10.17504/protocols.io.b5tjq6kn | https://www.protocols.io/view/overall-protocol-for-top-down-lc-ms-ms-of-human-he-b5tjq6kn | Jeannie Camarillo, Bryon Drown, Neil Kelleher | TITLE: Overall protocol for top-down LC-MS/MS of human heart tissue
AUTHORS: Jeannie Camarillo, Bryon Drown, Neil Kelleher
[DESCRIPTION]
Overview description of the process for acquiring top-down LC-MS/MS data on human heart tissue
[STEPS]
SECTION: Tissue Collection
1. Heart tissue was provided by University of Wa... | ["[Tissue Collection] Heart tissue was provided by University of Washington. Tissue was collected and prepared according to the following:", "[Sample Preparation] Perform LC based Proteomics on adjacent tissue sections:", "[Data Acquisition]", "[Sample Preparation]"] |
43,787 | EPM with room set-up and results | 3 | null | https://www.protocols.io/view/epm-with-room-set-up-and-results-bnzjmf4n | Lieselot Carrette, Marsida Kallupi, Olivier George | TITLE: EPM with room set-up and results
AUTHORS: Lieselot Carrette, Marsida Kallupi, Olivier George
[STEPS] | [] |
67,006 | Nuclear prep and FACS for 10x Genomics Chromium single-nucleus sequencing | 4 | dx.doi.org/10.17504/protocols.io.261genm5yg47/v1 | https://www.protocols.io/view/nuclear-prep-and-facs-for-10x-genomics-chromium-si-cdn6s5he | Matt Keefe | TITLE: Nuclear prep and FACS for 10x Genomics Chromium single-nucleus sequencing
AUTHORS: Matt Keefe
[DESCRIPTION]
Protocol is used for nuclear isolation and single cell RNA sequencing in the Nowakowski lab.
[STEPS]
SECTION: Introduction
1. Nuclear prep and FACS for 10x Genomics Chromium single-nucleus sequencing
(p... | ["[Introduction] Nuclear prep and FACS for 10x Genomics Chromium single-nucleus sequencing\n(protocol version 1.3.2, J. Brown, Arlotta lab)", "[Introduction] Partially from Habib et al., Massively parallel single-nucleus rna-seq with dronc-seq, Nature Methods 2017. (With additional commentary by Eugene Drokhlyansky and... |
80,624 | Protocol For Predicting Cognitive Outcomes After Spinal Surgery | 1 | dx.doi.org/10.17504/protocols.io.bp2l696odlqe/v1 | https://www.protocols.click/view/protocol-for-predicting-cognitive-outcomes-after-s-csyqwfvw | Keenan Smith, Christopher Hawthorne, Matthew Sheridan, Eric Jackson, Malcolm Watson, Martin Shaw, Shona McKay, Jonathan Cavanagh | TITLE: Protocol For Predicting Cognitive Outcomes After Spinal Surgery
AUTHORS: Keenan Smith, Christopher Hawthorne, Matthew Sheridan, Eric Jackson, Malcolm Watson, Martin Shaw, Shona McKay, Jonathan Cavanagh
[DESCRIPTION]
Background: Perioperative Neurocognitive Disorders range from short term (postoperative deliriu... | ["[Prior to Enrolment] Screening\n\nPatients awaiting non-emergency spinal surgery at the Queen Elizabeth University Hospital will be identified from electronic waiting lists and screened for eligibility.", "[Prior to Enrolment] Approaching Participants\n\nPatients eligible for inclusion will be asked by their clinical... |
96,932 | Protocol for ESBL-EC recovery from stool samples | 0 | dx.doi.org/10.17504/protocols.io.kxygxyk3dl8j/v1 | https://www.protocols.io/view/protocol-for-esbl-ec-recovery-from-stool-samples-dawc2faw | Sarah Gallichan | TITLE: Protocol for ESBL-EC recovery from stool samples
AUTHORS: Sarah Gallichan
[DESCRIPTION]
Understanding transmission pathways of important opportunistic, drug resistant pathogens, such as extended-spectrum beta-lactamase (ESBL) producing Escherichia coli, is essential to implementing targeted prevention strategie... | ["[Reagent preparation] Preparation of Sterile Buffered Peptone Water (BPW) pre-enrichment broth", "[Reagent preparation] Add 20 g of BPW powder to 1 L of distilled water.", "[Reagent preparation] Mix well and sterilise by autoclaving at 121 °C .", "[Reagent preparation] Store at room temperature for up to 1 month.",... |
44,624 | 3.1 Synthesis of Glutathione Beads | 4 | dx.doi.org/10.17504/protocols.io.bptqmnmw | https://www.protocols.io/view/3-1-synthesis-of-glutathione-beads-bptqmnmw | Peter Simons, Virginie Bondu, Angela Wandinger-Ness, Tione Buranda | TITLE: 3.1 Synthesis of Glutathione Beads
AUTHORS: Peter Simons, Virginie Bondu, Angela Wandinger-Ness, Tione Buranda
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Small, monomeric guanine triphosphate hydrolases (GTPases) are ubiquitous cellular integrators of signaling. A signal activates ... | ["[3.1 Synthesis of Glutathione Beads]\nHigh-site-density glutathione-derivatized beads used for flow cytometry have been synthesized previously from 13 μm dextran-cross-linked agarose beads [26, 27], and 4 μm amino polystyrene beads [20]. In this method, 5.4 μm Cyto-Plex™ carboxylated polystyrene bead sets are first c... |
98,019 | ReViBE: protocol for Refit Visualisation of lithic reduction sequences using the Blender Engine | 1 | dx.doi.org/10.17504/protocols.io.ewov1qxqkgr2/v2 | https://www.protocols.io/view/revibe-protocol-for-refit-visualisation-of-lithic-dbyb2psn | 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... |
59,279 | Statistical Analysis Plan for Validation of the STarTBack Tool for Management of Low Back Pain in the Military Health System | 3 | dx.doi.org/10.17504/protocols.io.b55pq85n | https://www.protocols.io/view/statistical-analysis-plan-for-validation-of-the-st-b55pq85n | Daniel I Rhon, Steve George, Emily Poehlein, Cindy Green | TITLE: Statistical Analysis Plan for Validation of the STarTBack Tool for Management of Low Back Pain in the Military Health System
AUTHORS: Daniel I Rhon, Steve George, Emily Poehlein, Cindy Green
[DESCRIPTION]
DISCLAIMER: The view(s) expressed herein are those of the author(s) and do not reflect the official... | [] |
54,586 | AU Test with IQTree | 5 | dx.doi.org/10.17504/protocols.io.e6nvw5w7zvmk/v1 | https://www.protocols.io/view/au-test-with-iqtree-bzi2p4ge | Dakota Betz | TITLE: AU Test with IQTree
AUTHORS: Dakota Betz
[DESCRIPTION]
Our protocols are constantly evolving and old versions will be deleted.
The documents here are not intended to be cited in publications
[STEPS]
SECTION: Programs and Dependencies
1. IQ-Tree
Download: http://www.iqtree.org/
Additional information/tutorials... | ["[Programs and Dependencies] IQ-Tree\nDownload: http://www.iqtree.org/\nAdditional information/tutorials: http://www.iqtree.org/doc/Advanced-Tutorial\n\nMesquite\nDownload: https://www.mesquiteproject.org/Installation.html\n\nRAxML-ng\nDownload: https://github.com/amkozlov/raxml-ng\nGUI 2.0 (compatible with ng): https... |
41,750 | Glass Milk preparation | 4 | dx.doi.org/10.17504/protocols.io.bkzwkx7e | https://www.protocols.io/view/glass-milk-preparation-bkzwkx7e | Martin Codyre | TITLE: Glass Milk preparation
AUTHORS: Martin Codyre
[STEPS]
?. [Glass Milk Preparation]
After acid washing for at room temperature , silica was pelleted by spinning two minutes at 5,000 xg and the supernatant was poured off.
