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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75,773 | FBS heat inactivation | 4 | null | https://www.protocols.io/view/fbs-heat-inactivation-cm85u9y6 | Andreas Sagen | TITLE: FBS heat inactivation
AUTHORS: Andreas Sagen
[DESCRIPTION]
The objective of heat inactivation is to destroy complement activity in the serum without affecting the growth-promoting characteristics of the product. Removal of complement activity from serum, such as fetal bovine serum, is not required for most cell... | ["[Inactivation] Preparation", "[Inactivation] Aliquot FBS into 50 mL or 100 mL units in a sterile environment", "[Inactivation] Prepare a water bath", "[Inactivation] Clean and add distilled water to an appropriate hight", "[Inactivation] FBS inactivation", "[Inactivation] Set temperature to 58 °C", "[Inactivation] Pr... |
85,681 | Total lipid content analysis for coral samples | 4 | dx.doi.org/10.17504/protocols.io.81wgbx681lpk/v1 | https://www.protocols.io/view/total-lipid-content-analysis-for-coral-samples-cxwrxpd6 | Keyla Plichon, Paola Furla | TITLE: Total lipid content analysis for coral samples
AUTHORS: Keyla Plichon, Paola Furla
[DESCRIPTION]
This protocol aims to extract and quantify total lipidic content from frozen coral samples. This method is adapted from the extraction protocol of Rowan et al., 2020 and the sulfo-phospho-vanillin protocol on 96-wel... | ["[Lipid extraction] Remove subsamples from the freeze dryer.\nTurn off the freeze-dryer and quickly tighten the screw caps to the vial to avoid moisture entering the subsample. Keep samples at -80°C until analysis.", "[Lipid quantifcation sulfo-phospho-vanillin method] Prepare a stock of cholesterol solution and prepa... |
78,939 | Tetiaroa Yellow Crazy Ant Sampling: Sugar and PB Protocol - 1/24/2023 | 4 | dx.doi.org/10.17504/protocols.io.n2bvj81rxgk5/v1 | https://www.protocols.io/view/tetiaroa-yellow-crazy-ant-sampling-sugar-and-pb-pr-crb3v2qn | Juliet Capriola, Kalani Alcala | TITLE: Tetiaroa Yellow Crazy Ant Sampling: Sugar and PB Protocol - 1/24/2023
AUTHORS: Juliet Capriola, Kalani Alcala
[DESCRIPTION]
Walked along a series of transects with ant sugar water and peanut butter vials. The experiment aimed to discover the extent of the invasive yellow crazy Ant ,Anoplolepis gracilipes, on Te... | ["[Preparation] Prepare 25 sugar plastic vials by soaking a napkin in sugar water and placing at the bottom of the vial", "[Preparation] Divide the atoll into a series of transects labeled A-Z. Then on each transect create points 1-X. The points should create a grid on the island.", "[Preparation] Prepare 12 PB plastic... |
null | null | null | dx.doi.org/10.17504/protocols.io.htrb6m6 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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92,442 | A polarized cell system amenable to subcellular resolution imaging of influenza virus infection | 1 | dx.doi.org/10.17504/protocols.io.36wgq3pmklk5/v1 | https://www.protocols.io/view/a-polarized-cell-system-amenable-to-subcellular-re-c6h2zb8e | Brault Jean-Baptiste, Thouvenot Catherine, Cannata Serio Magda, Paisant Sylvain, Fernandes Julien, Gény David, Danglot Lydia, Mallet Adeline, Naffakh Nadia | TITLE: A polarized cell system amenable to subcellular resolution imaging of influenza virus infection
AUTHORS: Brault Jean-Baptiste, Thouvenot Catherine, Cannata Serio Magda, Paisant Sylvain, Fernandes Julien, Gény David, Danglot Lydia, Mallet Adeline, Naffakh Nadia
[DESCRIPTION]
This protocol details a polarized ce... | ["[SEEDING AND POLARIZATION OF CACO-2/TC7 CELLS ON CYTODEX 3 BEADS] Prepare the repellent layer and seed the Caco-2/TC7 cells", "[SEEDING AND POLARIZATION OF CACO-2/TC7 CELLS ON CYTODEX 3 BEADS] Dissolve the Gelrite solution (0.8% Gelrite + 0.1% MgSO4 x7H2O w/v in PBS) in the microwave oven.", "[SEEDING AND POLARIZATIO... |
82,131 | L3 stage C. elegans dissociation for FACS isolation and RNA-seq analysis of intestine-specific cells | 4 | dx.doi.org/10.17504/protocols.io.14egn7zwmv5d/v2 | https://www.protocols.io/view/l3-stage-c-elegans-dissociation-for-facs-isolation-cuftwtnn | Robert TP Williams, Erin Osborne Nishimura | TITLE: L3 stage C. elegans dissociation for FACS isolation and RNA-seq analysis of intestine-specific cells
AUTHORS: Robert TP Williams, Erin Osborne Nishimura
[DESCRIPTION]
This protocol is for generating a single cell suspension suitable for isolation of intestine-specific cells through Fluorescence Activated Cell S... | ["[Before beginning] Prepare reagents in advance\n\n\nL15-10 Buffer: Mix 500 ml Leibovitz's L-15 Medium, 50 ml Fetal Bovine Serum (heat inactivated), 50 ul of 100x Penicillin-Streptomycin solution and 7.7 g sucrose. Filter with 0.2 micron pore filter. Store at 4ºC.\n\nEgg Buffer: Mix 29.5 ml of 2M NaCl, 12 ml of 2M KCl... |
71,205 | RNA-interference in Paramecium bursaria | 2 | dx.doi.org/10.17504/protocols.io.8epv5jzm4l1b/v1 | https://www.protocols.io/view/rna-interference-in-paramecium-bursaria-chsdt6a6 | Ben Jenkins | TITLE: RNA-interference in Paramecium bursaria
AUTHORS: Ben Jenkins
[DESCRIPTION]
RNA-interference based gene knock-down in Paramecium bursaria. This collection contains protocols for:
1) Paramecium cultures for RNAi - Filtering and preparing P. bursaria cultures for downstream RNAi
2) RNAi induction - Back-dilution,... | [] |
90,500 | stilPCR (single-tube Illumina long read PCR) increases the effective sequencing length of Illumina, targeted next-generation sequencing | 4 | dx.doi.org/10.17504/protocols.io.bp2l6xmn5lqe/v1 | https://www.protocols.io/view/stilpcr-single-tube-illumina-long-read-pcr-increas-c4mcyu2w | Jason D Limberis, Roland Nagel, Soumitesh Chakravorty, Dena Block, Scott Dewell, Alina Nalyvayko, Zach Howard, Grant Theron, Rouxjeane Venter, John Metcalfe | TITLE: stilPCR (single-tube Illumina long read PCR) increases the effective sequencing length of Illumina, targeted next-generation sequencing
AUTHORS: Jason D Limberis, Roland Nagel, Soumitesh Chakravorty, Dena Block, Scott Dewell, Alina Nalyvayko, Zach Howard, Grant Theron, Rouxjeane Venter, John Metcalfe
[DESCRIPTI... | ["[Stage 1 PCR] COMPONENT FINAL C. 50ul 5X Reaction Buffer 1X 10 5X GC Buffer 1X 10 10 mM dNTPs 200 µM 1 AtpE_stilPCRm1_F1 0.1µM 0.5 AtpE_stilPCRm1_R1 0.1µM 0.5 Rv0678_stilPCRm1_F1 0.1µM 0.5 Rv0678_stilPCRm1_R2 0.1µM 0.5 Template DNA – 2 Q5 High-Fidelity DNA Polymerase 0.... |
98,739 | A protocol for tissue clearing and three-dimensional imaging of human sigmoid mucosal biopsies | 0 | dx.doi.org/10.17504/protocols.io.6qpvr8dkblmk/v2 | https://www.protocols.io/view/a-protocol-for-tissue-clearing-and-three-dimension-dcnt2ven | Pu-Qing Yuan, Tao Li, Yvette Taché | TITLE: A protocol for tissue clearing and three-dimensional imaging of human sigmoid mucosal biopsies
AUTHORS: Pu-Qing Yuan, Tao Li, Yvette Taché
[DESCRIPTION]
This protocol was developed for tissue clearing and 3D imaging of human sigmoid mucosal biopsies by adapting and modifying the original CLARITY tissue clearin... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.ssyeefw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol is used to clarity the process of total DNA extration for L. maculatus genome.</p>
[STEPS]
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82,136 | Implant Surgery: Chronic recoverable Neuropixels in mice | 1 | dx.doi.org/10.17504/protocols.io.yxmvmnn2bg3p/v6 | https://www.protocols.click/view/implant-surgery-chronic-recoverable-neuropixels-in-cufywtpw | Emily A Aery Jones | TITLE: Implant Surgery: Chronic recoverable Neuropixels in mice
AUTHORS: Emily A Aery Jones
[DESCRIPTION]
This protocol collection explains how to build a low-cost, lightweight system to implant 1 Neuropixels 1.0 probe or 2 Neuropixels 2.0 probes into mice, record during freely moving behavior, then recover the probes... | ["[Prepare surgical tools and field] Sterilize tips of metal instruments, ground screw, and headbar in autoclave 25 min or hot bead sterilizer 5 s . Disinfect cotton swabs, toothpick, and a weigh boat under UV light 30 min .", "[Prepare surgical tools and field] Disinfect surgical field with 10% bleach. Lay absorbent ... |
19,445 | Adapted protocol to extract total RNA using TRIzol® (Invitrogen, Thermo) | null | dx.doi.org/10.17504/protocols.io.w8vfhw6 | null | Talita Gagliardi | TITLE: Adapted protocol to extract total RNA using TRIzol® (Invitrogen, Thermo)
AUTHORS: Talita Gagliardi
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Total RNA extraction using TRizol reagent.</div><div class = "text-block">Attention: for nasopharyngeal aspirates, we use regular TRizol reagent i... | ["Incubate the homogeneized sample for 5min at r.t.", "Add 150ul of chloroform", "Shake the tube vigorously by vortex for 15sec.", "Incubate for 3min at r.t.", "Centrifuge for 15min at 12,000 x g and 4ºC.", "The mixture separates into red lower phenol-chloroform phase, and interphase, and a colorless upper aqueous phas... |
null | null | null | dx.doi.org/10.17504/protocols.io.esxbefn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
For use in <a href="https://www.protocols.io/view/CviRI-Purification-From-XZ-6E-Virus-Infected-NC64A-er4bd8w" target="_blank">CviRI Purification From XZ-6E Virus Infected NC64A Chlorella</a>.
