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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59,242 | Stranded Mapping from Oriented Long Reads | 1 | dx.doi.org/10.17504/protocols.io.b54iq8ue | https://www.protocols.io/view/stranded-mapping-from-oriented-long-reads-b54iq8ue | David A Eccles | TITLE: Stranded Mapping from Oriented Long Reads
AUTHORS: David A Eccles
[DESCRIPTION]
This protocol demonstrates how to map strand-oriented long reads to a genome, and visualise them in a genome browser.
The general idea is to use minimap2 to create stranded BAM files, which are split for forward/reverse orientatio... | ["[Orient Reads] Orient reads as per protocol Preparing Reads for Stranded Mapping.\n\nIf this has been done, then the following command should produce output without errors:\n \nExample output:", "[Index Preparation] Prepare genome index for spliced alignment", "[Read Mapping] Map the long reads to the genome using mi... |
null | null | null | dx.doi.org/10.17504/protocols.io.kcfcstn | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
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?. | [] |
55,776 | MAVRICS: A Robust and Safe Magnetic Nanoparticle based RNA Extraction Method Compatible with Phenol-chloroform Inactivated Infectious Samples | 1 | dx.doi.org/10.17504/protocols.io.b2p8qdrw | https://www.protocols.io/view/mavrics-a-robust-and-safe-magnetic-nanoparticle-ba-b2p8qdrw | Mo Li, Gerardo Ramos-Mandujano | TITLE: MAVRICS: A Robust and Safe Magnetic Nanoparticle based RNA Extraction Method Compatible with Phenol-chloroform Inactivated Infectious Samples
AUTHORS: Mo Li, Gerardo Ramos-Mandujano
[DESCRIPTION]
Diagnosis and surveillance of emerging pathogens such as SARS-CoV-2 depend on nucleic acid isolation from clinica... | ["Silica magnetic nanoparticles (SiMNP) synthesis.\nSiMNP synthesis was done following the published protocols in BOMB.bio: BOMB magnetic core nanoparticles synthesis and BOMB coating ferrite MNPs with silica oxide.", "COVID-19 patient samples.\nOropharyngeal or nasopharyngeal swabs are steeped in 1 mL acid guanidinium... |
24,090 | Systemic analysis of injection site pain caused by subcutaneous administration of FKB327 and reference product via different delivery methods | null | dx.doi.org/10.17504/protocols.io.3r2gm8e | null | Takahiro Ito, Masayuki Takanuma, Yasumasa Arai | TITLE: Systemic analysis of injection site pain caused by subcutaneous administration of FKB327 and reference product via different delivery methods
AUTHORS: Takahiro Ito, Masayuki Takanuma, Yasumasa Arai
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">FKB327 is a biosimilar of the adalimumab refere... | ["Data to be analyzed in systemic analysisThe VAS data of injection site pain from FKB327-001, -002, -003, and -004 are integrated for the systemic analysis. All cumulative data will be analyzed for the randomized subjects with injection site pain data collected immediately after injection at Day 1. Some subjects had m... |
null | null | null | dx.doi.org/10.17504/protocols.io.j3xcqpn | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?. | [] |
61,966 | Chemically Labile Linkers | 6 | dx.doi.org/10.17504/protocols.io.36wgq7mexvk5/v1 | https://www.protocols.io/view/chemically-labile-linkers-b8rnrv5e | BOC Sciences | TITLE: Chemically Labile Linkers
AUTHORS: BOC Sciences
[DESCRIPTION]
The chemically labile linkers, which include acid-cleavable linkers and disulfide linkers, are extensively applied to ADCs due to their ability to undergo fracture, increasing the acidity of the endosomal-lysosomal pathway, as well as the concen... | [] |
97,917 | Filaggrin genotyping using Taqman SNP genotyping assays | 0 | dx.doi.org/10.17504/protocols.io.3byl492mogo5/v1 | https://www.protocols.io/view/filaggrin-genotyping-using-taqman-snp-genotyping-a-dbu52ny6 | Angie Fawkes, Katarzyna Hafezi, Lee Murphy | TITLE: Filaggrin genotyping using Taqman SNP genotyping assays
AUTHORS: Angie Fawkes, Katarzyna Hafezi, Lee Murphy
[DESCRIPTION]
The FLG gene encodes the filaggrin protein which is essential for epidermal barrier formation and hydration. Mutations in the filaggrin gene are associated with a broad range of skin and all... | ["[Prepare reaction mix] The tables below are for one sample based on 10μL reaction volume (2μL of DNA and 8μL of reaction mix). Multiply up reaction mix by number of samples plus extra for dead-volume. Ensure a sensible amount for accurate pipetting. \n(This means that for R501X and S3247X primers will be at 300nM & p... |
33,927 | Q5® Site-Directed Mutagenesis (E0554) | 1 | dx.doi.org/10.17504/protocols.io.bddfi23n | https://www.protocols.io/view/q5-site-directed-mutagenesis-e0554-bddfi23n | New England Biolabs | TITLE: Q5® Site-Directed Mutagenesis (E0554)
AUTHORS: New England Biolabs
[DESCRIPTION]
This is the protocol for the Q5® Site-Directed Mutagenesis Kit (E0554).
[GUIDELINES]
DESCRIPTION
The Q5® Site-Directed Mutagenesis Kit enables rapid, site-specific mutagenesis of double-stranded plasmid DNA in less than 2 hour... | ["[Exponential Amplification (PCR)] Assemble the following reagents in a thin-walled PCR tube.\n 25 μl RXN FINAL CONC. Q5 Hot Start High-Fidelity 2X Master Mix 12.5 μl 1X 10 μM Forward Primer 1.25 μl 0.5 μM 10 μM Reverse Primer 1.25 μl 0.5 μM Template DNA (1–25 ng/μl) 1 μl 1-25 ng Nuclease-free water 9.0 ... |
53,375 | DNA Ethanol Precipitation (SOP009.v1.1) | 4 | null | https://www.protocols.io/view/dna-ethanol-precipitation-sop009-v1-1-byc7pszn | Rory Kruithoff, Douglas Shepherd | TITLE: DNA Ethanol Precipitation (SOP009.v1.1)
AUTHORS: Rory Kruithoff, Douglas Shepherd
[DESCRIPTION]
Document Summary: This document, SOP002 - DNA Ethanol Precipitation, describes a method to concentrate or dry DNA using ethanol to reduce the solubility of dissolved DNA causing it to precipitate out of solution. ... | ["[Precipitate DNA] Add 1/10 volume of 3 M Na-Acetate pH 5.2, and 2 to 2.5 volumes of ice-cold 100% ethanol to the DNA sample.", "[Precipitate DNA] Mix, and store at -20 °C for at least 60 min to precipitate the DNA. Typically, DNA will be left at -20 °C 60 minbefore proceeding to part 2.", "[Pellet DNA and dry] Reco... |
31,453 | Association between circulating microRNA-122, microRNA-126-3p and microRNA-146a and inflammatory markers in patients with pre-diabetes and type 2 diabetes mellitus | 1 | dx.doi.org/10.17504/protocols.io.bax5ifq6 | https://www.protocols.io/view/association-between-circulating-microrna-122-micro-bax5ifq6 | Hassan Mozaffari-Khosravi, Fahime Zeinali, Seyed Mohsen Aghaei Zarch, Alireza Jahan-mihan, Shima Abdollahi, Seyed Mehdi Kalantar, Mohammad Yahya Vahidi Mehrjardi, Hossein Fallahzadeh, Mahdieh Hosseinzadeh-Shamsi-Anar, Masoud Rahmanian | TITLE: Association between circulating microRNA-122, microRNA-126-3p and microRNA-146a and inflammatory markers in patients with pre-diabetes and type 2 diabetes mellitus
AUTHORS: Hassan Mozaffari-Khosravi, Fahime Zeinali, Seyed Mohsen Aghaei Zarch, Alireza Jahan-mihan, Shima Abdollahi, Seyed Mehdi Kalantar, Mohammad Y... | ["[Real time PCR]\nReal time PCR", "[IL6 measurement]\nIL6 measurement by ELISA kit https://www.diaclone.com/documents/protocole/950.030_Human_IL-6_ELISA_kit_insert_v11.pdf", "[RNA extraction]\nRNA extraction http://tribioscience.com/files/315-150.pdf", "[RNA extraction]\nPrepare 750 ul RiboExTM LS in a 1.5 ml microcen... |
97,862 | Nuclei Isolation for Human Ovary Explants | 0 | dx.doi.org/10.17504/protocols.io.e6nvw1632lmk/v1 | https://www.protocols.io/view/nuclei-isolation-for-human-ovary-explants-dbte2nje | Nicolas Martin | TITLE: Nuclei Isolation for Human Ovary Explants
AUTHORS: Nicolas Martin
[DESCRIPTION]
This protocol uses fresh frozen human ovary explants to isolate nuclei suspension.
[GUIDELINES]
This protocol needs prior approval by the users' institutional review board (IRB) or equivalent ethics committee(s).
