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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39,141 | Eosin-5’-maleimide (EMA) binding test with fluorecent beads | 4 | dx.doi.org/10.17504/protocols.io.bigdkbs6 | https://www.protocols.io/view/eosin-5-maleimide-ema-binding-test-with-fluorecent-bigdkbs6 | Andreas Glenthoej, Jesper Petersen | TITLE: Eosin-5’-maleimide (EMA) binding test with fluorecent beads
AUTHORS: Andreas Glenthoej, Jesper Petersen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The flow cytometry-based eosin-5’-maleimide (EMA) binding test is used for reliable diagnostics of hereditary spherocytosis, a relatively com... | ["[Run samples on the Flow Cytometer]\nPrepare FACS-tubes for beads:Label 3 tubes for beads and add 500 µl PBS to each.Add 1 drop of beads to each tube (Calibration beads, Blank beads, and rainbow beads).Calibration beads and blank beads are part of a calibration kit from Agilent (#K011011-2)Rainbow beads are puchased ... |
null | null | null | dx.doi.org/10.17504/protocols.io.igzcbx6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Please contact Dr. Steven Wilhelm (wilhelm@utk.edu) for additional information regarding this protocol.</p>
[STEPS]
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53,418 | p1 21/09 | 1 | dx.doi.org/10.17504/protocols.io.byeiptce | https://www.protocols.io/view/p1-21-09-byeiptce | name go test surname | TITLE: p1 21/09
AUTHORS: name go test surname
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">test </div></div>
[STEPS]
?. test
?. test 2 | ["test", "test 2"] |
null | null | null | dx.doi.org/10.17504/protocols.io.t2ceqaw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Please see uploaded laboatory protocol in word and pdf-format.
[STEPS]
?. | [] |
37,336 | Making inexpensive light-powered Chlamydomonas reinhardtii (a green micro-alga) bead bracelets/necklaces for teaching the interplay of photosynthesis and cellular respiration to K4-K16 students. | 1 | dx.doi.org/10.17504/protocols.io.bgpyjvpw | https://www.protocols.io/view/making-inexpensive-light-powered-chlamydomonas-rei-bgpyjvpw | Mautusi Mitra, Sara Broom, Kysis Pinto , Sovi-Mya Doan Wellons , Ariel Dominique Roberts | TITLE: Making inexpensive light-powered Chlamydomonas reinhardtii (a green micro-alga) bead bracelets/necklaces for teaching the interplay of photosynthesis and cellular respiration to K4-K16 students.
AUTHORS: Mautusi Mitra, Sara Broom, Kysis Pinto , Sovi-Mya Doan Wellons , Ariel Dominique Roberts
[DESCRIPTION]... | ["Algal media and cultures: Maintain Chlamydomonas wild type strain 4A+ strain in the lab on Tris-Acetate Phosphate (TAP) agar media plates [17] in dim light intensities (15-20 µmol m-2s-1) at 25°C. Start a starter culture of 4A+ approximately 10-12 days before the lab activity by inoculating 10 mL of liquid TAP media ... |
94,572 | Imaging and analysis of mouse midbrain tissue labeled by RNAscope | 1 | null | https://www.protocols.io/view/imaging-and-analysis-of-mouse-midbrain-tissue-labe-c8kkzuuw | William S Conrad | TITLE: Imaging and analysis of mouse midbrain tissue labeled by RNAscope
AUTHORS: William S Conrad
[DESCRIPTION]
Below we describe imaging, analysis and cell counts of coronal sections of mouse substantia nigra and ventral
tegmental area labeled with Slc17a6 (VGLUT2), Slc32a1 (VGAT), and Slc18a2 (VMAT2).
[STEPS]
SECT... | ["[A. Imaging] Remove labeled slides from storage. If slides are not clean, spray both sides with a 70% ethanol 30% distilled water solution and wipe clean with lens paper.", "[A. Imaging] Turn on computer, confocal microscope, and lasers (helium-neon, diode-pumped solid-state, argon, and diode). Start ZEN Blac... |
90,291 | SDS-PAGE | 1 | dx.doi.org/10.17504/protocols.io.4r3l22er4l1y/v1 | https://www.protocols.io/view/sds-page-c4etyten | Alexander Röntgen | TITLE: SDS-PAGE
AUTHORS: Alexander Röntgen
[DESCRIPTION]
Protocol for running an SDS-PAGE.
[STEPS]
SECTION: Sample preparation
1. Dilute NuPAGE Sample Buffer 4X Concentrate into protein samples
SECTION: Sample preparation
2. Heat for 10 min at 95 °C
SECTION: Gel
3. Run gel at ~150 V for 35 min
SECTION: Gel
4. Inc... | ["[Sample preparation] Dilute NuPAGE Sample Buffer 4X Concentrate into protein samples", "[Sample preparation] Heat for 10 min at 95 °C", "[Gel] Run gel at ~150 V for 35 min", "[Gel] Incubate in staining solution until bands appear", "[Gel] Image using ChemiDoc MP Imaging system"] |
49,346 | SPARC_Bolser- Stimulation of Upper Airway Afferents with Capsaicin and Section of the Superior Laryngeal Nerve Modulate Mechanically Induced Coughing from the Tracheobronchial Airways | 1 | dx.doi.org/10.17504/protocols.io.bufantie | https://www.protocols.io/view/sparc-bolser-stimulation-of-upper-airway-afferents-bufantie | Donald Bolser | TITLE: SPARC_Bolser- Stimulation of Upper Airway Afferents with Capsaicin and Section of the Superior Laryngeal Nerve Modulate Mechanically Induced Coughing from the Tracheobronchial Airways
AUTHORS: Donald Bolser
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Airway diseases that induce coughing o... | ["Anesthetize animal with 2% sevoflurane. Once anesthetized, wean onto sodium pentobarbital anesthesia (28 mg/kg, iv). Animals will be allowed to spontaneously breathe.", "Place femoral venous and arterial catheters, a urinary catheter, and cannulate trachea. Record esophageal pressure via a balloon catheter placed in ... |
85,963 | Immunoblots | 4 | dx.doi.org/10.17504/protocols.io.n2bvj388wlk5/v1 | https://www.protocols.io/view/immunoblots-cx7jxrkn | wusj, Nancy C. Hernandez Villegas, Iona Thomas-Wright, Richard Wade-Martins, schekman | TITLE: Immunoblots
AUTHORS: wusj, Nancy C. Hernandez Villegas, Iona Thomas-Wright, Richard Wade-Martins, schekman
[DESCRIPTION]
This protocol describes a standard procedure for protein separation and identification of protein of interest.
Protocol overview:
The steps of this protocol is similar for different source... | ["[Immunoblots] Cell lysate, cytosol, or membrane samples, and EV samples were mixed with SDS sample loading\nbuffer. For cell lysate, cytosol or membrane samples, 20 μg proteins were loaded. For EV samples, the maximal amount up to 20uL were loaded.", "[Immunoblots] Samples with DNAJC5 and α-syn were heated at 55°C fo... |
null | null | null | dx.doi.org/10.17504/protocols.io.i4tcgwn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><em>Escherichia </em><em>C</em><em>oli</em><em>,</em> also known as <em>E. coli, </em>is the most widely studied prokaryotic model organism, and an important species in the field of biotechnology and microbiology, where it has served as the host organism for the majority of w... | [] |
32,069 | DNA quantification in plates (picogreen protocol) | null | dx.doi.org/10.17504/protocols.io.bbjdiki6 | null | Jenn Coughlan, Jen Modliszewski, Cathy Rushworth | TITLE: DNA quantification in plates (picogreen protocol)
AUTHORS: Jenn Coughlan, Jen Modliszewski, Cathy Rushworth
[STEPS]
?. [Sample Prep + Standard Curve]
Allow the Quant-iT PicoGreen reagent to warm to room temperature before opening the vial. PicoGreen is light sensitive; while thawing, wrap in aluminum foil, stic... | ["[Sample Prep + Standard Curve]\nAllow the Quant-iT PicoGreen reagent to warm to room temperature before opening the vial. PicoGreen is light sensitive; while thawing, wrap in aluminum foil, stick in desk drawer. Note: PicoGreen takes a long time to thaw—maybe an hour.", "[Sample Prep + Standard Curve]\nPrepare a 1x w... |
85,452 | What are the implications and impacts of current digital health interventions for children and adolescents with diagnoses ADHD? | 4 | dx.doi.org/10.17504/protocols.io.5jyl8p9d6g2w/v1 | https://www.protocols.io/view/what-are-the-implications-and-impacts-of-current-d-cxpkxmkw | ajamisam | TITLE: What are the implications and impacts of current digital health interventions for children and adolescents with diagnoses ADHD?
AUTHORS: ajamisam
[DESCRIPTION]
Attention deficit hyperactivity disorder (ADHD) has become increasingly relevant in
the wake of a technology centred and stimulation rich society. ADHD... | ["[Data extraction] Studies collected throughout the search process will be processed through Microsoft Excel and Rayyan (a free web based systematic review software), whereby any duplicates will be removed, and studies will be sorted to either be included or excluded based on the previously defined criteria.", "[Data ... |
88,815 | Graphing area from an image series using ImageJ: a simple method | 1 | dx.doi.org/10.17504/protocols.io.n2bvj326blk5/v1 | https://www.protocols.io/view/graphing-area-from-an-image-series-using-imagej-a-c2ypyfvn | Vanessa R Ho, Sally P Leys | TITLE: Graphing area from an image series using ImageJ: a simple method
AUTHORS: Vanessa R Ho, Sally P Leys
[DESCRIPTION]
This protocol provides a quick way to quantify change in area of an object in a large series of images, by pixel contrast. It's equivalent to rootpainter, except much simpler, but it does rely on g... | ["Create a workflow (macro) in ImageJ with the following steps: This will be run on all your images.\nOpen ImageJ\nOpening an image, \nSelecting Plugin>Macro>Record, which opens up a ‘recorder’ window.", "Recording the macro for image processing: \nSet image type to 8-bit grayscale\nSelect the rectangular selection too... |
101,436 | 100ml 5M Sodium Chloride (NaCl) | 0 | null | https://www.protocols.io/view/100ml-5m-sodium-chloride-nacl-dfa43igw | Menglin WANG | TITLE: 100ml 5M Sodium Chloride (NaCl)
AUTHORS: Menglin WANG
[DESCRIPTION]
This is a recipe for how to make 100ml 5M Sodium Chloride (NaCl).