[STEPS]
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27,578 | Isolation of Klebsiella strains from human or animal fecal material | null | dx.doi.org/10.17504/protocols.io.662hhge | null | Sylvain Brisse, virginie passet, Carla Rodrigues | TITLE: Isolation of Klebsiella strains from human or animal fecal material
AUTHORS: Sylvain Brisse, virginie passet, Carla Rodrigues
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is intended for isolation of Klebsiella strains from human or animal fecal material. It is derived from ... | ["Pre-treatment of sampleEnrich the sample by use of an enrichment broth. We typically use Luria-Bertani broth with 10 mg/L of ampicillin final concentration. Because they carry a constitutively expressed class A beta-lactamase (blaSHV type), the vast majority of Klebsiella isolates will grow/survive, whereas many othe... |
54,878 | FPCount protocol - Short protocol | 4 | dx.doi.org/10.17504/protocols.io.bzt6p6re | https://www.protocols.io/view/fpcount-protocol-short-protocol-bzt6p6re | Eszter Csibra, Guy-Bart Stan | TITLE: FPCount protocol - Short protocol
AUTHORS: Eszter Csibra, Guy-Bart Stan
[DESCRIPTION]
FPCount is a complete protocol for fluorescent protein calibration, consisting of:
1. FP expression/purification using Thermo's HisPur Cobalt Resin.
2. FP concentration determination in a microplate reader.
3. FP fluores... | ["[Harvesting and Washing] [ Day 2 ]\n\nBuffers:\nWash buffer = T50N150\n 50 mM Tris-Cl pH 7.5, 150 mM NaCl\n Doesn’t need protease inhibitors\n Can be substituted by T50N300\nResuspension buffer = T50N300+pi\n 50 mM Tris-Cl pH 7.5, 300 mM NaCl\n protease inhibitors (pi; 1 tablet/10ml) \n filter steri... |
44,314 | Immunoprecipitation Washes and RNA Dephosphorylation | 4 | dx.doi.org/10.17504/protocols.io.bph2mj8e | https://www.protocols.io/view/immunoprecipitation-washes-and-rna-dephosphorylati-bph2mj8e | Eric L. Van Nostrand, Thai B. Nguyen, Chelsea Gelboin-Burkhart, Ruth Wang, Steven M. Blue, Gabriel A. Pratt, Ashley L. Louie, Gene W. Yeo | TITLE: Immunoprecipitation Washes and RNA Dephosphorylation
AUTHORS: Eric L. Van Nostrand, Thai B. Nguyen, Chelsea Gelboin-Burkhart, Ruth Wang, Steven M. Blue, Gabriel A. Pratt, Ashley L. Louie, Gene W. Yeo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Profiling of RNA binding protein targets in v... | ["[Wash Beads (Pre-chill All Wash Buffers to 4 °C)]\nMagnetically separate beads, remove the supernatant (or store for western if desired).\nWe often perform intermediate washes with equal mixtures of the previous and current wash buffer, in order to decrease dramatic changes in buffer composition.", "[Wash Beads (Pre-... |
76,671 | Isolation of mouse embryonic fibroblasts (MEFs) from mouse embryos at E12.5 | 4 | dx.doi.org/10.17504/protocols.io.eq2ly713qlx9/v1 | https://www.protocols.io/view/isolation-of-mouse-embryonic-fibroblasts-mefs-from-cn47vgzn | Francesca Tonelli | TITLE: Isolation of mouse embryonic fibroblasts (MEFs) from mouse embryos at E12.5
AUTHORS: Francesca Tonelli
[DESCRIPTION]
Mouse embryo fibroblasts (MEFs) isolated from genetically altered mouse strains are a powerful resource for investigating the consequences of defined genetic mutations at the cellular level. Here... | ["Transfer the uterus containing the embryos to a dish with ice cold PBS.", "Separate the embryos by cutting through the uterus in the region between each embryo with scissors.", "Transfer each embryo to a new dish with ice cold PBS.", "Remove the placenta and other maternal tissues by gently pulling them off using for... |
20,048 | Transfection of primary endothelial cells with siRNA | null | dx.doi.org/10.17504/protocols.io.xtqfnmw | null | Thomas Mudersbach, Daniel Siuda, Karin Kohlstedt, Ingrid Fleming | TITLE: Transfection of primary endothelial cells with siRNA
AUTHORS: Thomas Mudersbach, Daniel Siuda, Karin Kohlstedt, Ingrid Fleming
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. [Preparing the endothelial cells for transfection (12-well plate)]
Cells were seeded the day before transfection at a density... | ["[Preparing the endothelial cells for transfection (12-well plate)]\nCells were seeded the day before transfection at a density of 3 x 104 cells/cm2.", "[Transfection ]\nCells were washed twice with PBS and than starved for at least in serum-free basal MCDB131 Medium at before incubation is finshed prepare the transfe... |
53,684 | Homology modeling using Phyre2 for Biochemistry I | 1 | null | https://www.protocols.io/view/homology-modeling-using-phyre2-for-biochemistry-i-bynupvew | Michael Friedman, Chris Berndsen | TITLE: Homology modeling using Phyre2 for Biochemistry I
AUTHORS: Michael Friedman, Chris Berndsen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol for homology modeling proteins for use in Biochemistry I at James Madison University. Protocol guides students to use the PHYRE2 web server (cit... | ["[NCBI BLAST]\nNavigate to NCBI BLAST (Basic Local Sequence Alignment Tool) and paste your sequence into the \"Enter Query Sequence\" box.", "[NCBI BLAST]\nThe standard settings for the search are shown in the table. ABC1Default SettingWhat it does2Enter Query Sequence3Query Subrange(Blank)Limits search to a part of ... |
94,565 | Purification of GST-LC3B | 1 | dx.doi.org/10.17504/protocols.io.3byl4qnbjvo5/v1 | https://www.protocols.io/view/purification-of-gst-lc3b-c8kdzus6 | Elias Adriaenssens | TITLE: Purification of GST-LC3B
AUTHORS: Elias Adriaenssens
[DESCRIPTION]
This protocol describes the purification of GST-LC3B.
[STEPS]
SECTION: Purification of GST-LC3B
1. To purify GST-LC3B, insert human LC3B cDNA in a pGEX-4T1 vector. Note, the last five amino acids of LC3B are deleted to mimic the cleavage by ATG... | ["[Purification of GST-LC3B] To purify GST-LC3B, insert human LC3B cDNA in a pGEX-4T1 vector. Note, the last five amino acids of LC3B are deleted to mimic the cleavage by ATG4.", "[Purification of GST-LC3B] After the transformation of the pGEX-4T1 vector encoding GST-LC3B in E.coli Rosetta (DE3) pLysS cells, grow the c... |
null | null | null | dx.doi.org/10.17504/protocols.io.dm448v | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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26,075 | Bradford protein assay – Protein concentration measurement (single 595 nm read) | 1 | dx.doi.org/10.17504/protocols.io.14egnxd3ml5d/v1 | https://www.protocols.io/view/bradford-protein-assay-protein-concentration-measu-5p3g5qn | Daniel C Moreira | TITLE: Bradford protein assay – Protein concentration measurement (single 595 nm read)
AUTHORS: Daniel C Moreira
[DESCRIPTION]
This protocol describes how to measure the concentration of total protein in a sample performing the Bradford's assay using microtiter plates. Procedures are slightly modifications based on t... | ["[Bradford's protein reagent preparation] Prepare a solution containing 0.01% (w/v) Coomassie Brilliant Blue G-250 (e.g., B0770, Sigma-Aldrich), 4.7% (v/v) ethanol, and 8.5% (v/v) phosphoric acid as described in the next steps.", "[Bradford's protein reagent preparation] Weight 100 mg of Coomassie Brilliant ... |
57,891 | YAP1 mKate:BSD HDR Knock-in (via Cas9 RNP lipofection) | 4 | null | https://www.protocols.io/view/yap1-mkate-bsd-hdr-knock-in-via-cas9-rnp-lipofecti-b4sbqwan | Emir Bora Akmeriç | TITLE: YAP1 mKate:BSD HDR Knock-in (via Cas9 RNP lipofection)
AUTHORS: Emir Bora Akmeriç
[DESCRIPTION]
s
[STEPS]
SECTION: Culturing Immortalized HUVECs
1. In a t25 flask, add 10 mL of EGM2 (with antibiotics). Incubate flask for 20 minutes
SECTION: Culturing Immortalized HUVECs
1.1. Thaw a 500k/1M CI-huVEC tube in a... | ["[Culturing Immortalized HUVECs] In a t25 flask, add 10 mL of EGM2 (with antibiotics). Incubate flask for 20 minutes", "[Culturing Immortalized HUVECs] Thaw a 500k/1M CI-huVEC tube in a 37C water bath\nand add the cells into the flask.", "[Culturing Immortalized HUVECs] Change media 6-8 hours later or when cells have ... |
62,617 | Prima United Kingdom | Boosts Level Of Power & Increases Assurance! | 3 | dx.doi.org/10.17504/protocols.io.3byl4bx82vo5/v1 | https://www.protocols.io/view/prima-united-kingdom-boosts-level-of-power-amp-inc-b9dzr276 | prima | TITLE: Prima United Kingdom | Boosts Level Of Power & Increases Assurance!