[STEPS]
SECTION: ... | ["[Nuclei Isolation Protocol for Human Ovary Explants] Chapter 1—Single Cell Gene Expression & Chromium Fixed RNA Profiling of the protocol CG000505 REV A was used to isolate nuclei from frozen human ovary explants with the following modifications: 1) a cordless motor pestle (VWR, Catalog number 47747-370) was used for... |
20,451 | iPSC PCR: For Screening Edited Clones | null | dx.doi.org/10.17504/protocols.io.x8bfrsn | null | Celeste Karch, Rita Martinez, Jacob Marsh | TITLE: iPSC PCR: For Screening Edited Clones
AUTHORS: Celeste Karch, Rita Martinez, Jacob Marsh
[STEPS]
?. [PCR]
This is the set up for a 50 µL reaction. ABC1Volumex# rxns25x Green GoTaq Flexi Buffer10 µl325mM MgCl26 µl425mM dNTPs0.8 µl5Forward Primer (10uM)2 µl6Reverse Primer (10uM)2 µl7GoTaq DNA Polymerase (5U/uL)0... | ["[PCR]\nThis is the set up for a 50 µL reaction. ABC1Volumex# rxns25x Green GoTaq Flexi Buffer10 µl325mM MgCl26 µl425mM dNTPs0.8 µl5Forward Primer (10uM)2 µl6Reverse Primer (10uM)2 µl7GoTaq DNA Polymerase (5U/uL)0.25 µl8Milli-Q H2026.95 µl9Quick Extract gDNA2 µl10Total50 µl\nABC1Volumex# rxns25x Green GoTaq Flexi Buf... |
92,384 | SOP for genome size estimations from collection specimens | 3 | dx.doi.org/10.17504/protocols.io.yxmvm3by9l3p/v1 | https://www.protocols.io/view/sop-for-genome-size-estimations-from-collection-sp-c6f8zbrw | Jean François Flot, Mohammed Tawfeeq, Ana Riesgo | TITLE: SOP for genome size estimations from collection specimens
AUTHORS: Jean François Flot, Mohammed Tawfeeq, Ana Riesgo
[DESCRIPTION]
Genome size data is crucial now for comparative studies with the goal of understanding the mechanisms of genomic change and their biological implications related to genome size diver... | [] |
52,282 | Growth rate determination of E. coli | 4 | dx.doi.org/10.17504/protocols.io.bxa2pige | https://www.protocols.io/view/growth-rate-determination-of-e-coli-bxa2pige | Ashwinuday | TITLE: Growth rate determination of E. coli
AUTHORS: Ashwinuday
[DESCRIPTION]
<div class = "text-blocks"><br/><div class = "text-block"><span>This is to measure the growth rate of </span><span style = "font-style:italic;">E. coli.</span></div><br/><div class = "text-block">The initially used culture is a primary cult... | ["Grow the bacteria in an overnight (14-18 hours) culture.", "Inoculate 50 ml autoclaved culture media in a conical flask with a part of the overnight grown culture equal to 2% volume of fresh media (i.e. 1ml) inside a laminar hood.", "Put the rest of the freshly inoculated flask into a shaking incubator at at .\n33\... |
null | null | null | dx.doi.org/10.17504/protocols.io.f7cbriw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>prepare 100 mL per 250 mL flask for each overnight culture</p>
<p>for </p>
<h1>CZV8CS - liquid media for flask culture</h1>
<p>prepare 100 mL per 250 mL flask for each overnight culture for</p>
<p> <strong><u>100 mL</u></s... | [] |
94,242 | Protocol3_HEK293T cells and mRNA transfections.pdf | 1 | dx.doi.org/10.17504/protocols.io.36wgq3zyklk5/v1 | https://www.protocols.io/view/protocol3-hek293t-cells-and-mrna-transfections-pdf-c8aazsae | angelica.gonzalez | TITLE: Protocol3_HEK293T cells and mRNA transfections.pdf
AUTHORS: angelica.gonzalez
[DESCRIPTION]
HEK293T cells and mRNA transfections
[STEPS] | [] |
90,197 | Immunohistochemistry protocol optimized at iMM-JLA | 1 | dx.doi.org/10.17504/protocols.io.j8nlkon2wv5r/v1 | https://www.protocols.io/view/immunohistochemistry-protocol-optimized-at-imm-jla-c4bvysn6 | Ana M Biscaia Santos, Ana M Cristóvão Pinto, Ana R Pires, Joana G Antunes | TITLE: Immunohistochemistry protocol optimized at iMM-JLA
AUTHORS: Ana M Biscaia Santos, Ana M Cristóvão Pinto, Ana R Pires, Joana G Antunes
[DESCRIPTION]
The immunohistochemistry (IHC) protocol is used to showcase the location of specific proteins in relation to the arquitecture of the tissue.
In this method, we use... | ["[Preparation of Wash Buffer] Measure 20 mL of 20X", "[Preparation of Wash Buffer] Make up with distilled water to 1 L of total volume", "[Antigen Retrieval] Perform antigen retrieval using PT Module by Thermo Scientific with a cycle of pre-heat to 65ºC and heat to 95ºC for 20 minutes.", "[Counterstain and mount] Clea... |
67,557 | Monkeypox virus multiplexed PCR amplicon sequencing (PrimalSeq) V.2. | 1 | dx.doi.org/10.17504/protocols.io.5qpvob1nbl4o/v2 | https://www.protocols.io/view/monkeypox-virus-multiplexed-pcr-amplicon-sequencin-cd8ds9s6 | Nicholas F.G. Chen*, Luc Gagne*, Matthew Doucette, Sandra Smole, Erika Buzby, Joshua Hall, Stephanie Ash, Rachel Harrington, Seana Cofsky, Selina Clancy, Curtis J Kapsak, Joel Sevinsky, Kevin Libuit, mallery.breban , Chrispin Chaguza, Nathan D. Grubaugh, Daniel J. Park, Glen R. Gallagher#, Chantal B.F. Vogels# | TITLE: Monkeypox virus multiplexed PCR amplicon sequencing (PrimalSeq) V.2.
AUTHORS: Nicholas F.G. Chen*, Luc Gagne*, Matthew Doucette, Sandra Smole, Erika Buzby, Joshua Hall, Stephanie Ash, Rachel Harrington, Seana Cofsky, Selina Clancy, Curtis J Kapsak, Joel Sevinsky, Kevin Libuit, mallery.breban , Chrispin ... | ["[Dilute and Pool Primers] Reagents:", "[Dilute and Pool Primers] If not already done, separate odd and even numbered primer pairs into two separate boxes. These will constitute the two pools", "[Dilute and Pool Primers] Label 164, 8-strip tubes with the corresponding odd-numbered primer name (e.g. 3 left)", "[Dilute ... |
null | null | null | dx.doi.org/10.17504/protocols.io.ci4ugv | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
How to make a 1M DTT Stock Solution
[STEPS]
?.
?.
?.
?. | [] |
25,877 | Permanent multiprofessional auditory assessment protocol for children with congenital zika virus syndrome | null | dx.doi.org/10.17504/protocols.io.5hvg366 | null | Klinger Vagner Teixeira da Costa, Pedro Menezes, Ana Frizzo | TITLE: Permanent multiprofessional auditory assessment protocol for children with congenital zika virus syndrome
AUTHORS: Klinger Vagner Teixeira da Costa, Pedro Menezes, Ana Frizzo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Trata-se de 0um protocolo de avaliação auditiva multiprofissional para... | [] |
36,353 | PCOS lifestyle program | null | dx.doi.org/10.17504/protocols.io.bfq9jmz6 | https://www.protocols.io/view/pcos-lifestyle-program-bfq9jmz6 | Geranne Jiskoot, J.S.E Laven, J.J. van Busschbach, C. de Klerk, J. de Niet | TITLE: PCOS lifestyle program
AUTHORS: Geranne Jiskoot, J.S.E Laven, J.J. van Busschbach, C. de Klerk, J. de Niet
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Obesity in women with polycystic ovary syndrome (PCOS)</div><div class = "text-block">negatively affects all clinical features, and a 5 to... | ["[Background]\nPolycystic ovary syndrome (PCOS) is a common endocrine disorder that affects 5–10% of women in their reproductive years [1]. According to the ESHRE/ASRM Rotterdam consensus [2], the diagnosis of PCOS requires at least 2 of the following 3 criteria: oligoovulation or anovulation (irregular or no menstrua... |
63,000 | Weight Crasher Keto Gummies | 3 | dx.doi.org/10.17504/protocols.io.bp2l61m8kvqe/v1 | https://www.protocols.io/view/weight-crasher-keto-gummies-b9ryr57w | H Douglas Morris | TITLE: Weight Crasher Keto Gummies
AUTHORS: H Douglas Morris
[DESCRIPTION]
Weight Crasher Keto Gummies is a natural enhancement proposed for weight reduction. These diet pills are intended for people who are now on the ketogenic diet and aim to improve their belongings.
[STEPS] | [] |
77,741 | Calcium fluorimetry with the FLIPR Calcium 6 kit on FlexStation 3 | 1 | dx.doi.org/10.17504/protocols.io.3byl4jdmjlo5/v1 | https://www.protocols.io/view/calcium-fluorimetry-with-the-flipr-calcium-6-kit-o-cp6mvrc6 | Angus Li | TITLE: Calcium fluorimetry with the FLIPR Calcium 6 kit on FlexStation 3
AUTHORS: Angus Li
[DESCRIPTION]
This protocol details an experimental procedure used to generate results described in the manuscript Li, A., Liu, S., Huang, R., Ahn, S., & Lefkowitz, R. J. (2023). Loss of biased signaling at a G protein-coupled r... | ["Plate U2OS-TetOn-AT1R in microplates (Black with clear bottom, lysine- coated Corning 3842) at 15000 cells/well 2 days prior to assay", "Add doxycycline and optionally PTX to wells 14 hours before replacement with loading buffer", "Remove one vial of Calcium 6 Assay Reagent (Component A, good for 2 plates) from the f... |
39,140 | S30-S30A-S30-Buffers- Haseloff Lab | 4 | dx.doi.org/10.17504/protocols.io.bigckbsw | https://www.protocols.io/view/s30-s30a-s30-buffers-haseloff-lab-bigckbsw | Fernando Guzman Chavez, Jim Haseloff | TITLE: S30-S30A-S30-Buffers- Haseloff Lab
AUTHORS: Fernando Guzman Chavez, Jim Haseloff
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:center"><span>Following this recipe, you will obtain 1L of</span><span style = "font-weight:bold;"> S30</span><span style... | ["[1. S30 Buffer]\nTo prepare S30 buffer, following compounds have to be ready-to-use:Tris-AcetateMagnesium acetate tetrahydratePotassium acetate1M DTT5M KOH", "[1. S30 Buffer]\n1. 1 Prepare for autoclavingVolumes indicated are sufficient for 1 L of S30 buffer Before useadd 2 mL of 1 M DTT(2mM, final concentration)For ... |
null | null | null | dx.doi.org/10.17504/protocols.io.cjjukm | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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85,936 | Whole-cell proteomics and Analysis with or without nutrient stress by Tandem Mass Tagging-based proteomics V2 | 4 | dx.doi.org/10.17504/protocols.io.yxmvm32nbl3p/v1 | https://www.protocols.io/view/whole-cell-proteomics-and-analysis-with-or-without-cx6qxrdw | Sharan Swarup, J. Wade Harper wade_harper@hms.harvard.edu, Kelsey Hickey | TITLE: Whole-cell proteomics and Analysis with or without nutrient stress by Tandem Mass Tagging-based proteomics V2
AUTHORS: Sharan Swarup, J. Wade Harper wade_harper@hms.harvard.edu, Kelsey Hickey
[DESCRIPTION]
The analysis of relative protein abundance has emerged as an important tool in cell biology. Typically, it... | ["[Harvest, precipitation and digestion] For whole proteome analysis, 50 µg is required for each replicate. Cells from step 2 are washed with PBS three times. Cells were lysed by in UREA denaturing buffer (8M Urea, 150mM NaCl, 50mM EPPS pH8.0, containing mammalian protease inhibitor cocktail (Sigma), and Phos-STOP)... |
49,235 | space_publications_versions protocol 1 v2 | 1 | null | https://www.protocols.io/view/space-publications-versions-protocol-1-v2-bubtnsnn | Maria Guliakina | TITLE: space_publications_versions protocol 1 v2
AUTHORS: Maria Guliakina
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">test</div></div>
[STEPS]
?. test
?. est 2
?.