[Possibly 4 to 8 hours]
0 Room temperature
Centrifuge: 5000 33, 2 min
?. [Glass Milk Prep... | ["[Glass Milk Preparation]\nAfter acid washing for at room temperature , silica was pelleted by spinning two minutes at 5,000 xg and the supernatant was poured off.\n[Possibly 4 to 8 hours]\n0 Room temperature\nCentrifuge: 5000 33, 2 min", "[Glass Milk Preparation]\nTo prepare glass milk, 325 mesh silicon dioxide (... |
67,362 | Functionality test (OpenVent polymerase, PCR Master Mixes) | 4 | null | https://www.protocols.io/view/functionality-test-openvent-polymerase-pcr-master-cd2as8ae | Nadine Mowoh, Stephane Fadanka, Shalo Minette | TITLE: Functionality test (OpenVent polymerase, PCR Master Mixes)
AUTHORS: Nadine Mowoh, Stephane Fadanka, Shalo Minette
[DESCRIPTION]
After production, we typically subject our products to a batch of quality control assays to ascertain their functionality, efficacy and ability to meet their intended purpos... | ["[Functionality test - PCR amplification] DNA polymerase Enzyme and PCR Master mix\n\n \n\nPreparing reagents\n\nThaw all reagents on ice in a bowl\nLabel reaction tubes (0.2 mL PCR tubes) according to the number of samples, and include controls in each run (negative and positive controls) as needed.\n\nPolymerase enz... |
12,753 | Field sampling of root-associated microbes for DNA/RNA extraction | null | dx.doi.org/10.17504/protocols.io.qprdvm6 | null | Roey Angel | TITLE: Field sampling of root-associated microbes for DNA/RNA extraction
AUTHORS: Roey Angel
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes a procedure for sampling plant roots in the field for future DNA and RNA extraction for microbiome analysis. The protocol is deliberate... | ["G\n M\n T\n \n \n ABCDEFGHI1\nDetect language\nAfrikaans\nAlbanian\nArabic\nArmenian\nAzerbaijani\nBasque\nBelarusian\nBengali\nBosnian\nBulgarian\nCatalan\nCebuano\nChichewa\nChinese (Simplified)\nChinese (Traditional)\nCroatian\nCzech\nDanish\nDutch\nEnglish\nEsperanto\nEstonian\nFilipino\nFinnish\nFrench\nGali... |
43,140 | Protcol 1: PCR Dry Lab | 5 | null | https://www.protocols.io/view/protcol-1-pcr-dry-lab-bndcma2w | TITLE: Protcol 1: PCR Dry Lab
AUTHORS:
[STEPS]
?. [Finding a Sequence of Interest: Human Genome Browser]
To find information on DNA region of interest, first go to the hgb website and find the Genomes tab. Click on SARS-coV-2 (COVID-19).
?. [Finding a Sequence of Interest: Human Genome Browser]
Once the genome is op... | ["[Finding a Sequence of Interest: Human Genome Browser]\nTo find information on DNA region of interest, first go to the hgb website and find the Genomes tab. Click on SARS-coV-2 (COVID-19).", "[Finding a Sequence of Interest: Human Genome Browser]\nOnce the genome is open, go to the bottom of the page and click defaul... | |
null | null | null | dx.doi.org/10.17504/protocols.io.uruev6w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
The dataset for population change, economic growth and carbon emissions in Nigeria is presented here.
[STEPS]
?. | ["null"] |
65,426 | Standard Operating Procedure: Mouse Stereotaxic Intracranial Injection Surgery | 1 | dx.doi.org/10.17504/protocols.io.rm7vzye28lx1/v1 | https://www.protocols.io/view/standard-operating-procedure-mouse-stereotaxic-int-cb5ssq6e | Hong-Yuan Chu | TITLE: Standard Operating Procedure: Mouse Stereotaxic Intracranial Injection Surgery
AUTHORS: Hong-Yuan Chu
[DESCRIPTION]
The intent of this Standard Operating Procedure (SOP) is to describe procedures for mouse stereotaxic intracranial injection surgery.
[GUIDELINES]
RESPONSIBILITY:
Principal investigator (PI), th... | ["[Surgical and Station Preparation:] Print the surgery documents and prepare them from Chu Lab SharePoint.", "[Surgical and Station Preparation:] Prepare solutions needed for target injections according Chu Lab Inventory and SOPs from the Chu Lab SharePoint. Place solutions on ice, if applicable.", "[Surgical and Sta... |
98,846 | READDI protocol: Crystallisation of CHIKV nsP3 macrodomain | 1 | dx.doi.org/10.17504/protocols.io.x54v92jzzl3e/v1 | https://www.protocols.io/view/readdi-protocol-crystallisation-of-chikv-nsp3-macr-dcr62v9e | Jasmin Aschenbrenner, Peter Marples, michael fairhead, Andre Schutzer de Godoy, Daren Fearon | TITLE: READDI protocol: Crystallisation of CHIKV nsP3 macrodomain
AUTHORS: Jasmin Aschenbrenner, Peter Marples, michael fairhead, Andre Schutzer de Godoy, Daren Fearon
[DESCRIPTION]
Chikungunya virus (CHIKV) causes severe fever, rash and debilitating joint pain that can last for months or even years. Millions of peopl... | ["[Crystallization experiment] Protein and buffer requirements:\n21.6 µL11 mg/mL \n2.88 mL \n10.08 µL Seeds, dilution 1:100", "[Crystallization experiment] Dispense 30 µL into SwissCI 3 lens plate reservoir wells using a 100 µl multi-channel pipette.\nDispense 75 nL11 mg/mL to each lens using the SPT mosquito.\nD... |
null | null | null | dx.doi.org/10.17504/protocols.io.rmud46w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Cas9 Nuclease, <em>S. pyogenes</em>, (Cas9) is a double-stranded DNA endonuclease that is guided to its target by sequence complementarity of a small RNA loaded into the protein. This protocol describes how to digest double-stranded DNA <em>in vitro</em> using Cas9 and a sing... | [] |
93,620 | Single cell CRISPRi screen to identify mechanoenhancer gene targets | 4 | dx.doi.org/10.17504/protocols.io.kqdg3xd7zg25/v1 | https://www.protocols.io/view/single-cell-crispri-screen-to-identify-mechanoenha-c7nuzmew | Brian D. Cosgrove, Lexi R. Bounds, Carson Key Taylor, Alan L. Su, Anthony J. Rizzo, Alejandro Barrera, Andrea R Daniel, Gregory E. Crawford, Brenton D. Hoffman, Charles A. Gersbach | TITLE: Single cell CRISPRi screen to identify mechanoenhancer gene targets
AUTHORS: Brian D. Cosgrove, Lexi R. Bounds, Carson Key Taylor, Alan L. Su, Anthony J. Rizzo, Alejandro Barrera, Andrea R Daniel, Gregory E. Crawford, Brenton D. Hoffman, Charles A. Gersbach
[DESCRIPTION]
This protocols describes methods for a s... | ["[gRNA library design and cloning] Following hit identification from combined migration and growth screens, a library is designed that includes the top 10 gRNA by pZ value across either screen for the 87 hit pRE (870 gRNA total).", "[gRNA library design and cloning] 100 non-targeting control gRNAs with similar sequenc... |
88,422 | Differentiation of RGC Induced Neurons (RGC-iNs) | 4 | dx.doi.org/10.17504/protocols.io.14egn2pqzg5d/v2 | https://www.protocols.io/view/differentiation-of-rgc-induced-neurons-rgc-ins-c2keycte | Devansh Agarwal, Kevin W. Mazo, Karl Wahlin | TITLE: Differentiation of RGC Induced Neurons (RGC-iNs)
AUTHORS: Devansh Agarwal, Kevin W. Mazo, Karl Wahlin
[DESCRIPTION]
This protocol is designed to convert human induced pluripotent stem cells (PSCs) into retinal ganglion cell induced neurons (RGC-iNs) using a doxycycline-inducible polycistronic transcription fact... | ["[PSC expansion step] Grow PSCs in mTeSR1 under hypoxia (5 % (v/v) O2/10 % (v/v) CO2) or normoxia (20 % (v/v) O2/5 % (v/v) CO2) at 37 °C.\n12-well plate (3.5 cm2): Plate 5,000 PSCs into each well of 12-well plates in mTeSR1 in the presence of 5 micromolar (µM) blebbistatin (blebb; 2,000x stock). Feed daily in mTeSR1 (... |
33,916 | A methodology for gathering and annotating the raw-data/characteristics of the documents citing a retracted article | 1 | dx.doi.org/10.17504/protocols.io.bdc4i2yw | https://www.protocols.io/view/a-methodology-for-gathering-and-annotating-the-raw-bdc4i2yw | Ivan Heibi, Silvio Peroni | TITLE: A methodology for gathering and annotating the raw-data/characteristics of the documents citing a retracted article
AUTHORS: Ivan Heibi, Silvio Peroni
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Giving a retracted article, we present a step-by-step methodology for gathering the raw-... | ["[Identifying and retrieving the citing entities]\nNow we need to get the list of the entities which have cited the retracted article. We will query the COCI dataset (https://opencitations.net/index/coci). This dataset contains details of all the citations that are specified by the open references to DOI-identified wo... |
106,764 | JAX-Sen: Collection and shipment of specimen for Visium Spatial Transcriptomics (vST/Visium ST) | 0 | dx.doi.org/10.17504/protocols.io.36wgqn193gk5/v2 | https://www.protocols.io/view/jax-sen-collection-and-shipment-of-specimen-for-vi-dkhk4t4w | Laura Robinson, Susan Sheehan, Gaven Garland, Ron Korstanje | TITLE: JAX-Sen: Collection and shipment of specimen for Visium Spatial Transcriptomics (vST/Visium ST)
AUTHORS: Laura Robinson, Susan Sheehan, Gaven Garland, Ron Korstanje
[DESCRIPTION]
These samples are part of the JAX-Sen project in the SenNet Consortium. Here we provide details on specimen collection and shipment p... | ["[Reagents and Materials:] 10% NBF fixative\nTweezers\nAppropriate container for fixing", "[Quality Key Points:] The tissue specimen should be always kept at 4 degrees Celsius and RNase-free. \nIt is crucial to not store the tissue specimen at RT to avoid any cell death, and tissue and/or RNA degradation.", "[Procedur... |
46,016 | 10Xv2 RNASeq Sample Processing | 1 | dx.doi.org/10.17504/protocols.io.bq68mzhw | https://www.protocols.io/view/10xv2-rnaseq-sample-processing-bq68mzhw | Allen Institute for Brain Science | TITLE: 10Xv2 RNASeq Sample Processing
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Allows for rapid generation of 3’ transcriptomic-NGS-ready- single-cell-libraries from pools of cells.</div><div class = "text-block"><span style = "font-weight:bold;">Not... | [] |
87,516 | Preparation of unilamellar liposomes | 1 | dx.doi.org/10.17504/protocols.io.5qpvo3ke7v4o/v1 | https://www.protocols.io/view/preparation-of-unilamellar-liposomes-czp4x5qw | Ayan Adhikari, Suzanne R Pfeffer | TITLE: Preparation of unilamellar liposomes
AUTHORS: Ayan Adhikari, Suzanne R Pfeffer
[DESCRIPTION]
We present here a protocol for preparing liposomes that can be used to monitor binding of proteins to vesicles of various membrane curvatures. We used this to study the association of the PPM1H phosphatase with highly ... | ["[Make lipid stocks] All lipids were purchased from Avanti Polar Lipids. PC and PS were obtained as 10mg/ml\nchloroform solutions. PI, PI(4)P and cholesterol sulfate were obtained as powders. Dissolve in chloroform to prepare 2mg/ml, 1mg/ml and 25mg/ml stock solutions respectively.", "[Prepare the lipid mixture] Prep... |
52,763 | Part 1: SmartSeq | 1 | dx.doi.org/10.17504/protocols.io.bxr3pm8n | https://www.protocols.io/view/part-1-smartseq-bxr3pm8n | cecilia , Suzie Alarcon, Alessandro Sette | TITLE: Part 1: SmartSeq
AUTHORS: cecilia , Suzie Alarcon, Alessandro Sette
[DESCRIPTION]
This protocol details the procedure of SmartSeq.