[STEPS]
SECTION: 5M Sodium Chloride (NaCl,100ml)
1. Weigh out an amount of 29.22 g of in an appropriate-size beaker or conical flask (1L volume). Add 80 mL of .
Precauti... | ["[5M Sodium Chloride (NaCl,100ml)] Weigh out an amount of 29.22 g of in an appropriate-size beaker or conical flask (1L volume). Add 80 mL of .\n\nPrecaution: Do not add 100 ml of deionized/Milli-Q water. In most cases, solution volume increases when a large amount of solute is dissolved in a solvent.", "[5M So... |
92,652 | Spatial N-glycomics with MALDI-MSI for human lung tissue | 1 | null | https://www.protocols.io/view/spatial-n-glycomics-with-maldi-msi-for-human-lung-c6qkzduw | Dusan Velickovic, Chris Anderton | TITLE: Spatial N-glycomics with MALDI-MSI for human lung tissue
AUTHORS: Dusan Velickovic, Chris Anderton
[DESCRIPTION]
This protocol describes the procedure to obtain high quality MALDI mass spectrometry images of N-linked glycans from formalin-fixed paraffin embedded tissue. This protocol is optimized for human lun... | ["[Scope] This protocol describes the procedure to obtain high quality matrix-assisted laser desorption/ionization (MALDI) mass spectrometry images of N-linked glycans from formalin-fixed paraffin embedded tissue.", "[Health and Safety] Wear nitrile gloves and safety glasses. Follow standard laboratory safety procedure... |
19,448 | Detection of respiratory viruses or housekeeping genes by qPCR (Taqman) – primers and probes | null | dx.doi.org/10.17504/protocols.io.w8yfhxw | null | José Luiz-Proença Modena, Flavia Escremim de Paula, Eurico Arruda | TITLE: Detection of respiratory viruses or housekeeping genes by qPCR (Taqman) – primers and probes
AUTHORS: José Luiz-Proença Modena, Flavia Escremim de Paula, Eurico Arruda
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. Detection of hRSV-A/B; hMPV-A/B (Duplex format of qPCR-Taqman). For final volume rea... | ["Detection of hRSV-A/B; hMPV-A/B (Duplex format of qPCR-Taqman). For final volume reaction of 15µl, add 3µL cDNA, 0.5µL Primer Foward A (10pM), 0.5µL Primer Reverse A (10pM), 0.5µL Primer Foward B (10pM), 0.5µL Primer Reverse B (10pM), 0.25µL Probe A (10pM), 0.25µL probe B (10pM).", "Detection of FLU-A, FLU-B, PIV-1, ... |
90,565 | DNA EXTRACTION Protocol Template | 1 | null | https://www.protocols.io/view/dna-extraction-protocol-template-c4pdyvi6 | Kathleen Pitz, Raissa.meyer | TITLE: DNA EXTRACTION Protocol Template
AUTHORS: Kathleen Pitz, Raissa.meyer
[DESCRIPTION]
A protocol template created through the BeBOP project for DNA Extraction.
[STEPS]
SECTION: MIOP: Minimum Information about an Omics Protocol
1.
MIOP Term
Value
methodology category
project
purpose
analyses
g... | ["[MIOP: Minimum Information about an Omics Protocol] MIOP Term\nValue\n \nmethodology category\n\n \nproject\n\n \npurpose\n\n \nanalyses\n\n \ngeographic location\n\n \nbroad-scale environmental context\n\n \nlocal environmental context\n\n \nenvironmental medium\n\n \ntarget\n\n \ncreator\n\n \nmaterials required\... |
null | null | null | dx.doi.org/10.17504/protocols.io.u2ueyew | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Surfactants are compounds that lower the surface tension between two liquids, between a gas and a liquid, or between a liquid and a solid. Surfactants can be used as detergents, wetting agents, emulsifiers, foaming agents and dispersants.
[STEPS] | [] |
69,597 | Infection of nalidixic-acid treated mice with bioluminescent derivatives of Citrobacter rodentium by oral gavage | 4 | dx.doi.org/10.17504/protocols.io.j8nlkwbjxl5r/v1 | https://www.protocols.io/view/infection-of-nalidixic-acid-treated-mice-with-biol-cf75trq6 | Hannah Read, Siouxsie Wiles | TITLE: Infection of nalidixic-acid treated mice with bioluminescent derivatives of Citrobacter rodentium by oral gavage
AUTHORS: Hannah Read, Siouxsie Wiles
[DESCRIPTION]
Citrobacter rodentium is a Gram-negative bacterium which infects laboratory mice in a similar way to how enteropathogenic Escherichia coli (EPEC) an... | ["[Preparation of bioluminescent Citrobacter rodentium derivatives] At least two days before needed, revive bacteria from frozen stocks stored at –80°C. Plate onto LB-Lennox media. At this stage, you can grow them with or without kanamycin 50 ug/mL . Incubate 1440 min at 37 °C", "[Preparation of bioluminescent Citrob... |
71,354 | Discovery of RNA and DNA viruses using next-generation sequencing: Metagenomics | 4 | dx.doi.org/10.17504/protocols.io.261ge34zol47/v1 | https://www.protocols.io/view/discovery-of-rna-and-dna-viruses-using-next-genera-chw2t7ge | Lily Tong, Katherine Smollett, Jenna Nichols, Kirsty Kwok, Kyriaki Nomikou, Ma. Jowina Galarion, Daniel Mair, Ana Filipe | TITLE: Discovery of RNA and DNA viruses using next-generation sequencing: Metagenomics
AUTHORS: Lily Tong, Katherine Smollett, Jenna Nichols, Kirsty Kwok, Kyriaki Nomikou, Ma. Jowina Galarion, Daniel Mair, Ana Filipe
[DESCRIPTION]
Next-generation sequencing is a powerful tool for viral genomics. Viruses often constit... | ["[Initial sample preparation] Split each nucleic acid extract into two subsamples for RNA and DNA virus detection.", "[Initial sample preparation] If required, make up each sample to 50 µL with Nuclease-free water.", "[Initial sample preparation] Prepare two 0.2 mL PCR tubes per sample labelled with R (for the RNA pre... |
null | null | null | dx.doi.org/10.17504/protocols.io.ejjbckn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Adenosine-to-inosine (A-to-I) deamination is a functionally important modification of RNA that occurs in many metazoan nuclear transcripts, in several types tRNAs, and in mitochondrial transcripts of diplonemid protists. Several conceptually different methods exists to identify ... | [] |
97,934 | Processing of pediatric bronchoalveolar lavage samples for single cell analysis v 3 | 4 | dx.doi.org/10.17504/protocols.io.6qpvr8ox2lmk/v1 | https://www.protocols.io/view/processing-of-pediatric-bronchoalveolar-lavage-sam-dbvn2n5e | Shivanthan Shanthikumar, Liam Gubbels, Melanie R Neeland | TITLE: Processing of pediatric bronchoalveolar lavage samples for single cell analysis v 3
AUTHORS: Shivanthan Shanthikumar, Liam Gubbels, Melanie R Neeland
[DESCRIPTION]
This protocol describes the collection, processing, cryopreservation and thawing of pediatric bronchoalveolar lavage (BAL) samples for downstream si... | ["[COLLECTION OF BRONCHOALVEOLAR LAVAGE (BAL)] After obtaining informed consent from family and/or patient, obtain any excess BAL fluid collected at the time of clinically indicated bronchoscopy and lavage.", "[COLLECTION OF BRONCHOALVEOLAR LAVAGE (BAL)] For guidelines on how to safely perform bronchoscopy and lavage i... |
50,513 | Expression and purification protocol of GST-OPTN or (S177D, S473D) | 1 | dx.doi.org/10.17504/protocols.io.bvjrn4m6 | https://www.protocols.io/view/expression-and-purification-protocol-of-gst-optn-o-bvjrn4m6 | Chunmei Chang, Chunmei Chang | TITLE: Expression and purification protocol of GST-OPTN or (S177D, S473D)
AUTHORS: Chunmei Chang, Chunmei Chang
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol details the expression and purification protocol of GST-OPTN or (S177D, S473D).</div></div>
[STEPS]
?. [Protein expression]
... | ["[Protein expression]\nTransform the E.Coli BL21DE3 cells with plasmid encoding for GST-OPTN and plated them on Amp plate.", "[Protein expression]\nCarry out the protein expression in LB medium, induce with IPTG (isopropyl- -d-thiogalactopyranoside) to an OD600 of 0.8 and grow at .\n1.5 L\n18 °C", "[Protein express... |
59,372 | Minimal Basal Medium (liquid) | 1 | dx.doi.org/10.17504/protocols.io.b58kq9uw | https://www.protocols.io/view/minimal-basal-medium-liquid-b58kq9uw | Christa Smith | TITLE: Minimal Basal Medium (liquid)
AUTHORS: Christa Smith
[DESCRIPTION]
A defined artificial seawater medium for growing bacteria.
[BEFORE_START]
Acid wash all glassware with 10% HCl and rinse well with dH2O.