?. test 4 | ["test", "est 2", "test 4"] |
63,866 | Chemotaxonomy-based Drug Discovery | 4 | dx.doi.org/10.17504/protocols.io.36wgq7yw5vk5/v1 | https://www.protocols.io/view/chemotaxonomy-based-drug-discovery-cak2scye | contact.microbialtec | TITLE: Chemotaxonomy-based Drug Discovery
AUTHORS: contact.microbialtec
[DESCRIPTION]
With the large numbers of already known microbial and plant metabolites, one of the major challenges in modern natural product discovery is to detect already known and trivial compounds rapidly. This relies on information managemen... | [] |
81,575 | Protocol for t-DNA insertional mutagenesis in the chickpea Fusarium wilt pathogen, Fusarium oxysporum f. sp. ciceris for identification of virulence genes | 4 | null | https://www.protocols.io/view/protocol-for-t-dna-insertional-mutagenesis-in-the-ctwfwpbn | Ramawatar Nagar | TITLE: Protocol for t-DNA insertional mutagenesis in the chickpea Fusarium wilt pathogen, Fusarium oxysporum f. sp. ciceris for identification of virulence genes
AUTHORS: Ramawatar Nagar
[DESCRIPTION]
Chickpea is the third most consumed grain legume in the world. It serves as a valuable source of protein and micronutr... | ["Preparing Fusarium spore suspension", "A wilting isolate (on the genotype JG62) of the Foc was cultured on PDA plates containing cefotaxime (50mg/L) at 25 °C for 7-10 days", "Spores were collected from the plant by adding 4 mL of double-distilled autoclave water to the plate and gently brushing the mycelium with a cl... |
null | null | null | dx.doi.org/10.17504/protocols.io.jgacjse | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<ol>
<li><strong> DNA Extraction</strong></li>
</ol>
<ul>
<li>Extract DNA from sample using the phenol/chloroform procedure or your kit of choice. We typically use the Mo Bio Power Soil DNA extraction kit for extracting DNA from soil and plant litter samples.</li>
<li>Use the Na... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.qv8dw9w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Adapted from Tara Oceans extraction protocol (see citation).</p>
[STEPS]
?.
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26,168 | Make NGM medium | null | dx.doi.org/10.17504/protocols.io.5syg6fw | null | Cancer Research UK / Wellcome Trust Gurdon Institute media kitchen | TITLE: Make NGM medium
AUTHORS: Cancer Research UK / Wellcome Trust Gurdon Institute media kitchen
[STEPS]
?.
?. Add bacto peptone and NaCl
?. Measure approx 4.8L double distilled H2O in 5L bell jar with a magnetic flea.
?. Stir until all solutes are dissolved.
?. Dispense approx 972ml NGM media per 1L bottle OR 48... | ["Add bacto peptone and NaCl", "Measure approx 4.8L double distilled H2O in 5L bell jar with a magnetic flea.", "Stir until all solutes are dissolved.", "Dispense approx 972ml NGM media per 1L bottle OR 486ml NGM into a 500ml bottle.", "Dispense 17g of agar and a magnetic flea to each 1L bottle OR 8.5g of agar and a ... |
61,925 | PNA/DNA Chimera Synthesis | 6 | dx.doi.org/10.17504/protocols.io.j8nlkkmnwl5r/v1 | https://www.protocols.io/view/pna-dna-chimera-synthesis-b8qdrvs6 | Cathy Miller | TITLE: PNA/DNA Chimera Synthesis
AUTHORS: Cathy Miller
[DESCRIPTION]
Pure PNA has significant binding properties, but it has completely different properties from DNA and RNA. For example, it cannot be recognized as a substrate when it interacts with nucleic acid modifying enzymes. On the one hand, this is an advantag... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.ibccaiw | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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102,752 | HEP-TILE: HBV whole genome sequencing (nanopore protocol) | 1 | dx.doi.org/10.17504/protocols.io.5jyl82bedl2w/v1 | https://www.protocols.io/view/hep-tile-hbv-whole-genome-sequencing-nanopore-prot-dgj83urw | Sheila Lumley, Chris Kent, Josh Quick, Philippa Matthews | TITLE: HEP-TILE: HBV whole genome sequencing (nanopore protocol)
AUTHORS: Sheila Lumley, Chris Kent, Josh Quick, Philippa Matthews
[DESCRIPTION]
This protocol describes the HEP-TILE tiled amplicon protocol for whole genome sequencing of Hepatitis B virus (HBV) on the nanopore MinION.
We developed a pan-genotypic (gen... | ["[Multiplex PCR] Set up the two PCR reactions per sample as follows in strip-tubes or plates. Gently mix by pipetting and pulse spin the tube to collect liquid at the bottom of the tube.", "[Multiplex PCR] Add 2.5 µL cDNA to each of the PCR reactions, gently mix by pipetting and pulse spin the tube to collect liquid a... |
58,678 | Minimum Inhibitory Concentration | 4 | null | https://www.protocols.io/view/minimum-inhibitory-concentration-b5iwq4fe | Amanda T Alker, Nicholas J Shikuma | TITLE: Minimum Inhibitory Concentration
AUTHORS: Amanda T Alker, Nicholas J Shikuma
[DESCRIPTION]
Protocol for determining the minimum inhibitory concentration of antibiotics for marine bacteria.
[STEPS]
SECTION: Day 1
1. Streak out marine microbes onto Marine Agar plates and incubate overnight at 25-28ºC.
SECTI... | ["[Day 1] Streak out marine microbes onto Marine Agar plates and incubate overnight at 25-28ºC.", "[Day 2] Inoculate a single colony into 5mL Marine Broth (2216) media in the late afternoon/ early evening. Incubate overnight at 25ºC, shaking at 200 rpm.", "[Day 3] Measure optical density (OD600) of overnight culture gr... |
63,431 | 20 Reasons You Need to Stop Stressing About Prima Slimming Pills UK | 1 | dx.doi.org/10.17504/protocols.io.q26g746bqgwz/v1 | https://www.protocols.io/view/20-reasons-you-need-to-stop-stressing-about-prima-b97fr9jn | buddymurphyz | TITLE: 20 Reasons You Need to Stop Stressing About Prima Slimming Pills UK
AUTHORS: buddymurphyz
[DESCRIPTION]
Prima Slimming Pills UK : Offers!
Prima Slimming Pills UK Obesity issues are growing rapidly in the world. If you will not take care of your health and will keep on eating unhealthy food regularly, then it ... | ["[20 Reasons You Need to Stop Stressing About Prima Slimming Pills UK]"] |
65,880 | Golden Revive Plus Reviews: [Scam Exposed 2022] Read Ingredients, Side Effects Price & Where To Buy? | 3 | dx.doi.org/10.17504/protocols.io.kxygxzx7kv8j/v1 | https://www.protocols.io/view/golden-revive-plus-reviews-scam-exposed-2022-read-ccjysupw | G | TITLE: Golden Revive Plus Reviews: [Scam Exposed 2022] Read Ingredients, Side Effects Price & Where To Buy?
AUTHORS: G
[DESCRIPTION]
Golden Reviews Plus Reviews
[STEPS] | [] |
86,815 | Deparaffinization for tissue and organoids | 4 | null | https://www.protocols.io/view/deparaffinization-for-tissue-and-organoids-cyz7xx9n | Gabriela Vallejo Flores, Annika Fendler | TITLE: Deparaffinization for tissue and organoids
AUTHORS: Gabriela Vallejo Flores, Annika Fendler
[DESCRIPTION]
This protocol is to withdraw the paraffin from formalin-fixed paraffin-embedded tissue and organoids and to recover the protein structure of your sample.