[STEPS]
SECTION: INPUT:
1. Use total RNA, ranging between 10 pg-30 pg up to 10 ng. 2.6 µL will be used per sample.
SECTION: ANNEAL PRIMERS:
2. on ice, add each sample (2.6 µL to... | ["[INPUT:] Use total RNA, ranging between 10 pg-30 pg up to 10 ng. 2.6 µL will be used per sample.", "[ANNEAL PRIMERS:] on ice, add each sample (2.6 µL total RNA) to a thin-walled 0.2 mL PCR tube and add:\n \n Item Volume (uL) ______xMM Lot# oligo-dT primer (10uM) 1 ... |
106,138 | Purification of CCPG1-GST | 0 | dx.doi.org/10.17504/protocols.io.e6nvw14dzlmk/v1 | https://www.protocols.io/view/purification-of-ccpg1-gst-djv24n8e | Elias Adriaenssens | TITLE: Purification of CCPG1-GST
AUTHORS: Elias Adriaenssens
[DESCRIPTION]
This protocol details the purification of CCPG1-GST, its analysis by SDS-PAGE and Coomassie staining.
[STEPS]
SECTION: Purification procedure
1. To purify CCPG1-GST, fuse the cytosol-exposed domain of CCPG1 (1-212aa) to a C-terminal GST-tag th... | ["[Purification procedure] To purify CCPG1-GST, fuse the cytosol-exposed domain of CCPG1 (1-212aa) to a C-terminal GST-tag through gene synthesis and Gibson cloning into a pET-DUET1 vector.", "[Purification procedure] Collect the cells by centrifugation and resuspend in lysis buffer. \n\nLysis Buffer:", "[Purification ... |
86,349 | LRRK2:DARPins complex preparation | 1 | dx.doi.org/10.17504/protocols.io.j8nlkowxxv5r/v1 | https://www.protocols.io/view/lrrk2-darpins-complex-preparation-cyjmxuk6 | Marta Sanz Murillo | TITLE: LRRK2:DARPins complex preparation
AUTHORS: Marta Sanz Murillo
[DESCRIPTION]
Protocol used to create LRRK2-RCKW: DARPin complex for cryo-EM grid preparation.
[STEPS]
SECTION: LRRK2:DARPins complex preparation
1.
His6-Z-TEV-LRRK2-RCKW was expressed and purified as described in a previous protocol
SE... | ["[LRRK2:DARPins complex preparation] His6-Z-TEV-LRRK2-RCKW was expressed and purified as described in a previous protocol", "[LRRK2:DARPins complex preparation] Prepare LRRK2 buffer exchange: Keep it at 4ºC.\n20 millimolar (mM) HEPES pH=7.4\n150 millimolar (mM) NaCl\n2.5 millimolar (mM) MgCl2\n20 micromolar (µM) GDP\n... |
83,659 | Enzymatic padlock probe preparation | 4 | dx.doi.org/10.17504/protocols.io.n92ldm3pxl5b/v1 | https://www.protocols.io/view/enzymatic-padlock-probe-preparation-cvxjw7kn | Chien-Ju Chen, Kian Kalhor, Kun Zhang | TITLE: Enzymatic padlock probe preparation
AUTHORS: Chien-Ju Chen, Kian Kalhor, Kun Zhang
[DESCRIPTION]
This protocol accompanies the manuscript Mapping Human Tissues with Highly Multiplexed RNA in situ Hybridization (https://doi.org/10.1101/2023.08.16.553610). It protocol outlines the steps for the enzymatic amplific... | ["[PCR mass production] Prepare PCR production mix in a 15mL tube and add load 100 µL to each well of a 96-well plate\n\n \nrun PCR program to amplify the oligo pool \n98 °C , 1 min -> (98 °C , 30 s ->55 °C 45 s ->72 °C 45 s )x14 cycles ->72 °C , 2 min -> 4 °C , hold", "[oligo pool pre-amplification] Resuspend the oli... |
62,290 | Synchronized spinal nerve and dorsal root ganglia stimulation | 1 | dx.doi.org/10.17504/protocols.io.36wgq7b4ovk5/v1 | https://www.protocols.io/view/synchronized-spinal-nerve-and-dorsal-root-ganglia-b83sryne | Longtu Chen, Bin Feng | TITLE: Synchronized spinal nerve and dorsal root ganglia stimulation
AUTHORS: Longtu Chen, Bin Feng
[DESCRIPTION]
Assessing the instantaneous effect of dorsal root ganglia (DRG) stimulation on the transmission of electrically evoked action potentials from the spinal nerve via the ex vivo preparation with mouse L6 sp... | ["[Ex vivo spinal nerve-dorsal root ganglia-dorsal root (SN-DRG-DR) preparation] C57BL/6 mice (8-16 weeks, 25-35 g, and either sex) were anesthetized by isoflurane inhalation followed by intraperitoneal and intramuscular injection of a ketamine/xylazine cocktail (100/10 mg per kg weight).", "[Determine DRG stimulation ... |
null | null | null | dx.doi.org/10.17504/protocols.io.jaycifw | null | null | TITLE: No Title
AUTHORS:
[STEPS] | [] |
78,534 | 2. Data collection protocols | 1 | dx.doi.org/10.17504/protocols.io.6qpvr4w93gmk/v1 | https://www.protocols.io/view/2-data-collection-protocols-cqxevxje | Haydeh Payami | TITLE: 2. Data collection protocols
AUTHORS: Haydeh Payami
[DESCRIPTION]
This is a collection of protocols for data and specimen collection, designed for self-administration by subject. It includes the Environmental & Family History Questionnaire, the Gut Microbiome Questionnaire, instructions for saliva collection, a... | ["[Data collection protocols]", "[Data collection protocols]", "[Data collection protocols]", "[Data collection protocols]"] |
42,775 | SocialInclusionIOS | 1 | dx.doi.org/10.17504/protocols.io.bmzxk77n | https://www.protocols.io/view/socialinclusionios-bmzxk77n | j.vyrastekova | TITLE: SocialInclusionIOS
AUTHORS: j.vyrastekova
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Online questionnaire to assess social inclusion of the SEN students as reported by their parents/care-takers, see attached:</div></div>
[STEPS]
?. Collect data from parents of special education needs s... | ["Collect data from parents of special education needs students (SEN) age 4-12, by distributing the online questionnaire among parents/care-takers of the SEN students."] |
37,906 | Quick Protocol for Oligonucleotide Cleanup Using the Monarch® PCR & DNA Cleanup Kit (5 μg) (NEB #T1030) | 1 | dx.doi.org/10.17504/protocols.io.bg9sjz6e | https://www.protocols.io/view/quick-protocol-for-oligonucleotide-cleanup-using-t-bg9sjz6e | New England Biolabs | TITLE: Quick Protocol for Oligonucleotide Cleanup Using the Monarch® PCR & DNA Cleanup Kit (5 μg) (NEB #T1030)
AUTHORS: New England Biolabs
[DESCRIPTION]
Quick Protocol for Oligonucleotide Cleanup Using the Monarch® PCR & DNA Cleanup Kit (5 μg) (NEB #T1030)
[BEFORE_START]
All centrifugation steps should be car... | ["Add 100 µL to the 50 µL.", "Add 300 µL. Mix well by pipetting up and down or flicking the tube. Do not vortex.", "Insert column into collection tube and load sample onto column and close the cap.", "Spin at 16000 x g for 1 min, then discard flow-through.", "Re-insert column into collection tube.", "Add 500 µL and spi... |
27,673 | Interventions for incarcerated adults with opioid use disorder in the United States: A systematic review with a focus on social determinants of health | null | dx.doi.org/10.17504/protocols.io.69zhh76 | null | Olivia Sugarman, Marcus A. Bachhuber, Ashley Wennerstrom, Todd Bruno, Benjamin F. Springgate | TITLE: Interventions for incarcerated adults with opioid use disorder in the United States: A systematic review with a focus on social determinants of health
AUTHORS: Olivia Sugarman, Marcus A. Bachhuber, Ashley Wennerstrom, Todd Bruno, Benjamin F. Springgate
[DESCRIPTION]
<div class = "text-blocks"><div class = "text... | ["[Identify articles]\nConduct PubMed search", "[Identify articles]\nApply filters to PubMed search:Publication dates: 5 yearsSpecies: HumanAges: 19+ yearsLanguages: EnglishSort: Most recentText availability: Full text", "[Identify articles]\nUse boolean term:(substance use OR medically assisted treatment OR opioid OR ... |
