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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42,520 | Affinity purification of ookinetes in coverslips | 4 | dx.doi.org/10.17504/protocols.io.bmryk57w | https://www.protocols.io/view/affinity-purification-of-ookinetes-in-coverslips-bmryk57w | Benito Recio Totoro | TITLE: Affinity purification of ookinetes in coverslips
AUTHORS: Benito Recio Totoro
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The ookinetes, as they come from the ookinete culture, are suspended in a solution that also contains blood cells and other parasite stages. Often, it is necessary to... | ["[Purification from cardiac puncture-derived ookinete culture.]\nThaw an aliquot of ECM gel overnight at in ice.\n4 °C\nKeep the ECM gel in ice at all times. ECM gel starts to form a gel at 20°C", "[Purification from cardiac puncture-derived ookinete culture.]\nPlace the desired number of clean and sterile coverslips... |
24,640 | The Black identity, hair product use, and breast cancer scale | null | dx.doi.org/10.17504/protocols.io.4a8gshw | null | Dede Teteh, Marissa Ericson, Sabine Monice, Lenna Dawkins-Moultin, Nasim Bahadorani, Phyllis Clark, Eudora Mitchell, Lindsey S. Treviño, Adana Llanos, Rick Kittles, Susanne Montgomery | TITLE: The Black identity, hair product use, and breast cancer scale
AUTHORS: Dede Teteh, Marissa Ericson, Sabine Monice, Lenna Dawkins-Moultin, Nasim Bahadorani, Phyllis Clark, Eudora Mitchell, Lindsey S. Treviño, Adana Llanos, Rick Kittles, Susanne Montgomery
[DESCRIPTION]
<div class = "text-blocks"><div class = "te... | ["[Qualitative Study Focus Group and Key Informant Interview Questions]\nParticipant type: Young women. 1. How important are hair styles for women like you? How important is your hair to you? a. What is the meaning of hair in black culture as you see it? b. Does that differ from what you see somewhat older wo... |
96,576 | FindingNemo (v.kit14): A Toolkit for DNA Extraction, Library Preparation and Purification for Ultra Long Nanopore Sequencing | 1 | dx.doi.org/10.17504/protocols.io.5jyl8p38rg2w/v1 | https://www.protocols.io/view/findingnemo-v-kit14-a-toolkit-for-dna-extraction-l-dai82chw | Inswasti Cahyani, John Tyson, Nadine Holmes, Josh Quick, Nicholas Loman, Matthew Loose | TITLE: FindingNemo (v.kit14): A Toolkit for DNA Extraction, Library Preparation and Purification for Ultra Long Nanopore Sequencing
AUTHORS: Inswasti Cahyani, John Tyson, Nadine Holmes, Josh Quick, Nicholas Loman, Matthew Loose
[DESCRIPTION]
This collection of protocols is designed to enable ultra-long (UL) reads on N... | ["[UHMW DNA Extraction - Monarch Kit Direct Lysis] A DNA extraction protocol that yields clean and homogeneous UHMW DNA is essential for a good ultra-long (UL) sequencing output. We have routinely used the New England Biolabs (NEB) Monarch HMW DNA Extraction Kit for Cells & Blood (T3050) for UL library preparations, wi... |
null | null | null | dx.doi.org/10.17504/protocols.io.h9fb93n | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?. | [] |
22,827 | Cas9/sgRNA ribonucleoprotein nucleofection using Lonza 4D nucleofector with lower amount of RNP (final best version-tested) | null | dx.doi.org/10.17504/protocols.io.2ijgccn | null | Bao Thai | TITLE: Cas9/sgRNA ribonucleoprotein nucleofection using Lonza 4D nucleofector with lower amount of RNP (final best version-tested)
AUTHORS: Bao Thai
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. [Prepare cells (part 1)]
-Trypsinize cells: Leave cells in trypsin (2 mL for a 10cm plate) at 37C for 3-5 minu... | ["[Prepare cells (part 1)]\n-Trypsinize cells: Leave cells in trypsin (2 mL for a 10cm plate) at 37C for 3-5 minutes.Note: don't leave cells in trypsin for a long period of time. -Add in warm media to neutralize trypsin (8 mL for a 10cm plate).-Pellet cells at 500 x g for 5 mins.", "[Prepare cells (part 1)]\nRemove med... |
40,047 | FCMPASS - Acquisition and gating of fluorescence reference materials | 1 | dx.doi.org/10.17504/protocols.io.bjcpkivn | https://www.protocols.io/view/fcmpass-acquisition-and-gating-of-fluorescence-ref-bjcpkivn | Joshua Welsh, Jennifer Jones | TITLE: FCMPASS - Acquisition and gating of fluorescence reference materials
AUTHORS: Joshua Welsh, Jennifer Jones
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol outlines the steps required to acquire fluorescence reference material data for use with the FCMPASS software. This is one o... | ["[MESF Bead Calibration]\nVortex each fluorescence reference bead bottle before use.", "[MESF Bead Calibration]\nAdd 1 drop (~50 µL) of each bead population to separate FACS tubes containing 250 µL of DPBS.", "[MESF Bead Calibration]\nDue to the high autofluorescence of the ‘Blank’ beads, their use is not recommended ... |
91,901 | hsqc_metab.nan | 5 | dx.doi.org/10.17504/protocols.io.5jyl8pd2dg2w/v3 | https://www.protocols.io/view/hsqc-metab-nan-c5y5y7y6 | NAN KB, John Glushka, Mario Uchimiya, Saraa Al Jawad, Christopher Esselman, Leandro I Ponce, Laura Morris, Arthur Edison | TITLE: hsqc_metab.nan
AUTHORS: NAN KB, John Glushka, Mario Uchimiya, Saraa Al Jawad, Christopher Esselman, Leandro I Ponce, Laura Morris, Arthur Edison
[DESCRIPTION]
This is a protocol for running the Bruker pulse program "hsqcetgpsisp2".