AUTHORS: prima
[DESCRIPTION]
Prima United Kingdom
[STEPS] | [] |
90,668 | Regional Mouse Brain Analysis (Modified QUINT) | 2 | dx.doi.org/10.17504/protocols.io.kqdg3xbkzg25/v1 | https://www.protocols.io/view/regional-mouse-brain-analysis-modified-quint-c4skywcw | Michael X. Henderson | TITLE: Regional Mouse Brain Analysis (Modified QUINT)
AUTHORS: Michael X. Henderson
[DESCRIPTION]
This is series of protocols that has been adapted from published and unpublished protocols broadly referred to as the QUINT workflow. Note that the original QUINT workflow was generated by Yates and colleagues, and all cr... | [] |
11,431 | Liposome binding assay | null | dx.doi.org/10.17504/protocols.io.pefdjbn | null | Christa Testerink, Anne Froyd-Rankenberg | TITLE: Liposome binding assay
AUTHORS: Christa Testerink, Anne Froyd-Rankenberg
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Standard protocol to examine lipid binding of the proteins isolated from the E.coli with the GST tag</div></div>
[STEPS]
?. Mix lipids in chloroform in the right molecular... | ["Mix lipids in chloroform in the right molecular ratios. Per sample 400 nmole (total) lipid is required. For (poly) phosphoinositides add MeOH (C:M 20:9)", "Dry lipid mixtures for 30’ in the speed vac. Store at -20C", "Add 500ul extrusion buffer per tube with lipid mixture. Vortex and let lipids rehydrate for 1-1.5 h ... |
62,294 | Superior Nutra Keto | 3 | dx.doi.org/10.17504/protocols.io.x54v9ykjzg3e/v1 | https://www.protocols.io/view/superior-nutra-keto-b83wrype | H H | TITLE: Superior Nutra Keto
AUTHORS: H H
[DESCRIPTION]
Superior Nutra Keto are most commonly offered in conjunction with a high-deductible health plan. As a rule, these plans keep premium costs low
[STEPS] | [] |
75,228 | Preparing MEF-cultured hPSCs for nucleofection | 4 | dx.doi.org/10.17504/protocols.io.bp2l611ddvqe/v2 | https://www.protocols.io/view/preparing-mef-cultured-hpscs-for-nucleofection-cmp4u5qw | Hanqin Li, Oriol Busquets, Steven Poser, Dirk Hockemeyer, Frank Soldner | TITLE: Preparing MEF-cultured hPSCs for nucleofection
AUTHORS: Hanqin Li, Oriol Busquets, Steven Poser, Dirk Hockemeyer, Frank Soldner
[DESCRIPTION]
This protocol describes the procedure or preparing MEF-cultured human pluripotent stem cells (hPSCs) for the delivery of plasmids, mRNA or ribonucleoprotein (RNP) using ... | ["When MEF-cultured hPSCs reach 50% confluency, change medium to hPSCs medium + Rock inhibitor, preparing for nucleofection the next day. For each 20 µl nucleofection reaction, prepare half to 1 well of cells.\n\nA detailed protocol on maintaining MEF-cultured hPSCs can be found in the collection \"Maintenance and inac... |
20,493 | Western blot analysis | null | dx.doi.org/10.17504/protocols.io.x9mfr46 | null | Kiichi Hirota | TITLE: Western blot analysis
AUTHORS: Kiichi Hirota
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. [Cell lysis]
Scrape cells and transfer the suspension to a 1.5 ml microcentrifuge tube.
?. [Cell lysis]
Centrifuge at 10,000 x g for 5 minutes at 4°C and collect the supernatant in a new microcentrifuge tube... | ["[Cell lysis]\nScrape cells and transfer the suspension to a 1.5 ml microcentrifuge tube.", "[Cell lysis]\nCentrifuge at 10,000 x g for 5 minutes at 4°C and collect the supernatant in a new microcentrifuge tube.", "[Cell lysis]\nDetermine protein concentration by using DC™ Protein Assay Kit.", "[Separation of proteins... |
null | null | null | dx.doi.org/10.17504/protocols.io.rhnd35e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>End-stage renal disease (ESRD) is related to high morbidity, mortality, and impaired health-related quality of life. While hemodialysis (HD) is the current life-saving standard of treatment for patients with ESRD, their quality of life (QoL) remains far from desirable. Online... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.pumdnu6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol describes how to make chemically competent <em>Vibrio natriegens</em> cells.</p>
<p>The protocol was described and published by Weinstock et al., 2016</p>
[BEFORE_START]
<p>Make sure you have all solutions there:</p>
<ul>
<li><strong>Brain heart infusion + V<su... | [] |
35,786 | ddPCR Titration of Lentivirus Vectors | 1 | dx.doi.org/10.17504/protocols.io.be7ijhke | https://www.protocols.io/view/ddpcr-titration-of-lentivirus-vectors-be7ijhke | Addgene The Nonprofit Plasmid Repository | TITLE: ddPCR Titration of Lentivirus Vectors
AUTHORS: Addgene The Nonprofit Plasmid Repository
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol describes ddPCR titration of Lentivirus vectors. To see the full abstract and additional resources, visit </span><a href="https://www.add... | ["[Transducing Cells]\nThaw the virus.\non ice", "[Transducing Cells]\nPrepare the following dilution series of virus in DMEM complete: ABCD1Dilution FactorVirusMediaTotal Volume22.5160µL viral stock240µL400µL35200µL of 2.5-fold dilution200µL400µL410200µL of 5-fold dilution 200µL400µL520200µL of 10-fold dilution200µL... |
104,832 | Mouse brain, gut and plasma collection | 0 | dx.doi.org/10.17504/protocols.io.14egn3pkzl5d/v2 | https://www.protocols.io/view/mouse-brain-gut-and-plasma-collection-dik84czw | Livia Hecke Morais | TITLE: Mouse brain, gut and plasma collection
AUTHORS: Livia Hecke Morais
[DESCRIPTION]
Protocol used in the Mazmanian lab for collecting brain and gut tissues and plasma from mouse for metabolomics. Protocol has been approved by the California Institute of Technology’s Institutional Animal Care
and Use Committee (IA... | ["[Mouse brain, gut and plasma collection] At 4 months of age, mice is euthanized inside chemical hood by decapitation using scissors (as approved by IACUC protocol)", "[Mouse brain, gut and plasma collection] The head is separated from the rest of the body for brain and gut dissections using straight scissors", "[Mous... |
null | null | null | dx.doi.org/10.17504/protocols.io.p4zdqx6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>We used the NEPA electroportor to transform Emiliania huxleyi cells. </p>
<p>We were able to establish that this method can be used to introduce proteins into the cells. </p>
[STEPS]
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23,772 | Allende HRTEM study | null | dx.doi.org/10.17504/protocols.io.3f4gjqw | null | H. I. Cruz-Rosas, F. Riquelme, P. Santiago, L. Rendón, T. Buhse, F. Ortega-Gutiérrez, R. Borja-Urby, D. Mendoza, C. Gaona, P. Miramontes, G. Cocho. | TITLE: Allende HRTEM study
AUTHORS: H. I. Cruz-Rosas, F. Riquelme, P. Santiago, L. Rendón, T. Buhse, F. Ortega-Gutiérrez, R. Borja-Urby, D. Mendoza, C. Gaona, P. Miramontes, G. Cocho.
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;"> </span><span style = "font-weight... | [] |
69,180 | Nasal Lavage Sample collection and processing | 1 | null | https://www.protocols.io/view/nasal-lavage-sample-collection-and-processing-cfs4tngw | maria.xylaki | TITLE: Nasal Lavage Sample collection and processing
AUTHORS: maria.xylaki
[DESCRIPTION]
This protocol describes the nasal lavage fluid sampling that can be used for Omics (for Proteome analysis, see Schoenebeck et al, 2015; for Microbiome analysis see Heintz-Buschart et al, 2017) or RT-QuIC. Collection proceedure wa... | ["[Nasal Lavage Sample collection] Two nasal lavage samples (NLS) are collected per person in each step, one from each nostril.\nBoth nasal cavities are pre-washed with 2 mL of physiological NaCl solution with the use of a plastic disposable pipette to remove bacterial impurities.", "[Nasal Lavage Sample collection] Af... |
null | null | null | dx.doi.org/10.17504/protocols.io.qnmdvc6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Protocol for add azide modified nucleotide to 3' end of unmodified DNA olgionucleotide using terminal transferase. Protocol adapted from <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4787804/" target="_blank" rel="noopener noreferrer">Winz et al. 2015</a>. </p>
[STEP... | [] |
48,928 | Ethanol extraction protocol | 1 | null | https://www.protocols.io/view/ethanol-extraction-protocol-btz8np9w | Nannie | TITLE: Ethanol extraction protocol
AUTHORS: Nannie
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Developed for IBA at the NRM DNA lab.</div></div>
[STEPS]
?. Decant the ethanol through a mesh and add new ethanol to the insects.