[BEFORE_START]
Prepare the steamer and the cook ... | ["[Antigen retrieval solution] Transfer the slide into the antigen retrieval solution in the steamer, turn on the cook heater and incubate 5 min after the valve is up, turn off the cook heater and wait till the valve get down again.", "[Antigen retrieval solution] Transfer the slides into destillated water, now the sli... |
78,074 | Preparation of Encoding Probes SOP005.v1.5 (PCR, In-vitro Transcription, Reverse Transcription and USER ENZYME Digest) | 4 | dx.doi.org/10.17504/protocols.io.kqdg36zxqg25/v3 | https://www.protocols.io/view/preparation-of-encoding-probes-sop005-v1-5-pcr-in-cqg2vtye | Rory Kruithoff, Douglas Shepherd | TITLE: Preparation of Encoding Probes SOP005.v1.5 (PCR, In-vitro Transcription, Reverse Transcription and USER ENZYME Digest)
AUTHORS: Rory Kruithoff, Douglas Shepherd
[DESCRIPTION]
Document Summary:This document, Preparation of Encoding Probes (SOP005), describes the proc... | ["[Part 1 - PCR Amplification - Step 1: Prepare the PCR reaction] In a 1.7 mL Eppendorf tube, mix the following:\n- 40 µL ;\n- 2 µL ;\n- 2 µL ; \n- 1 µL ; \n- 355 µL ; \n- 400 µL .", "[Part 1 - PCR Amplification - Step 1: Prepare the PCR reaction] Aliquot 25 µL into 32 PCR tubes.", "[Part 1 - PCR Amplification - ... |
null | null | null | dx.doi.org/10.17504/protocols.io.hjpb4mn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This is a variation of the CagA translocation assay performed in our lab.</p>
<p>This protocol has been used in the publication DOI: <a href="https://doi.org/10.1111/cmi.12166" target="_blank">10.1111/cmi.12166</a> </p>
<p> </p>
[STEPS]
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97,156 | 10x Protocols: Chromium Single Cell/Nuclei Gene Expression Flex Multiplex -- University of Minnesota TMCs (CG000527 Rev E) | 1 | dx.doi.org/10.17504/protocols.io.bp2l6x81klqe/v2 | https://www.protocols.io/view/10x-protocols-chromium-single-cell-nuclei-gene-exp-da5c2g2w | IOx Genomics, Laura Niedernhofer, David A Bernlohr | TITLE: 10x Protocols: Chromium Single Cell/Nuclei Gene Expression Flex Multiplex -- University of Minnesota TMCs (CG000527 Rev E)
AUTHORS: IOx Genomics, Laura Niedernhofer, David A Bernlohr
[DESCRIPTION]
10x Genomics Chromium Single Cell Expression flex protocol for library construction.
Note: These protocols may no... | ["[Preparation] Complete single cell or nuclei isolation and 10x fixation prior to starting this protocol", "[Library Preparation]", "[FASTQ Generation] BCL data from Illumina sequencer is demultiplexed and converted into FASTQ format using bcl2fastq version 2.20.0"] |
53,852 | Batch extraction of morphological and color metrics from invertebrate samples. | 1 | dx.doi.org/10.17504/protocols.io.byt4pwqw | https://www.protocols.io/view/batch-extraction-of-morphological-and-color-metric-byt4pwqw | Michael D Weiser, Katie E. Marshall, Cameron D. Siler, Michael Kaspari | TITLE: Batch extraction of morphological and color metrics from invertebrate samples.
AUTHORS: Michael D Weiser, Katie E. Marshall, Cameron D. Siler, Michael Kaspari
[DESCRIPTION]
This protocol is the complete methods used to extract abundance, morphology and color data from samples of invertebrates. We developed th... | ["[Camera Setup] We use a Canon EOS 5Ds (Model DS526521) camera fitted with a Canon EF 35mm f/2 IS USM Lens (Model 9523B002). To avoid having to recharge the battery we use a fixed power supply (Glorich Model #WP-AC08030V). The camera is mounted on a Diagnostic Instruments Heavy Duty Boom stand.", "[Camera Setup] At... |
91,576 | hsqc_metab.nan | 5 | dx.doi.org/10.17504/protocols.io.5jyl8pd2dg2w/v2 | https://www.protocols.io/view/hsqc-metab-nan-c5nyy5fw | NAN KB, John Glushka, Mario Uchimiya, Saraa Al Jawad, Christopher Esselman, Leandro I Ponce, Laura Morris, Arthur Edison | TITLE: hsqc_metab.nan
AUTHORS: NAN KB, John Glushka, Mario Uchimiya, Saraa Al Jawad, Christopher Esselman, Leandro I Ponce, Laura Morris, Arthur Edison
[DESCRIPTION]
This is a protocol for running the Bruker pulse program "hsqcetgpsisp2".
[BEFORE_START]
This protocol assumes:
Your sample is loaded, locked, tuned for ... | ["[Create a new dataset]", "[Create a new dataset] A new window opens. On the right top bar, select\nSource = /opt/NAN_METAB/par\n \nIn the list, select the one you want to use:\n\nFor serum and plasma samples:\nHSQC_br600_serum.par: Parameter set using an acquisition mode \"traditional planes\"\nHSQC_NUS_br600_serum.p... |
null | null | null | dx.doi.org/10.17504/protocols.io.nxsdfne | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Counting cells with a hemocytometer is an easy way to determine relatively accurate numbers of viable cells. After determining cell counts, cells can be passaged, frozen away, or used for an experiment at a particular density. </p>
[GUIDELINES]
<p>Keep cells sterile by wea... | [] |
88,807 | UPitt TriState SenNet TMC Cryopreserved Tissue Grinding | 1 | dx.doi.org/10.17504/protocols.io.q26g7px41gwz/v1 | https://www.protocols.io/view/upitt-tristate-sennet-tmc-cryopreserved-tissue-gri-c2yfyftn | Marta Bueno | TITLE: UPitt TriState SenNet TMC Cryopreserved Tissue Grinding
AUTHORS: Marta Bueno
[DESCRIPTION]
This document outlines the tissue pulverization protocol of lung and heart specimens at the TriState SenNet TMC Biospecimen Core at the University of Pittsburgh, as part of the Cellular Senescence Network Program (SenNet)... | ["[Tissue pulverization] Pour liquid nitrogen into a mortar and pestle until frozen.", "[Tissue pulverization] Remove tissue from tube and place into liquid nitrogen with a clean cold spatula (precool in liquid\nnitrogen).", "[Tissue pulverization] Grind up the sample with liquid nitrogen using the mortar and pestle.",... |
71,463 | Co-existing OSA reduce Nuss surgery efficacy | 3 | dx.doi.org/10.17504/protocols.io.n2bvj86rbgk5/v1 | https://www.protocols.io/view/co-existing-osa-reduce-nuss-surgery-efficacy-ch2ft8bn | Mei-Chen Yang | TITLE: Co-existing OSA reduce Nuss surgery efficacy
AUTHORS: Mei-Chen Yang
[DESCRIPTION]
Nuss surgery is effective for pectus excavatum (PE), with a recurrence rate of 1.2–27%. Re-do surgery is effective, but still has a 6% failure rate. Patients with obstructive sleep apnea (OSA) experience repetitive PE-associated s... | [] |
70,953 | Modified one-step growth (mOSG) assay | 4 | dx.doi.org/10.17504/protocols.io.4r3l2op9pv1y/v2 | https://www.protocols.io/view/modified-one-step-growth-mosg-assay-chiht4b6 | Eva JP. Lievens | TITLE: Modified one-step growth (mOSG) assay
AUTHORS: Eva JP. Lievens
[DESCRIPTION]
This protocol describes a modified one-step growth assay, as presented in the manuscript "Life history diversity and signals of trade-offs in a large group of chloroviruses" (Lievens et al., bioRxiv). It is designed to quantify the ads... | ["[Preparation (can be done the day beforehand)] Prepare the 1:1000 dilution plates.", "[Preparation (can be done the day beforehand)] Prepare the 1:10000 dilution plates.", "[Preparation (can be done the day beforehand)] If following the alternative 1:1000 dilution option (see step 9.1):\nPrepare the 1:10 intermediate... |
18,459 | Protocols for activity changes in Neuron-Astrocyte Networks in Culture Under the Effect of Norepinephrine | null | dx.doi.org/10.17504/protocols.io.v93e98n | null | Yasmin Bar El, Sivan Kanner | TITLE: Protocols for activity changes in Neuron-Astrocyte Networks in Culture Under the Effect of Norepinephrine
AUTHORS: Yasmin Bar El, Sivan Kanner
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Protocols for Primary cortical neuronal-astrocyte cell culture, Isolated astrocyte cell culture,... | [] |
93,561 | External Quality Control for inter-Batch comparison (English) | 1 | dx.doi.org/10.17504/protocols.io.dm6gp36ydvzp/v1 | https://www.protocols.io/view/external-quality-control-for-inter-batch-compariso-c7kzzkx6 | Ricardo M. Borges | TITLE: External Quality Control for inter-Batch comparison (English)
AUTHORS: Ricardo M. Borges
[DESCRIPTION]
External Quality Control (QCExt): The sample containing the strain code CCMR0280, cultivated in parallel with all batches, will serve as a reference for comparative studies between the strains of the CCMR (Cul... | ["[Material] 2 mL microtubes with screw cap\n50 mL Falcon type centrifuge tube\nAnalytical balance (AUW220, Shimadzu)", "[Material in Stock] Initially, a starting batch composed of 25 replicas of the cultivation of the strain code CCMR0280 was (i) cultivated, (ii) collected and combined, (iii) subjected to lyophilizat... |
null | null | null | dx.doi.org/10.17504/protocols.io.pnddma6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Rich medium comonly used for Escherichia coli growth and maintenance.</p>
[STEPS]
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96,434 | Exp_01 Taza | 0 | dx.doi.org/10.17504/protocols.io.6qpvr31povmk/v1 | https://www.protocols.io/view/exp-01-taza-daes2bee | Mayleth Medina Cárdenas, Estefanía Sauceda Camacho, Sofía Morga Benítez | TITLE: Exp_01 Taza
AUTHORS: Mayleth Medina Cárdenas, Estefanía Sauceda Camacho, Sofía Morga Benítez
[DESCRIPTION]
Este experimento consiste en la medición de la temperatura de 250 mL de agua contenida en una taza, desde que el agua se encuentra a una temperatura de 84ºC, hasta llegar a una temperatura ambiente de 22ºC... | ["[Circuito Arduino y software] Armar el siguiente circuito:", "[Circuito Arduino y software] Conectar el cable USB 2.0 a la placa de Arduino y a la laptop.", "[Experimentación] Hervir agua y con esta vaciar por completo una tasa de 250 mL", "[Resultados de mediciones] Las mediciones registradas en el archivo .txt obte... |
81,814 | TS Procure 812 - primary fixation Karnovsky's - transwells (TM - 013) | 4 | dx.doi.org/10.17504/protocols.io.e6nvwjwpwlmk/v1 | https://www.protocols.io/view/ts-procure-812-primary-fixation-karnovsky-39-s-tra-ct5wwq7e | sandra.crameri | TITLE: TS Procure 812 - primary fixation Karnovsky's - transwells (TM - 013)
AUTHORS: sandra.crameri
[DESCRIPTION]
The method is used to Karnovsky's EM fixed transwells to Procure 812 resin blocks. The presence of 4% paraformaldehyde is only used to satisfy microsecurity requirements.