[BEFORE_START]
This protocol assumes:
Your sample is loaded, locked, tuned for ... | ["[Create a new dataset]", "[Create a new dataset] A new window opens. On the right top bar, select\nSource = /opt/NAN_METAB/par\n \nIn the list, select the one you want to use:\n\nFor serum and plasma samples:\nHSQC_br600_serum.par: Parameter set using an acquisition mode \"traditional planes\"\nHSQC_NUS_br600_serum.p... |
84,237 | A Programmable DNA Roadblock System Using dCas9 and Multivalent Target Sites | 1 | dx.doi.org/10.17504/protocols.io.36wgq422kvk5/v3 | https://www.protocols.click/view/a-programmable-dna-roadblock-system-using-dcas9-an-cwhmxb46 | priceal, ekmatozel, parzialest | TITLE: A Programmable DNA Roadblock System Using dCas9 and Multivalent Target Sites
AUTHORS: priceal, ekmatozel, parzialest
[DESCRIPTION]
A protein roadblock forms when a protein binds DNA and hinders translocation of other DNA binding proteins. These roadblocks can have significant effects on gene expression and regu... | ["[PCR Preparation] Gather the materials used in Step 1 (See Materials section). Thaw components before use. Keep all on ice.", "Dilute the primers for (See Materials) to 10 uM before using.", "[PCR reaction] Combine the components from Step 1 into PCR tube(s) in order, for the desired final volume. Use Table 1 for ref... |
65,194 | LDM protocol for estimating plasmid conjugation rates | 4 | dx.doi.org/10.17504/protocols.io.e6nvwk812vmk/v3 | https://www.protocols.io/view/ldm-protocol-for-estimating-plasmid-conjugation-ra-cbwispce | Olivia Kosterlitz, Claire Wate, Adamaris Muñiz Tirado, Benjamin Kerr | TITLE: LDM protocol for estimating plasmid conjugation rates
AUTHORS: Olivia Kosterlitz, Claire Wate, Adamaris Muñiz Tirado, Benjamin Kerr
[DESCRIPTION]
This is a general protocol to implement the LDM approach for estimating plasmid conjugation rates. This version of the protocol was originally submitted with th... | ["[Phase 1: Minimum inhibitory concentration assay with the transconjugant-selecting medium.] Prepare bacterial cultures.\n\n Start cultures from freezer stocks for the donor, recipient, and transconjugant. Supplement the donor and transconjugant growth culture medium with the appropriate selective agents to maintain t... |
81,826 | NCEM Drop Agar (TM-014) | 4 | dx.doi.org/10.17504/protocols.io.rm7vzb4n5vx1/v1 | https://www.protocols.io/view/ncem-drop-agar-tm-014-ct6awrae | sandra.crameri | TITLE: NCEM Drop Agar (TM-014)
AUTHORS: sandra.crameri
[DESCRIPTION]
drop agar
[STEPS]
SECTION: HEADER
1. SAN:
SPEC No:
OPERATOR:
SECTION: Adsorption & Staining
4. Place 5 µL sample on surface of agar square. Immediately float carbon coated formvar filmed grid face down on the droplet and leave until t... | ["[HEADER] SAN:\n\n\n\n\nSPEC No:\n\n\n\n\nOPERATOR:", "[Adsorption & Staining] Place 5 µL sample on surface of agar square. Immediately float carbon coated formvar filmed grid face down on the droplet and leave until the droplet diffuses into the agar.", "[Adsorption & Staining] Stain 1 min", "[Adsorption &am... |
40,447 | Immunoblot analyses for investigating SpLA binding to purified mammalian and avian immunoglobulins. | 6 | dx.doi.org/10.17504/protocols.io.bjq7kmzn | https://www.protocols.io/view/immunoblot-analyses-for-investigating-spla-binding-bjq7kmzn | Angel Justiz-Vaillant | TITLE: Immunoblot analyses for investigating SpLA binding to purified mammalian and avian immunoglobulins.
AUTHORS: Angel Justiz-Vaillant
[STEPS]
?. Aliquots of 2 µg/µl purified immunoglobulins from birds, laboratory, wild, farm animals and pets are applied to the gels of SDS-PAGE as described elsewhere.
?. Gels are ... | ["Aliquots of 2 µg/µl purified immunoglobulins from birds, laboratory, wild, farm animals and pets are applied to the gels of SDS-PAGE as described elsewhere.", "Gels are transferred to nitrocellulose membranes (Immobilon-Nc, pore size 0.45 µm, Sigma-Aldrich Co, St Louis, Missouri) during 75 minutes at 40 mAmps using a... |
null | null | null | dx.doi.org/10.17504/protocols.io.g6vbze6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Rapid, cheap, and effective DNA extraction for PCR. Easily scaled up to 96-well plates. This originates with Truett et al (2000) <a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=10907076%5Buid%5D" target="_blank">PMID:10907076</a></p>
<p> </p>
<p>This protocol is very well ... | [] |
45,109 | Multicolor adeno-associate virus labeling and 3D digital tracing of enteric plexus in mouse proximal colon | 1 | dx.doi.org/10.17504/protocols.io.bqavmse6 | https://www.protocols.io/view/multicolor-adeno-associate-virus-labeling-and-3d-d-bqavmse6 | Lixin Wang, Collin Challis, Honghui Liang, Songlin Li, Charless Fowlkes, Aidan Sullivan, Kumar SR, Yvette Taché | TITLE: Multicolor adeno-associate virus labeling and 3D digital tracing of enteric plexus in mouse proximal colon
AUTHORS: Lixin Wang, Collin Challis, Honghui Liang, Songlin Li, Charless Fowlkes, Aidan Sullivan, Kumar SR, Yvette Taché
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Using a multicolo... | ["[Viral constructs]\nProduction of a tunable two-component multicolor four-vector system (AAV-PHP.S:hSyn-tTA:TRE-XFP) is described in details in a previous publication: Challis RC, Ravindra Kumar S, Chan KY, Challis C, Beadle K, Jang MJ, et al. Systemic AAV vectors for widespread and targeted gene delivery in rodents.... |
22,977 | Pig- Heart Neuonal and Fiber Immunocytochemistry | null | dx.doi.org/10.17504/protocols.io.2n9gdh6 | null | Pradeep Rajendran, John Tompkins, Kalyanam Shivkumar | TITLE: Pig- Heart Neuonal and Fiber Immunocytochemistry
AUTHORS: Pradeep Rajendran, John Tompkins, Kalyanam Shivkumar
[STEPS]
?. Animal: Yucatan Minipig 1427-Gender: Male-Weight: 28.4Kg
?. Tissue Fixation:-Flush heart with PBS, RT, and heparin then inject 4% paraformaldehyde in PBS into coronaries. -Removed heart and... | ["Animal: Yucatan Minipig 1427-Gender: Male-Weight: 28.4Kg", "Tissue Fixation:-Flush heart with PBS, RT, and heparin then inject 4% paraformaldehyde in PBS into coronaries. -Removed heart and fix overnight at 4 degrees C in 4% PFA/PBS.-Transfer to container with 0.01M PBS+0.02M Na Azide+20% Sucrose on 6/15/2018..", "T... |
39,298 | ChIP-seq | 4 | dx.doi.org/10.17504/protocols.io.bimakc2e | https://www.protocols.io/view/chip-seq-bimakc2e | José Terrón-Bautista, Francisco Gómez-Vela, Irene Delgado-Sainz, Federico Divina, Miguel Garcíıa-Torres, Pedro Manuel Martínez-García | TITLE: ChIP-seq
AUTHORS: José Terrón-Bautista, Francisco Gómez-Vela, Irene Delgado-Sainz, Federico Divina, Miguel Garcíıa-Torres, Pedro Manuel Martínez-García
[STEPS]
?. [Crosslinking]
Fix cells adding formaldehyde to a final concentration of 1% and incubation at 37ºC for 10 min.