[GUIDELINES]
Increase or decrease amount proportionally to prepare stock quantities as needed. Add dry re... | ["[Sea Salt Solution] Add 20 g Sigma Sea Salts into a 1 L glass bottle.", "[Sea Salt Solution] Add 699 mL dH2O to sea salts in bottle and mix well to dissolve.", "[Sea Salt Solution] Set prepared sea salt solution aside until ready to autoclave.", "[FeEDTA Stock] Add 50 mg FeEDTA into a 250 mL glass bottle.", "[FeEDTA ... |
101,820 | Direct Detection of poliovirus and Nanopore Sequencing (DDNS) - Stool | 4 | dx.doi.org/10.17504/protocols.io.rm7vzbyyxvx1/v4 | https://www.protocols.io/view/direct-detection-of-poliovirus-and-nanopore-sequen-dfn43mgw | Alex Shaw, Catherine Troman, Joyce Akello, Erika Bujaki, Manasi Majumdar, Shannon Fitz, Ben Bellekom, Aine OToole, c.ansley, rachel.colquhoun, arshady, khurshida, alammu, Andrew Rambaut, Javier Martin, Nick Grassly | TITLE: Direct Detection of poliovirus and Nanopore Sequencing (DDNS) - Stool
AUTHORS: Alex Shaw, Catherine Troman, Joyce Akello, Erika Bujaki, Manasi Majumdar, Shannon Fitz, Ben Bellekom, Aine OToole, c.ansley, rachel.colquhoun, arshady, khurshida, alammu, Andrew Rambaut, Javier Martin, Nick Grassly
[DESCRIPTION]
This... | ["[First Round PCR (semi-nest)] Prepare a master mix using the reaction volumes detailed in the table below for the number of samples you have plus negative controls. The reaction mix and SSIII enzyme are provided in \n\n\nForward primer: Y7 [GGGTTTGTGTCAGCCTGTAATGA] \n\nReverse Primers: Cre [TCAATACGGTGTTTGCTCTTGAAC... |
null | null | null | dx.doi.org/10.17504/protocols.io.rv3d68n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><strong>Introduction</strong></p>
<p>As biopharmaceutical technology becomes more widely used in the treatment of diseases such as rheumatology, cancer and other chronic diseases, professionals in the pharmaceutical industry predict that half of the newly approved drugs will ... | [] |
68,514 | Generation of human colon organoids from healthy and inflammatory bowel disease mucosa | 4 | dx.doi.org/10.17504/protocols.io.rm7vz3wr4gx1/v2 | https://www.protocols.io/view/generation-of-human-colon-organoids-from-healthy-a-ce6athae | Isabella Dotti, Aida Mayorgas, Azucena Salas | TITLE: Generation of human colon organoids from healthy and inflammatory bowel disease mucosa
AUTHORS: Isabella Dotti, Aida Mayorgas, Azucena Salas
[DESCRIPTION]
Ulcerative colitis and Crohn’s Disease are chronic inflammatory bowel diseases (IBD) of unknown cause characterized by a relapsing-remitting behavior. Gro... | ["[1. Intestinal crypt isolation (day 1)] Collect 4-8 colonic biopsies (from non-IBD or IBD subject) obtained during the colonoscopy procedure, in a 15 mL Falcon tube containing 10 mL HBSS, preferably cold. \n\n \n\n \n\nALTERNATIVE PROTOCOL: For isolation of intestinal crypts from a surgical sample, follow Steps 14-31... |
51,201 | Immuno-correlative light and electron microscopy (iCLEM) using STEM | 4 | dx.doi.org/10.17504/protocols.io.bv89n9z6 | https://www.protocols.io/view/immuno-correlative-light-and-electron-microscopy-i-bv89n9z6 | Viola Oorschot, Jillian C Danne, Benjamin Lindsey, Jan Kaslin, Georg Ramm | TITLE: Immuno-correlative light and electron microscopy (iCLEM) using STEM
AUTHORS: Viola Oorschot, Jillian C Danne, Benjamin Lindsey, Jan Kaslin, Georg Ramm
[DESCRIPTION]
Immuno- correlative light and electron microscopy (iCLEM) combines ultrastructural information obtained from high resolution electron microscopy... | ["[Tissue fixation] Dissect out the tissue of interest (example, forebrain of Tg(proliferating cell nuclear antigen:GFP) transgenic adult zebrafish with olfactory bulbs attached for tissue orientation) on a teflon plate or dental wax sheet using fine forceps and a scalpel blade, at room temperature and place in fixativ... |
30,568 | Detection of Batrachochytrium dendrobatidis (Bd) and amphibians DNA metabarcoding | null | dx.doi.org/10.17504/protocols.io.94gh8tw | null | Omneya Ahmed Osman, Alexander Eiler, Mats Töpel, Tomas Larsson, Johan Andersson | TITLE: Detection of Batrachochytrium dendrobatidis (Bd) and amphibians DNA metabarcoding
AUTHORS: Omneya Ahmed Osman, Alexander Eiler, Mats Töpel, Tomas Larsson, Johan Andersson
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">This protocol explain the qPCR assay for... | [] |
25,399 | ABTS decolorization assay – in vitro antioxidant capacity | null | dx.doi.org/10.17504/protocols.io.42xgyfn | null | Daniel C. Moreira | TITLE: ABTS decolorization assay – in vitro antioxidant capacity
AUTHORS: Daniel C. Moreira
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:justify">This protocol describes how to perform the ABTS decolorization assay to assess potential in vitro antioxidan... | ["[ABTS radical preparation]\nPrepare a 7 mM ABTS (e.g., A1888, Sigma-Aldrich) stock solution in ultrapure water.Example: Dilute 3.8408 mg in a final volume of 1,000 µL1.1Note that you will need 570 µL (190 µL for each replicate) of the final ABTS• stock solution per sample; 400 µL of the ABTS solution produces approxi... |
106,765 | JAX-Sen: Collection and shipment of specimen for single-cell RNA sequencing (scRNA-Seq) | 0 | dx.doi.org/10.17504/protocols.io.kxygxy4b4l8j/v2 | https://www.protocols.io/view/jax-sen-collection-and-shipment-of-specimen-for-si-dkhm4t46 | Laura Robinson, Susan Sheehan, Gaven Garland, Ron Korstanje | TITLE: JAX-Sen: Collection and shipment of specimen for single-cell RNA sequencing (scRNA-Seq)
AUTHORS: Laura Robinson, Susan Sheehan, Gaven Garland, Ron Korstanje
[DESCRIPTION]
These samples are part of the JAX-Sen project in the SenNet Consortium. Here we provide details on specimen collection and shipment to the Ro... | ["[Reagents and Materials:] 2mL Eppendorf tubes or 5 ml Eppendorf tubes\nMACS tissue storage Solution (#130-100-008, MACS Miltenyi Biotech), \ncold storage (4 degrees Celsius)\nTweezers (clean, sterile)", "[Quality Key Points:] The tissue specimen should be kept at 4 degrees Celsius and RNAse-free from its excision unt... |
18,132 | microC-protocol | null | dx.doi.org/10.17504/protocols.io.vxue7nw | null | Dimitrios Voukantsis, Kenneth Kahn, Martin Hadley, Rowan Wilson, Francesca M Buffa | TITLE: microC-protocol
AUTHORS: Dimitrios Voukantsis, Kenneth Kahn, Martin Hadley, Rowan Wilson, Francesca M Buffa
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">microC is a multiscale virtual microenvironment for perturbation biology. It enables experiments that link genotype to phenotype taking i... | ["[Accessing microC]\nmicroC is available via microc.org. During the first visit this step might take several seconds. This will not be the case in future visits.", "[Preparing an experiment]\nExperiments are specified via the microC main web page (Figure 1). The user may set a number of numerical parameters via slider... |
50,105 | An Optimized Protocol for the Generation of Cortical Neurons from human iPSCs under Defined Conditions | 1 | dx.doi.org/10.17504/protocols.io.bu6znzf6 | https://www.protocols.io/view/an-optimized-protocol-for-the-generation-of-cortic-bu6znzf6 | Clare L Parish, Lachlan L Thompson | TITLE: An Optimized Protocol for the Generation of Cortical Neurons from human iPSCs under Defined Conditions
AUTHORS: Clare L Parish, Lachlan L Thompson
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is about cortical differentiation.</div></div>
[STEPS]
?. [Day -1:]
Coat plastic ce... | ["[Day -1:]\nCoat plastic cell culture plate (laminin 521 ).Make single cells of hPSCs using accutase for - @ .Seed cells @ 375K/cm2.\n37 °C", "[d0:]\nmTESR1 media change ~1-2 hrs (up to 6 hrs) prior to differentiation initiation.", "[d0:]\nWash cells with PBS-/- ( for 48 wells, for 96 wells).\n500 µl\n200 µl", "[d0:]... |
95,504 | Extraction of Total Nucleic Acid from Environmental Samples for the Detection of Bacterial and Viral Targets | 4 | dx.doi.org/10.17504/protocols.io.5jyl8pyzdg2w/v1 | https://www.protocols.io/view/extraction-of-total-nucleic-acid-from-environmenta-c9hqz35w | Dilip Abraham, Venkata Raghava Mohan, Mami Taniuchi, Nirmal kumar | TITLE: Extraction of Total Nucleic Acid from Environmental Samples for the Detection of Bacterial and Viral Targets
AUTHORS: Dilip Abraham, Venkata Raghava Mohan, Mami Taniuchi, Nirmal kumar
[DESCRIPTION]
This procedure describes a modified extraction procedure to isolate both DNA and RNA from wastewater samples using... | ["[Total Nucleic Acid extraction (TNA)] Kit used", "[Total Nucleic Acid extraction (TNA)] For Moore swab samples: Add the cut membrane filter strips to 2ml Screw Cap Micro Tubes containing ~ 370 mg (one 2 ml eppendorf tube capful) of acid-washed glass beads.", "[Total Nucleic Acid extraction (TNA)] Include one extra ... |
89,023 | Bulk RNASeq Delivery | 5 | dx.doi.org/10.17504/protocols.io.rm7vzxx9rgx1/v2 | https://www.protocols.io/view/bulk-rnaseq-delivery-c267yhhn | Tyler Stahl | TITLE: Bulk RNASeq Delivery
AUTHORS: Tyler Stahl
[DESCRIPTION]
This protocol will give an overview of the grc data delivery structure and results files
[STEPS]
SECTION: Analysis Overview
1. In brief, the RNASeq analysis follows pre-processing (quality control/filtering/trimming), alignment, post-processing, and dif... | ["[Analysis Overview] In brief, the RNASeq analysis follows pre-processing (quality control/filtering/trimming), alignment, post-processing, and differential expression analysis between sample groups with DESeq2. A detailed overview of the analysis can be found in the README.txt and methods.txt file. Also, please see ... |
null | null | null | dx.doi.org/10.17504/protocols.io.k74czqw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>RNA coIP from gradients</p>
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.ibdcai6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol offers a optimal timing of vitrification after TE biopsy. The findings are useful for further enhancing the clinical outcomes obtained from vitrified euploid embryos.</p>
[STEPS]
?.