[GUIDELINES]
Sample is not o... | ["[HEADER] SAN:\n\n\n\n\nSPEC No:\n\n\n\n\nOPERATOR & STEPS:\n\n\n\n\nOPERATOR & STEPS:", "[Conventional] Karnovsky's fixative: 2.5 % volume and 4 % volume in 0.1 Molarity (M) Sorenson's Phosphate buffer (pH 7.2, 300mosmol/kg) for at least 40 min or overnight", "[Conventional] 0.1 Molarity (M) buffer 15 min", "[Co... |
99,994 | HEPES-Sucrose Cutting Solution | 1 | dx.doi.org/10.17504/protocols.io.5jyl8peq8g2w/v2 | https://www.protocols.io/view/hepes-sucrose-cutting-solution-ddv2268e | Allen Institute | TITLE: HEPES-Sucrose Cutting Solution
AUTHORS: Allen Institute
[DESCRIPTION]
This protocol is used for preparing HEPES-Sucrose Cutting Solution, used for animal perfusion following anesthesia.
Note: Research reported in this publication was supported by the National Institute Of Mental Health of the National Institut... | [] |
92,922 | Terrific Broth Medium | 1 | dx.doi.org/10.17504/protocols.io.x54v9pb24g3e/v1 | https://www.protocols.io/view/terrific-broth-medium-c6y2zfye | is Sparrow, Steven J Burgess | TITLE: Terrific Broth Medium
AUTHORS: is Sparrow, Steven J Burgess
[DESCRIPTION]
Tartoff, K.D. and Hobbs, C.A. (1987) Improved Media for Growing Plasmid and Cosmid Clones. Bethesda Research Laboratories Focus, 9, 12.
[GUIDELINES]
Prepare the stock solutions and autoclave separately before combining when cooled to cre... | ["[Prepare stock solutions] Combine the following components for 1L TB buffer\n24 g \n20 g \n4 mL Glycerol\nMake up volume to 900 mL with dH2O\n\nAutoclave 121 °C 30 min", "[Prepare medium] Allow solutions to cool to 60 °C then add\n100 mL of 10x TB salts to 900 mL TB buffer.", "[Prepare medium] Store at Room tempe... |
null | null | null | dx.doi.org/10.17504/protocols.io.dqh5t5 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
For use in "Isolation of cyanophages by plaque assyays"
[BEFORE_START]
Prepare 100 mL portions of 0.4 to 0.5% (w/v) of purified agar, agarose or low-melting point (LMP) agarose (i.e., Invitrogen #15517-022) in your media of choice. Although LMP agarose can be quite expensive, i... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.fyrbpv6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div class="page" title="Page 1">
<div class="layoutArea">
<div class="column">
<p>The SensiFAST™ HRM Kit has been developed for fast, highly reproducible High Resolution Melt (HRM) analysis and has been validated on commonly used real-time instruments. A combination of the late... | [] |
91,524 | Isolation of natural killer (NK) cells from human blood products | 1 | dx.doi.org/10.17504/protocols.io.81wgbp94yvpk/v3 | https://www.protocols.io/view/isolation-of-natural-killer-nk-cells-from-human-bl-c5mcy42w | Philippa R Kennedy | TITLE: Isolation of natural killer (NK) cells from human blood products
AUTHORS: Philippa R Kennedy
[DESCRIPTION]
Standard isolation procedure for peripheral blood mononuclear cells (PBMC) from human blood leukopheresis products.
[GUIDELINES]
One trimacone will generally provide 500 million - 2 billion PBMCs.
NK c... | ["[Overview] Healthy donor blood products (Leukopaks) were obtained from Memorial Blood Bank (Minneapolis, MN). All samples were de-identified and their use was approved by the University of Minnesota and NMDP institutional review board in accordance with the Declaration of Helsinki.", "[Overview] Peripheral blood mono... |
51,739 | Digital Scanning Recommended Practice | 1 | dx.doi.org/10.17504/protocols.io.bwr3pd8n | https://www.protocols.io/view/digital-scanning-recommended-practice-bwr3pd8n | Patrick Walston, Madalyn Massey | TITLE: Digital Scanning Recommended Practice
AUTHORS: Patrick Walston, Madalyn Massey
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">A protocol regarding digitization of documents stored in paper format. Topics covered: minimum standards, best practices, digital scanning hardware, software, file st... | ["[Introduction]\nWhat is it?Digitization is the process of turning physical information into digital data. The USGS and National Geological and Geophysical Data Preservation Program (NGGDPP), aim to preserve and curate historical geological information using Digitization. By following standard processes, scientists ca... |
34,196 | Protein expression in Bacillus subtilis | 1 | dx.doi.org/10.17504/protocols.io.bdmui46w | https://www.protocols.io/view/protein-expression-in-bacillus-subtilis-bdmui46w | Kristoffer Bach Falkenberg, Cristina Hernandez Rollan, Maja Rennig, Andreas Birk Bertelsen, Morten Norholm | TITLE: Protein expression in Bacillus subtilis
AUTHORS: Kristoffer Bach Falkenberg, Cristina Hernandez Rollan, Maja Rennig, Andreas Birk Bertelsen, Morten Norholm
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-style:italic;">B. subtilis </span><span>is a gram-positive bacteria u... | ["[Cal18-2 media preparations]\nPrepare a stock solution of 2.0g/L Na2MoO4. Sterilize by filtration", "[Cal18-2 media preparations]\nAdd a magnetic stirrer to the blue cap bottle and place the bottle on a stirring plate. Turn on the stirring, and make sure it's mixing well.", "[Cal18-2 media preparations]\nAdd the foll... |
67,518 | A versatile nuclei extraction protocol for single nucleus sequencing in non model species – optimization in various Atlantic salmon tissues. | 4 | null | https://www.protocols.io/view/a-versatile-nuclei-extraction-protocol-for-single-cd66s9he | Rose Ruiz Daniels, Richard S Taylor, Ross Dobie, Sarah Salisbury, Emily Clark, Dan Macqueen, Diego Robledo | TITLE: A versatile nuclei extraction protocol for single nucleus sequencing in non model species – optimization in various Atlantic salmon tissues.
AUTHORS: Rose Ruiz Daniels, Richard S Taylor, Ross Dobie, Sarah Salisbury, Emily Clark, Dan Macqueen, Diego Robledo
[DESCRIPTION]
Single cell RNA sequencing has rapidly be... | ["[Nucleus isolation workflow for ST-based buffers] on ice, place a piece of frozen tissue into one well of a 6-well tissue culture plate with 1 mL TST.", "[Nucleus isolation workflow for ST-based buffers] on ice, mince tissue initially using Tungsten Carbide scissors for 30 s and then with Noyes Spring Scissors for ... |
28,111 | Co-Incubation protocol for transforming heterotrophic dinoflagellates (e.g. Oxyrrhis marina) | null | dx.doi.org/10.17504/protocols.io.7pphmmn | null | Lu Wang, Brittany Sprecher, Huan Zhang, and Senjie Lin | TITLE: Co-Incubation protocol for transforming heterotrophic dinoflagellates (e.g. Oxyrrhis marina)
AUTHORS: Lu Wang, Brittany Sprecher, Huan Zhang, and Senjie Lin
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. [Prepare vector and transform into Escherichia coli]
Prepare a plasmid carrying proper promo... | ["[Prepare vector and transform into Escherichia coli]\nPrepare a plasmid carrying proper promoter, selection marker, and reporter gene. Transform this plasmid into E. coli cells using standard heat shock protocol.", "[Grow transformed E. coli]\nGrow E. coli cells at a volume equal to 1/10 the desired volume of dinofla... |
18,638 | GYROS | null | dx.doi.org/10.17504/protocols.io.wfnfbme | null | Anish Chhetri | TITLE: GYROS
AUTHORS: Anish Chhetri
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">I would absolutley go for StrainControl Laboratory Manager. I find this software extremely good and easy to use. Lets you manage strains, plasmids, oligos, antibodies and inventories.</div></div>
[STEPS]
?. [1]
Prim... | ["[1]\nPrime the instrument 200%", "[1]\nDownload the sequence file", "[1]\nMRD of samples 1:2", "[1]\nCapture Prep\n10 Mass/Volume Percent", "[1]\nDetector Prep", "[1]\nOpen the Gyros Software"] |
null | null | null | dx.doi.org/10.17504/protocols.io.m9vc966 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><strong>Background</strong></p>
<p>The use of mobile technology such as phone applications (apps) has been proposed as an efficient means of providing health and clinical information in a variety of healthcare settings. We developed the Health-e Babies app as an Android smart... | [] |
44,047 | BSCI:414--Lab 9: Cloning the SARS-CoV-2 Spike Protein into a E. coli Protein Expression Vector | 1 | null | https://www.protocols.io/view/bsci-414-lab-9-cloning-the-sars-cov-2-spike-protei-bn9pmh5n | Harley King | TITLE: BSCI:414--Lab 9: Cloning the SARS-CoV-2 Spike Protein into a E. coli Protein Expression Vector
AUTHORS: Harley King
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The SARS-CoV-2 spike protein does not express solubly in E. coli cells. This may be due to E. coli's inability to glycosylate... | ["[Explore the Spike Protein]\nExplore the structure of the SARS-CoV-2 spike protein using Cov3D.", "[Explore the Spike Protein]\nRead abstract of Zuo et al. concerning previous attempts at expressing SARS-CoV spike protein fused with SUMO tag.", "[Clone spike -sumo into pET28.]\nUsing a Gibson cloning strategy in Benc... |
35,043 | Generating cloned sheep embryos by zona-free somatic cell transfer | 1 | dx.doi.org/10.17504/protocols.io.begbjbsn | https://www.protocols.io/view/generating-cloned-sheep-embryos-by-zona-free-somat-begbjbsn | Zachariah Mclean, Sarah Appleby, Lisanne Fermin, Bjorn Oback | TITLE: Generating cloned sheep embryos by zona-free somatic cell transfer