?. [Crosslinking]
Quench fixation addi... | ["[Crosslinking]\nFix cells adding formaldehyde to a final concentration of 1% and incubation at 37ºC for 10 min.", "[Crosslinking]\nQuench fixation adding glycine to a final concentration of 125 mM at cell culture plates and incubate at RT for 5 min.", "[Crosslinking]\nAfter two washes with cold PBS, in the presence o... |
null | null | null | dx.doi.org/10.17504/protocols.io.nw9dfh6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol describes the preparation of aorta samples from mouse for Western blot analysis.</p>
[STEPS]
?.
?.
?.
?.
?.
?. | [] |
55,039 | Chromatin loops and expression QTL colocalization reveal novel gene targets for T1D-associated GWAS variants in immune cells | 5 | null | https://www.protocols.io/view/chromatin-loops-and-expression-qtl-colocalization-bzy7p7zn | Joaquin Reyna, Sourya Bhattacharyya, Nikhil Rao, Abhijit Chakraborty, Ferhat Ay | TITLE: Chromatin loops and expression QTL colocalization reveal novel gene targets for T1D-associated GWAS variants in immune cells
AUTHORS: Joaquin Reyna, Sourya Bhattacharyya, Nikhil Rao, Abhijit Chakraborty, Ferhat Ay
[DESCRIPTION]
Type 1 diabetes (T1D) is a disease characterized by the destruction of β cell popul... | ["[Main Colocalization Pipeline] Download the GWAS summary statistics (uses GRCh38 coordinates)\nDownload GWAS summary statistics from the GWAS catalogue. \nDownload link: http://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/GCST90014001-GCST90015000/GCST90014023/GCST90014023_buildGRCh38.tsv", "[Main Colocalizati... |
105,947 | Stanford FAP Colectomy SOP - HTAN | 1 | dx.doi.org/10.17504/protocols.io.eq2lywqoevx9/v1 | https://www.protocols.io/view/stanford-fap-colectomy-sop-htan-djp34mqn | Aaron Horning, Roxanne Chiu, Rozelle Laquindanum | TITLE: Stanford FAP Colectomy SOP - HTAN
AUTHORS: Aaron Horning, Roxanne Chiu, Rozelle Laquindanum
[DESCRIPTION]
Stanford FAP Colectomy SOP
Due to the time and temperature sensitive nature of tissue collection, we must be fully prepared with all supplies for the procedure and that all persons involved in the collecti... | ["[Gross Room Set Up] The gross room area will be set up with 2 main stations.", "[Description of roles] Roles and typical persons involved (SWAT team):\n●Cutter : The Cutter will clean the colon and cut out the samples. The Cutter is responsible for laying the colon out with the descending colon on the left and ascend... |
63,525 | Weight Crasher Keto Gummies Reviews & Latest Update | 1 | dx.doi.org/10.17504/protocols.io.j8nlkk2oxl5r/v1 | https://www.protocols.io/view/weight-crasher-keto-gummies-reviews-amp-latest-upd-caadsaa6 | weightcrashers | TITLE: Weight Crasher Keto Gummies Reviews & Latest Update
AUTHORS: weightcrashers
[DESCRIPTION]
✅ Name – Weight Crasher Keto Gummies
✅ Category – Weight Loss
✅ Composition—NATURAL
✅ Main Benefits – Burn Fat
✅ Side Effects - No Major Side Effects
✅ Rating - ⭐⭐⭐⭐⭐
✅Availability – Online
>>>Click to Buy — Purc... | [] |
28,452 | Glycemic effect of post-meal walking compared to one prandial insulin injection in type 2 diabetic patients treated with basal insulin: a randomized controlled cross-over study | null | dx.doi.org/10.17504/protocols.io.72chqaw | null | Onnicha Suntornlohanakul, Chatchalit Rattarasarn, Atiporn Ingsathit, Chatvara Areevut, Sunee Saetung | TITLE: Glycemic effect of post-meal walking compared to one prandial insulin injection in type 2 diabetic patients treated with basal insulin: a randomized controlled cross-over study
AUTHORS: Onnicha Suntornlohanakul, Chatchalit Rattarasarn, Atiporn Ingsathit, Chatvara Areevut, Sunee Saetung
[DESCRIPTION]
<div class ... | [] |
44,815 | Protocol PCR Wet Lab | 5 | dx.doi.org/10.17504/protocols.io.bpzpmp5n | https://www.protocols.io/view/protocol-pcr-wet-lab-bpzpmp5n | TITLE: Protocol PCR Wet Lab
AUTHORS:
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. DNA ExtractionDNA Extraction: Saliva (Bento lab) This protocol extracts DNA from Saliva using a microcentrifuge and thermocycler. The microcentrifuge separates the cells in the sample into a pellet at the bottom of th... | ["DNA ExtractionDNA Extraction: Saliva (Bento lab) This protocol extracts DNA from Saliva using a microcentrifuge and thermocycler. The microcentrifuge separates the cells in the sample into a pellet at the bottom of the microcentrifuge tube. Extra liquid is drawn out of the microcentrifuge tube. Cells are then heated... | |
88,504 | HEPES-Sucrose Cutting Solution | 1 | dx.doi.org/10.17504/protocols.io.5jyl8peq8g2w/v1 | https://www.protocols.io/view/hepes-sucrose-cutting-solution-c2nyydfw | Allen Institute | TITLE: HEPES-Sucrose Cutting Solution
AUTHORS: Allen Institute
[DESCRIPTION]
This protocol is used for preparing HEPES-Sucrose Cutting Solution, used for animal perfusion following anesthesia.