?.
?.
?.
?. | [] |
36,536 | Electrophysiological recording of electrically-evoked compound action potentials | 1 | dx.doi.org/10.17504/protocols.io.bfwyjpfw | https://www.protocols.io/view/electrophysiological-recording-of-electrically-evo-bfwyjpfw | James Fallon, Sophie Payne | TITLE: Electrophysiological recording of electrically-evoked compound action potentials
AUTHORS: James Fallon, Sophie Payne
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Recording electrically-evoked compound action potentials (ECAPs) is performed to confirm that the electrode array is appropriate... | ["[Electrophysiological testing]\nThis procedure is performed immediately following implantation surgery or in awake, unrestrained animals. The electrical impedance of the array are tested using a custom stimulation to assess any open or short circuiting of wires.", "[Electrophysiological testing]\nMeasure the impedanc... |
86,840 | L-Leucine based supramolecular gelator | 6 | dx.doi.org/10.17504/protocols.io.5qpvo3349v4o/v1 | https://www.protocols.io/view/l-leucine-based-supramolecular-gelator-cy2yxyfw | Raviraj Kusanur, Trilokchandran B, G Vijaya Kumar, M R Padmini, Sushma C, Namrata Patil, Rajalaxmi.S | TITLE: L-Leucine based supramolecular gelator
AUTHORS: Raviraj Kusanur, Trilokchandran B, G Vijaya Kumar, M R Padmini, Sushma C, Namrata Patil, Rajalaxmi.S
[DESCRIPTION]
Gels are basically made up of polymers which, are either cross-linked or entangled in order to form a solid-like network. A new class of gels know... | ["[ESTERIFICATION] L-Leucine (C6H13NO2) 2.62g (0.02 mol) and Cetyl alcohol (C16H34O) 4.85g (0.02mol) were dissolved in toluene (75 ml). P-toluene sulphonic acid monohydrate (C7H8O3S.H2O) 7.60g (0.04mol) was added.", "[ESTERIFICATION] The reaction mixture was refluxed at 95℃ for 10 hours.", "[ESTERIFICATION] The progres... |
76,799 | qPCR assay for Aquarickettsia spp. | 4 | null | https://www.protocols.io/view/qpcr-assay-for-aquarickettsia-spp-cn87vhzn | Ana Palacio, Grace Klinges, Stephanie Rosales | TITLE: qPCR assay for Aquarickettsia spp.
AUTHORS: Ana Palacio, Grace Klinges, Stephanie Rosales
[DESCRIPTION]
qPCR for the quantification of Aquarickettsia spp. ( Klinges et al., 2022) a putative parasite found in the coral A. cervicornis. This protocol has been altered by incorporating a recently published A. cervi... | ["[Prepare for qPCR] Remove PCR reagents from freezer and allow reagents to thaw on ice or at room temperature.\nWipe down PCR hood with bleach and ethanol. \nPlace consumables such as tubes, plates, plate sealers, and water in PCR hood and turn on UV light for 20 min\nOnce everything is thawed vortex PCR reagents, spi... |
85,741 | Western Blotting | 4 | dx.doi.org/10.17504/protocols.io.3byl4qbnrvo5/v1 | https://www.protocols.io/view/western-blotting-cxymxpu6 | Tae-Un Han, sidranse | TITLE: Western Blotting
AUTHORS: Tae-Un Han, sidranse
[DESCRIPTION]
We got a great result to detect alpha-synuclein and GCase protein using this WB protocol
[STEPS]
1. Prepare loading buffer as a 1:9 ratio of 2-Mercaptoethanol (4 °C) to 4x Leammli sample loading buffer (ie., 50 mL2-Mercaptoethanol + 450 mL Leammli bu... | ["Prepare loading buffer as a 1:9 ratio of 2-Mercaptoethanol (4 °C) to 4x Leammli sample loading buffer (ie., 50 mL2-Mercaptoethanol + 450 mL Leammli buffe).", "Denature protein by boiling at99 °C for 5 min in the Thermocycler.", "Select right concentration of TGX precast gel (Biorad) to run and remove comb from the ca... |
83,082 | Synapse Staining - IHC - VGluT1 and PSD95 - Mouse Brain Sections | 4 | dx.doi.org/10.17504/protocols.io.6qpvr3x4zvmk/v1 | https://www.protocols.click/view/synapse-staining-ihc-vglut1-and-psd95-mouse-brain-cvdiw24e | Justin T Savage, Juan Ramirez, Dolores Irala, Cagla Eroglu | TITLE: Synapse Staining - IHC - VGluT1 and PSD95 - Mouse Brain Sections
AUTHORS: Justin T Savage, Juan Ramirez, Dolores Irala, Cagla Eroglu
[DESCRIPTION]
Instructions to stain for pre- and post-synaptic markers used to quantify the number of synapses in mouse brain. This protocol specifically labels VgluT1+ inputs whi... | ["[Day 1: Buffer preparation] Prepare 50 mL of 0.2% Triton in 1X TBS (TBST) by combining 1 mL of Triton X-100 with 49 mL of 1X TBS. Vortex to mix well.", "[Day 1: Buffer preparation] Prepare 7.5 mL of 5% Normal Goat Serum in TBST (NGST) by combining 375 μL of Goat serum with 7.125 mL of 0.2% TBST. Vortex to mix well. A... |
26,492 | Manuscript Citation | null | dx.doi.org/10.17504/protocols.io.544g8yw | null | State Key Laboratory of Water Resources and Hydropower Engineering Science, Peng Cheng | TITLE: Manuscript Citation
AUTHORS: State Key Laboratory of Water Resources and Hydropower Engineering Science, Peng Cheng
[STEPS]
?.
?. | [] |
42,031 | Protocol for mass capturing, handling, and fitting tracking devices and patagial tags on vultures | 4 | dx.doi.org/10.17504/protocols.io.bmapk2dn | https://www.protocols.io/view/protocol-for-mass-capturing-handling-and-fitting-t-bmapk2dn | M. T. Hirschauer, W. Neser, K. Wolter | TITLE: Protocol for mass capturing, handling, and fitting tracking devices and patagial tags on vultures
AUTHORS: M. T. Hirschauer, W. Neser, K. Wolter
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">VulPro is a vulture conservation organization in South Africa which has contributed to vulture resea... | ["[Tag Placement]\nWorking with the bird on its sternum, have one person hold the wing out slightly so that you have room to work but can clearly see the bend in the leading edge of the patagium by the elbow.", "[Tag Placement]\nThe piercing should be at least one centimeter away from the pro-patagial tendon.", "[Tag P... |
null | null | null | dx.doi.org/10.17504/protocols.io.g9tbz6n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p style="text-align: center;"><img style="display: block; margin-left: auto; margin-right: auto;" src="https://s3.amazonaws.com/pr-journal/hnnfjtn.png" width="100" height="90" data-src="https://s3.amazonaws.com/pr-journal/hnnfjtn.png" data-ofn="nehirarma-üst-Tr.png" /> </p>
<p... | [] |
19,917 | U Mass - Alanine Transferase | null | dx.doi.org/10.17504/protocols.io.xpmfmk6 | null | Jason Kim | TITLE: U Mass - Alanine Transferase
AUTHORS: Jason Kim
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span><span style = "font-weight:bold;"> </span></div><div class = "text-block">
This experiment involves a spectrophotometric measurement using Roche Cob... | ["Load each sample into a specialized micro-sample cup for the clinical chemistry analyzer.", "Select ALT test on display and run the analysis.", "Collect and analyze the data.", "Perform daily quality control assessment of instrumentation before analysis."] |
28,470 | Reading Sample Fluorescence (PDMPO) via Fluorometer | null | dx.doi.org/10.17504/protocols.io.72whqfe | null | Brittany Zepernick, Matthew Saxton, Steven Wilhelm | TITLE: Reading Sample Fluorescence (PDMPO) via Fluorometer
AUTHORS: Brittany Zepernick, Matthew Saxton, Steven Wilhelm
[STEPS]
?. [Calibration]
From the home screen of the device, perform the following:
?. [Calibration]
Select the 1. Button for “set-up”
?. [Calibration]
Select the 1. Button again for “mode”
?. [Calibr... | ["[Calibration]\nFrom the home screen of the device, perform the following:", "[Calibration]\nSelect the 1. Button for “set-up”", "[Calibration]\nSelect the 1. Button again for “mode”", "[Calibration]\nConfirm machine reads “simple multi-operational” (which is the mode) press ENTER.", "[Calibration]\nSelect the 2. Butt... |
37,580 | Genomic DNA extraction from anaerobic digester samples | null | null | https://www.protocols.io/view/genomic-dna-extraction-from-anaerobic-digester-sam-bgxkjxkw | Abhijeet Singh | TITLE: Genomic DNA extraction from anaerobic digester samples
AUTHORS: Abhijeet Singh
[STEPS]
?. [Kit]
Genomic DNA extraction from anaerobic digester samples using FastDNA
?. [Cell lysis]
In Lysing matrix E, weigh 250 mg solid/semi-solid sample OR add 200 µl of liquid sample* Label the lysing matrix tube on the side ... | ["[Kit]\nGenomic DNA extraction from anaerobic digester samples using FastDNA", "[Cell lysis]\nIn Lysing matrix E, weigh 250 mg solid/semi-solid sample OR add 200 µl of liquid sample* Label the lysing matrix tube on the side of the tube and not on the top of the cap (chances of label being disappear during the process)... |
35,032 | SARS-CoV-2 Genome Sequencing Using Long Pooled Amplicons on Illumina Platforms | null | dx.doi.org/10.17504/protocols.io.befyjbpw | null | John-Sebastian Eden, Eby Sim | TITLE: SARS-CoV-2 Genome Sequencing Using Long Pooled Amplicons on Illumina Platforms
AUTHORS: John-Sebastian Eden, Eby Sim
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes methods to sequence SARS-CoV-2 with pooled amplicons (14 x 2.5kb) using Illumina Platforms.</div></div>