?. Filter the ethanol: method 2.1 or 2.2
?. Vacuum pumpPut the Steri... | ["Decant the ethanol through a mesh and add new ethanol to the insects.", "Filter the ethanol: method 2.1 or 2.2", "Vacuum pumpPut the Sterivex filters on the vacuum pump with the large syringe attached to the filter. Turn on the pump and pour the ethanol into the syringe.The filtered ethanol will not be saved.", "Manu... |
49,605 | Cardiodynamic variables measured by Impedance Cardiography during a 6-minute walk test are reliable predictors of peak oxygen consumption in young healthy adults | 1 | dx.doi.org/10.17504/protocols.io.bupdnvi6 | https://www.protocols.io/view/cardiodynamic-variables-measured-by-impedance-card-bupdnvi6 | Fang Liu, Raymond Tsang, Alice YM Jones, Minchao Zhou, Kaiwen Xue, Miaoling Chen, Yulong Wang | TITLE: Cardiodynamic variables measured by Impedance Cardiography during a 6-minute walk test are reliable predictors of peak oxygen consumption in young healthy adults
AUTHORS: Fang Liu, Raymond Tsang, Alice YM Jones, Minchao Zhou, Kaiwen Xue, Miaoling Chen, Yulong Wang
[DESCRIPTION]
<div class = "text-blocks"><div... | ["Invitation emails were sent via the student portal of all students registered at the School of Rehabilitation of a local university affiliated with the hospital where this project was conducted.", "Exclusion criteria were: (1) students with known cardiovascular, pulmonary or musculoskeletal disorders that might limit... |
29,169 | ChroPlate - ProteinA/G | null | dx.doi.org/10.17504/protocols.io.8qrhvv6 | null | David Frommholz, Alexandra Ehl, Nadine Stefanczyk | TITLE: ChroPlate - ProteinA/G
AUTHORS: David Frommholz, Alexandra Ehl, Nadine Stefanczyk
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Purification Guide for the Isolation of Antibodies with ChroPlate Filtration Plates by DALEX Biotech.</span></div><div class = "t... | ["[Load and Wash]\nPlace the ChroPlate on a clean deep-well plate. Add up to 1.5 ml sample to every well. Centrifuge 2 - 10 minutes at 400 g in a swing-out rotor.\nIt is advisable to keep the flow-through and wash fractions for later analysis, e.g. SDS-PAGE.The centrifugation time depends on the sample's volume and vis... |
42,869 | MRM-LC-MS/MS Assay for inflammatrory associated proteins in serum | 1 | dx.doi.org/10.17504/protocols.io.bm4vk8w6 | https://www.protocols.io/view/mrm-lc-ms-ms-assay-for-inflammatrory-associated-pr-bm4vk8w6 | TITLE: MRM-LC-MS/MS Assay for inflammatrory associated proteins in serum
AUTHORS:
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Multiplex targeted proteomic assay to measure human proteins associated with inflammation in serum. A unique peptide is selected to represent a protein and is measured ... | ["[Sample preparation]\nsamples are prepared for targeted mass spectrometric analysis utilising 20 μL serum.", "[Sample preparation]\nPrior to preparation, 5 pmol yeast enolase 1 protein (ENO1) (sigma UK) were added to each 20 μL serum sample to act as an internal standard, accounting for variation in sample preparati... | |
39,736 | Materials and Methods: First report of the bat fly species Basilia italica in Romania | 3 | dx.doi.org/10.17504/protocols.io.bi2ykgfw | https://www.protocols.io/view/materials-and-methods-first-report-of-the-bat-fly-bi2ykgfw | aronpeter92 , Sándor D. Attila, Andrei D. Mihalca | TITLE: Materials and Methods: First report of the bat fly species Basilia italica in Romania
AUTHORS: aronpeter92 , Sándor D. Attila, Andrei D. Mihalca
[STEPS] | [] |
71,801 | Tissue Sectioning - Stanford | 1 | dx.doi.org/10.17504/protocols.io.j8nlkwkr1l5r/v1 | https://www.protocols.io/view/tissue-sectioning-stanford-ciczuax6 | emonte | TITLE: Tissue Sectioning - Stanford
AUTHORS: emonte
[DESCRIPTION]
Tissue sectioning preparation (FF and FFPE)
[STEPS]
1. Tissue sectioning protocol can be found here:
| ["Tissue sectioning protocol can be found here:"] |
53,420 | p2 21/09 | 1 | null | https://www.protocols.io/view/p2-21-09-byekptcw | name go test surname | TITLE: p2 21/09
AUTHORS: name go test surname
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">test</div></div>
[STEPS]
?. est | ["est"] |
53,638 | Auger/Auspice/UShER SARS-CoV-2 Cluster Detection Workflow for the Terra Platform | 5 | null | https://www.protocols.io/view/auger-auspice-usher-sars-cov-2-cluster-detection-w-bymepu3e | Anusha Ginni, Jill V Hagey, Michael Weigand, Technical Outreach and Assistance for States Team | TITLE: Auger/Auspice/UShER SARS-CoV-2 Cluster Detection Workflow for the Terra Platform
AUTHORS: Anusha Ginni, Jill V Hagey, Michael Weigand, Technical Outreach and Assistance for States Team
[DESCRIPTION]
The Titan_Augur workflow processes concatenated assembly fasta data for SARS-CoV-2 phylogenetic analysis and ... | ["[Setup Terra and Google Cloud Accounts]", "[Import Augur workflows from Dockstore] Importing the Titan_Augur Workflows from Dockstore to the Terra User Workspace\n\nNote: The Augur workflow includes two steps: Titan_Augur_Prep and Titan_Augur_Run.\n\nThe Titan_Augur_Prep workflow prepares the metadata and assembly fa... |
46,664 | Laser Capture Microdissection | 4 | null | https://www.protocols.io/view/laser-capture-microdissection-brtgm6jw | Angela Kruse, Carrie Romer, Jamie Allen, Danielle Gutierrez, Jeff Spraggins | TITLE: Laser Capture Microdissection
AUTHORS: Angela Kruse, Carrie Romer, Jamie Allen, Danielle Gutierrez, Jeff Spraggins
[DESCRIPTION]
Laser Capture Microdissection (LCM) is used to excise specific tissue regions for in-solution analysis. Tissue sections are mounted on membrane-coated slides, and a combination... | ["[Turning on the instrument and software] Turn on the computer and microscope in the following order.", "[Loading a Sample] Load a sample mounted on a suitable membrane-coated slide.", "[Turning on the instrument and software] Turn key to ON position.", "[Turning on the instrument and software] Turn on computer.", "[T... |
63,755 | Mitochondrial Bioenergetics | 4 | dx.doi.org/10.17504/protocols.io.q26g746n3gwz/v1 | https://www.protocols.io/view/mitochondrial-bioenergetics-cahjsb4n | mitsjoecohen | TITLE: Mitochondrial Bioenergetics
AUTHORS: mitsjoecohen
[DESCRIPTION]
Mitochondrial bioenergetics plays a key role in a variety of basic cellular processes, such as energy production, nucleotide biosynthesis, and metabolism. Not only the basic system of cell production and death (apoptosis), it is also necessary fo... | [] |
99,539 | USDA LTAR Common Experiment measurement: Obtaining quality metrics in forage aboveground biomass | 0 | dx.doi.org/10.17504/protocols.io.n2bvjn6wpgk5/v1 | https://www.protocols.io/view/usda-ltar-common-experiment-measurement-obtaining-ddft23nn | Kimberly A. Cassida, Harold Collins | TITLE: USDA LTAR Common Experiment measurement: Obtaining quality metrics in forage aboveground biomass
AUTHORS: Kimberly A. Cassida, Harold Collins
[DESCRIPTION]
Harvesting crops for potential use as livestock forage must include nutritional value measurements to understand how these feedstuffs will meet the consumpt... | ["[Sample collection] Sampling for forage quality requires the collection of biomass samples in addition to those samples outlined in the LTAR aboveground biomass protocol. These additional samples are necessary to capture a sample that reflects the cutting height of forage harvesting equipment or animal grazing. To be... |
31,278 | HuBMAP: Embedding Fixed Frozen OCT Samples | null | dx.doi.org/10.17504/protocols.io.basniede | null | Marda Jorgensen, Jerelyn Nick | TITLE: HuBMAP: Embedding Fixed Frozen OCT Samples
AUTHORS: Marda Jorgensen, Jerelyn Nick
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The purpose of this Standard Operating Procedure (SOP) is to outline procedures for the OCT embedding of HuBMAP frozen fixed specimens.</div></div>
[STEPS]
?. [Re... | ["[Reagent Preparation]\nPrepare 1x PBSPBS is required to prepare reagents needed for this procedure. Dilute 10x PBS 1:10 in deionized water to make working 1x solution.", "[Reagent Preparation]\nPrepare a 4% paraformaldehyde solution.\nParaformaldehyde is toxic. Use gloves, wear a lab coat and work in a fume hood.", "... |
null | null | null | dx.doi.org/10.17504/protocols.io.nradd2e | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
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?.
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?.
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?.
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?. | [] |
29,756 | Enzymatic Assay of Trypsin Inhibition | null | dx.doi.org/10.17504/protocols.io.9a4h2gw | null | Neilier Junior | TITLE: Enzymatic Assay of Trypsin Inhibition
AUTHORS: Neilier Junior
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol has been standardized for analysis of protease inhibitors in soybean leaf extract, but can be easily adjusted for other biological samples.</div></div>
[STEPS]
?. [Prep... | ["[Prepare the solutions and the workspace]\nPreparation of solutionsTrypsin solution:Dilute 1.25 mg of bovine trypsin in 1 mL of water pH 3.0 (adjust with HCl).L-BApNA stock solution:Dilute 130.47 mg L-BApNA in 5 mL DMSO (concentration: 6.0 10-2 M). Store at -20 °C and protected from light.L-BApNA usage solution (fres... |
93,810 | DNA Extraction from Inoculated Broth for WGS using the Maxwell RSC Cultured Cells DNA Kit | 1 | dx.doi.org/10.17504/protocols.io.6qpvr3z5zvmk/v1 | https://www.protocols.io/view/dna-extraction-from-inoculated-broth-for-wgs-using-c7usznwe | Julie Haendiges, Ruth Timme | TITLE: DNA Extraction from Inoculated Broth for WGS using the Maxwell RSC Cultured Cells DNA Kit
AUTHORS: Julie Haendiges, Ruth Timme
[DESCRIPTION]
The Maxwell® RSC Cultured cells DNA Kit is used with the Maxwell RSC or Maxwell RSC 48 Instrument from Promega. This extraction method purifies genomic DNA (gDNA) efficien... | ["[Pre-processing of Gram Positive Cultures] Gram-Negative cultures do not require any steps prior to extraction on the Maxwell RSC instrument and can proceed to the Cultured Cells DNA Cartridge Preparation step. However, due to the thick peptidoglycan layer of Gram-Positive bacteria extra lysing is necessary. Follow t... |
82,164 | 8. Taxon Group: Echinodermata | 4 | dx.doi.org/10.17504/protocols.io.4r3l27d63g1y/v2 | https://www.protocols.io/view/8-taxon-group-echinodermata-cuguwtww | Kesella Scott-Somme, Chris Fletcher, Inez Januszczak | TITLE: 8. Taxon Group: Echinodermata
AUTHORS: Kesella Scott-Somme, Chris Fletcher, Inez Januszczak
[DESCRIPTION]
This is part of the collection "DToL Taxon-specific Standard Operating Procedures (SOPs) for Marine Metazoa", lead by the Other Metazoa Working Group. The SOP collection contains guidance on how to process ... | [] |
68,847 | Genomic DNA isolation from fixed cells | 1 | dx.doi.org/10.17504/protocols.io.eq2lynm9qvx9/v1 | https://www.protocols.io/view/genomic-dna-isolation-from-fixed-cells-cfgptjvn | Herschel Dhekne, Ebsy Jaimon, Suzanne R Pfeffer | TITLE: Genomic DNA isolation from fixed cells
AUTHORS: Herschel Dhekne, Ebsy Jaimon, Suzanne R Pfeffer
[DESCRIPTION]
This protocol details the procedure of genomic DNA isolation from fixed cells.