[STEPS] | [] |
79,936 | Modified protocol for genome-wide mapping of uncapped transcripts (GMUCT) in eukaryotes | 4 | dx.doi.org/10.17504/protocols.io.yxmvm2jjbg3p/v1 | https://www.protocols.io/view/modified-protocol-for-genome-wide-mapping-of-uncap-csa8wahw | Diep R Ganguly, Garima Bhatia, Susheel Sagar Bhat, Brian D Gregory | TITLE: Modified protocol for genome-wide mapping of uncapped transcripts (GMUCT) in eukaryotes
AUTHORS: Diep R Ganguly, Garima Bhatia, Susheel Sagar Bhat, Brian D Gregory
[DESCRIPTION]
This is a modified protocol to perform genome-wide mapping of uncapped and cleaved transcripts (GMUCT; Willmann et al, 2014 Methods, 1... | ["[Poly-A selection] For each sample, dilute 5 - 30 μg total RNA in 100 μL of nuclease-free water (or 10 mM Tris-Cl pH 7.5).", "[Poly-A selection] Perform poly-A RNA selection using Dynabeads mRNA purification kit as per the manufacturer's instructions (see attachments).\n\nNote, the capacity of these beads are 75 μg t... |
89,348 | Set Shifting ASAP Operant Behavior_LernerLab | 1 | null | https://www.protocols.io/view/set-shifting-asap-operant-behavior-lernerlab-c3hcyj2w | jillian.seiler | TITLE: Set Shifting ASAP Operant Behavior_LernerLab
AUTHORS: jillian.seiler
[DESCRIPTION]
Protocol for set shifting task used by the Lerner Lab for ASAP work
[STEPS]
SECTION: Magazine Training
1. Food restrict animals overnight prior to beginning magazine training. For the remainder of training animals should be rest... | ["[Magazine Training] Food restrict animals overnight prior to beginning magazine training. For the remainder of training animals should be restricted to 85% of their free feeding weight.", "[Magazine Training] Place animals in operant box with dummy patch cords attached and allow ~5 minutes to habituate", "[Magazine T... |
55,838 | 622.2 URMC HTC Rapid Clearing of Thick Human Lung Tissue Sections | 1 | dx.doi.org/10.17504/protocols.io.q26g7bzp9lwz/v2 | https://www.protocols.io/view/622-2-urmc-htc-rapid-clearing-of-thick-human-lung-b2r6qd9e | Cory Poole, Gloria S Pryhuber | TITLE: 622.2 URMC HTC Rapid Clearing of Thick Human Lung Tissue Sections
AUTHORS: Cory Poole, Gloria S Pryhuber
[DESCRIPTION]
Purpose and Scope of the Procedure:
Provide a relatively rapid clearing of lung tissue sections up to 1 millimeter thick for immunofluorescence staining and imaging with confocal or multiph... | ["[Preparing Reagents] 1X Phosphate Buffered Saline\nAdd 50 mL of 10X Phosphate Buffered Saline to 450 mL ultrapure water and mix the solution well. Store at room temperature.\n\n100% CUBIC-L\nAdd 16 g of ultrapure water to a 50 mL conical followed by 2 g of Triton X-100. Swirl the tube until the Triton X-100 completel... |
98,781 | Stickleback IVF Breeding (Clutch generation and maintenance) | 0 | dx.doi.org/10.17504/protocols.io.81wgbz753gpk/v1 | https://www.protocols.io/view/stickleback-ivf-breeding-clutch-generation-and-mai-dcp52vq6 | Helen Spence-Jones | TITLE: Stickleback IVF Breeding (Clutch generation and maintenance)
AUTHORS: Helen Spence-Jones
[DESCRIPTION]
IVF generation of clutches of stickleback embryos from gravid females and males in breeding condition. This protocol requires euthanisation of the male and leaves the female unharmed.