... | ["[Viral RNA extraction]\nAdd to each 200 μl sample and mix well by gentle vortexing.\n[Viral RNA Buffer]", "[Viral RNA extraction]\nTransfer the mixture into a Zymo-Spin IC column placed in a collection tube. Centrifuge at for to bind viral RNA to matrix.\nCentrifuge: 12000 34", "[Viral RNA extraction]\nTransfer th... |
63,437 | Nanopore genome sequencing with barcode | 4 | dx.doi.org/10.17504/protocols.io.dm6gpb2wjlzp/v1 | https://www.protocols.click/view/nanopore-genome-sequencing-with-barcode-b97mr9k6 | phangguanjie | TITLE: Nanopore genome sequencing with barcode
AUTHORS: phangguanjie
[DESCRIPTION]
The modified version of official protocol using Kappa chemicals
[STEPS]
SECTION: Step1. End-prep & A-Tailing
1. In a 200μl PCR tube, mix the following:
SECTION: Step1. End-prep & A-Tailing
1.1. Ensure the components are tho... | ["[Step1. End-prep & A-Tailing] In a 200μl PCR tube, mix the following:", "[Step1. End-prep & A-Tailing] Ensure the components are thoroughly mixed by pipetting, and spin down.", "[Step1. End-prep & A-Tailing] Using a thermal cycler, incubate at 20 °C for30 min and65 °C for 30 min. Hold at4 °C", "[Step2. Ba... |
36,027 | Passaging cancer organoid cultures | 1 | dx.doi.org/10.17504/protocols.io.bfe3jjgn | https://www.protocols.io/view/passaging-cancer-organoid-cultures-bfe3jjgn | Hazel Rogers, Laura Letchford, Sara Vieira, Maria Garcia-Casado, Mya Fekry-Troll, Charlotte Beaver, Rachel Nelson, Hayley Francies, Mathew Garnett | TITLE: Passaging cancer organoid cultures
AUTHORS: Hazel Rogers, Laura Letchford, Sara Vieira, Maria Garcia-Casado, Mya Fekry-Troll, Charlotte Beaver, Rachel Nelson, Hayley Francies, Mathew Garnett
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the passaging of organoid cult... | ["[Process Diagram]", "[Protocol]\nUsing a P1000 pipette, detach BME2 drops from the plate. (Optional - detach BME2 drops using a cell-scraper; recommended for passaging a large number of plates).", "[Protocol]\nPipette suspension up and down multiple times to dissociate organoids from BME2 and transfer to an approproa... |
56,861 | Long-read plant genome assembly and annotation: assembly | 5 | null | https://www.protocols.io/view/long-read-plant-genome-assembly-and-annotation-ass-b3r5qm86 | Scott Ferguson, Ashley Jones, Justin Borevitz | TITLE: Long-read plant genome assembly and annotation: assembly
AUTHORS: Scott Ferguson, Ashley Jones, Justin Borevitz
[DESCRIPTION]
With the introduction of long-read, third generation sequencing (e.g. Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio) and associated bioinformatics tools, we can n... | ["[Data Input] De novo genome assembly works best if long-read sequencing has been performed. For best results, optimise a high-molecular weight DNA extraction, for example we use: High-molecular weight DNA extraction, clean-up and size selection for long-read sequencing (https://journals.plos.org/plosone/article?id=10... |
71,651 | Discharge of LiPo Batteries Using Saltwater Electrolysis | 1 | dx.doi.org/10.17504/protocols.io.14egn274mg5d/v1 | https://www.protocols.io/view/discharge-of-lipo-batteries-using-saltwater-electr-ch8bt9sn | marshall.bennett | TITLE: Discharge of LiPo Batteries Using Saltwater Electrolysis
AUTHORS: marshall.bennett
[DESCRIPTION]
Procedure developed using information gathered from the following sources:
How To Dispose Of Lipo Batteries? - Standard Battery (standardbatteryinc.com)
Discharging & Disposing of LiPo Batteries – HeliDirect Suppo... | ["Dissolve non-iodized salt into water in a bucket following the measurements outlined in the chart below.", "Place the battery into a container that is sealable with a vented lid, such as a five gallon bucket.", "Carefully pour the salt/water solution into the container holding the battery so that it is completely sub... |
18,662 | Laboratory protocols for the detection and genotyping of Cervical high-risk human papillomavirus (HR-HPV) among adult women living in N'Djamena the capital city of Chad. | null | dx.doi.org/10.17504/protocols.io.wgefbte | null | Ralph-Sydney Mboumba Bouassa, Zita Aleyo Nodjikouambaye, Damtheou Sadjoli, Chatté Adawaye, Hélène Péré, David Veyer, Mathieu Matta, Leman Robin, Serge Tonen-Wolyec, Ali Mahamat Moussa, Donato Koyalta and Laurent Belec., Laurent Bélec | TITLE: Laboratory protocols for the detection and genotyping of Cervical high-risk human papillomavirus (HR-HPV) among adult women living in N'Djamena the capital city of Chad.
AUTHORS: Ralph-Sydney Mboumba Bouassa, Zita Aleyo Nodjikouambaye, Damtheou Sadjoli, Chatté Adawaye, Hélène Péré, David Veyer, Mathieu Matta, Le... | [] |
53,587 | Extraction of High Molecular Weight DNA from Aureococcus anophagefferens Virus | 1 | null | https://www.protocols.io/view/extraction-of-high-molecular-weight-dna-from-aureo-byjtpunn | Alex Truchon, Eric Gann, Steven W Wilhelm | TITLE: Extraction of High Molecular Weight DNA from Aureococcus anophagefferens Virus
AUTHORS: Alex Truchon, Eric Gann, Steven W Wilhelm
[DESCRIPTION]
High molecular weight DNA has become a necessary resource with the advancement of long-read sequencing from Nanopore ONT and PacBio SMRT. Often times excessive treatm... | ["[Viral Particle Preparation and Lysis] Infect 1 L of Aureococcus anophagefferens CCMP1984 with 10 mL of Aureococcus anophagefferens Virus (AaV) lysate.", "[Viral Particle Preparation and Lysis] Incubate cultures at 19 degrees C on a 14:10 light-dark cycle until complete lysis of the culture (~10 days).", "[Viral Part... |
null | null | null | dx.doi.org/10.17504/protocols.io.jfbcjin | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><u>Background</u>: Community nasal meningococcal carriage rates are high across Africa.</p>
<p>Meningococcal infections are major causes of morbidity and mortality in the continent;</p>
<p>especially among children and adolescents. This study aimed to determine the prevalence... | [] |
82,921 | Enriching and isolating phages in liquid culture | 4 | dx.doi.org/10.17504/protocols.io.ewov1oeeylr2/v1 | https://www.protocols.click/view/enriching-and-isolating-phages-in-liquid-culture-cu8hwzt6 | Adair Borges | TITLE: Enriching and isolating phages in liquid culture
AUTHORS: Adair Borges
[DESCRIPTION]
This protocol explains how we isolate phage from microbial communities using liquid enrichment. For a protocol on enriching and isolating on solid agar plates, check out our companion protocol.
[STEPS]
SECTION: Liquid growth e... | ["[Liquid growth enrichment] Set up cultures of your target host strains. We use this protocol for cheese bacterial isolates, which grow best in LB at 25 °C with shaking at 200 rpm, and reach high density after two days.", "[Liquid growth enrichment] After cells have grown to high density, prepare your infection media.... |
81,303 | Populus Microcuttings | 4 | null | https://www.protocols.io/view/populus-microcuttings-ctmxwk7n | Lotus Lofgren | TITLE: Populus Microcuttings
AUTHORS: Lotus Lofgren
[DESCRIPTION]
This is the protocol I use for micropropagation of trees in the genus Populus to generate germ-free plant material for microbiome/mycobiome studies. I have successfully used this protocol to generate clones of P. trichocarpa (Black cottonwood), P. delto... | ["[Make media tubes] Make .5 strength MS media. If pre-mixed (often this is the case because we go through a lot of MS) supplement with agar to increase the osmolarity to a gel, since our MS comes with agar already in it and we're making .5 strength - I supplement with 6g agar/L. Autoclave for 45 mins. \n\nAfter autoc... |
108,293 | High-throughput Smart-seq3 | 0 | dx.doi.org/10.17504/protocols.io.ewov196jolr2/v1 | https://www.protocols.io/view/high-throughput-smart-seq3-dmzd4726 | Kai-Hui Sun, Hsiu-Chun Chuang | TITLE: High-throughput Smart-seq3
AUTHORS: Kai-Hui Sun, Hsiu-Chun Chuang
[DESCRIPTION]
We built upon the Smart-seq3 protocol to develop the high-throughput Smart-seq3 (HT Smart-seq3) workflow, an automated workflow with a detailed and optimized protocol.
[STEPS]
SECTION: Single Cell Collection via FACS
1. Prepare Cel... | ["[Single Cell Collection via FACS] Prepare Cell Lysis Buffer Master Mix on the same day as single cell collection via FACS, and keep it on ice.", "[Cell Lysis] Remove the 96-well plates from the -80 °C freezer and incubate them in a thermocycler at 72 °C for 10 min, followed by a hold at 4 °C.", "[Reverse Transcriptio... |
94,175 | Hot alkaline lysis gDNA extraction from formalin-fixed archival tissues | 4 | dx.doi.org/10.17504/protocols.io.yxmvm32p6l3p/v2 | https://www.protocols.io/view/hot-alkaline-lysis-gdna-extraction-from-formalin-f-c777zrrn | Erin E Hahn, marina.alexander, Alicia Grealy, clare.holleley | TITLE: Hot alkaline lysis gDNA extraction from formalin-fixed archival tissues
AUTHORS: Erin E Hahn, marina.alexander, Alicia Grealy, clare.holleley
[DESCRIPTION]
The widespread practice of formalin preservation has historically limited genomic analysis of archival museum specimens.