11,438 | El-cheep-o bacterial DNA isolation / miniprep | null | dx.doi.org/10.17504/protocols.io.pendjde | null | Magdalena Julkowska | TITLE: El-cheep-o bacterial DNA isolation / miniprep
AUTHORS: Magdalena Julkowska
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a protocol for cheep miniprep isolation. Be aware that the DNA quality might not be sufficient to use this protocol for cloning purposes. It works very well for t... | ["Spin 3ml of the overnight culture to pellet cells (1.5 ml per time) @13000 rpm for 5 min", "·Remove the supernatant", "Add 250 ul of P1 solution + Rnase 5ul and vortex to resuspend the cells", "Incubate 15 min @ room temperature", "Add 250 ul of P2 solution and mix gently", "Incubate 5 min @ room temperature", "Add 3... |
32,867 | Emma's Snickerdoodles | null | dx.doi.org/10.17504/protocols.io.bccbissn | null | Emma Slayton | TITLE: Emma's Snickerdoodles
AUTHORS: Emma Slayton
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Emma's Snickerdoodles</div><div class = "text-block"><ul style = "list-style-type:disc;"><li style = "counter-reset:ol0;list-style-type:disc;">1 cup packed brown sugar</li><li style = "counter-rese... | [] |
31,444 | Isolation of Klebsiella strains from water samples | null | dx.doi.org/10.17504/protocols.io.baxuifnw | null | MedVetKlebs consortium | TITLE: Isolation of Klebsiella strains from water samples
AUTHORS: MedVetKlebs consortium
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is intended for isolation of Klebsiella strains from water samples. </div><div class = "text-block"><span>It is derived from the initial description... | ["[Pre-treatment of sample]\nWater samples are collected in 5L sterile containers and transported to the laboratory. Six samples are collected at each site to give a total of 30 litres per sample.\nThe water samples are processed using the CapE system by placing the submersible pump into the pooled water samples.NOTE: ... |
76,675 | Addgene paper recovery | 4 | dx.doi.org/10.17504/protocols.io.14egn2n8qg5d/v1 | https://www.protocols.io/view/addgene-paper-recovery-cn5bvg2n | Guilherme Barbosa | TITLE: Addgene paper recovery
AUTHORS: Guilherme Barbosa
[DESCRIPTION]
Simple steps to recover plasmid from paper.
[BEFORE_START]
Have the plasmid on paper
[GUIDELINES]
Follow the protocol for simple plasmid recovery from paper
[STEPS]
SECTION: To recover your plasmid on paper:
1.
Use a clean razor blade to cut o... | ["[To recover your plasmid on paper:] Use a clean razor blade to cut out one of the circles containing your DNA.", "[To recover your plasmid on paper:] Immerse the circle in 30 µL of TE and pipette to mix.", "[To recover your plasmid on paper:] After waiting for at least 10 min, use 2 µL to transform competent bacteria... |
50,507 | Expression and purification protocol of FIP200 full length or FIP200∆641–779 | 1 | dx.doi.org/10.17504/protocols.io.bvjjn4kn | https://www.protocols.io/view/expression-and-purification-protocol-of-fip200-ful-bvjjn4kn | Xiaoshan Shi | TITLE: Expression and purification protocol of FIP200 full length or FIP200∆641–779
AUTHORS: Xiaoshan Shi
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol describes the expression and purification of FIP200 full length or FIP200</span><span style = "vertical-align:super;">∆641–779... | ["[1- Protein expression:]\nTransfect DNA in cells at a concentration of 2.5–3×106/mL using polyethylenimine (Polysciences) and harvest after expression, harvest and lyse cells with lysis buffer.", "[2- Protein Purification:]\nGlutathione Sepharose 4B (GE Healthcare) followed by MBP-tag affinity purifications.I... |
null | null | null | dx.doi.org/10.17504/protocols.io.hdrb256 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>sgRNA template assembly, in vitro T7 transcription, and SPRI bead cleanup</p>
[GUIDELINES]
The primers used are: one long, variable oligo that carries the T7 promoter and desired guide sequence; an 82-nt constant oligo that carries the 3' end of the sgRNA; two short external... | [] |
37,639 | The impact of delayed treatment on progression of uncomplicated P. falciparum malaria to severe malaria: a pooled multicentre individual-patient meta-analysis. | 1 | dx.doi.org/10.17504/protocols.io.bgzfjx3n | https://www.protocols.io/view/the-impact-of-delayed-treatment-on-progression-of-bgzfjx3n | Andria Mousa, Dr Joseph Challenger, Dr Lucy Okell | TITLE: The impact of delayed treatment on progression of uncomplicated P. falciparum malaria to severe malaria: a pooled multicentre individual-patient meta-analysis.
AUTHORS: Andria Mousa, Dr Joseph Challenger, Dr Lucy Okell
[STEPS]
?. [Research Question, study design and conditions being studied]
Research Question: ... | ["[Research Question, study design and conditions being studied]\nResearch Question: What is the impact of improved access to treatment in reducing progression from uncomplicated P. falciparum malaria to severe disease?Study design: An individual-participant meta-analysis of observational studies of hospital admission ... |
null | null | null | dx.doi.org/10.17504/protocols.io.j77crrn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
In plaque-assay based viral discovery many more plaques are often generated than can be examined at any one time, it is therefore of value to be able to archive plaques for future investigation. To address the potential for differences among viruses in tolerance to storage, this... | ["[Cataloging Plaques (Day 1)] {\"blocks\":[{\"key\":\"12n5h\",\"text\":\"Mark\\u00a0the plaques: Mark all plaques to be archived by writing a number adjacent to the plaque on the bottom of the petri dish.\",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[{\"offset\":0,\"length\":17,\"style\":\"bold\"}],\"enti... |
26,723 | DNA extraction for HMW DNA | null | dx.doi.org/10.17504/protocols.io.6cbhasn | null | Natalie Solonenko, Marie Burris | TITLE: DNA extraction for HMW DNA
AUTHORS: Natalie Solonenko, Marie Burris
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is intended for extraction of HMW DNA from bacterial or viral samples.</div></div>
[STEPS]
?. [Lyse cells/viruses]
Add 600ul lysis buffer to less than 500ul of sa... | ["[Lyse cells/viruses]\nAdd 600ul lysis buffer to less than 500ul of sample in a 2mL tube.\n[lysis buffer]\nTo make lysis buffer, add the following to 10mL of 1X TE:1. 300ul 20% SDS2. 60ul 20mg/mL protK", "[Extract DNA]\nAdd 1 vol phenol:chloroform and mix by inversion.\nAlways work with phenol:chloroform in a fume hoo... |
82,294 | Investigation and identification of somatic and germline variants for colorectal cancer exomes using the NGS pipeline: a computational analysis perspective | 5 | dx.doi.org/10.17504/protocols.io.x54v9dqxqg3e/v1 | https://www.protocols.io/view/investigation-and-identification-of-somatic-and-ge-cukwwuxe | Chandrashekar K, Anagha S Setlur, Vidya Niranjan | TITLE: Investigation and identification of somatic and germline variants for colorectal cancer exomes using the NGS pipeline: a computational analysis perspective