Depending on source pop... | ["[Selection of breeding pair] Gravid female should have a distinctive swollen, ‘pebbled’ abdomen, with eggs visible through vent upon (very) gentle squeezing. Not much pressure is required to begin release of eggs; if too much force is required to start egg release, the clutch may be too early and is unlikely to be su... |
23,149 | Molecular and serological surveys of canine distemper virus: a meta-analysis of cross-sectional studies | null | dx.doi.org/10.17504/protocols.io.2umgeu6 | null | Vivaldo Costa, Marielena Saivish, Roger Rodrigues, Rebeca de Lima Silva, Marcos Moreli, Ricardo Krüger | TITLE: Molecular and serological surveys of canine distemper virus: a meta-analysis of cross-sectional studies
AUTHORS: Vivaldo Costa, Marielena Saivish, Roger Rodrigues, Rebeca de Lima Silva, Marcos Moreli, Ricardo Krüger
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Background: Although studies ... | ["Literature searchThis protocol conforms to the Preferred Reporting Items for Systematic Review and Meta-analysis protocols (PRISMA-P) guidelines for reporting a protocol for a systematic review and meta-analysis [1].\n\t\t\t\t\t\t\t .justify:after {\n\t\t\t\t\t\t\t content: \"\";\n\t\t\t\t\t\t\t display:inline... |
66,899 | ONT Sequencing IT/Compute Pop!_OS 22.04 Setup | 5 | dx.doi.org/10.17504/protocols.io.14egn7kzmv5d/v1 | https://www.protocols.io/view/ont-sequencing-it-compute-pop-os-22-04-setup-cdjts4nn | Stephen Douglas Russell | TITLE: ONT Sequencing IT/Compute Pop!_OS 22.04 Setup
AUTHORS: Stephen Douglas Russell
[DESCRIPTION]
The IT requirements for processing MinION data should be carefully reviewed before purchasing a MinION device. You will want to go with a Linux system. System76 is really the primary/best vendor for laptops. Pay... | ["The final setup I went with can be found below. It was expensive (around for the laptop), but should be able to achieve live basecalling for two MinION devices at the same time. Overall specs of my laptop: \n\n \n\nMinimum IT requirements for MinION from ONT:", "The process at this link was instrumental to this p... |
38,481 | Packaging and Shipping of Flash Frozen Non-Islet Pancreatic (Acinar)Tissue | 4 | dx.doi.org/10.17504/protocols.io.bhtrj6m6 | https://www.protocols.io/view/packaging-and-shipping-of-flash-frozen-non-islet-p-bhtrj6m6 | Integrated Islet Distribution Program | TITLE: Packaging and Shipping of Flash Frozen Non-Islet Pancreatic (Acinar)Tissue
AUTHORS: Integrated Islet Distribution Program
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:left"><span>To define a standardized method for packaging and cold shipping of r... | ["[Preparation of Supplies and Reagents]\nThe IIDP will provide each center with the following supplies necessary for islet culture:Gemini Human AB Serum (ABS)-Heat Inactivated (HI)PIM(G)®PIM(T)®Ciprofloxacin Hydrochloride. Either MP Biomedicals™ MP219902005 or Corning™ MT61277RG (61277RF is available in 1 gm bottles a... |
36,741 | Zooarchaeology by Mass Spectrometry (ZooMS)- Pretreatment protocols for bone material | 2 | dx.doi.org/10.17504/protocols.io.bf5djq26 | https://www.protocols.io/view/zooarchaeology-by-mass-spectrometry-zooms-pretreat-bf5djq26 | Samantha Brown, Sandra Hebestreit, Naihui Wang, Nicole Boivin, Katerina Douka, Kristine Richter | TITLE: Zooarchaeology by Mass Spectrometry (ZooMS)- Pretreatment protocols for bone material
AUTHORS: Samantha Brown, Sandra Hebestreit, Naihui Wang, Nicole Boivin, Katerina Douka, Kristine Richter
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This collection details some of the different establis... | [] |
85,335 | Gewebesammlung Frischgewebe Zystektomie | 1 | null | https://www.protocols.io/view/gewebesammlung-frischgewebe-zystektomie-cxjxxkpn | Annika Fendler, Bettina Ergün | TITLE: Gewebesammlung Frischgewebe Zystektomie
AUTHORS: Annika Fendler, Bettina Ergün
[DESCRIPTION]
Dieses Protokoll beschreibt die Schritte für die Sammlung von Frischgewebe, Gefriergewebe (Fresh-frozen), und Blut von Patienten mit Harnblasenkarzinom nach Zystektomie.
Verwandte Dokumente:
Protokoll zur Blutaufarb... | ["[Dokumentation] Patientendaten in Datei hinterlegen und korrespondierende Liquidnummer eintragen: \\\\Charite.de\\Centren\\C08\\UR\\FO\\Intern\\PROBEN_PATIENTEN\\01-Gewebe\\Gewebe_FF\\ Biobank_Gewebe_ab01012019.xlsx", "[Dokumentation] In der Liquid-Sammelliste die korresspondierende Gewebenummer eintragen: \\\\Charit... |
26,549 | UC Davis - Microvascular Permeability and Lipoprotien Flux | null | dx.doi.org/10.17504/protocols.io.56vg9e6 | null | John Rutledge | TITLE: UC Davis - Microvascular Permeability and Lipoprotien Flux
AUTHORS: John Rutledge
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">One of the three indices of arterial function that are compromised to a varying d... | ["Mice are anesthetized with an intraperitoneal injection with 50 mg pentobarbital/kg weight.", "All treatments are administered into the left femoral vein by bolus injection. FITC-albumin (40 mg/mL) in 100 µL: a. PBS b. VLDL (150 mg/dL) c. VLDL (150mg/dL) + LpL (2 U/mL) d. LpL (2 U/mL) in PBS", "Alterna... |
13,287 | Anaerobic (vinyl) tent maintenance | 1 | dx.doi.org/10.17504/protocols.io.q8fdztn | https://www.protocols.io/view/anaerobic-vinyl-tent-maintenance-q8fdztn | Eva Petrova, Roey Angel | TITLE: Anaerobic (vinyl) tent maintenance
AUTHORS: Eva Petrova, Roey Angel
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The </span><a href="https://coylab.com/products/anaerobic-chambers/vinyl-anaerobic-chambers/" style = "text-decoration:underline;color:blue;cursor:pointer;"><span style =... | ["[Preventive maintenance - once a week]\nrejuvenate the catalyst (bake it in an oven at 125 - 200°C for 2 hours)rejuvenate the desicant (bake it in an oven at 125 - 200°C for 2 hours)refresh hydrogen levels (let 1/4 of atmosphere volume off from a tent and then refill it with 95%N2/5%H2 gas mixture)clean the airlock s... |
95,478 | Automated concentration of viral particles in wastewater samples using Nanotrap Microbiome A Beads | 4 | dx.doi.org/10.17504/protocols.io.261gedz7dv47/v1 | https://www.protocols.io/view/automated-concentration-of-viral-particles-in-wast-c9gwz3xe | Ashlie McCunn, Dagmara Antkiewicz, Adelaide Roguet | TITLE: Automated concentration of viral particles in wastewater samples using Nanotrap Microbiome A Beads
AUTHORS: Ashlie McCunn, Dagmara Antkiewicz, Adelaide Roguet
[DESCRIPTION]
This method describes how to concentrate viral particles in water samples using magnetic beads (Nanotrap‱ Microbiome A Particles) to enable... | ["[Concentration Preparation] For the Sample plates (Sample 1 and Sample 2): Inside the BSC, add 5 mL of wastewater sample into matching wells of the remaining two KingFisher Deep Well 24 Plates (10mL total are processed). Repeat this step for all samples listed on the plate map.", "[Concentration Preparation] Add 50 µ... |