AUTHORS: Zachariah Mclean, Sarah Appleby, Lisanne Fermin, Bjorn Oback
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol summarises zona-free sheep cloning by somatic cell transfer (SCT), adapted from a simila... | ["[Induce donor cell quiescence by serum starvation]\nInduce donor cells into quiescence (or G0) by serum starvation", "[In vitro maturation of oocytes]\nRetrieve oocytes from slaughterhouse ovaries\nSheep (ovine) is a seasonally reproductive species and SCT experiments are best carried out during the extended breeding... |
95,131 | BAF_Protocol_005 Database Search Proteome Discoverer into Scaffold | 1 | dx.doi.org/10.17504/protocols.io.q26g7p28kgwz/v1 | https://www.protocols.io/view/baf-protocol-005-database-search-proteome-discover-c853zy8n | nesf | TITLE: BAF_Protocol_005 Database Search Proteome Discoverer into Scaffold
AUTHORS: nesf
[DESCRIPTION]
This protocol lays out the basic steps for taking a Thermo RAW file and doing a standard database search in Proteome Discoverer 2.5+ and putting the search results into Scaffold 5.3+ for display. Included is also the ... | ["[Proteome Discoverer 2.5 Database Searching] Thermo RAW files are set up to search in PD 2.5 software (Proteome Discoverer) to produce an output MSF file. The RAW files for an individual project are placed in a folder and a sub folder is created with the MSF files produced by PD 2.5 inside. The MSF files will be load... |
null | null | null | dx.doi.org/10.17504/protocols.io.ucwesxe | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol is used to dissociate adult (8-10 wk) mouse ear "on ice" (in order to reduce gene expression artifacts). The cell yield is 9000 cells/mg (213000 cells total from 23 mg tissue), with 98% viable. The protocol involves a 2-layered dissociation, incubating on ice with ... | ["[Isolating tissue] Dissect out ear tissue and place in ice-cold hypothermosol on ice.", "[Isolating tissue] {\"blocks\":[{\"key\":\"jm3a\",\"text\":\"Using forceps, transfer ear tissue to petri dish on ice. Mince ear tissue thoroughly on ice for 3-4 min on ice into 1-mm3 pieces using razor blade while manipulating ti... |
31,737 | Methods and protocols from Chaiyarat et al. (2019) for systematic reintroduction of bateng (Bos javanicus) | null | dx.doi.org/10.17504/protocols.io.ba8zihx6 | null | Rattanawat Chaiyarat, Namphung Youngpoy, Praeploy Kongsurakan, Seree Nakbun | TITLE: Methods and protocols from Chaiyarat et al. (2019) for systematic reintroduction of bateng (Bos javanicus)
AUTHORS: Rattanawat Chaiyarat, Namphung Youngpoy, Praeploy Kongsurakan, Seree Nakbun
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Banteng (</span><span style = "font-style:itali... | [] |
56,827 | Miraprep: Fast Plasmid Prep | 1 | dx.doi.org/10.17504/protocols.io.b3q3qmyn | https://www.protocols.io/view/miraprep-fast-plasmid-prep-b3q3qmyn | Zaki Molvi | TITLE: Miraprep: Fast Plasmid Prep
AUTHORS: Zaki Molvi
[DESCRIPTION]
An adaptation of the original miraprep protocol published by Pronobis et al. PLoS One (2016).
[STEPS]
SECTION: Introduction
1. My adaptation of the miraprep method originally published by Pronobis et al. The miraprep method is highly preferred sinc... | ["[Introduction] My adaptation of the miraprep method originally published by Pronobis et al. The miraprep method is highly preferred since plasmid prep kits larger than minipreps take too long and require scarier, louder centrifuges.", "[Protocol] Inoculate an overnight culture in 2xYT and appropriate antibiotic1\nThe... |
104,401 | Transfections for gene delivery and genome editing in S. rosetta (VERSION 4) | 1 | dx.doi.org/10.17504/protocols.io.j8nlk86o5l5r/v1 | https://www.protocols.io/view/transfections-for-gene-delivery-and-genome-editing-dh7r39m6 | David Booth | TITLE: Transfections for gene delivery and genome editing in S. rosetta (VERSION 4)
AUTHORS: David Booth
[DESCRIPTION]
This protocol details the preparation and execution of CRISPR/Cas9 genome editing in S. rosetta. The protocol builds on a method to transfect macromolecules into S. rosetta for delivering a purified ... | ["[Culture Cells] Seed a large culture of S. rosetta.", "[Culture Cells] Two days prior to transfection, inoculate 80 mL of media (15% Red Algae + 2% Peptone-Yeast-Glycerol) with a culture of S. rosetta feeding on E. pacifica (ATCC PRA-390) to a final concentration of S. rosetta of 1.5*10^4 cells/ml. Also add 400 µLo... |
95,586 | Protocol for "ventriculography-assisted stereotaxic surgery in non-human primates | 0 | dx.doi.org/10.17504/protocols.io.e6nvwd3w7lmk/v1 | https://www.protocols.io/view/protocol-for-34-ventriculography-assisted-stereota-c9kaz4se | jlanciego | TITLE: Protocol for "ventriculography-assisted stereotaxic surgery in non-human primates
AUTHORS: jlanciego
[DESCRIPTION]
An stept-by-step procedure describing ventriculography-assisted stereotaxic surgery in non-human primates is provided here, including (i) animal pre-surgical preparation, (ii) stereotaxic surge... | ["[Animal preparation] Pre-surgical anesthesia: to be induced with ketamine (5 mg/Kg) and midazolam (0.5 mg/Kg), administered intramuscularly.", "[Animal preparation] Surgical shaving: comprising left and right superior and inferior limbs and thorax for the placement of adhesive EKG electrodes.", "[Animal preparation] ... |
52,287 | cDNA Synthesis Using SuperScript III First-Strand Synthesis System for RT-PCR | 4 | dx.doi.org/10.17504/protocols.io.bxa7pihn | https://www.protocols.io/view/cdna-synthesis-using-superscript-iii-first-strand-bxa7pihn | Lynn Doran | TITLE: cDNA Synthesis Using SuperScript III First-Strand Synthesis System for RT-PCR
AUTHORS: Lynn Doran
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The SuperScript® III First-Strand Synthesis System for RT-PCR is used to synthesize first-strand cDNA from purified total RNA. RNA targets from 1... | ["Allow reagents to thaw completely, mix, and briefly minicentrifuge 10 mM dNTP mix and 50 ng/ul random hexamers before use. Store on ice when not in use.", "Label two PCR tubes per sample, RT and NRT.\nBest practice for qPCR is to prepare a no reverse transcriptase (NRT) reaction for each of your samples to ensure tha... |
null | null | null | dx.doi.org/10.17504/protocols.io.c2dya5 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol is designed to purify single- or double-stranded DNA fragments from PCR and other enzymatic reactions (see page 8). For cleanup of other enzymatic reactions, follow the protocol as described for PCR samples or use the MinElute Reaction Cleanup Kit. Fragments rangin... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.mayc2fw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><strong>A protocol for isolation of RNA from blood and RT-PCR for detection of live Brucella organisms in cattle</strong></p>
[STEPS] | [] |
70,086 | LRRK2 Staining in mouse brain sections | 4 | dx.doi.org/10.17504/protocols.io.e6nvwj64dlmk/v1 | https://www.protocols.io/view/lrrk2-staining-in-mouse-brain-sections-cgpetvje | Chuyu Chen | TITLE: LRRK2 Staining in mouse brain sections
AUTHORS: Chuyu Chen
[DESCRIPTION]
LRRK2 is a widely expressed, multifunctional protein.LRRK2 mutations are the major cause to inherited and sporadic PD. Staining of LRRK2 in mouse brain can be challenging. This protocol provides an optimised way to achieve LRRK2 staining ... | ["Prepare brain cryosections in 20μm thickness", "Blocking with 5% serum (preferably same serum as host of secondary antibody) 30 min RT", "Wash with PBS 5 min 2x", "Permeabilize with 0.5% Triton 15 min RT", "Wash with PBS 5 min 2x", "VECTOR® antigen unmasking solution 48ul/5ml water (in small glass sample vial). Micr... |
15,196 | K and K+Si medium | null | dx.doi.org/10.17504/protocols.io.s34egqw | null | Roscoff Culture Collection | TITLE: K and K+Si medium
AUTHORS: Roscoff Culture Collection
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Medium to grow most phytoplankton species in small eukaryotes (Mamiellophyceae, Pelagophyceae etc...).</div><div class = "text-block">When using for diatoms and coccolithophorids add silica (... | ["Filter 1L of old seawater of at least two months on prefilter and filter 0,2 microns", "Heat seawater during 20min at 100°C", "Under hood, to seawater, add these nutriments that have been autoclaved (excepted vitamin) : ABC1Quantity\nCompound\nStock Solution\n21.0 mL\nSodium Nitrate (NaNO3)\n75.0 g/L of H2O\n31.0 mL... |
null | null | null | dx.doi.org/10.17504/protocols.io.n43dgyn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>A real-time PCR targeting the DNA-dependent RNA polymerase of Orthopoxviruses.</p>
<p>This protocol was designed and developed at this laboratory.</p>
[GUIDELINES]
<ul>
<li>If using a different brand or model of real-time thermocycler, check the concentration of ROX is adequ... | [] |
88,426 | JMN-MSMP Muscle Bulk RNAseq | 1 | dx.doi.org/10.17504/protocols.io.rm7vzxjz4gx1/v2 | https://www.protocols.io/view/jmn-msmp-muscle-bulk-rnaseq-c2kiycue | ccherry | TITLE: JMN-MSMP Muscle Bulk RNAseq
AUTHORS: ccherry
[DESCRIPTION]
RNA sequencing of muscle
[STEPS]
SECTION: Bulk RNA sequencing
1. cDNA synthesis and library preparation were performed using the TruSeq RNA Library Prep Kit V2 following the manufacturer's protocol.