AUTHORS: Chandrashekar K, Anagha S Setlur, Vidya Niranjan
[DESCRIPTION]
A thorough analysis on colorectal cancer exomes reveals potential mutations such as... | ["[COLORECTAL CANCER EXOME RETRIEVAL] Retrieval of colorectal cancer exomes\n\nThis protocol was run with colorectal cancer exome datasets. However, the SRR-IDs of datasets have not been mentioned to make this protocol universal. Therefore, NCBI-SRA database (https://www.ncbi.nlm.nih.gov/sra) was employed to retrieve t... |
101,221 | Directed cardiomyocte generation from human pluripotent stem cells using a chemically defined protocol (GiWi2) | 0 | dx.doi.org/10.17504/protocols.io.ewov199k7lr2/v1 | https://www.protocols.io/view/directed-cardiomyocte-generation-from-human-plurip-de4d3gs6 | Fan Li, Jingli Cai, Wenli Yang, Hao Wu | TITLE: Directed cardiomyocte generation from human pluripotent stem cells using a chemically defined protocol (GiWi2)
AUTHORS: Fan Li, Jingli Cai, Wenli Yang, Hao Wu
[DESCRIPTION]
The GSK3 inhibitor and Wnt inhibitor, named GiWi2, are utilized for robust differentiation of human pluripotent stem cells (hPSCs) into car... | ["[Materials] Matrigel (life science, cat# 354230)\nY27632 (Tocris, cat# 1254), 5 mM Y27632 stock (1:1000)\nTeSR-E8 (Stem Cell Technologies, cat# 05990): Thaw TeSR-E8 25X Supplement at room temperature (15-25℃) or overnight at 2 - 8℃. Add 20 mL of TeSR-E8 25X Supplement to 480 mL of TeSR-E8 Basal Medium. Mix thoroughly... |
71,464 | Tissue Cyclic Immunofluorescence (t-CyCIF) version 3 | 1 | null | https://www.protocols.io/view/tissue-cyclic-immunofluorescence-t-cycif-version-3-ch2gt8bw | Jia Ren Lin, Benjamin Izar, Zoltan Maliga, Yu-An Chen, Giorgio Gaglia, Ziming Du, Clarence Yapp, Shaolin Mei, Sandro Santagata, Peter Sorger | TITLE: Tissue Cyclic Immunofluorescence (t-CyCIF) version 3
AUTHORS: Jia Ren Lin, Benjamin Izar, Zoltan Maliga, Yu-An Chen, Giorgio Gaglia, Ziming Du, Clarence Yapp, Shaolin Mei, Sandro Santagata, Peter Sorger
[DESCRIPTION]
The architecture of normal and diseased tissues strongly influences the development and progres... | ["[Pre-Staining and Background Determination] Pre-staining and Background Determination takes approximately 16-24 hours.\n\nMake fluorophore bleaching solution. Combine 25 mL 1X PBS, 4.5 mL 30% (wt/vol) H2O2, and 0.8 mL 1 Molarity (M) NaOH in a 50-ml centrifuge tube. The final working concentration is 4.5% (wt/vol) H2O... |
96,840 | Bioinformatics Protocol for Investigating Novel Biomarkers, Conducting Statistical Analysis, and Exploring Molecular Pathways: A Unified Approach for Alzheimer's Disease | 0 | dx.doi.org/10.17504/protocols.io.5qpvokxyxl4o/v1 | https://www.protocols.io/view/bioinformatics-protocol-for-investigating-novel-bi-datg2ejw | Shreya Satyanarayan Bhat, Adarsh Vishal, Spoorthi Anil Bandikatte, Vidya Niranjan | TITLE: Bioinformatics Protocol for Investigating Novel Biomarkers, Conducting Statistical Analysis, and Exploring Molecular Pathways: A Unified Approach for Alzheimer's Disease
AUTHORS: Shreya Satyanarayan Bhat, Adarsh Vishal, Spoorthi Anil Bandikatte, Vidya Niranjan
[DESCRIPTION]
This protocol paper presents a co... | ["[Identification of RNA-Seq Dataset]", "[Identification of RNA-Seq Dataset] Retrieval of Samples", "[Identification of RNA-Seq Dataset]", "[Alignment] All 32 RNA-Seq samples were aligned to the human reference genome obtained from the National Center for Biotechnology Information (NCBI). The alignment was performed us... |
82,861 | TIANprep Mini Plasmid Kit Protocol | 4 | dx.doi.org/10.17504/protocols.io.dm6gpj4n5gzp/v1 | https://www.protocols.click/view/tianprep-mini-plasmid-kit-protocol-cu6mwzc6 | TIANGEN Biotech | TITLE: TIANprep Mini Plasmid Kit Protocol
AUTHORS: TIANGEN Biotech
[DESCRIPTION]
TIANprep Mini Plasmid Kit is based on alkaline lysis technology followed by adsorption of DNA onto silica membrane in the presence of high salt. Plasmid DNA purified with TIANprep Mini Plasmid Kit is immediately readyfor use. Phenol extra... | ["[Preparation of Bacterial Cells] Centrifiguation of 1-5 mL of bacterial cells in a microcentrifuge tube at 12000 rpm, 1 min", "[Preparation of Bacterial Cells] Direct drainage of supernatant by opening and inverting the tube.", "[Preparation of Bacterial Cells] Complete resuspension of the bacteria pellet in 250 µL... |
90,470 | C-SOP-401: Quality Control (QC) of DNA Libraries for Whole Genome Sequencing | 4 | null | https://www.protocols.io/view/c-sop-401-quality-control-qc-of-dna-libraries-for-c4keyute | Mihir Kekre, Ben Pascoe | TITLE: C-SOP-401: Quality Control (QC) of DNA Libraries for Whole Genome Sequencing
AUTHORS: Mihir Kekre, Ben Pascoe
[DESCRIPTION]
The success of fragmentation and size selection is best confirmed using an electrophoretic instrument designed for automated and high throughput use, suitable for applications such as NGS.... | ["[Before Starting] Prior to initiating the protocol, ensure that all active workbenches are cleaned with 80% ethanol, all relevant personal protective clothing is worn and the work area is prepared according to local GLP guidelines for molecular methods.\n\nCreate an organised bench space by clearing away all clutter ... |
44,748 | SOLUTION- 13 - Complete culture medium | 3 | dx.doi.org/10.17504/protocols.io.bpxkmpkw | https://www.protocols.io/view/solution-13-complete-culture-medium-bpxkmpkw | Marco Cosentino, Elisa Storelli, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Marco Ferrari, Franca Marino | TITLE: SOLUTION- 13 - Complete culture medium
AUTHORS: Marco Cosentino, Elisa Storelli, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Marco Ferrari, Franca Marino
[STEPS] | [] |
40,859 | Data Handling and Recordkeeping (Part 8 of Phase 3 study of Vaccine Candidate for COVID-19) | 1 | dx.doi.org/10.17504/protocols.io.bj53kq8n | https://www.protocols.io/view/data-handling-and-recordkeeping-part-8-of-phase-3-bj53kq8n | Chris Ockenhouse, Chris Gast, Renee Holt, Jorge Flores | TITLE: Data Handling and Recordkeeping (Part 8 of Phase 3 study of Vaccine Candidate for COVID-19)
AUTHORS: Chris Ockenhouse, Chris Gast, Renee Holt, Jorge Flores
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This is Part 8 of "Phase 3 randomized, double-blinded, placebo-controlled trial to ... | [] |
43,327 | Electroporation | 1 | dx.doi.org/10.17504/protocols.io.bni7mchn | https://www.protocols.io/view/electroporation-bni7mchn | Jiaxin Li | TITLE: Electroporation
AUTHORS: Jiaxin Li
[STEPS]
?. Separate the bacterial liquid in shaking tube into 1.5 mL (2 tubes) per tube, centrifuge quickly for 90 s at 4℃ and 12000 rpm.
?. Add 1 mL of 300 mM sucrose solution to each tube of bacterial liquid, centrifuge for 2 min at 12000 rpm and 4℃, and pour it out.