[STEPS]
SECTION: Genomic DNA isolation from fixed cells
1. Resuspend 1-3 X106 cells in 250 µL of PBS and transfer to a 2 m... | ["[Genomic DNA isolation from fixed cells] Resuspend 1-3 X106 cells in 250 µL of PBS and transfer to a 2 mL tube (this would represent one dish of 3T3 cells).", "[Genomic DNA isolation from fixed cells] Add 200 µg Proteinase K (from a 20 mg/mL stock) and 200 µg RNase A (from a 20 mg/mL stock).", "[Genomic DNA isolat... |
null | null | null | dx.doi.org/10.17504/protocols.io.ci7uhm | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
How to make a 50 mg/ml Rifampicin Stock Solution
[GUIDELINES]
Make a 50 mg/ml Rifampicin Stock Solution
[STEPS]
?.
?.
?. | [] |
101,901 | Sonication of α-synuclein Fibrils for injection into the mouse brain | 1 | dx.doi.org/10.17504/protocols.io.14egn337zl5d/v2 | https://www.protocols.io/view/sonication-of-synuclein-fibrils-for-injection-int-dfrm3m46 | Vijay Singh, Marta Castellana-Cruz, Nunilo Cremades, Laura Volpicelli-Daley | TITLE: Sonication of α-synuclein Fibrils for injection into the mouse brain
AUTHORS: Vijay Singh, Marta Castellana-Cruz, Nunilo Cremades, Laura Volpicelli-Daley
[DESCRIPTION]
Animal models that accurately recapitulate the accumulation of alpha-synuclein (α-syn) inclusions, progressive neurodegeneration of the nigrost... | ["[Sonicating Fibrils] Thaw and pipet 25-22 µL in 1.5 mL polystyrene sonication tube.", "[Sonicating Fibrils] WePFFs Fill Qsonica water reservoir with about 900 mL.", "[Sonicating Fibrils] Attach cooling system to Qsonica and set the temperature at 10 °C.", "[Sonicating Fibrils] Place 1.5 mL sonication tube with fibril... |
82,896 | CZ ID Workflow for Assembling Viral Consensus Genomes | 1 | dx.doi.org/10.17504/protocols.io.bp2l69ojklqe/v1 | https://www.protocols.click/view/cz-id-workflow-for-assembling-viral-consensus-geno-cu7qwzmw | Karyna Rosario Cora, Elizabeth Fahsbender, CZ ID Team | TITLE: CZ ID Workflow for Assembling Viral Consensus Genomes
AUTHORS: Karyna Rosario Cora, Elizabeth Fahsbender, CZ ID Team
[DESCRIPTION]
CZ ID's Viral Consensus Genome pipeline is designed to quickly assemble consensus genomes in bulk for any virus. Users can get started on their analysis by simply uploading Illumina... | ["[Upload Data] Log in to your CZ ID account.", "[Upload Data] Navigate to the Upload page from the Discovery page by clicking the \"Upload\" link next to your username. Note that the upload process is divided into three general sections, including Samples, Metadata, and Review pages.", "[Upload Data] Select a project,... |
60,311 | Virtual Screening | 6 | dx.doi.org/10.17504/protocols.io.n92ldzr6ov5b/v1 | https://www.protocols.io/view/virtual-screening-b65xrg7n | BOC Sciences | TITLE: Virtual Screening
AUTHORS: BOC Sciences
[DESCRIPTION]
Virtual screening has been widely applied in early-stage drug discovery. As an alternative or complementary approach to high-throughput screening (HTS) assays with high cost and low hit rate, virtual screeningis an efficient computational method to identify... | [] |
49,016 | Grinding Tissue with the Qiagen Tissuelyzer (Soybean, Cowpea, Tobacco) | 4 | null | https://www.protocols.io/view/grinding-tissue-with-the-qiagen-tissuelyzer-soybea-bt4ynqxw | Steven Burgess, Lynn Doran | TITLE: Grinding Tissue with the Qiagen Tissuelyzer (Soybean, Cowpea, Tobacco)
AUTHORS: Steven Burgess, Lynn Doran
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Grinding tissue using the Qiagen Tissuelyzer for DNA extraction, RNA extraction, or Immunoblotting.</div><div class = "text-block"><span s... | ["Pre-cool components for tissue lysis.", "Pre-cool and sterilize 4mm SPEX stainless steel grinding beads in 100% ethanol in a beaker at for\n-80 °C", "Pre-cool the empty TissueLyser inserts for LN2 for by lowering the inserts into a full liquid nitrogen dewar with the extra-long tongs.\nWear lab coat, goggles, cryo... |
11,410 | Electrocompetent Agrobacterium preparation | null | dx.doi.org/10.17504/protocols.io.pdsdi6e | null | Magdalena Julkowska | TITLE: Electrocompetent Agrobacterium preparation
AUTHORS: Magdalena Julkowska
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Preparing electrocompetent Agrobacterium - used for the GV301 strain that we currently have in stock in Salt Lab</div></div>
[STEPS]
?. Grow seed culture to saturation (36-... | ["Grow seed culture to saturation (36-48 hours), you will need ~5mL", "Inoculate 1 L of YEP media (20g peptone, 10 g yeast/ 1L) 1:200 with saturated agro. Alternatively inoculate 500ml YEP 1:100. Grow culture to an OD600 of 1.5 (24 hours or so). If you dont have YEP, just use normal LB media. Proceed on ice.", "Spin c... |
103,202 | Mouse brain slice electrophysiology | 0 | dx.doi.org/10.17504/protocols.io.rm7vzj7y8lx1/v1 | https://www.protocols.io/view/mouse-brain-slice-electrophysiology-dg2a3yae | Shiyi Wang | TITLE: Mouse brain slice electrophysiology
AUTHORS: Shiyi Wang
[DESCRIPTION]
Mouse brain slice electrophysiology
[STEPS]
1. **Animal Handling**
1.1. - Anesthetize 3-4 mice of each genotype (WT and LRRK2 G2019Ski/ki) and condition using 200 mg/kg tribromoethanol (Avertin).