28,724 | Protein Purification for OnePot PURE cell-free system | null | dx.doi.org/10.17504/protocols.io.8auhsew | null | Konstantinos Ragios | TITLE: Protein Purification for OnePot PURE cell-free system
AUTHORS: Konstantinos Ragios
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">In this protocol we explain the procedure of protein purification with a single coculture and a single Ni-NTA affinity His-tag purification to produce the protein... | ["[Small cell culture ]\nPrepare 10ml of autoclaved LB medium and supplement it with 100μg/ml Ampicillin\nWork under flame Sterilize the bench with 70% Ethanol", "[Small cell culture ]\nFill 35 of the wells of a 96 deep-well plate with 0.3 ml of the LB medium according to the pattern of the stored strains.\nWe assumed... |
72,683 | Downstream Analysis of ebFRET Data | 1 | null | https://www.protocols.io/view/downstream-analysis-of-ebfret-data-ci8juhun | Clark Fritsch | TITLE: Downstream Analysis of ebFRET Data
AUTHORS: Clark Fritsch
[DESCRIPTION]
This protocol follows from the "Using ebFRET for Hidden Markov Modeling" protocol and is the fourth and final step towards analyzing your single-molecule FRET traces using Hidden Markov Modeling. In this protocol, I describe some of the que... | ["After creating your \"2stateHMM_practice_Analysis.dat\", as described in the \"Using ebFRET for Hidden Markov Modeling\" protocol, you can then calculate / retrieve various types of information from your data.", "The downstream analysis that I have done so far for the ebFRET data can be divided into the following que... |
63,449 | Preparation of primary hippocampal neurons | 4 | dx.doi.org/10.17504/protocols.io.j8nlkk241l5r/v1 | https://www.protocols.io/view/preparation-of-primary-hippocampal-neurons-b97zr9p6 | Arpine Sokratian, yuan.yuan, andrew.west west | TITLE: Preparation of primary hippocampal neurons
AUTHORS: Arpine Sokratian, yuan.yuan, andrew.west west
[DESCRIPTION]
This protocol details preparation of the primary hippocampal neuron culture. The protocol involves extraction ofdissecting hippocampi from rodent embryos P1 from nTg or transgenic mice, enzymatic dige... | ["[Plate preparation] Wash 48 well plates with distilled H2O", "[Plate preparation] Treat each well with 0.5 mL PDL at 37 °C for 60 min.", "[Plate preparation] Wash with distilled H2O.", "[Plate preparation] Place 0.5 mL plating media into each well at 37 °C.", "[Dissection] Collect the hippocampi of 1-day postnatal ... |
null | null | null | dx.doi.org/10.17504/protocols.io.rf4d3qw | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?. | [] |
22,270 | LB borth or agar | 1 | null | https://www.protocols.io/view/lb-borth-or-agar-zy6f7ze | Adrien Assie, Buck Samuel | TITLE: LB borth or agar
AUTHORS: Adrien Assie, Buck Samuel
[DESCRIPTION]
LB broth or agar recipe
[STEPS]
1. Start with 900 mL
2. 10 gBacto-tryptone
3. 5 g Bacto-yeast
4. 5 gNaCl
5. Adjust pH to 7.0 using 5 Molarity (M)NaOH
6. For LB Agar add 15 g
7. Adjust water to 1000 mL
8. Autoclave | ["Start with 900 mL", "10 gBacto-tryptone", "5 g Bacto-yeast", "5 gNaCl", "Adjust pH to 7.0 using 5 Molarity (M)NaOH", "For LB Agar add 15 g", "Adjust water to 1000 mL", "Autoclave"] |
78,715 | Primary Data Analysis - Basecalling, Demultiplexing, and Consensus Building for ONT Fungal Barcodes | 5 | dx.doi.org/10.17504/protocols.io.dm6gpbm88lzp/v3 | https://www.protocols.io/view/primary-data-analysis-basecalling-demultiplexing-a-cq43vyyn | Stephen Douglas Russell | TITLE: Primary Data Analysis - Basecalling, Demultiplexing, and Consensus Building for ONT Fungal Barcodes
AUTHORS: Stephen Douglas Russell
[DESCRIPTION]
This protocol assumes that your MinION run has been completed and the data from the run has been saved. It should take you from raw data to usable FASTA files ... | ["[Initial Post-Run Preparation] This protocol assumes the experiment name is \"FirstRun.\"\n\nCreate a new working folder on the desktop. Ex - FirstRun. Within that create a new folder called \"fast5,\" another called \"Programs,\" and a final one called \"NGSpeciesID.\"\n\nI will start by copying all of the fast5 fil... |
36,748 | Mild Hypothermia to prevent Acute kidney injury in Liver Transplantation (MHALT) Trial - Statistical Analysis Plan for the Interim Analysis, v1.0 | null | dx.doi.org/10.17504/protocols.io.bf5kjq4w | https://www.protocols.io/view/mild-hypothermia-to-prevent-acute-kidney-injury-in-bf5kjq4w | Michael Bokoch, Claus Niemann, Dieter Adelmann, Rishi Kothari | TITLE: Mild Hypothermia to prevent Acute kidney injury in Liver Transplantation (MHALT) Trial - Statistical Analysis Plan for the Interim Analysis, v1.0
AUTHORS: Michael Bokoch, Claus Niemann, Dieter Adelmann, Rishi Kothari
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Acute kidney injury (AKI), ... | ["[STATISTICAL CONSIDERATIONS]\nStatistical Analysis Plan for the Interim AnalysisNCT03534141UCSF IRB # 17-22384Version 1.0May 7, 2020", "Analysis PopulationsThe following populations will be used for the summaries and analyses of the study data. These populations are defined as follows:Randomized:The Randomized popula... |
78,915 | Slide-TCR-Seq v3 (IVT) | 4 | dx.doi.org/10.17504/protocols.io.n92ldp6w8l5b/v2 | https://www.protocols.io/view/slide-tcr-seq-v3-ivt-crbbv2in | Sophia Liu, Ruth Raichur, Fei Chen | TITLE: Slide-TCR-Seq v3 (IVT)
AUTHORS: Sophia Liu, Ruth Raichur, Fei Chen
[DESCRIPTION]
T cells mediate antigen-specific immune responses to disease through the specificity and diversity of their clonotypic T cell receptors (TCRs). Determining the spatial distributions of T cell clonotypes in tissues is essential to u... | ["[PCR to add T7 to cDNA libraries] This protocol amplifies TCRs from unfragmented, full-length cDNA from Slide-Seq. \nPrepare two 10-nanogram* dilutions of all samples into 12.25 μL of ultrapure water for amplifying TCR alpha and beta sequences in separate reactions. \n*We have successfully tested down to 2 ng for low... |
44,522 | Role and effects of zinc supplementation in HIV-infected patients with immunovirological discordance: A randomized, double blind, case control study. | 1 | dx.doi.org/10.17504/protocols.io.bpqimmue | https://www.protocols.io/view/role-and-effects-of-zinc-supplementation-in-hiv-in-bpqimmue | Macarena Silva, Carmen G Montes, Andrea Canals, Maria J Mackenna, Marcelo Wolff | TITLE: Role and effects of zinc supplementation in HIV-infected patients with immunovirological discordance: A randomized, double blind, case control study.