?. Resu... | ["Separate the bacterial liquid in shaking tube into 1.5 mL (2 tubes) per tube, centrifuge quickly for 90 s at 4℃ and 12000 rpm.", "Add 1 mL of 300 mM sucrose solution to each tube of bacterial liquid, centrifuge for 2 min at 12000 rpm and 4℃, and pour it out.", "Resuspend the competent cells (tube one) by adding 100 μ... |
47,161 | Gene CRISpy | 5 | dx.doi.org/10.17504/protocols.io.bsaznaf6 | https://www.protocols.io/view/gene-crispy-bsaznaf6 | Eric Smith | TITLE: Gene CRISpy
AUTHORS: Eric Smith
[STEPS]
?. [HTTP]
Datafire
?. [HTTP]
MATLAB
?. [HTTP]
?. [HTTP] | ["[HTTP]\nDatafire", "[HTTP]\nMATLAB", "[HTTP]", "[HTTP]"] |
44,549 | Nuclei preparation from human lung using grinding for snRNA-seq | 4 | dx.doi.org/10.17504/protocols.io.bprdmm26 | https://www.protocols.io/view/nuclei-preparation-from-human-lung-using-grinding-bprdmm26 | Center for Epigenomics UCSD | TITLE: Nuclei preparation from human lung using grinding for snRNA-seq
AUTHORS: Center for Epigenomics UCSD
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol describing nuclei isolation from frozen tissue including lung using grinding for droplet-based single nucleus RNA-seq.</div></div>
[ST... | [] |
32,845 | Less invasive surfactant administration in preterm neonates with respiratory distress syndrome: a network meta-analysis | null | dx.doi.org/10.17504/protocols.io.bcbmisk6 | null | Ioannis Bellos, Georgia Fitrou, Aakash Pandita | TITLE: Less invasive surfactant administration in preterm neonates with respiratory distress syndrome: a network meta-analysis
AUTHORS: Ioannis Bellos, Georgia Fitrou, Aakash Pandita
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Preterm birth is often associated with respiratory distress syndrome,... | ["Review title: Less invasive surfactant administration in preterm neonates with respiratory distress syndrome: a network meta-analysis 2: Review question: The meta-analysis aims to compare adverse clinical outcomes in neonates treated with less invasive surfactant administration compared to those treated with the InSu... |
null | null | null | dx.doi.org/10.17504/protocols.io.fmibk4e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Protocol for the cultivatio of Alternaria Solani.</p>
<p> </p>
<p>This protocol has been used for many years at the chair of Phytopathology at the Technical University of Munich.</p>
<p> </p>
<p>SNA Medium was first described by Nirenberg in 1981.</p>
[GUIDELINES]
<p>Work un... | [] |
57,793 | Preparation of mouse embryonic fibroblast (MEF) feeder plates for hPSC cultures | 4 | dx.doi.org/10.17504/protocols.io.b4n9qvh6 | https://www.protocols.io/view/preparation-of-mouse-embryonic-fibroblast-mef-feed-b4n9qvh6 | Hanqin Li, Oriol Busquets, Steven Poser, Dirk Hockemeyer, Frank Soldner | TITLE: Preparation of mouse embryonic fibroblast (MEF) feeder plates for hPSC cultures
AUTHORS: Hanqin Li, Oriol Busquets, Steven Poser, Dirk Hockemeyer, Frank Soldner
[DESCRIPTION]
This protocol describes the preparation of mouse embryonic fibroblasts (MEFs) as feeder cells for human pluripotent stem cell (hPSC) cul... | ["[A. Starting with frozen irradiated or Mitomycin C inactivated MEFs (optional)] To recover frozen stocks of irradiated or Mitomycin C inactivated MEFs (up to passage P4), thaw MEF tubes in in a water bath at 37 °C by gently shaking.", "[A. Starting with frozen irradiated or Mitomycin C inactivated MEFs (optional)] ... |
99,893 | DAB Detection of Biocytin Labeled Tissue | 1 | dx.doi.org/10.17504/protocols.io.eq2ly3xkegx9/v6 | https://www.protocols.io/view/dab-detection-of-biocytin-labeled-tissue-ddsv26e6 | Allen Institute for Brain Science | TITLE: DAB Detection of Biocytin Labeled Tissue
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
This protocol describes the process for diaminobenzidine (DAB) detection of biocytin filled cells. This protocol is optimized for use with brain slices cut at 350 µm thick, in which cells are first filled with bio... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.mcdc2s6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol provides an efficient way to observe proteins in samples. </p>
[BEFORE_START]
<p>Prepare acrylamide gels a few hours before running the gels; acrylamide percentage depends on protein sizes. Prepare SDS-PAGE buffers beforehand as well. </p>
[STEPS]
?.
?.
?.
... | [] |
45,370 | Immunofluorescent methods for antibody test in mouse colon | 1 | dx.doi.org/10.17504/protocols.io.bqi2muge | https://www.protocols.io/view/immunofluorescent-methods-for-antibody-test-in-mou-bqi2muge | Lixin Wang, Pu-Qing Yuan, Honghui Liang, Yvette Tache | TITLE: Immunofluorescent methods for antibody test in mouse colon
AUTHORS: Lixin Wang, Pu-Qing Yuan, Honghui Liang, Yvette Tache
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">A table listed the information of antibodies used in the mouse colon. The protocol described the methods of colon tissues s... | ["[Tissue Collection]\nMice were euthanized by an overdose of 5% isoflurane in oxygen.", "[Tissue Collection]\nAfter thoracotomy, perfusion cannula (18G) was inserted into the aorta via the left ventricle.", "[Tissue Collection]\nSaline was perfused for ~1 min to flush out the blood.", "[Tissue Collection]\nThe colon w... |
89,626 | Immunohistochemistry Protocol for Free-floating Fixed Tissue | 1 | dx.doi.org/10.17504/protocols.io.rm7vzx725gx1/v1 | https://www.protocols.io/view/immunohistochemistry-protocol-for-free-floating-fi-c3r2ym8e | Jeffrey Kordower, Yaping Chu | TITLE: Immunohistochemistry Protocol for Free-floating Fixed Tissue
AUTHORS: Jeffrey Kordower, Yaping Chu
[DESCRIPTION]
Immunohistochemistry protocol for staining free-floating fixed tissue in the Kordower Laboratory.
[GUIDELINES]
HISTO- NOTES:
Primate tissue staining dishes use 100 mLsolution per dish
Rodent tissue ... | ["[DAY 1 (4 hrs)] Wash sections (6 x 10 min) in Dilution Media (DM) (0.2 Molarity (M)TBS plus 0.05 % volumeTriton X-100).", "[DAY 1 (4 hrs)] Endogenous peroxidase inhibition (20 min). 0.1 Molarity (M) Sodium meta-periodate in TBS.\n100 mL 0.2 Molarity (m)Tris-buffered saline (TBS)\n2.13 g Sodium meta-periodate", "[DAY ... |
85,934 | Gene editing of YIPF3, YIPF4, CALCOCO1, FIP200, and ATG7 in HEK293 and HeLa cells V2 | 4 | dx.doi.org/10.17504/protocols.io.6qpvr3462vmk/v1 | https://www.protocols.io/view/gene-editing-of-yipf3-yipf4-calcoco1-fip200-and-at-cx6nxrde | Harper JW, Kelsey Hickey, sharan_swarup | TITLE: Gene editing of YIPF3, YIPF4, CALCOCO1, FIP200, and ATG7 in HEK293 and HeLa cells V2
AUTHORS: Harper JW, Kelsey Hickey, sharan_swarup
[DESCRIPTION]
This protocol describes the creation of YIPF3, YIPF4, FIP200, CALCOCO1, and ATG7 knockout cell lines in HEK293 and HeLa cells using CRISPR-Cas9.
[STEPS]
SECTION: C... | ["[Cell line maintenance] Maintain HEK293 and/or HeLa cells in Dulbecco’ Modifies Eagles Medium (DMEM) with 10% fetal bovine serum and optional 1% penicillin-streptomycin.", "[Targeted knock-out specific genes including YIPF3, YIPF4, CALCOCO1, FIP200, or ATG7: targeting vector creation] For YIPF4 knock-out, the followi... |
88,642 | Bacterial DNA extraction using modified Zymobiomics for short- and long-read sequencing | 1 | dx.doi.org/10.17504/protocols.io.36wgq36wolk5/v1 | https://www.protocols.io/view/bacterial-dna-extraction-using-modified-zymobiomic-c2tayeie | Thidathip Wongsurawat | TITLE: Bacterial DNA extraction using modified Zymobiomics for short- and long-read sequencing
AUTHORS: Thidathip Wongsurawat
[DESCRIPTION]
Description:
The Bacterial DNA Extraction protocol leverages the robustness of the Zymobiomics DNA extraction method, introducing specific modifications to ensure the yield of hig... | ["ZymoBIOMICS‱ DNA Extraction (following the manufacturer’s instruction except for beat beating time) (reference no. 1)\n1.1. Add 750 µl ZymoBIOMICS‱ Lysis Solution to the ZR BashingBead‱ Lysis Tubes. \n1.2 Pick up bacterial isolates (whole plate) using inoculate loop and add them to the tube and cap tightly. \n1.3. Se... |
104,436 | Quick and simple removal of endotoxins from purified protein solutions with magnetic beads | 0 | dx.doi.org/10.17504/protocols.io.yxmvmeze5g3p/v1 | https://www.protocols.io/view/quick-and-simple-removal-of-endotoxins-from-purif-dh8u39ww | Gudrun Baersch | TITLE: Quick and simple removal of endotoxins from purified protein solutions with magnetic beads
AUTHORS: Gudrun Baersch
[DESCRIPTION]
Endotoxins (lipopolysaccharides) can affect the results of protein solutions in many ways, so it is important to eliminate them before in vitro and in vivo testing. There are several... | ["[Working protocol] Performing of the isolation:\nThe user should use 10µl of magnetic beads for 250µl solution, from which the endotoxins are to be removed. If the user has 1 ml of solution, 40µl of magnetic beads should be used.", "[Working protocol] The user must first wash the specified quantity of magnetic beads ... |
46,320 | Tissue Punching Protocol | 1 | null | https://www.protocols.io/view/tissue-punching-protocol-brgqm3vw | McKenzie Pavlich, Lani Tieu, Brent Boomhower, Lisa Maturin, Giordano De Guglielmo, Olivier George | TITLE: Tissue Punching Protocol