1.2. - Ensure proper anesthesia depth and con... | ["**Animal Handling**", "- Anesthetize 3-4 mice of each genotype (WT and LRRK2 G2019Ski/ki) and condition using 200 mg/kg tribromoethanol (Avertin).", "- Ensure proper anesthesia depth and confirm absence of reflexes before proceeding.", "**Brain Extraction and Slicing**", "- Decapitate the mice and immediately immerse... |
84,921 | Feline Respiratory Pathogen Detection Assays | 1 | dx.doi.org/10.17504/protocols.io.ewov1q4z2gr2/v1 | https://www.protocols.io/view/feline-respiratory-pathogen-detection-assays-cw6zxhf6 | Come J Thieulent, Mariano Carossino, Laura Peak, Udeni B. R. Balasuriya | TITLE: Feline Respiratory Pathogen Detection Assays
AUTHORS: Come J Thieulent, Mariano Carossino, Laura Peak, Udeni B. R. Balasuriya
[DESCRIPTION]
The Feline Respiratory Pathogen (FRP) Detection Assays is intended as an in vitro veterinary reagent set, based on quantitative PCR (qPCR) and Reverse Transcription qPCR (R... | ["Thaw all reagents on ice.", "Centrifuge all reagents on a benchtop centrifuge to ensure no liquid is in cap and keep on ice", "Setup the Master Mix according to the following table 1:", "[PROGRAMMING THE THERMOCYCLER] Select the following fluorescence channels: ABYTM, Cy5, FAMTM, and VICTM.", "[PROGRAMMING THE THERMO... |
93,454 | Systematic Perturb-seq to discover endothelial cell programs related to CAD | 4 | dx.doi.org/10.17504/protocols.io.261ged73yv47/v1 | https://www.protocols.io/view/systematic-perturb-seq-to-discover-endothelial-cel-c7hnzj5e | Gavin R. Schnitzler, Helen Kang, Glen Munson, Philine Guckelberger, Drew Bergman, Brian Cleary, Eric S Lander, Jesse Engreitz, Rajat M. Gupta | TITLE: Systematic Perturb-seq to discover endothelial cell programs related to CAD
AUTHORS: Gavin R. Schnitzler, Helen Kang, Glen Munson, Philine Guckelberger, Drew Bergman, Brian Cleary, Eric S Lander, Jesse Engreitz, Rajat M. Gupta
[DESCRIPTION]
Linking variants from genome-wide association studies (GWAS) to underly... | ["[General considerations for culturing of TeloHAEC] Telomerase-immortalized human aortic endothelial cells (TeloHAEC) were purchased from ATCC (CRL-4052), and grown in Lifeline VEGF endothelial cell media (LL-0005) with 1x Penn/Strep (ThermoFisher #15070063 or equivalent, used at 1:100 dilution) in place of the provid... |
87,256 | Lee et al. Digestion and Seeding (adapted from. Annika) | 4 | null | https://www.protocols.io/view/lee-et-al-digestion-and-seeding-adapted-from-annik-czfyx3pw | Annika Fendler | TITLE: Lee et al. Digestion and Seeding (adapted from. Annika)
AUTHORS: Annika Fendler
[DESCRIPTION]
This Protocol is adapted from Lee et a. (2018) (https://www.sciencedirect.com/science/article/pii/S0092867418302976?via%3Dihub)
The authors have established organoids from clusters of bladder cancer cells after TURB. ... | ["[Prepare medium and enzyme mixes] Heat the shaking incubator to 37°C", "[Prepare medium and enzyme mixes] Prepare and adequate volume of Lee Organoid Medium and HBSS Washing Solution.", "[Thaw fragments]", "[Thaw fragments] Thaw 1 or more aliquots of fragments at 37 °C until only a small piece of ice remains", "[Prep... |
36,003 | Separating the Protein of Interest from MBP after TEV Protease Cleavage (NEB #E8201) | null | dx.doi.org/10.17504/protocols.io.bfebjjan | https://www.protocols.io/view/separating-the-protein-of-interest-from-mbp-after-bfebjjan | New England Biolabs | TITLE: Separating the Protein of Interest from MBP after TEV Protease Cleavage (NEB #E8201)
AUTHORS: New England Biolabs
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><ul style = "list-style-type:disc;"><li style = "counter-reset:ol0;list-style-type:disc;"><span>Both the MBP-tag and TEV Protease ... | ["[Resin Preparation]\nGently shake the Ni Resin bottle to completely resuspend the slurry and transfer desired amount to a closed column; allow resin to settle.", "[Resin Preparation]\nOpen column and allow storage buffer to flow through.", "[Resin Preparation]\nEquilibrate the resin by adding 5 column volumes (CV) of... |
39,234 | Performing CUT&RUN on adherent cells in a multi-well cell culture plate | 4 | dx.doi.org/10.17504/protocols.io.bijakcie | https://www.protocols.io/view/performing-cut-amp-run-on-adherent-cells-in-a-mult-bijakcie | Michi Miura | TITLE: Performing CUT&RUN on adherent cells in a multi-well cell culture plate
AUTHORS: Michi Miura
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol describes a variant of the standard CUT&RUN procedure (Skene et al. </span><span style = "font-style:italic;">eLife</span><span> 201... | ["[Cell seeding]\nSeed adherent cells in a standard 24-well cell culture plateSeed the cells at an appropriate density so that the cells are 70 to 90% confluent when performing CUT&RUN.", "[CUT&RUN]\nPerform CUT&RUNBefore cell permeabilisation (step 2.2),Remove the cell culture mediumWash the cells with PBS (Optional) ... |
28,417 | 17 Inhibition Kinetics Measurement | null | dx.doi.org/10.17504/protocols.io.7y9hpz6 | null | TJUSLS China | TITLE: 17 Inhibition Kinetics Measurement
AUTHORS: TJUSLS China
[STEPS]
?. [IC50 in vitro test]
Soak the 96-well plates in 75% ethanol and put the container in ultrasonic cleaner for 30min to 1 hour, then use ddH2O to wash these plates several times. Put these clean plates in drying oven at 55°C.
?. [IC50 in vitro tes... | ["[IC50 in vitro test]\nSoak the 96-well plates in 75% ethanol and put the container in ultrasonic cleaner for 30min to 1 hour, then use ddH2O to wash these plates several times. Put these clean plates in drying oven at 55°C.", "[IC50 in vitro test]\nDilute inhibitors using 100%DMSO to 8mM (a.k.a. 80μM in reaction syst... |
21,152 | UC Davis - RadioImmuno Assay (RIA) Protocol | null | dx.doi.org/10.17504/protocols.io.yv8fw9w | null | Peter Havel | TITLE: UC Davis - RadioImmuno Assay (RIA) Protocol
AUTHORS: Peter Havel
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">The RIA (RadioImmuno Assay) is an assay method used for the quantification of various proteins. A ... | ["Follow kit instructions for preparing standards and all reagents.", "Follow kit instructions for volumes and incubation times. Pipet standards and samples . Pipet antibody and tracer. Incubate.", "Follow kit instructions for volumes and incubation times. Add precipitating reagent. Incubate.", "Centrifuge.", "Aspirate... |
30,700 | Anti-DYKDDDDK Tag (L5) Affinity Gel Protocol | null | dx.doi.org/10.17504/protocols.io.98kh9uw | null | Sam Li | TITLE: Anti-DYKDDDDK Tag (L5) Affinity Gel Protocol
AUTHORS: Sam Li
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. [Part I. Cell Lysate Preparation - A. Purifying DYKDDDDK-tag fusion proteins from crude E.coli extracts]
Grow the bacteria cells under the condition that induce production of DYKDDDDK-tag fus... | ["[Part I. Cell Lysate Preparation - A. Purifying DYKDDDDK-tag fusion proteins from crude E.coli extracts]\nGrow the bacteria cells under the condition that induce production of DYKDDDDK-tag fusion proteins.", "[Part I. Cell Lysate Preparation - A. Purifying DYKDDDDK-tag fusion proteins from crude E.coli extracts]\nHar... |
35,930 | Automated transfer of inactivated virus samples from individual 2ml tubes to 96-well plate | null | dx.doi.org/10.17504/protocols.io.bfb2jiqe | https://www.protocols.io/view/automated-transfer-of-inactivated-virus-samples-fr-bfb2jiqe | Efthymios Fidanis, Sophia Ward, Laura Cubitt, Amelia Edwards, Debbie Hughes, Michael Hubank, Jerome Nicod | TITLE: Automated transfer of inactivated virus samples from individual 2ml tubes to 96-well plate
AUTHORS: Efthymios Fidanis, Sophia Ward, Laura Cubitt, Amelia Edwards, Debbie Hughes, Michael Hubank, Jerome Nicod
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Purpo... | ["[Transfer of inactivated virus to 96 well plates]\nSample tubes will arrive from the CL2/3 facility after virus inactivation at . Working in the reception area (in a separate room), wipe outside of tube with alcohol wipe, invert tube twice, and place in centrifuge. Pulse spin tubes.\n0 Room temperature", "[Transfer o... |
106,252 | Immunofluorescence for pSer129 alpha-synuclein and total alpha-synuclein in mouse brain | 0 | dx.doi.org/10.17504/protocols.io.5jyl82819l2w/v1 | https://www.protocols.io/view/immunofluorescence-for-pser129-alpha-synuclein-and-djzk4p4w | Laura Volpicelli-Daley, mamenard | TITLE: Immunofluorescence for pSer129 alpha-synuclein and total alpha-synuclein in mouse brain
AUTHORS: Laura Volpicelli-Daley, mamenard
[DESCRIPTION]
This protocol details the immunofluorescence of brain section for phopho-serine129-alpha-synuclein and total alpha-synuclein
[STEPS]
SECTION: Day 1
1. Pre-warm sodium... | ["[Day 1] Pre-warm sodium citrate buffer to 37 °C.", "[Day 1] Place sections in netwell inserts (Fisher Scientific 07-200-213) in 6-well plate.", "[Day 1] Wash 3X in cold 1X TBS for 5 min each with shaking (around 2 mL per well).", "[Day 1] Incubate at 37 °C for 60 min in pre-heated sodium citrate buffer (about 2 mL/we... |
58,865 | Plate Protein Expression on Autoinduction media | 4 | dx.doi.org/10.17504/protocols.io.b5qrq5v6 | https://www.protocols.io/view/plate-protein-expression-on-autoinduction-media-b5qrq5v6 | Stephane Fadanka, Chiara Gandini | TITLE: Plate Protein Expression on Autoinduction media
AUTHORS: Stephane Fadanka, Chiara Gandini
[DESCRIPTION]
The current protocol describes the preparation and use of 2X YT autoinduction medium for recombinant protein expression on Petri dishes. This protocol allows for reproducible and time effective expression ex... | ["[Preparation of the Overnight Pre-inoculum] Grow culture 10 mL of desired bacteria strain in LB broth supplemented with the appropriate antibiotic, grow overnight at 37 °C in an incubator.", "[Preparation of Auto-induction media] Prepare the needed amount of 4xYT autoinduction agar medium \n\n(It is recommended to p... |
42,698 | Thin Layer Chromatography (TLC) Bioautography | 1 | dx.doi.org/10.17504/protocols.io.bmxik7ke | https://www.protocols.io/view/thin-layer-chromatography-tlc-bioautography-bmxik7ke | Dane Lyddiard | TITLE: Thin Layer Chromatography (TLC) Bioautography
AUTHORS: Dane Lyddiard
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">A TLC bioautography protocol to test the constituents of plant extracts and essential oils for antibacterial activity was adapted and optimised from the methods described in Sm... | ["Grow Bacteria (Overnight)Prepare streak plates of bacteria on appropriate solid agar media (e.g., nutrient or Mueller-Hinton agars). Incubate overnight (aerobically) at 35°C ±1°C", "Select TLC Solvent SystemCut TLC plates (handle with gloves) to 9 x 9 cm (or smaller for testing solvent systems). Using a TLC spotter o... |
89,018 | Preparing Cholesterol for use in NGM | 1 | dx.doi.org/10.17504/protocols.io.36wgq3oe5lk5/v1 | https://www.protocols.io/view/preparing-cholesterol-for-use-in-ngm-c262yhge | Bonnie Evans | TITLE: Preparing Cholesterol for use in NGM
AUTHORS: Bonnie Evans
[DESCRIPTION]
C. elegans requires cholesterol to progress through the four larval stages.
[STEPS]