SECTION: Bulk RNA sequencing
2. The Agilent BioAnaly... | ["[Bulk RNA sequencing] cDNA synthesis and library preparation were performed using the TruSeq RNA Library Prep Kit V2 following the manufacturer's protocol.", "[Bulk RNA sequencing] The Agilent BioAnalyzer system was used to perform quality control on samples during the library prep process as suggested in the manufac... |
48,205 | IHC AD neuropathology protocol | 4 | dx.doi.org/10.17504/protocols.io.btbmnik6 | https://www.protocols.io/view/ihc-ad-neuropathology-protocol-btbmnik6 | Christiana Bjorkli | TITLE: IHC AD neuropathology protocol
AUTHORS: Christiana Bjorkli
[DESCRIPTION]
Immunohistochemical processing was conducted on tissue from chronically implanted animals, as well as non-implanted transgenic mice for characterization of AD neuropathology.
[STEPS]
SECTION: Day 1 fluorescent IHC
1. Heat-induced antigen... | ["[Day 1 fluorescent IHC] Heat-induced antigen retrieval on all tissue at 60 °C for 2 hours in phosphate buffer (PB).", "[Day 1 fluorescent IHC] Wash sections 3 x 10min in PB containing 0.2 % Triton X-100 (PBT+).", "[Day 1 fluorescent IHC] Block sections using 5 % normal goat serum in PBT+ for 1 hour.", "[Day 1 fluor... |
54,354 | Revival of S. elongatus from plates | 4 | dx.doi.org/10.17504/protocols.io.bzbsp2ne | https://www.protocols.io/view/revival-of-s-elongatus-from-plates-bzbsp2ne | Akashdutta | TITLE: Revival of S. elongatus from plates
AUTHORS: Akashdutta
[DESCRIPTION]
On receiving wild type or tranformed S. elongatus plates, one needs to revive them for further studies. Revival of S. elongatus involves making its liquid culture in BG-11 medium. The following protocol describes the liquid culture preparat... | ["Take a 50 mL autoclaved flask.", "Take a 10 mL aliquot of BG-11 solution in a falcon tube and transfer it into the flask. Keep the flask aside", "Dip the pipette tip in the aliquot of the BG-11 medium and gently mix.", "Take the cyanobacteria plate and gently scrape it with the tip of a 1 mL loaded micropipette.", ... |
57,027 | Acetylation of lysines on affinity-purification matrices to reduce co-digestion of bead-bound ligands | 4 | dx.doi.org/10.17504/protocols.io.kxygxzexkv8j/v2 | https://www.protocols.io/view/acetylation-of-lysines-on-affinity-purification-ma-b3xbqpin | David M. Hollenstein, Margarita Maurer-Granofszky, Dorothea Anrather, Thomas Gossenreiter, Natascha Hartl, Markus Hartl | TITLE: Acetylation of lysines on affinity-purification matrices to reduce co-digestion of bead-bound ligands
AUTHORS: David M. Hollenstein, Margarita Maurer-Granofszky, Dorothea Anrather, Thomas Gossenreiter, Natascha Hartl, Markus Hartl
[DESCRIPTION]
In mass-spectrometry-based interaction proteomics on-bead digestion... | ["[Acetylation protocol] Wash beads 3x with 100µl Reaction buffer, using the magnetic rack. \nRemove supernatant after the final wash.", "[Acetylation protocol] Add 19 µl Reaction buffer and 1 µl Sulfo-NHS-Acetate (100 mM) to obtain a final concentration of 5 mM Sulfo-NHS-Acetate. \nIncubate 1h at room temperature with... |
52,480 | Microfluidics Lithography 1 Mold Fabrication: Spin Coating of Photoresist (version s2) | 1 | dx.doi.org/10.17504/protocols.io.bxg8pjzw | https://www.protocols.io/view/microfluidics-lithography-1-mold-fabrication-spin-bxg8pjzw | C. Yunus Sahan, Serhat S | TITLE: Microfluidics Lithography 1 Mold Fabrication: Spin Coating of Photoresist (version s2)
AUTHORS: C. Yunus Sahan, Serhat S
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:center"></div></div><div style = "text-align :; float : ;"><img style = "" src =... | ["[SpinCoater Instrument Adjustment]\nDispense 1ml of photoresist (SU8) resin for each inch (25mm) of Si wafer substrate diameter.Spin at 500 rpm for 10 seconds with an acceleration of 100 rpm/second.Spin at \"N\" rpm for 30 seconds with an acceleration of 300 rpm/second.Expected results of photoresist thickness: 40u... |
null | null | null | dx.doi.org/10.17504/protocols.io.khxct7n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Adapted from Core LJ, Waterfall JJ, Lis JT. Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science. 2008;322(5909):1845-8. PubMed PMID: 19056941.</p>
<p>This method can be used to detect nascent transcripts. The conditions given... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.cpkvkv | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?. | [] |
107,703 | Tissue preparation and tissue imaging for MERFISH | 0 | dx.doi.org/10.17504/protocols.io.14egn6opyl5d/v1 | https://www.protocols.io/view/tissue-preparation-and-tissue-imaging-for-merfish-dmex43fn | Cameron Oram | TITLE: Tissue preparation and tissue imaging for MERFISH
AUTHORS: Cameron Oram
[DESCRIPTION]
MERSCOPE Sample preparation protocol and imaging protocol
[STEPS]
SECTION: Perfusion and sectioning of brain
1. C57Bl6 male mice were housed in groups until 2-3 months of age.
SECTION: Perfusion and sectioning of brain
2. 4% ... | ["[Perfusion and sectioning of brain] C57Bl6 male mice were housed in groups until 2-3 months of age.", "[Perfusion and sectioning of brain] 4% PFA solution was made from 32% PFA concentrate in 1x PBS.", "[Perfusion and sectioning of brain] Mice were perfused first with 25 mL of chilled 1x PBS (DNAse, RNAse free) follo... |
32,625 | Surgical Isolation of Stellate Ganglia and Electrophysiology | 1 | dx.doi.org/10.17504/protocols.io.bb4riqv6 | https://www.protocols.io/view/surgical-isolation-of-stellate-ganglia-and-electro-bb4riqv6 | Mark Doyle | TITLE: Surgical Isolation of Stellate Ganglia and Electrophysiology
AUTHORS: Mark Doyle
[DESCRIPTION]
Surgical Isolation of Stellate Ganglia and Electrophysiology
[STEPS]
1. The thorax of adult mice of either sex were removed under deep Isoforane anesthesia according to approved protocols by the Institutional Animal... | ["The thorax of adult mice of either sex were removed under deep Isoforane anesthesia according to approved protocols by the Institutional Animal Care and Use Committee at Oregon Health and Science University, and guidelines of the National Institutes of Health. The heart and SG were perfused with modified Ringers that... |
41,462 | R editing of HMMSEARCH output: heatmap with associated with gene tree and protein illustration | 5 | dx.doi.org/10.17504/protocols.io.bkqwkvxe | https://www.protocols.io/view/r-editing-of-hmmsearch-output-heatmap-with-associa-bkqwkvxe | Kanae Nishii | TITLE: R editing of HMMSEARCH output: heatmap with associated with gene tree and protein illustration
AUTHORS: Kanae Nishii
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">R codes used for phyml tree and profile HMM heatmap visualization, protein domain illustration</div></div>
[STEPS]
?. [R librar... | ["[R libraries]\n#libraries for tree drawinglibrary(ggtree)library(ape)library(phytools)#libraries for heatmaplibrary(reshape2)library(dplyr)library(ggplot2)library(aplot)", "[tree drawing]\n#rooting tree#midpoint rooted treetree2 #rooted by outgroup samplestree2 #check tree2ggtree(tree2)", "[tree drawing]\n#read Newic... |
91,658 | Visium Direct Mount Fresh Frozen -- University of Minnesota TMCs | 1 | dx.doi.org/10.17504/protocols.io.6qpvr3qdovmk/v1 | https://www.protocols.io/view/visium-direct-mount-fresh-frozen-university-of-min-c5riy54e | Laura J Niedernhofer, David A Bernlohr | TITLE: Visium Direct Mount Fresh Frozen -- University of Minnesota TMCs
AUTHORS: Laura J Niedernhofer, David A Bernlohr
[DESCRIPTION]
The Visium Spatial Gene Expression Solution measures the total mRNA in tissue sections and requires a Visium Spatial slide with intact tissue sections as input. This protocol outlines m... | ["[Tissue Optimization]", "[Fixation, H&E Staining & Imaging]", "[Library Preparation & Sequencing]", "[FASTQ Generation] BCL data from Illumina sequencer is demultiplexed and converted into FASTQ format using bcl2fastq version 2.20.0"] |
92,592 | Populating NCBI template for submissions using BioNumerics | 1 | dx.doi.org/10.17504/protocols.io.36wgq3ejylk5/v2 | https://www.protocols.io/view/populating-ncbi-template-for-submissions-using-bio-c6nqzddw | Ruth Timme, Maria Balkey, Julie Haendiges, Brian Sauders, Tina.Pfefer | TITLE: Populating NCBI template for submissions using BioNumerics
AUTHORS: Ruth Timme, Maria Balkey, Julie Haendiges, Brian Sauders, Tina.Pfefer
[DESCRIPTION]
PURPOSE: to define the standard operating procedure for collecting isolate metadata using BioNumerics for submission of food/environmental isolates to NCBI.