AUTHORS: McKenzie Pavlich, Lani Tieu, Brent Boomhower, Lisa Maturin, Giordano De Guglielmo, Olivier George
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">SOP for brain punching for the Biobanks</div></div>
[STEPS]
?. [Beginning Prep]
Take brain out of -80° freeze... | ["[Beginning Prep]\nTake brain out of -80° freezer and leave in -20 ° freezer overnight.", "[Beginning Prep]\nMake sure the cryostat is at -14° and the stage matches the cryostat temperature. If you plan on leaving the lid to the cryostat open during punching, you may want to turn the temperature a few degrees colder a... |
59,399 | Standardized Protocol for Soil Survey and Archaeological Diagnosis for the DOPAMICS Research Program | 1 | dx.doi.org/10.17504/protocols.io.14egn768pv5d/v1 | https://www.protocols.io/view/standardized-protocol-for-soil-survey-and-archaeol-b59fq93n | Marc Testé, Kevin Mabobet, Julien Engel, Louise Brousseau | TITLE: Standardized Protocol for Soil Survey and Archaeological Diagnosis for the DOPAMICS Research Program
AUTHORS: Marc Testé, Kevin Mabobet, Julien Engel, Louise Brousseau
[DESCRIPTION]
We describe the protocol developed as part of the ERC-funded DOPAMICS research program for palm sampling in three forested pre-Col... | ["[Soil sampling] Every 50 meters along the central line (at the position of pickets \"Cstart\", \"C1\", \"C2\", etc.) and at the position of additional pits (\"RH\" and \"AH\"),\n\nCollect soil samples every 5 cm in depth, starting from the surface to 120 cm in depth\nPut the soil samples in zip-lock plastic bags\nWit... |
51,318 | Slime away: a simple CTAB-based high molecular weight DNA and RNA extraction protocol for "difficult" invertebrates (rev20200518) | 4 | dx.doi.org/10.17504/protocols.io.bwcwpaxe | https://www.protocols.io/view/slime-away-a-simple-ctab-based-high-molecular-weig-bwcwpaxe | Sergio Vargas, Cüneyt Caglar, Gabi Büttner, Simone Schätzle, Fabian Deister, Gert Woerheide | TITLE: Slime away: a simple CTAB-based high molecular weight DNA and RNA extraction protocol for "difficult" invertebrates (rev20200518)
AUTHORS: Sergio Vargas, Cüneyt Caglar, Gabi Büttner, Simone Schätzle, Fabian Deister, Gert Woerheide
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocols for ... | ["[Protocol]\nMix the CTAB Buffer in a 15ml falcon tube and preheat it to before starting the extraction.\n60 °C", "[Protocol]\nAdd β-Mercaptoethanol to the preheated CTAB Buffer under the fume-hood directly before you start with the extraction.\n100 µl", "[Protocol]\nCut a small piece of tissue and place it in a 2ml... |
28,318 | Aggregating expert-elicited data for prediction: A scoping review of statistical methods, experiments, and applications | null | dx.doi.org/10.17504/protocols.io.7v6hn9e | null | Thomas McAndrew, Nutcha Wattanachit, G. Casey Gibson, Nicholas G. Reich | TITLE: Aggregating expert-elicited data for prediction: A scoping review of statistical methods, experiments, and applications
AUTHORS: Thomas McAndrew, Nutcha Wattanachit, G. Casey Gibson, Nicholas G. Reich
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Combining forecasts from experts, compared t... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.mrcc52w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Computer-Aided Nodule Assessment and Risk Yield (CANARY) is a novel computed tomography (CT) tool developed at Mayo Clinic (Rochester, MN) that characterizes early lung adenocarcinoma by detecting nine distinct voxel classes, representing a spectrum of lepidic to invasive gro... | [] |
71,194 | Label-free quantification (LFQ) proteomic data analysis from DIA-NN output files | 5 | dx.doi.org/10.17504/protocols.io.5qpvobk7xl4o/v2 | https://www.protocols.io/view/label-free-quantification-lfq-proteomic-data-analy-chr2t58e | Yan Chen, Christopher J Petzold | TITLE: Label-free quantification (LFQ) proteomic data analysis from DIA-NN output files
AUTHORS: Yan Chen, Christopher J Petzold
[DESCRIPTION]
This protocol details the analysis of label-free quantification (LFQ) data from data independent acquisition (DIA) discovery (shotgun) proteomic experiments and generates a ser... | ["[Data processing: Relative Counts] We start with a DIA data acquisition peptide search output file the DIANN search (DIA; link to DIA-NN paper) and we trim out unused columns in the reports to simplify the analysis.\n\nDIA-NN report restricted to:\nProtein Group\nProtein Name\nGenes\nProtein Description\nPeptide Sequ... |
57,093 | Mechanical Model | 1 | null | https://www.protocols.io/view/mechanical-model-b3zdqp26 | Wolfram Moebius | TITLE: Mechanical Model
AUTHORS: Wolfram Moebius
[DESCRIPTION]
Mechanical Model
[STEPS]
5. To simulate our device, COMSOL discretises the model spatially and temporally. The spatial discretisation is defined by a mesh of points, created in the Mesh 1 menu. COMSOL will automatically design a mesh, but this should be o... | ["To simulate our device, COMSOL discretises the model spatially and temporally. The spatial discretisation is defined by a mesh of points, created in the Mesh 1 menu. COMSOL will automatically design a mesh, but this should be optimised for different parts of the design manually.\n\nSelect the Mesh 1 menu. In the sett... |
76,223 | DengueSeq: A pan-serotype whole genome amplicon sequencing protocol for dengue virus | 4 | dx.doi.org/10.17504/protocols.io.kqdg39xxeg25/v2 | https://www.protocols.io/view/dengueseq-a-pan-serotype-whole-genome-amplicon-seq-cnn7vdhn | Chantal Vogels, Chrispin Chaguza, Mallery I Breban, Afeez Sodeinde, Emma Taylor-Salmon, Abigail J. Porzucek, Nathan D Grubaugh | TITLE: DengueSeq: A pan-serotype whole genome amplicon sequencing protocol for dengue virus
AUTHORS: Chantal Vogels, Chrispin Chaguza, Mallery I Breban, Afeez Sodeinde, Emma Taylor-Salmon, Abigail J. Porzucek, Nathan D Grubaugh
[DESCRIPTION]
Version 2 updates:
Updated the DENV3 primer file (DENV3_Primer-Scheme.xlsx) w... | ["[Dengue Serotype Identification / Plate Setup] There are two primer scheme options available for use: Single-Serotype and Pan-Serotype.", "[Prepare Working Primer Solutions] Briefly centrifuge all primers", "[Prepare Working Primer Solutions] Within each serotype, organize odd and even-numbered primers into two separ... |
70,102 | Protocol for in vivo electrophysiological and optogenetic manipulation of basal ganglia neurons in awake head-fixed mice | 4 | dx.doi.org/10.17504/protocols.io.rm7vzbn94vx1/v1 | https://www.protocols.io/view/protocol-for-in-vivo-electrophysiological-and-opto-cgpwtvpe | Mark Bevan | TITLE: Protocol for in vivo electrophysiological and optogenetic manipulation of basal ganglia neurons in awake head-fixed mice
AUTHORS: Mark Bevan
[DESCRIPTION]
Step by step procedure for in vivo electrophysiological and optogenetic manipulation of basal ganglia neurons in awake head-fixed mice
[STEPS]
SECTION: In v... | ["[In vivo recording preparation] Before and after any procedures, spray down working lab surfaces and equipment with 5% Nolvasan to disinfect the surgical area.", "[In vivo recording preparation] Autoclave all surgical instruments and ensure that sterility is maintained throughout the procedure.", "[In vivo recording ... |
83,796 | Sample collection, embedding and freezing tissue | 4 | dx.doi.org/10.17504/protocols.io.bp2l6x43rlqe/v1 | https://www.protocols.click/view/sample-collection-embedding-and-freezing-tissue-cv3uw8nw | Paul PN Norton, Emily Stephenson, Keval Sidhpura, Chloe Admane, Mohi Miah | TITLE: Sample collection, embedding and freezing tissue
AUTHORS: Paul PN Norton, Emily Stephenson, Keval Sidhpura, Chloe Admane, Mohi Miah
[DESCRIPTION]
Sample collection, embedding and freezing paediatric skin tissue
[STEPS]
SECTION: Day 1 - Sample collection
1. Take 6mm punch biopsy of skin and place in a vial of H... | ["[Day 1 - Sample collection] Take 6mm punch biopsy of skin and place in a vial of Hypothermosol that has been pre-chilled at 4oC. Record time of biopsy.", "[Day 1 - Sample collection] Proceed to embed and freeze the tissue as soon as possible, no longer than 24 hours later, ensuring that the sample is kept in Hypother... |
null | null | null | dx.doi.org/10.17504/protocols.io.qf5dtq6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The use of genetically encoded ‘self-labeling tags’ with chemical fluorophore ligands enables rapid labeling of specific cells in neural tissue. To improve the chemical tagging of neurons, we synthesized and evaluated new fluorophore ligands based on Cy, Janelia Fluor, Alexa ... | [] |
40,286 | Effective identification of DNA-bound protein complexes using Chromatin Immunoprecipitation | 4 | dx.doi.org/10.17504/protocols.io.bjj6kkre | https://www.protocols.io/view/effective-identification-of-dna-bound-protein-comp-bjj6kkre | Georgios I Laliotis, Philip N. Tsichlis | TITLE: Effective identification of DNA-bound protein complexes using Chromatin Immunoprecipitation
AUTHORS: Georgios I Laliotis, Philip N. Tsichlis