AUTHORS: Macarena Silva, Carmen G Montes, Andrea Canals, Maria J Mackenna, Marcelo Wolff
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.hgqb3vw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div class="row bibliography-item-info">
<div class="bibliography-item-copy-text content col-md-12" data-clipboard-target="copy-target-228943496" data-redirect-target="/items/228943496/copy">Adapted from: Van Etten, J. (n.d.). Titering of <em>Chlorella </em>Viruses. Retrieved fr... | [] |
104,073 | Standard operating procedure for dead-end ultrafiltration water sampling in the field for bacterial pathogens using REXEED 25S replacement filters | 0 | dx.doi.org/10.17504/protocols.io.j8nlk8nydl5r/v1 | https://www.protocols.io/view/standard-operating-procedure-for-dead-end-ultrafil-dhvh3636 | Julie Ann Kase | TITLE: Standard operating procedure for dead-end ultrafiltration water sampling in the field for bacterial pathogens using REXEED 25S replacement filters
AUTHORS: Julie Ann Kase
[DESCRIPTION]
This protocol details the standard operating procedure for dead-end ultrafiltration water sampling in the field for bacterial p... | ["[SCOPE AND APPLICABILITY] This standard operating procedure (SOP) will be used to filter up to 100 L of water using an ultrafilter at a field sampling site to collect bacteria for pathogen analyses in the laboratory.", "[SUMMARY OF METHOD] Using a field-portable peristaltic pump, volumes up to 100 L of water are pass... |
null | null | null | dx.doi.org/10.17504/protocols.io.qpcdviw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Commonly used protocol to isolate peripheral blood mononuclear cells from whole human blood or apheresis packs</p>
[BEFORE_START]
<ul>
<li>Make sure to repeatedly label sample with donor number, especially if working with multiple donors</li>
<li>The protocol here is optimiz... | [] |
62,237 | Keto Start ACV Gummies | 3 | dx.doi.org/10.17504/protocols.io.dm6gpbx8jlzp/v1 | https://www.protocols.io/view/keto-start-acv-gummies-b8z5rx86 | Keto Start ACV Gummies | TITLE: Keto Start ACV Gummies
AUTHORS: Keto Start ACV Gummies
[DESCRIPTION]
Keto Start ACV Gummies
[STEPS] | [] |
25,140 | Reverse transcription using SuperScript IV | null | dx.doi.org/10.17504/protocols.io.4sugwew | null | Amin Mahpour | TITLE: Reverse transcription using SuperScript IV
AUTHORS: Amin Mahpour
[STEPS]
?. Mix the following reagents from the kit. Please scale up if more RT reaction is desired. AB1ReagentAmount (uL)2Primer (Random or dT)0.53dNTP (10mM)14RNA11
AB1ReagentAmount (uL)2Primer (Random or dT)0.53dNTP (10mM)14RNA11
?. Incubate th... | ["Mix the following reagents from the kit. Please scale up if more RT reaction is desired. AB1ReagentAmount (uL)2Primer (Random or dT)0.53dNTP (10mM)14RNA11\nAB1ReagentAmount (uL)2Primer (Random or dT)0.53dNTP (10mM)14RNA11", "Incubate the mixture at for . Then, incubate samples on ice for few minutes.\n72 °C\nThis ... |
78,502 | [Modified] DNeasy PowerSoil Pro Kit_Increased Sediment Volume & Optional Concentration | 1 | dx.doi.org/10.17504/protocols.io.rm7vzb9x4vx1/v1 | https://www.protocols.io/view/modified-dneasy-powersoil-pro-kit-increased-sedim-cqwevxbe | Grayson Huston | TITLE: [Modified] DNeasy PowerSoil Pro Kit_Increased Sediment Volume & Optional Concentration
AUTHORS: Grayson Huston
[DESCRIPTION]
Protocol (both increased sediment amount up to 2.0g as well as concentrating DNA post-extraction) unsuccessful at detecting fish sedDNA from lakes in Maine, USA.
Both protocols succ... | ["[Modified PowerSoil Pro extraction - sample preparation & cell lysis] CENTRIFUGE sediment samples briefly to separate pore water\n\nDISCARD pore water to retain only sediment samples", "[Modified PowerSoil Pro extraction - sample preparation & cell lysis] SPIN the PowerBead Pro Tube briefly to ensure that the... |
56,786 | The perfect Crème Brûlée | 1 | dx.doi.org/10.17504/protocols.io.b3psqmne | https://www.protocols.io/view/the-perfect-cr-me-br-l-e-b3psqmne | René Bernard | TITLE: The perfect Crème Brûlée
AUTHORS: René Bernard
[DESCRIPTION]
Crème Brûlée has a short ingredient list and does not require specific skills to make, but to get it right, several steps need to be carefully executed to receive the creme, not a pudding that, that is still grainy or liquid. With a caramel crust tha... | ["[Preparation of creme] Take a midsize stainless steel pot and add500 mL of heavy whipping cream and add 100 g sugar.", "[Preparation of creme] Take one Bourbon Vanilla bean and with a small and pointy knife cut itopen lengthwise. \n \nRemove the sticky vanilla mark with the knife and at it to the cream-sugar-mix. Wh... |
null | null | null | dx.doi.org/10.17504/protocols.io.vede3a6 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
SECTION: Cell Culture
?.