1. Prepare 5 mg/ml in Ethanol by resuspending the whole 250mg vial in 50 ml ~100% ethanol.
2. Filter sterilise using vacuum pump.
3. Store at 4 degree... | ["Prepare 5 mg/ml in Ethanol by resuspending the whole 250mg vial in 50 ml ~100% ethanol.", "Filter sterilise using vacuum pump.", "Store at 4 degrees protected from the light"] |
27,589 | Protocol- Romantic relationships and family in Spaniards emerging adults | null | dx.doi.org/10.17504/protocols.io.67dhhi6 | null | Marta Díez | TITLE: Protocol- Romantic relationships and family in Spaniards emerging adults
AUTHORS: Marta Díez
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The exploration of and search for romantic relationships is one of the developmental tasks that characterize emerging adulthood, a new developmental ph... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.e46bgze | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>SWIFT™ Western Transfer Pads For Efficient High & Low MW Protein Transfer</p>
<p>(Cat. # <a href="http://www.gbiosciences.com/ResearchProducts/swift-desc.aspx" target="_blank">786‐370 to 786‐375, 786‐370S, 786‐373S</a>)</p>
[BEFORE_START]
<p>Combine 50ml of supplied SWIF... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.ijpccmn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Please contact Dr. Steven Wilhelm (wilhelm@utk.edu) for additional information regarding this protocol.</p>
<p> </p>
<p>Adapted from Wetzel and Likens 2000. Limnological Analyses, Springer NY</p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?. | [] |
75,316 | MDL-LDA Agile Method | 1 | dx.doi.org/10.17504/protocols.io.n2bvj82mxgk5/v2 | https://www.protocols.io/view/mdl-lda-agile-method-cmsuu6ew | Freddie Prianes | TITLE: MDL-LDA Agile Method
AUTHORS: Freddie Prianes
[DESCRIPTION]
As a guide in modeling the document labels using Latent Dirichlet allocation for archived documents in an Integrated Quality Assurance System (IQAS), the researchers used the agile method as it promotes flexibility, speed, and, most importantly, contin... | ["[MDL-LDA Methodology] Plan: the researchers collected previous documents involved in the accreditation process, such as compliance reports under the areas of student, faculty, facility, library, and administration. Also, understanding of the existing problems in tracking, tagging, and duplication of these documents d... |
79,602 | Collecting needle and branch samples for terpenoid and expression analysis | 1 | null | https://www.protocols.io/view/collecting-needle-and-branch-samples-for-terpenoid-crysv7we | Vidya S Vuruputoor, Victoria Burton, Jill Wegrzyn | TITLE: Collecting needle and branch samples for terpenoid and expression analysis
AUTHORS: Vidya S Vuruputoor, Victoria Burton, Jill Wegrzyn
[DESCRIPTION]
This protocol is used by the PCG group for sampling needle and branch tissue from hemlock conifers for terpenoid analysis, as well as RNA expression analysis.
[STE... | ["Open Treesnap (https://treesnap.org/), record the accession number on the tree and fill in notes for hemlock woolly adelgid infestation (HWA) levels (scale provided by the app).", "Use the comment field to enter: EHS present OR EHS absent to record the hemlock scale.", "Take at least 3 photos with TreeSnap. This incl... |
94,452 | Propionylation and tryptic digestion | 1 | dx.doi.org/10.17504/protocols.io.5jyl8pz36g2w/v1 | https://www.protocols.io/view/propionylation-and-tryptic-digestion-c8guztww | Laura Corveleyn, Sigrid Verhelst | TITLE: Propionylation and tryptic digestion
AUTHORS: Laura Corveleyn, Sigrid Verhelst
[DESCRIPTION]
Protocol to derivatize (propionylation) and digest histone proteins into peptides with the purpose of bottom-up label free LC-MS/MS analysis. In this method, aspecific overpropionylation at serine (S), threonine (T) and... | ["[First propionylation] Start with vacuum dried sample (20 µg/sample)", "[First propionylation] Add 20 µL 1M triethylammonium bicarbonate (TEAB)", "[First propionylation] Add 20 µL prop-reagent (Isopropylalcohol:propionic anhydride (79:1))", "[First propionylation] Spin down & Incubate at room temperature for 30 minut... |
38,945 | Investigation of ancestral alleles in the Bovinae subfamily | 5 | dx.doi.org/10.17504/protocols.io.bh99j996 | https://www.protocols.io/view/investigation-of-ancestral-alleles-in-the-bovinae-bh99j996 | Maulana Naji, Yuri Utsunomiya, Johann Sölkner, Benjamin Rosen, Gábor Mészáros | TITLE: Investigation of ancestral alleles in the Bovinae subfamily
AUTHORS: Maulana Naji, Yuri Utsunomiya, Johann Sölkner, Benjamin Rosen, Gábor Mészáros
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">In evolutionary theory, divergence and speciation can arise from long periods of reproductive isol... | ["[Reads alignment and variant calling on individuals separately]\nDownload Read Sequences in format of SRA FASTQ", "[Reads alignment and variant calling on individuals separately]\nMapping with BWA-Mem", "[Reads alignment and variant calling on individuals separately]\nIndividual Haplotype Calling", "[Joint analysis o... |
108,999 | Effects of Intraoperative Hypothermia on Patients Undergoing Laparoscopic Surgery: A Retrospective Cohort Study | 0 | dx.doi.org/10.17504/protocols.io.14egn6d2yl5d/v1 | https://www.protocols.io/view/effects-of-intraoperative-hypothermia-on-patients-dnpf5djn | maliwan oofuvong | TITLE: Effects of Intraoperative Hypothermia on Patients Undergoing Laparoscopic Surgery: A Retrospective Cohort Study
AUTHORS: maliwan oofuvong
[DESCRIPTION]
This study aims to explore the association between intraoperative hypothermia and
outcomes in adult patients undergoing laparoscopic surgery. A retrospective an... | ["[Methodology] This study was approved by the Institutional Ethics Committee of the Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand in 11 July 2022 (REC 65-226-8-9). Since this is a retrospective study, informed consent was waived by the Institutional Ethics Committee of the Faculty of Medicine, ... |
49,940 | OMS Atlas FFPE Spatial Mapping | 1 | dx.doi.org/10.17504/protocols.io.buzunx6w | https://www.protocols.io/view/oms-atlas-ffpe-spatial-mapping-buzunx6w | Brett Johnson, Danielle Galipeau, Todd Camp, George Thomas | TITLE: OMS Atlas FFPE Spatial Mapping
AUTHORS: Brett Johnson, Danielle Galipeau, Todd Camp, George Thomas
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the procedure by which the OMS Atlas serially sections a FFPE block, prepares the resulting slides, and then distributes t... | ["[Preparation]\nVerify the identity of the FFPE block to be cut against written request for sectioning.", "[Preparation]\nLabel each Tanner slide with a unique BEMS ID and slide number, corresponding to the written request and FFPE spatial map (below).Note: Slides #1-4 compose the official OMS Atlas Dataset. ABC1Slid... |
64,426 | Fluxactive Complete Reviews – What are the Customers Saying? | 3 | dx.doi.org/10.17504/protocols.io.rm7vzyqp5lx1/v1 | https://www.protocols.io/view/fluxactive-complete-reviews-what-are-the-customers-ca6ishce | healthy | TITLE: Fluxactive Complete Reviews – What are the Customers Saying?
AUTHORS: healthy
[DESCRIPTION]
Fluxactive Complete has been released as a prostate wellness supplement that can support prostate health in men, which in turn helps keep their bladders and reproductive system healthy.
[STEPS] | [] |
92,381 | Protocol for "Development and characterization of a non-human primate model of diseeminated synucleinopathy" | 2 | dx.doi.org/10.17504/protocols.io.81wgbxwnylpk/v1 | https://www.protocols.io/view/protocol-for-34-development-and-characterization-o-c6f5zbq6 | jlanciego, Alberto J. Rico, Julia Chocarro, Goiaz Ariznabarreta, Elvira Roda, Adriana Honrubia, Patricia Arnaiz, Almudena Corcho | TITLE: Protocol for "Development and characterization of a non-human primate model of diseeminated synucleinopathy"
AUTHORS: jlanciego, Alberto J. Rico, Julia Chocarro, Goiaz Ariznabarreta, Elvira Roda, Adriana Honrubia, Patricia Arnaiz, Almudena Corcho
[DESCRIPTION]
Here we took advantage of a retrogradely-sp... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.hasb2ee | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol (like its companion protocol for liposome suspension and extrusion) was original created by <a href=""http://www.whoi.edu/sbl/liteSite.do?litesite" target="_blank">Krista Longnecker</a> and <a href="http://jamesrco.github.io/" target="_blank">Jamie Collins<... | [] |
95,838 | Treatment and staining of iPSC-derived neurons for lysosomal phenotype analysis | 0 | dx.doi.org/10.17504/protocols.io.e6nvwdwedlmk/v1 | https://www.protocols.io/view/treatment-and-staining-of-ipsc-derived-neurons-for-c9t6z6re | Jessica Chedid, Adahir Labrador-Garrido, Nicolas Dzamko | TITLE: Treatment and staining of iPSC-derived neurons for lysosomal phenotype analysis
AUTHORS: Jessica Chedid, Adahir Labrador-Garrido, Nicolas Dzamko
[DESCRIPTION]
This protocol describes the preparation and treatment of neuronal cultures to be imaged for its analysis using the Opera Phenix high-content screening sy... | ["[Live Cell experimental outline] 1. Prepare: DQ-red-BSA 1:100, Cytopainter green cell proliferation reagent 1:500 and Hoechst 1:100 in complete cell culture media. \nAlternatively prepare: Mitotracker 1:10.000, Lysosomal staining 1:500, Cytopainter 1:500 and Hoechst 1:100 in complete cell culture media. \n\n2. Gently... |
49,208 | Multiplexed, single-cell profiling of histone modifications with SCEPTRE | 4 | dx.doi.org/10.17504/protocols.io.buaynsfw | https://www.protocols.io/view/multiplexed-single-cell-profiling-of-histone-modif-buaynsfw | Marcus A Woodworth, Hao Yuan Kueh, Joshua C. Vaughan | TITLE: Multiplexed, single-cell profiling of histone modifications with SCEPTRE
AUTHORS: Marcus A Woodworth, Hao Yuan Kueh, Joshua C. Vaughan
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Genome architecture and activity are tightly regulated during an organism’s development and function. Histone... | ["[Cell Culture and Fixation]\nWash three times with of 1× PBS.\n250 µl", "[Immunofluorescence]\nWash cells three times with of 1× PBS.\n250 µl", "[Immunofluorescence]\nIncubate in of blocking solution for at .\n250 µl\n0 Room temperature", "[Immunofluorescence]\nIncubate in of primary solution at .\n250 µl... |
26,103 | Infant formula sample preparation for element analysis using PIXE/RBS | null | dx.doi.org/10.17504/protocols.io.5qxg5xn | null | Seth H. Frisbie, Erika J. Mitchell, Stéphane Roudeau, Florelle Domart, Asuncion Carmona, Richard Orterga | TITLE: Infant formula sample preparation for element analysis using PIXE/RBS
AUTHORS: Seth H. Frisbie, Erika J. Mitchell, Stéphane Roudeau, Florelle Domart, Asuncion Carmona, Richard Orterga
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol was developed to quantify chemical elements fro... | ["Work under a clean atmosphere to avoid dust contamination.", "Use a disposable plastic spatula to deliver between 1.0000 grams (g) and 1.0099 g of powdered product to a laboratory-grade plastic centrifuge tube.", "Add 10.00 milliliters (mL) of ultra-trace elemental analysis grade water (Water OptimaTM).", "Vortex unt... |
73,112 | A new metabarcoding approach to survey diversity at the species level of Arcellinida (Amoebozoa: Tubulinea) | 1 | dx.doi.org/10.17504/protocols.io.yxmvm2389g3p/v1 | https://www.protocols.click/view/a-new-metabarcoding-approach-to-survey-diversity-a-cjmyuk7w | R. González-Miguéns | TITLE: A new metabarcoding approach to survey diversity at the species level of Arcellinida (Amoebozoa: Tubulinea)
AUTHORS: R. González-Miguéns
[DESCRIPTION]
PCR protocol for the paper:" A needle in a haystack: a new metabarcoding approach to survey diversity at the species level of Arcellinida (Amoebozoa: Tubulinea)"... | ["[Polymerase Chain Reaction protocol] First PCR\n\nPrimers:\nPrimer forward: LCO 1490 (5´ GGTCAACAAATCATAAAGATATTGG 3´)\nPrimer reverse: HCO 2198 (5´ TAAACTTCAGGGTGACCAAAAAATCA 3´)\n\nReagents for the PCR:\n \nTotal reaction mix per sample= 10 μL\n\n\nThermocycler program:\n \n\nDenaturation temperatures and times may... |
79,877 | Virus production | 1 | dx.doi.org/10.17504/protocols.io.8epv5jpkjl1b/v1 | https://www.protocols.io/view/virus-production-cr9dv926 | michela.deleidi | TITLE: Virus production
AUTHORS: michela.deleidi
[DESCRIPTION]
Lentiviral production protocol
[STEPS]
SECTION: Virus production
2. HEK 293 T cells were seeded in a 10-cm dish to reach 80% confluency the day after
transfection.The next day, the medium was changed.