Here we describe sample selection... | ["[Specimen vetting] Measure the pH of the media.", "[Specimen vetting] Visually assess the specimen. If the specimen appears decomposed, consider selecting an alternative specimen. Generally, specimens with discernible internal organs tend to have higher likelihood of success. If the internal organs have been removed,... |
null | null | null | dx.doi.org/10.17504/protocols.io.kwzcxf6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Isolated human islets were dispersed into single cells using Accutase (Millipore), ~1500-2000 islet equivalents/ml. 20,000-65,000 islet cells were transferred to individual wells of a 96 well culture plate (CELLSTAR, Greiner Bio-one) for immediate staining for flow cytometry ... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.chjt4m | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.dn95h5 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol gives two methods for prophage induction in heterotrophic bacterioplankton; one with no viral reduction and the other with viral reduction (see guidelines).<br /><br />Paul, J. H., and M. Weinbauer. 2010. Detection of lysogeny in marine environments, p. 30–33... | [] |
46,499 | nCoV-2019 environmental sample sequencing protocol | 1 | dx.doi.org/10.17504/protocols.io.brnbm5an | https://www.protocols.io/view/ncov-2019-environmental-sample-sequencing-protocol-brnbm5an | Sam Diaz-Munoz, Ivy Jose, AJ Campbell | TITLE: nCoV-2019 environmental sample sequencing protocol
AUTHORS: Sam Diaz-Munoz, Ivy Jose, AJ Campbell
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">ARTIC amplicon MinION sequencing protocol for nCoV-2019 starting from environmental samples</div><div class = "text-block">This protocol is a modif... | ["[cDNA preparation]\nMix the following components in an 0.2mL 8-strip tube;Component Volume50µM random hexamers 10mM dNTPs mix (10mM each) Template RNA Total\n1 µl\n1 µl\n11 µl\n13 µl\nViral RNA input from a clinical sample sho... |
null | null | null | dx.doi.org/10.17504/protocols.io.cikucv | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
The working concentration of <a href="http://store.p212121.com/blasticidin-s-hcl/">blasticidin S HCl</a> for use in mammalian cell gene selection can range anywhere from 2-100μg/mL depending on the cell lines used.<br /><br />Optimal doses typically range from 2-20μg/mL<br... | [] |
78,806 | NCBI submission protocol for microbial pathogen surveillance | 1 | dx.doi.org/10.17504/protocols.io.4r3l284pql1y/v7 | https://www.protocols.io/view/ncbi-submission-protocol-for-microbial-pathogen-su-cq7wvzpe | Ruth Timme, Julie Haendiges, Tina.Pfefer, Errol Strain, Maria Balkey | TITLE: NCBI submission protocol for microbial pathogen surveillance
AUTHORS: Ruth Timme, Julie Haendiges, Tina.Pfefer, Errol Strain, Maria Balkey
[DESCRIPTION]
PURPOSE: Step-by-step instructions for submitting pathogen whole genome sequence data to NCBI and to the NCBI Pathogen Detection portal. This protocol covers ... | ["[Establish submission environmnet at NCBI] Set up a new NCBI submission environment for your lab:\n\n1.1: Create an NCBI user account\n1.2: Set up an NCBI submission user group for your lab\n1.4: Bookmark the link to your submission portal\n1.5. Identify or establish new BioProjects (detailed in Step 3)\n\n\nReady fo... |
48,695 | Development of a reporter line for assessing the changes in gene expression of PfSir2a | 4 | dx.doi.org/10.17504/protocols.io.btsxnnfn | https://www.protocols.io/view/development-of-a-reporter-line-for-assessing-the-c-btsxnnfn | Linda Anagu | TITLE: Development of a reporter line for assessing the changes in gene expression of PfSir2a
AUTHORS: Linda Anagu
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>A luciferase reporter line of the malaria parasite, </span><span style = "font-style:italic;">Plasmodium falciparum</span><span>, ... | ["[Cloning of reporter luciferase gene under PfSir2A promoter]\nExtraction and Digestion of the Vector Backbone : The vector pLNSir2aGFP (or pLNSir2AGFP) with the GFP gene under PfSir2A promoter (reffered to as pLNSG vector here) and containing the AmpR gene was amplified by cloning this vector into competent E. coli (... |
64,633 | GFP-TBK1: expression and purification | 4 | dx.doi.org/10.17504/protocols.io.81wgb6wy1lpk/v1 | https://www.protocols.io/view/gfp-tbk1-expression-and-purification-cbczsix6 | Elias Adriaenssens, Justyna Sawa-Makarska | TITLE: GFP-TBK1: expression and purification
AUTHORS: Elias Adriaenssens, Justyna Sawa-Makarska
[DESCRIPTION]
This protocol describes how to express and purify human TBK1 tagged N-terminally with eGFP.
[STEPS]
SECTION: Expression
1. To generate GFP-TBK1 constructs the insect codon optimized TBK1 gene was purchased f... | ["[Expression] To generate GFP-TBK1 constructs the insect codon optimized TBK1 gene was purchased from GenScript and cloned with respective tags (GST-TEV-eGFP-TBK1) into pFastBac_Dual (Addgene ID: 187830). Generated construct was used for expression in Sf9 insect cells using the Bac-to-Bac system (ThermoFischer Scienti... |
90,938 | Environmental DNA (eDNA) 12S Metabarcoding PCR Protocol (with Platinum SuperFi II Taq) | 1 | null | https://www.protocols.io/view/environmental-dna-edna-12s-metabarcoding-pcr-proto-c422yyge | Kathleen Pitz, jbaker | TITLE: Environmental DNA (eDNA) 12S Metabarcoding PCR Protocol (with Platinum SuperFi II Taq)
AUTHORS: Kathleen Pitz, jbaker
[DESCRIPTION]
The 12S protocol is aimed at amplifying the hypervariable region of the mitochondrial DNA 12S rRNA gene in eukaryotes. The primers (MiFish-U-F & MiFish-U-R) used in this protocol ... | ["[MIOP: Minimum Information about an Omics Protocol] MIOP Term\nValue\n \nmethodology category\n\n \nproject\n\n \npurpose\n\n \nanalyses\n\n \ngeographic location\n\n \nbroad-scale environmental context\n\n \nlocal environmental context\n\n \nenvironmental medium\n\n \ntarget\n\n \ncreator\n\n \nmaterials required\... |
39,979 | SARS-CoV-2 McGill Nanopore sequencing protocol SuperScript IV_42C_ArticV3 | 1 | dx.doi.org/10.17504/protocols.io.bjajkicn | https://www.protocols.io/view/sars-cov-2-mcgill-nanopore-sequencing-protocol-sup-bjajkicn | Sarah Reiling, Shu-Huang Chen, Anne-Marie Roy, Josh Quick, Ioannis Ragoussis | TITLE: SARS-CoV-2 McGill Nanopore sequencing protocol SuperScript IV_42C_ArticV3
AUTHORS: Sarah Reiling, Shu-Huang Chen, Anne-Marie Roy, Josh Quick, Ioannis Ragoussis
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">SARS-CoV-2 McGill Nanopore sequencing protocol SuperScript IV_42C_ArticV3</div></div>... | ["[cDNA preparation]\nMix the following components in a 0.2 mL 8-strip tube:Component Volume50 µM random hexamers 10 mM dNTPs mix (10 mM each) Template RNA Total\n1 µl\n1 µl\n11 µl\n13 µl\... |
48,396 | Buffer Recipes | 3 | null | https://www.protocols.io/view/buffer-recipes-bthknj4w | Clark Fritsch | TITLE: Buffer Recipes
AUTHORS: Clark Fritsch
[DESCRIPTION]
Recipes for a variety of buffers that I have used for my work.
[STEPS] | [] |
77,864 | High-throughput screening of multiple Caenorhabditis elegans strains | 4 | null | https://www.protocols.io/view/high-throughput-screening-of-multiple-caenorhabdit-cqagvsbw | Tanara Peres | TITLE: High-throughput screening of multiple Caenorhabditis elegans strains
AUTHORS: Tanara Peres
[DESCRIPTION]
I developed this method for growing worms to avoid the steps of bleaching, refeeding and washing worms off plates. When using hundreds of strains these are very time consuming. Eggs will hatch on 24 well pla... | ["[Preparing plates] Prepare 60 mm NGM plates for worm maintenance. Dry plates for 1 hour under flow hood. If using 40 strains per week, you need at least 120 seeded plates per week (chunking Monday, Wednesday and Friday).\n\nAlways use the same agar, peptone and LB throughout the project (do not change reagents mid pr... |
30,662 | Isolation and Culture of Primary Mouse Astrocytes | null | dx.doi.org/10.17504/protocols.io.97eh9je | null | Sam Li | TITLE: Isolation and Culture of Primary Mouse Astrocytes
AUTHORS: Sam Li
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><a href="https://www.biolegend.com/en-us/astrocytes" style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;:UNDERLINE;">Astrocytes</span></a><a href="#" ... | ["Note: Use aseptic techniques if you need to sort and grow cells in culture.Pre-warm 30 mL SFM and all ACM in water bath at 37°C.", "Harvest brains and transfer to a 35 mm tissue culture dish placed on ice.", "Gently rinse brains in cold SFM.", "Carefully aspirate the medium and transfer brains to a new 35 mm tissue c... |
59,331 | cDNA Synthesis Using SuperScript III First-Strand Synthesis System for RT-PCR | 4 | null | https://www.protocols.io/view/cdna-synthesis-using-superscript-iii-first-strand-b57bq9in | Lynn Doran | TITLE: cDNA Synthesis Using SuperScript III First-Strand Synthesis System for RT-PCR
AUTHORS: Lynn Doran
[DESCRIPTION]
The SuperScript® III First-Strand Synthesis System for RT-PCR is used to synthesize first-strand cDNA from purified total RNA. RNA targets from 100 bp to >12 kb can be detected with this system.