[STEPS]
?. [Chemicals Required]
1. Cytosolic Lysis Buffer (200 ml) ; 5 mM PIPES (pH 8.0), 85 mM KCl, 0.5% NP40 + PI PIPES 0.3 g =>Adjust pH 8.0 2M KCl ... | ["[Chemicals Required]\n1. Cytosolic Lysis Buffer (200 ml) ; 5 mM PIPES (pH 8.0), 85 mM KCl, 0.5% NP40 + PI PIPES 0.3 g =>Adjust pH 8.0 2M KCl 8.5 ml 10% NP40 10 ml 2. Nuclear Lysis Buffer (50 ml) ; 50 mM Tris (pH 8.0), 10 mM EDTA, 0.5% SDS 1 M Tris (pH 8.0) 2... |
21,402 | PCR Reaction for Experiments | null | dx.doi.org/10.17504/protocols.io.y52fy8e | null | Kenneth Schackart | TITLE: PCR Reaction for Experiments
AUTHORS: Kenneth Schackart
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">How to run nucleic acid amplification using the Thermo scientific PCR Master Mix kit.</div><div class = "text-block">Each reaction produces 50 μL.</div><div class = "text-block"><span>For t... | ["[Prepare Work Area]\nSpray entire work area with 70% EtOH including pipettes, tip holder used for holding PCR tubes, and work surface. Wipe with a paper towel.", "[Prepare Work Area]\nSpray entire work area with RNAway.", "[Gather Materials]\nTake styrofoam container to Marley 527 (directly across from Marley 509) an... |
50,106 | Transplantation of Fetal Midbrain Dopamine Progenitors into a Rodent Model of Parkinson’s Disease | 1 | dx.doi.org/10.17504/protocols.io.bu62nzge | https://www.protocols.io/view/transplantation-of-fetal-midbrain-dopamine-progeni-bu62nzge | Lachlan H. Thompson, Clare L. Parish | TITLE: Transplantation of Fetal Midbrain Dopamine Progenitors into a Rodent Model of Parkinson’s Disease
AUTHORS: Lachlan H. Thompson, Clare L. Parish
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Cell therapy is a promising experimental treatment for Parkinson’s disease (PD). It is based on the ... | ["[3.1 Preparation of Cell Suspensions]\nRemove the uterus immediately from euthanized or terminally anesthetized animals via caesarian section, place in cold L15 medium (see Note 2) and store .\non ice", "[3.1 Preparation of Cell Suspensions]\nPlace the embryos in a petri dish containing ice-cold L15 medium. Under ... |
109,140 | Immunohistochemistry (IHC) on mouse brain slices | 0 | dx.doi.org/10.17504/protocols.io.5qpvokmq7l4o/v1 | https://www.protocols.io/view/immunohistochemistry-ihc-on-mouse-brain-slices-dntu5enw | Gerard Michael Coughlin | TITLE: Immunohistochemistry (IHC) on mouse brain slices
AUTHORS: Gerard Michael Coughlin
[DESCRIPTION]
This protocol provides a starting point for immunohistochemical localization and visualization of proteins in mouse brain tissue. This can be useful for marking cell types of interest or investigating the effect of e... | ["[Reagent set up] General note on reagents and consumables", "[Reagent set up] Prepare 1x PBS, by combining: \n\n1 PBS packet\nMilliQ water (or equivalent): 1 L \n\nShake to combine and store at Room temperature for up to 3 months.\n\n(Optional) Treat 1x PBS with DEPC- or DMPC-treat to inactivate RNases. Add 1 mL of D... |
null | null | null | dx.doi.org/10.17504/protocols.io.fccbisw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><strong>Purpose:</strong> To quantify virus-like particles in culture or environmental samples.</p>
<p><strong>Summary:</strong> Host cells and virus-like particles are enumerated from the same glutaraldehyde-fixed sample. For virus counts, an aliquot is diluted in 0.02-µm-fi... | [] |
43,743 | Efficient Depletion of Fission Yeast Condensin by Combined Transcriptional Repression and Auxin-Induced Degradation | 4 | dx.doi.org/10.17504/protocols.io.bnx7mfrn | https://www.protocols.io/view/efficient-depletion-of-fission-yeast-condensin-by-bnx7mfrn | Yasutaka Kakui, Frank Uhlmann | TITLE: Efficient Depletion of Fission Yeast Condensin by Combined Transcriptional Repression and Auxin-Induced Degradation
AUTHORS: Yasutaka Kakui, Frank Uhlmann
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Structural maintenance of chromosomes (SMC) complexes play pivotal roles in controlling ch... | ["[Depletion of the Condensin SMC2/Cut14 Subunit]\nCulture cells in PGM at until OD595 reaches 0.2–0.4 (4–8 × 106 cells/mL).\n25 °C\nTo prepare a culture with suitable density in the next morning, an inoculation at OD595 = 0.05 (approximately 1 × 106 cells/mL) and growth is recommended.", "[Depletion of the Condensi... |
null | null | null | dx.doi.org/10.17504/protocols.io.h2mb8c6 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
85,728 | Sectioning Mouse Brain with Sliding Microtome | 1 | dx.doi.org/10.17504/protocols.io.5jyl8p97rg2w/v1 | https://www.protocols.io/view/sectioning-mouse-brain-with-sliding-microtome-cxx8xprw | Naveen Ouellette, daphne.toglia, Holly Myers | TITLE: Sectioning Mouse Brain with Sliding Microtome
AUTHORS: Naveen Ouellette, daphne.toglia, Holly Myers
[DESCRIPTION]
This is a protocol that details sectioning a mouse brain fixed in 4% PFA and 30% sucrose on a sliding microtome. This protocol details the microtome set up, the mounting of the brain on the microtom... | ["[Setup] Microtome setup:", "[Setup] Ensure lock handle for knife is in the closed position before making any adjustments to, or mounting tissue onto, the microtome.", "[Setup] Attach the stage to the microtome and ensure that it is level.", "[Setup] Take microtome knife out of its case and use 70% ethyl alcohol and a... |
null | null | null | dx.doi.org/10.17504/protocols.io.fyxbpxn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div class="page" title="Page 1">
<div class="layoutArea">
<div class="column">
<p>The SensiFAST™ Probe No-ROX Kit has been developed for fast, highly reproducible real-time PCR and has been validated on commonly used real-time PCR instruments. The kit has been formulated for us... | [] |
88,610 | Steps for setup of AWS organization, S3 data storage, and EC2 computing for using Python notebooks | 5 | dx.doi.org/10.17504/protocols.io.rm7vz3z4xgx1/v2 | https://www.protocols.io/view/steps-for-setup-of-aws-organization-s3-data-storag-c2sayeae | Daniel J. Pollak, Gautam Chawla, Andrey Andreev, David A. Prober | TITLE: Steps for setup of AWS organization, S3 data storage, and EC2 computing for using Python notebooks
AUTHORS: Daniel J. Pollak, Gautam Chawla, Andrey Andreev, David A. Prober
[DESCRIPTION]
With the oncoming age of big data, biologists are encountering more use cases for cloud-based computing to streamline data pr... | ["[Setting organization and budget management] Setting up a Root account", "[Setting organization and budget management] Create “root” account for your organization, using Business account type", "[Setting organization and budget management] If you are using GMail account to manage other services in your lab, for examp... |
80,078 | Hairy root generation in common bean (Phaseolus vulgaris L.) and selection of Agrobacterium rhizogenes clones | 4 | dx.doi.org/10.17504/protocols.io.261ge3bpjl47/v1 | https://www.protocols.io/view/hairy-root-generation-in-common-bean-phaseolus-vul-csfnwbme | Ronal Pacheco, Georgina Estrada-Navarrete, Noreide Nava, Jorge Solismiranda, carmen.quinto | TITLE: Hairy root generation in common bean (Phaseolus vulgaris L.) and selection of Agrobacterium rhizogenes clones
AUTHORS: Ronal Pacheco, Georgina Estrada-Navarrete, Noreide Nava, Jorge Solismiranda, carmen.quinto
[DESCRIPTION]
The common bean (Phaseolus vulgaris L.) is one of the legumes used to study the molecula... | ["[Seeds disinfection (when necessary)] Immerse the common bean seeds in 96 % volume ethanol for 5 min and wash them three times with sterile water.", "[Seeds disinfection (when necessary)] Immerse the seeds in 2 % volume sodium hypochlorite for 5 min and wash them three times with sterile water.", "[Seeds disinfecti... |
null | null | null | dx.doi.org/10.17504/protocols.io.efgbbjw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Long-standing questions in marine viral ecology are centered on understanding how viral assemblages change along gradients in space and time. However, investigating these fundamental ecological questions has been challenging due to incomplete representation of naturally occurrin... | [] |
38,041 | Packaging and Cold Shipping of Human Islets | 1 | dx.doi.org/10.17504/protocols.io.bhdzj276 | https://www.protocols.io/view/packaging-and-cold-shipping-of-human-islets-bhdzj276 | Integrated Islet Distribution Program | TITLE: Packaging and Cold Shipping of Human Islets
AUTHORS: Integrated Islet Distribution Program
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This SOP defines a standardized method for packaging and cold shipping of research quality islets to approved investigators of human isolated islet prepar... | ["[Materials]\nThe IIDP will provide each center with the supplies necessary for shipments as listed in the materials section. Standard lab supplies will be provided by the IIDP Centers as listed below.", "[Materials]\nSupplies provided by the IIDP Centers:Islets for distributionRoutine lab supplies for transferring i... |
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