... | ["Metadata SampleSheet preparation \n\nBefore uploading your sequencing run or linking NCBI sequencing records at the BioNumerics platform make sure to fill out the metadata spreadsheet form. \n\nPlease download the template and guidelines included in the file \n\nCreate the fields NCBI_bioproject, Attribute_package... |
44,592 | Functional Analysis of Membrane Proteins Produced by Cell-Free Translation | 4 | dx.doi.org/10.17504/protocols.io.bpsqmndw | https://www.protocols.io/view/functional-analysis-of-membrane-proteins-produced-bpsqmndw | Srujan Kumar Dondapati, Doreen A. Wüstenhagen, Stefan Kubick | TITLE: Functional Analysis of Membrane Proteins Produced by Cell-Free Translation
AUTHORS: Srujan Kumar Dondapati, Doreen A. Wüstenhagen, Stefan Kubick
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Cell-free production is a valuable and alternative method for the synthesis of membrane protei... | ["[3.1 Preparation of Nanodiscs (NDs)]\nFirst prepare () containing , with and .\n[MSP protein solution]\n[Tris]\n[NaCl]\n[EDTA]", "[3.1 Preparation of Nanodiscs (NDs)]\nDissolve DMPC, DOTAP and DOPG lipids in cholate buffer at a concentration of (see Note 2).", "[3.1 Preparation of Nanodiscs (NDs)]\nSet up the rea... |
40,387 | Effective identification of RNA-binding proteins using RNA Immunoprecipitation | 4 | dx.doi.org/10.17504/protocols.io.bjpbkmin | https://www.protocols.io/view/effective-identification-of-rna-binding-proteins-u-bjpbkmin | Georgios I Laliotis, Philip N. Tsichlis | TITLE: Effective identification of RNA-binding proteins using RNA Immunoprecipitation
AUTHORS: Georgios I Laliotis, Philip N. Tsichlis
[STEPS]
?. [Chemicals Required]
For 100ml1.28M sucrose 43.21g
.justify:after {
content: "";
display:inline-block;
width: 100%;
... | ["[Chemicals Required]\nFor 100ml1.28M sucrose 43.21g\n\t\t\t\t\t\t\t .justify:after {\n\t\t\t\t\t\t\t content: \"\";\n\t\t\t\t\t\t\t display:inline-block;\n\t\t\t\t\t\t\t width: 100%;\n\t\t\t\t\t\t\t }\n\t\t\t\t\t\t\t1M Tris-HCL 7.5 4ml\n\t\t\t\t\t\t\t .justify:after {\n\t\t\t\t\t\t\t cont... |
50,707 | Intrahepatic implantation of tumor cells | 4 | dx.doi.org/10.17504/protocols.io.bvrtn56n | https://www.protocols.io/view/intrahepatic-implantation-of-tumor-cells-bvrtn56n | Shubhangi Agarwal, Robert Bok, donna.peehl , Renuka Sriram | TITLE: Intrahepatic implantation of tumor cells
AUTHORS: Shubhangi Agarwal, Robert Bok, donna.peehl , Renuka Sriram
[DESCRIPTION]
This protocol describes the steps required for successful implantation of small cell neuroendocrine prostate cancer patient-derived xenograft (PDX) cells in the liver. Liver is one of... | ["[Preparation before surgery] Preparation of surgical instruments and supplies: All of the instruments and supplies should be sterilized.", "Preparation of the PDX cells for implantation", "[Preparation of cells for implantation from frozen biobank] Retrieve cryovials containing cells from liquid nitrogen storage. Tha... |
45,459 | m9_media | 4 | null | https://www.protocols.io/view/m9-media-bqmtmu6n | Elizabeth Fozo | TITLE: m9_media
AUTHORS: Elizabeth Fozo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">M9 media protocols</div></div>
[STEPS]
?. [M9 minimal media: low osmolarity media for E. coli, resulting in slower growth rate]
Mix the ingredients (forms white precipitate but is dissolved after steering), filt... | ["[M9 minimal media: low osmolarity media for E. coli, resulting in slower growth rate]\nMix the ingredients (forms white precipitate but is dissolved after steering), filter sterilize, and store at room temperature.M9 Salts1X5X200100Magnesium sulfate2mM1M21Calcium chloride0.1mM1M0.10.05Vitamin B11ug/mL10mg.mL0.10.05Ca... |
76,661 | Illumina Amplicon Sequencing using two step PCR | 1 | null | https://www.protocols.io/view/illumina-amplicon-sequencing-using-two-step-pcr-cn4vvgw6 | Lindsay Kate Newbold, Joetay, Jonathan Warren, Daniel S Read, kerry.walsh, Amy Thorpe | TITLE: Illumina Amplicon Sequencing using two step PCR
AUTHORS: Lindsay Kate Newbold, Joetay, Jonathan Warren, Daniel S Read, kerry.walsh, Amy Thorpe
[DESCRIPTION]
This document is designed to provide the researcher with all of the information required to undertake two step amplicon sequencing using the Illumina MiSeq... | ["[Nextera index plates- Prepared prior to Step 1 PCR] Order indexing primers direct from oligo manufacturer (For example IDT, Sigma genosys or MWG) suspended in water 0.5 µM scale, Desalt purification and10 µM concentration. These indexing primers consist of: an Illumina Nextra adapter i5 (Forward primer) AATGATACGG... |
91,221 | Housing and Care for Hymenochirus boettgeri | 1 | dx.doi.org/10.17504/protocols.io.ewov1qxdpgr2/v1 | https://www.protocols.io/view/housing-and-care-for-hymenochirus-boettgeri-c5bvy2n6 | Tamilie Carvalho, Catherine Si, Rebecca A. Clemons, Evelyn Faust, Timothy Y. James | TITLE: Housing and Care for Hymenochirus boettgeri
AUTHORS: Tamilie Carvalho, Catherine Si, Rebecca A. Clemons, Evelyn Faust, Timothy Y. James
[DESCRIPTION]
This protocol provides an overview of housing and care procedures for H. boettgeri in a controlled laboratory environment, encompassing feeding at all life stages... | ["[Housing] Juvenile or adult frogs", "[Housing] Animals can be kept in groups or individually as needed. House animal groups in 38 L glass tanks (standard system; Figure 1A) with a density of at least 1.5 L of water per individual. House animals individually in 1 L plastic tanks (static system; Figure 1B).", "[Housing... |
null | null | null | dx.doi.org/10.17504/protocols.io.gdfbs3n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Find the words in common between two files. It is suggested to use hashes, but Sets and Bags would also useful for the more advanced student.</p>
[STEPS]
?.
?.
?. | [] |
29,050 | Folding of FluoroCubes | 1 | dx.doi.org/10.17504/protocols.io.8k2huye | https://www.protocols.io/view/folding-of-fluorocubes-8k2huye | Stefan Niekamp, Nico Stuurman, Ronald D. Vale | TITLE: Folding of FluoroCubes
AUTHORS: Stefan Niekamp, Nico Stuurman, Ronald D. Vale
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Photobleaching limits extended imaging of fluorescent biological samples. Here, we developed DNA based “FluoroCubes” that are similar in size to the green fluorescent ... | ["[Design]\nPick a dye that you would like to use for the six dye FluoroCube. We have tested ATTO 488, ATTO 565, ATTO 647N, Cy3, Cy3N (sulfonated Cy3), and Cy5. Based on our experience, ATTO 647N and Cy3N work very well as six dye FluoroCubes and we recommend using these two dyes.", "[Design]\nOrder the modified oligon... |
43,539 | Tetraspanin (CD9, CD63, CD81) Western Blot for Extracellular Vesicles | 4 | dx.doi.org/10.17504/protocols.io.bnrtmd6n | https://www.protocols.io/view/tetraspanin-cd9-cd63-cd81-western-blot-for-extrace-bnrtmd6n | Dima Ter-Ovanesyan, Wendy Trieu , Maia Norman, Roey Lazarovits, George Church, David Walt | TITLE: Tetraspanin (CD9, CD63, CD81) Western Blot for Extracellular Vesicles
AUTHORS: Dima Ter-Ovanesyan, Wendy Trieu , Maia Norman, Roey Lazarovits, George Church, David Walt
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Extracellular vesicles (EVs) are released by all mammalian cells and are tho... | ["[Day 1 ]\nAdd Bolt 4x LDS sample buffer to samples for a final concentration of 1x LDS or resuspend in 1x LDS directly if the samples are pellets.", "[Day 1 ]\nVortex, spin down, and denature the samples in heat block at 70 °C for 10 minutes.", "[Day 1 ]\nFill the Western Blot mini gel tank with 1x MES running buffer... |
39,175 | Statistical Analysis Plan for Development of Injury Prediction Models for the MP3 Return to Duty Study | 1 | dx.doi.org/10.17504/protocols.io.bihfkb3n | https://www.protocols.io/view/statistical-analysis-plan-for-development-of-injur-bihfkb3n | Dan Rhon, Tina Greenlee, Jeff Sorensen, Garrett Bullock | TITLE: Statistical Analysis Plan for Development of Injury Prediction Models for the MP3 Return to Duty Study
AUTHORS: Dan Rhon, Tina Greenlee, Jeff Sorensen, Garrett Bullock
[STEPS]
?. [Adminstrative Information]
ADMINISTRATIVE INFORMATIONThe SAP below is written following the Guidelines for Content of Statistical An... | ["[Adminstrative Information]\nADMINISTRATIVE INFORMATIONThe SAP below is written following the Guidelines for Content of Statistical Analysis Plans in Clinical Trials (adapted for the purposes of this cohort study) JAMA Reference: http://dx.doi.org/10.1001/jama.2017.18556", "[Adminstrative Information]\nTitle and Tria... |
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