... | ["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.", "Treat gloves and pipettes with RNase away and sterilize work area with 70% ethanol before pipetting reagents.", "I... |
null | null | null | dx.doi.org/10.17504/protocols.io.frzbm76 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The image is the Github logo.</p>
[STEPS]
?.
?.
?.
?.
?.
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.mctc2wn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Preparation of Yeast-Sucrose-Broth, that is used as liquid media for growing <em>Zt.</em> This is called 'YSB' in Bruce McDonald lab.<br /><br />Have a look for example: Zain, M. E., et al. 'Influence of growth medium on diagnostic characters of Aspergillus and Penicillium s... | [] |
39,886 | CoVan RT-LAMP protocol | 1 | null | https://www.protocols.io/view/covan-rt-lamp-protocol-bi7nkhme | David O'Connor, Shelby O'Connor, Amelia Haj, Mitchell Ramuta, Christina Newman, Dawn Dudley | TITLE: CoVan RT-LAMP protocol
AUTHORS: David O'Connor, Shelby O'Connor, Amelia Haj, Mitchell Ramuta, Christina Newman, Dawn Dudley
[STEPS]
?. [Saliva collection area]
Prepare saliva collection tube by placing a p1000 pipet tip in a 1.5 ml tube
?. [Saliva collection area]
Obtain ~300 µl of saliva – have the individual ... | ["[Saliva collection area]\nPrepare saliva collection tube by placing a p1000 pipet tip in a 1.5 ml tube", "[Saliva collection area]\nObtain ~300 µl of saliva – have the individual spit into a tube using a P1000 pipet tip to funnel saliva into the tube\nInfection control: Have individual throw the p1000 pipet tip away ... |
30,757 | Rare Trees Survey outside Plots (Megantic Only) | null | dx.doi.org/10.17504/protocols.io.baadiaa6 | null | Sabine St-Jean | TITLE: Rare Trees Survey outside Plots (Megantic Only)
AUTHORS: Sabine St-Jean
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Here, we describe the standardized protocol used by the </span><a href="http://www.caboscience.org" style = "text-decoration:underline;color:blue;cursor:pointer;"><spa... | ["[Tree Selection and Scouting]\nIdentify the tree species represented by\nTo do so, export the .csv file from Fulcrum → Vegetation Surveys: Large Trees → [filter: appropriate site]. Then, in Excel, filter the records by species and Crown class.", "[Tree Selection and Scouting]\nFor these species, find individual tree... |
58,996 | Direct RT-qPCR assay for the detection of SARS-CoV-2 in saliva samples | 3 | dx.doi.org/10.17504/protocols.io.b5uuq6ww | https://www.protocols.io/view/direct-rt-qpcr-assay-for-the-detection-of-sars-cov-b5uuq6ww | Francesco Saverio Tarantini, Siyu Wu, Harry Jenkins, Ana Tellechea Lopez, Hannah Tomlin, Ralph Hyde, Katarzyna Lis-Slimak, Jamie Louise Thompson, Sara Pijuan-Galitó, Danielle Scales, Kazuyo Kaneko, Jayasree Dey, Emily Park, Jack Hill, I-Ning Lee, Lara Doolan, Asta Arendt-Tranholm, Chris Denning, Claire Seedhouse, Andre... | TITLE: Direct RT-qPCR assay for the detection of SARS-CoV-2 in saliva samples
AUTHORS: Francesco Saverio Tarantini, Siyu Wu, Harry Jenkins, Ana Tellechea Lopez, Hannah Tomlin, Ralph Hyde, Katarzyna Lis-Slimak, Jamie Louise Thompson, Sara Pijuan-Galitó, Danielle Scales, Kazuyo Kaneko, Jayasree Dey, Emily Park, Jack Hill... | [] |
41,174 | Vegetation Monitoring Protocol for measuring and collecting ecological data | 1 | dx.doi.org/10.17504/protocols.io.bkfwktpe | https://www.protocols.io/view/vegetation-monitoring-protocol-for-measuring-and-c-bkfwktpe | Rebecca Hufft, Christina Alba, Amy Sahud | TITLE: Vegetation Monitoring Protocol for measuring and collecting ecological data
AUTHORS: Rebecca Hufft, Christina Alba, Amy Sahud
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol outlines the basic methods for measuring understory percent cover, soil moisture, tree canopy cover, and ... | ["[Describing Surevy Location]\nBefore collecting ecological data, we need to record information describing the survey location in a standardized way. Describe the location with the following physical location descriptors:Country.1st political division (state).2nd political division (county).Nearest population center, ... |
null | null | null | dx.doi.org/10.17504/protocols.io.mccc2sw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol provides an efficient and rapid way to concentrate proteins present in supernatants using Vivaspin columns (3,000 MWCO).</p>
[BEFORE_START]
<p>Prepare a 25 mM Ambic (Ammonium bicarbonate) solution:</p>
<p>19.77 g Ambic in 10 ml Ultrapure H2O.</p>
[STEPS]
?.
?... | [] |
43,258 | Calibrating a pH pmeter | 1 | null | https://www.protocols.io/view/calibrating-a-ph-pmeter-bng2mbye | PMAT0001 | TITLE: Calibrating a pH pmeter
AUTHORS: PMAT0001
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Step-by-step instructions on calibrating a pH meter</div></div>
[STEPS]
?. [Main steps]
Dip in pH 4
?. [Main steps]
Press “Cal”
?. [Main steps]
Press “✔️”
?. [Main steps]
Press “✔️”
?. [Main steps]
Dip... | ["[Main steps]\nDip in pH 4", "[Main steps]\nPress “Cal”", "[Main steps]\nPress “✔️”", "[Main steps]\nPress “✔️”", "[Main steps]\nDip in pH 7", "[Main steps]\nRinse pH meter", "[Main steps]\nPress “✔️”", "[Main steps]\nDip into sample; Note percentage purity as well", "[Important notes]\n- When liquid level falls way b... |
50,945 | Quality Indicators for Acute Cardiovascular Diseases: Protocol for Scoping Review | 1 | dx.doi.org/10.17504/protocols.io.bvy9n7z6 | https://www.protocols.io/view/quality-indicators-for-acute-cardiovascular-diseas-bvy9n7z6 | Koshiro Kanaoka, Yoshitaka Iwanaga, Yasushi Tsujimoto, Akihiro Shiroshita, Takaaki Suzuki, Michikazu Nakai, Yoshihiro Miyamoto | TITLE: Quality Indicators for Acute Cardiovascular Diseases: Protocol for Scoping Review
AUTHORS: Koshiro Kanaoka, Yoshitaka Iwanaga, Yasushi Tsujimoto, Akihiro Shiroshita, Takaaki Suzuki, Michikazu Nakai, Yoshihiro Miyamoto
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight... | [] |
55,611 | Pilot Exercise: Generating the Illumina SampleSheet and sharing data via BaseSpace | 1 | dx.doi.org/10.17504/protocols.io.b2i3qcgn | https://www.protocols.io/view/pilot-exercise-generating-the-illumina-samplesheet-b2i3qcgn | Ruth Timme, Maria Balkey, Tunc Kayikcioglu, Candace Bias, Cameron Boerner, James Pettengill | TITLE: Pilot Exercise: Generating the Illumina SampleSheet and sharing data via BaseSpace
AUTHORS: Ruth Timme, Maria Balkey, Tunc Kayikcioglu, Candace Bias, Cameron Boerner, James Pettengill
[DESCRIPTION]
This protocol describes the required steps to generate Illumina SampleSheet and provides guidelines for sharing... | ["[Generating Sequencing SampleSheet] Create your SampleSheet using Excel or a text editor. Name your sample sheet according your internal protocols, and use a *.csv extension. The sample sheet is organized in sections titled Header, Reads, Settings and Data. Section headings are case-sensitive and shown in bra... |
46,165 | Measure Effects of Manufacturing Variations of ENDS on coil Lifetime and Aerosol Generation | 1 | dx.doi.org/10.17504/protocols.io.brbvm2n6 | https://www.protocols.io/view/measure-effects-of-manufacturing-variations-of-end-brbvm2n6 | Qutaiba Saleh, Edward Hensel, Nathan C. Eddingsaas, Risa Robinson | TITLE: Measure Effects of Manufacturing Variations of ENDS on coil Lifetime and Aerosol Generation
AUTHORS: Qutaiba Saleh, Edward Hensel, Nathan C. Eddingsaas, Risa Robinson
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Manufacturing variations in coil resistance, initial pod mass, and e-liquid co... | ["[Samples (pods) Preparation]\nSelect the pods to be included in this experiment and execute all steps in this section on each pod.", "[Samples (pods) Preparation]\nDocument the UID for all pods.", "[Samples (pods) Preparation]\nVisually inspect the color of the e-liquid in the pods and classify the pods based on e-li... |
null | null | null | dx.doi.org/10.17504/protocols.io.gqfbvtn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The SpinSmart PCR purification and gel extraction technologies utilize a lysis buffer containing chaotropic salts that allow DNA to bind to a silica membrane. Binding buffer PCR 1 is added to a PCR reaction or agarose gel slice; the mixture is subsequently loaded directly ont... | [] |
97,696 | Purification of Lactococcus lactis OpuA and reconstitution in MSP nanodiscs | 0 | dx.doi.org/10.17504/protocols.io.bp2l624pzgqe/v1 | https://www.protocols.io/view/purification-of-lactococcus-lactis-opua-and-recons-dbm82k9w | Marco van den Noort, Panagiotis Drougkas, Cristina Paulino, Bert Poolman | TITLE: Purification of Lactococcus lactis OpuA and reconstitution in MSP nanodiscs
AUTHORS: Marco van den Noort, Panagiotis Drougkas, Cristina Paulino, Bert Poolman
[DESCRIPTION]
This is an optimized purification protocol which has been optimized in the context of:
Van Den Noort, M., Drougkas, P., Paulino, C., and Poo... | ["[Preparation of crude membrane vesicles] Use cells with an OD600 of 150-200, which are resuspended in 50 mM KPi pH 7.5 plus 20% (v/v) glycerol. Perform all steps of this procedure on ice or in a cooled environment (4 to 8 °C), unless otherwise indicated.", "[Preparation of crude membrane vesicles] Add 100 μg/ml DNAse... |