SECTION: Virus production
3. On days 4 and 5 after tra... | ["[Virus production] HEK 293 T cells were seeded in a 10-cm dish to reach 80% confluency the day after\ntransfection.The next day, the medium was changed.", "[Virus production] On days 4 and 5 after transfection, the medium was collected and filtered through a0.45-\nμm PVDF membrane.", "[Virus production] For lentivira... |
61,999 | Annexin V/PI- Assay: Flow Based Medium Throughput Assessment of Apoptotic Response to Two and Three Drug Combinations | 4 | dx.doi.org/10.17504/protocols.io.14egn7my6v5d/v1 | https://www.protocols.io/view/annexin-v-pi-assay-flow-based-medium-throughput-as-b8sprwdn | Dennis Juarez, dfruman | TITLE: Annexin V/PI- Assay: Flow Based Medium Throughput Assessment of Apoptotic Response to Two and Three Drug Combinations
AUTHORS: Dennis Juarez, dfruman
[DESCRIPTION]
Basic principals and protocol for medium throughput cell viability screening in suspension cells using Annexin V/PI staining on the Attune NXT used... | ["[Basic Principals and Planning Before Proceeding] Cells in culture can only tolerate small amounts of the vehicle in which a drug is dissolved in.\n\nAs such, you should minimize and standardize the amount of vehicle used in an experiment across all treatments.", "[Basic Principals and Planning Before Proceeding] I c... |
null | null | null | dx.doi.org/10.17504/protocols.io.rv5d686 | null | null | TITLE: No Title
AUTHORS:
[STEPS] | [] |
35,631 | DNA and RNA stabilization | null | dx.doi.org/10.17504/protocols.io.be2pjgdn | https://www.protocols.io/view/dna-and-rna-stabilization-be2pjgdn | Neilier Junior | TITLE: DNA and RNA stabilization
AUTHORS: Neilier Junior
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">DNA and RNA stabilization solution is an aqueous and non-toxic tissue storage reagent that rapidly permeates tissues to stabilize and protect nucleic acids in fresh specimens. Tissue pieces are h... | ["[Stabilization solution preparation (1.5 L)]\n935 mL of autoclaved MilliQ water700 g ammonium sulfateStir until dissolved Add 25 mL of 1 M sodium citrateAdd 40 mL of 0.5 M EDTAAdjust to pH 5.2 using concentrated H2SO4Complete the volume to 1.5 L with autoclaved MilliQ water700 g ammonium sulfateStir until dissolved A... |
80,199 | "Midnight" SARS-CoV2 genome sequencing protocol using 1200bp amplicon primer set v2 and the Nanopore Rapid library kit | 1 | null | https://www.protocols.io/view/34-midnight-34-sars-cov2-genome-sequencing-protoc-csjfwcjn | Nikki Freed, Lydia Murphy, Benjamin Schwessinger, Olin Silander | TITLE: "Midnight" SARS-CoV2 genome sequencing protocol using 1200bp amplicon primer set v2 and the Nanopore Rapid library kit
AUTHORS: Nikki Freed, Lydia Murphy, Benjamin Schwessinger, Olin Silander
[DESCRIPTION]
This protocols is part of the ANU Biosecurity mini-research project #2 "An SARS-COV2 incursion sc... | ["[cDNA preparation] You will receive a PCR strip of eight with 6 tubes containing 2uL Lunascript RT supermix. Label the tubes with 1-6 and your RG name. Note down which sample corresponds to which number.\n\nMix the following components in an 0.2mL 8-strip tube on ice; \n\nComponent ... |
49,790 | Parzenie herbaty | 1 | null | https://www.protocols.io/view/parzenie-herbaty-buu6nwze | tomasz.zielinski | TITLE: Parzenie herbaty
AUTHORS: tomasz.zielinski
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol is part of the lesson within the </span><a href="https://carpentries-incubator.github.io/fair-bio-practice/" style = "text-decoration:underline;color:blue;cursor:pointer;"><span sty... | ["[Preparation of water and tea]\nNapełnij czajnik wodą, co najmniej 300ml wody.", "[Preparation of water and tea]\nW międzyczasie przygotuj herbatę, rozpakuj ją i umieść jedna torebkę w szklance. Pamiętaj wyłożyć etykietkę na zewnątrz szklanki.", "[Preparation of water and tea]\nJak tylko woda się zagotuje wlej szybko... |
17,559 | Comparison of two column agglutination tests for red blood cell antibody testing | null | dx.doi.org/10.17504/protocols.io.vdxe27n | null | Jonas Sawierucha, Marion Posset, Viola Hähnel, Christian L. Johnson, James A. Hutchinson, Norbert Ahrens | TITLE: Comparison of two column agglutination tests for red blood cell antibody testing
AUTHORS: Jonas Sawierucha, Marion Posset, Viola Hähnel, Christian L. Johnson, James A. Hutchinson, Norbert Ahrens
[STEPS]
?. [Dataset] | ["[Dataset]"] |
78,284 | Synthetic Procedure of 3,3'-dimethoxy-5,5'-dipropyl-2,2'-biphenyldiol | 6 | dx.doi.org/10.17504/protocols.io.yxmvm2mr6g3p/v1 | https://www.protocols.io/view/synthetic-procedure-of-3-3-39-dimethoxy-5-5-39-dip-cqpkvvkw | Lisa.Stanley, rui.katahira, Gregg T. Beckham | TITLE: Synthetic Procedure of 3,3'-dimethoxy-5,5'-dipropyl-2,2'-biphenyldiol
AUTHORS: Lisa.Stanley, rui.katahira, Gregg T. Beckham
[DESCRIPTION]
A direct understanding of the degradation reaction pathways of lignin polymers in biomass is difficult due to the complexity of lignin’s structure. To overcome th... | ["[Synthetic Procedure]", "[Synthetic Procedure] 4-propylguaiacol (5.00 g , 0.03 mol) was dissolved in acetone (75 mL ) then diluted with 500 mL of acetic acid buffer (pH 5) [see Note 1]. Oxygen gas (O2) was bubbled through the buffer solution for 30 minutes. 75 mg of laccase (>0.5 U/mg) was then added to the solution.... |
15,876 | Legume-rhizobia interactions in a complex microbiome | null | dx.doi.org/10.17504/protocols.io.trcem2w | null | Ming-Dao Chia | TITLE: Legume-rhizobia interactions in a complex microbiome
AUTHORS: Ming-Dao Chia
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Contains all documented protocols used for Ming-Dao Chia's Honours project, "Legume-rhizobia interactions in a complex microbiome"</div></div>
[STEPS] | [] |
62,100 | Superior Keto: KETOGENIC DIET INGREDIENTS, BENEFITS AND POSSIBLE SIDE EFFECTS? | 3 | dx.doi.org/10.17504/protocols.io.bp2l6136rvqe/v1 | https://www.protocols.io/view/superior-keto-ketogenic-diet-ingredients-benefits-b8vurw6w | Superior Keto | TITLE: Superior Keto: KETOGENIC DIET INGREDIENTS, BENEFITS AND POSSIBLE SIDE EFFECTS?
AUTHORS: Superior Keto
[DESCRIPTION]
Superior Keto
[STEPS] | [] |
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