66,553 | Modified RNeasy Mini Kit protocol for filter extractions | 4 | dx.doi.org/10.17504/protocols.io.8epv59qd6g1b/v1 | https://www.protocols.io/view/modified-rneasy-mini-kit-protocol-for-filter-extra-cc8zszx6 | Margaret M. Brisbin | TITLE: Modified RNeasy Mini Kit protocol for filter extractions
AUTHORS: Margaret M. Brisbin
[DESCRIPTION]
RNA extraction protocol for filters - modification of RNeasy mini kit protocol
[STEPS]
SECTION: Prep
1. UV sterilize hood and clean all surfaces with RNAse-away
SECTION: Prep
4. Take out and label tubes:
Each... | ["[Prep] UV sterilize hood and clean all surfaces with RNAse-away", "[Prep] Take out and label tubes: \n \nEach sample needs: \n 1x bead-bashing tube\n 2x Lo-bind Eppendorf tubes\n 1x RNeasy filter column\n 1x RNeasy capped collection tube \n\nnumber tubes consecutively from last extraction (if last extrac... |
31,598 | Protocol for Geostatistical Determination of Radiation Dosimetry Maps of Population-Scale Exposures | null | dx.doi.org/10.17504/protocols.io.ba4nigve | https://www.protocols.io/view/protocol-for-geostatistical-determination-of-radia-ba4nigve | Eliseos Mucaki, Peter Rogan | TITLE: Protocol for Geostatistical Determination of Radiation Dosimetry Maps of Population-Scale Exposures
AUTHORS: Eliseos Mucaki, Peter Rogan
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Accurate radiation dose estimates are critical for determining eligibility for therapies by timely triaging ... | ["[Derivation and Processing of ground-truth HPAC radiation plumes]\nNuclear detonation scenarios created by the Hazard Prediction and Capability software (HPAC; https://www.acq.osd.mil/ncbdp/nm/narp/Radiation_Data/Specialized_Radiological.htm) were derived for 22 North American cities and surrounding regions (simulati... |
30,847 | Intracellular Flow Cytometry Staining Protocol | null | dx.doi.org/10.17504/protocols.io.bac7iazn | null | Sam Li | TITLE: Intracellular Flow Cytometry Staining Protocol
AUTHORS: Sam Li
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. [Fixation]
If staining intracellular antigens (e.g. IFN-γ or IL-4), first perform cell surface antigen staining as described in BioLegend’s Cell Surface Immunofluorescence Staining Protocol... | ["[Fixation]\nIf staining intracellular antigens (e.g. IFN-γ or IL-4), first perform cell surface antigen staining as described in BioLegend’s Cell Surface Immunofluorescence Staining Protocol, then fix cells in 0.5 ml/tube Fixation Buffer in the dark for 20 minutes at room temperature.Tip: For gentler fixation (partic... |
68,233 | Enhancing lithic analysis: Introducing 3D-EdgeAngle as a semi-automated 3D digital method to systematically quantify stone tool edge angle and design | 1 | dx.doi.org/10.17504/protocols.io.81wgb6j51lpk/v1 | https://www.protocols.click/view/enhancing-lithic-analysis-introducing-3d-edgeangle-cevhte36 | Lisa Schunk, Anja Cramer, Konstantin Bob, Ivan Calandra, Guido Heinz, Olaf Jöris, Joao Marreiros | TITLE: Enhancing lithic analysis: Introducing 3D-EdgeAngle as a semi-automated 3D digital method to systematically quantify stone tool edge angle and design
AUTHORS: Lisa Schunk, Anja Cramer, Konstantin Bob, Ivan Calandra, Guido Heinz, Olaf Jöris, Joao Marreiros
[DESCRIPTION]
This protocol describes a method ("3D-Edge... | ["[Samples] To demonstrate the applicability of the method, three samples have been selected:\n\n1x experimental flake (EAP-flake)\n1x Keilmessser (BU-072)\n1x calibrated standard angle (WEM-60; gauge block)", "[Sample documentation] Sample documentation is separated into two part: generating the 3D model via scanning ... |
null | null | null | dx.doi.org/10.17504/protocols.io.d5i84d | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
METAVIR is a web server designed to annotate viral metagenomic sequences (raw reads or assembled contigs). A set of published viromes, identified as "public projects", is already available, and your own data sets can be processed in a private environment.
[GUIDELINES]
<strong>V... | [] |
76,806 | Ethanol precipitation of nucleic acid | 4 | null | https://www.protocols.io/view/ethanol-precipitation-of-nucleic-acid-cn9evh3e | Andreas Sagen | TITLE: Ethanol precipitation of nucleic acid
AUTHORS: Andreas Sagen
[DESCRIPTION]
Simple protocol to precipitate nucleic acids
[STEPS]
SECTION: Sodium acetate (3 M, pH 5.2)
1. Add 25 mL distilled water to a 50 mL canonical tube
SECTION: Precipitation
5. Add 100 µL lysate in a reaction tube
SECTION: Precipitation
6. A... | ["[Sodium acetate (3 M, pH 5.2)] Add 25 mL distilled water to a 50 mL canonical tube", "[Precipitation] Add 100 µL lysate in a reaction tube", "[Precipitation] Add 10 µL Sodium acetate (3 Molarity (M), pH 5.2), 2 µL 250 µg/mL glycogen and 333 µL absolute ethanol\n\nMaterial:", "[Precipitation] Vortex solution, then pre... |
88,408 | Qubit dsDNA HS Assay | 1 | dx.doi.org/10.17504/protocols.io.kxygx3zrwg8j/v2 | https://www.protocols.io/view/qubit-dsdna-hs-assay-c2jyycpw | Lakme Caceres | TITLE: Qubit dsDNA HS Assay
AUTHORS: Lakme Caceres
[DESCRIPTION]
How to use the Qubit 2.0 fluorometer to quantify dsDNA samples. It is most accurate for sample concentrations from 5 pg/uL to 120 ng/uL.
[GUIDELINES]
Allow reagents to equilibriate to room temperature before use:
HS Buffer (ambient)
HS Reagent (4C - dar... | ["To prepare the Qubit working solution, a mixture of HS Reagent and HS Buffer, take the number of samples you will be running and multiply that by 199 uL. Then add 380 for the HS Standards. Round this number up to the nearest tenth (for excess). This is the amount of HS Buffer you will need. Divide this number by 200 ... |
59,976 | Assessment of PKC-dependent activation of LRRK1 in vitro | 4 | dx.doi.org/10.17504/protocols.io.5jyl89d5rv2w/v1 | https://www.protocols.io/view/assessment-of-pkc-dependent-activation-of-lrrk1-in-b6tgrejw | Athanasios Karapetsas, Asad Malik, Dario R Alessi | TITLE: Assessment of PKC-dependent activation of LRRK1 in vitro
AUTHORS: Athanasios Karapetsas, Asad Malik, Dario R Alessi
[DESCRIPTION]
We describe a non-radioactive assay that we deploy for analysing the kinase activity of recombinant LRRK1 following in vitro activation by Protein kinase C (PKC) isoforms. This assa... | ["[Preparation of lipid vesicles for PKC activation] Clean a disposable glass culture tube by washing. Allow to air-dry.", "[Preparation of lipid vesicles for PKC activation] Pipette 0.5 µL of Diacylglycerol (stock concentration is 10 mg/mL) and 5 µL of Phosphatidylserine (stock concentration is 10 mg/mL) into the clea... |
82,762 | Blood Sample collection and PBMC isolation JAGUAR.v4 | 4 | dx.doi.org/10.17504/protocols.io.e6nvwjx4zlmk/v1 | https://www.protocols.click/view/blood-sample-collection-and-pbmc-isolation-jaguar-cu3iwyke | Carla Jones, Pablo Romagnoli, Gosia Trynka | TITLE: Blood Sample collection and PBMC isolation JAGUAR.v4
AUTHORS: Carla Jones, Pablo Romagnoli, Gosia Trynka
[DESCRIPTION]
AIM: This protocol aims to isolate and cryopreserve PBMC from healthy donors from JAGUAR sites for multimodal single cell analysis and blood for DNA extraction for genotyping.
[BEFORE_START]
c... | ["[Blood Collection] Collect blood (21g needle) into the tube using the standard technique for CPT tube (3 tubes per donor). After collection, store tubes upright at room temperature (RT, 18-25oC) for up to 2hr (if longer times are required keep tubes on ice until processing).", "[Blood Collection]", "[PBMC cryopreserv... |
null | null | null | dx.doi.org/10.17504/protocols.io.rpnd5me | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Protocol to grow different accessions of cowpea seeds within a greenhouse in controlled conditions.</p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
39,101 | Vaginal swabbing | 1 | null | https://www.protocols.io/view/vaginal-swabbing-bie5kbg6 | Sharona Sedighim, Olivier George | TITLE: Vaginal swabbing
AUTHORS: Sharona Sedighim, Olivier George
[STEPS]
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.hfqb3mw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The workflow applied to Tara Oceans raw sequence data for generating assemblies suitable for genomic binning.</p>
<p> </p>
<p>Used in:</p>
<p>"290 Metagenome-assembled Genomes from the Mediterranean Sea: Ongoing Effort to Generate Genomes from the Tara Oceans Dataset" - bioRx... | [] |
43,137 | Protocol 1: Making Agar Plates | 4 | null | https://www.protocols.io/view/protocol-1-making-agar-plates-bnc9maz6 | TITLE: Protocol 1: Making Agar Plates
AUTHORS:
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol will assist you in making the agar plates for the CRISPR experiment. As you may have discovered in your prelab, the agar provides the bacteria with the nutrients needed to grow. Once your p... | ["To prepare for this lab, start by putting on your PPE gear, gathering your materials, and watching this video.Watch this video before boiling the agar.", "Add agar and water to erlynmeyer flask. To caculate the amount of LB media use the following equations:\\frac{7g \\;Agar}{20\\;Agar\\;plates} = \\frac{g\\;of\\;Aga... |
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