SECTION: Fixation, permeabilization, and staining
?.
SECTION: Fixation, permeabilization, and staining
?.
SECTION: Fixation, permeabilization, and staining
?.
SECTION: Fixation, permeabilization, and staining
?.
SECTION: Fixation, permeabilization, and st... | ["[Cell Culture] Culture primary T cells using standard tissue culture techniques", "[Fixation, permeabilization, and staining] {\"blocks\":[{\"key\":\"513mp\",\"text\":\"Collect 200K to 1 million cells and sping them at 300g for \",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[],\"entityRanges\":[{\"offset... |
70,807 | big redesign protocol PUBLISHED | 1 | dx.doi.org/10.17504/protocols.io.n2bvj8y7pgk5/v2 | https://www.protocols.io/view/big-redesign-protocol-published-chdxt27n | Maria Gul, katarina, rober, Monika MF Frolova | TITLE: big redesign protocol PUBLISHED
AUTHORS: Maria Gul, katarina, rober, Monika MF Frolova
[DESCRIPTION]
abstract
Lorem ipsum dolor sit amet, consectetuer adipiscing elit. Integer in sapien. Praesent id justo in neque elementum ultrices. Cras elementum. Sed ac dolor sit amet purus malesuada congue. Nunc auctor. Q... | ["[section 1] Lorem ipsum dolor sit amet, consectetuer adipiscing elit. Integer in sapien. Praesent id justo in neque elementum ultrices. Cras elementum. Sed ac dolor sit amet purus malesuada congue. Nunc auctor. Quis autem vel eum iure reprehenderit qui in ea voluptate velit esse quam nihil molestiae consequatur, vel ... |
70,375 | Relative hypotension in emergency care | 1 | dx.doi.org/10.17504/protocols.io.14egn2876g5d/v1 | https://www.protocols.io/view/relative-hypotension-in-emergency-care-cgyftxtn | James D van Oppen, Lucy Beishon, Rhiannon Owen, Tim Coats | TITLE: Relative hypotension in emergency care
AUTHORS: James D van Oppen, Lucy Beishon, Rhiannon Owen, Tim Coats
[DESCRIPTION]
Investigation for the effect (on mortality & length of hospital stay) of hypotension at emergency care attendance relative to an individual's baseline
[STEPS]
SECTION: Preparation
2. Dataset ... | ["[Preparation] Dataset generation", "[Preparation] Regulatory approvals", "[Data processing] Dataset linking and cleaning", "[Data processing] Summary statistics", "[Data analysis] Regression models"] |
88,738 | m6A visualization/immunofluorescence of DamID | 4 | dx.doi.org/10.17504/protocols.io.e6nvwdz6zlmk/v1 | https://www.protocols.io/view/m6a-visualization-immunofluorescence-of-damid-c2wayfae | Lucian Dipeso, Emily Hatch | TITLE: m6A visualization/immunofluorescence of DamID
AUTHORS: Lucian Dipeso, Emily Hatch
[DESCRIPTION]
Used for visualizing Dam activity by immunofluorescence in mammalian cells. This protocol stains N-6 methyladenosine (m6A) modified DNA by immunofluorescence while preserving other epitopes, avoiding harsh denaturati... | ["[Protocol] Fix cells in 100% MeOH for 10 min at -20 °C", "[Protocol] Block, and RNase treat in 2 ug/mL RNase A in blocking buffer (3% BSA, 0.04% TritonX-100, 0.02% sodium azide in PBS) at 37 °C for 30 min", "[Protocol] Wash cells 2x in PBS for 5 min at room temperature", "[Protocol] Digest in 50 U/mL DpnI (NEB #r0176... |
27,546 | Crossmatch testing before blood component transfusion | null | dx.doi.org/10.17504/protocols.io.652hg8e | null | Grace HJ Chung, Mina Hur, Sang Gyeu Choi, Hyun-Kyung Lee, Hanah Kim, Hee-Won Moon, Yeo-Min Yun | TITLE: Crossmatch testing before blood component transfusion
AUTHORS: Grace HJ Chung, Mina Hur, Sang Gyeu Choi, Hyun-Kyung Lee, Hanah Kim, Hee-Won Moon, Yeo-Min Yun
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:left"><span style = "font-weight:bold;">1.</... | ["[5.\tPROCEDURE]\n1st saline phase/room temperature immediate spin Saline room temperature is done to detect Major ABO incompatibility and complete (IgM) antibodies/cold antibodies like M, N, S, P, Lewis, Lutheran, etc. This crossmatching method can be done for the issuance of blood in emergencies. A.\tTake a test tub... |
93,687 | Uppsala Fungal Barcoding using ONT: DNA extraction -> Library preparation V1 | 6 | null | https://www.protocols.io/view/uppsala-fungal-barcoding-using-ont-dna-extraction-c7qxzmxn | Karl Soler | TITLE: Uppsala Fungal Barcoding using ONT: DNA extraction -> Library preparation V1
AUTHORS: Karl Soler
[DESCRIPTION]
Abstract
This protocol was developed by Uppsala Svampklubb (fungal society), in cooperation with Evolutionary Biology Centre (EBC) at Uppsala University, as a cost efficient method to help amateurs... | ["[Fungal collecting, storing and documentation] Before starting:\nIn order to maximize the chances that your barcoding is successful there are several things to consider when collecting, storing and documenting your fungal specimens. Collections coupled with a DNA sequence are also more valuable when donated to a herb... |
78,721 | Modified Promega Wizard Extraction for Barcoding Macrofungi | 1 | dx.doi.org/10.17504/protocols.io.rm7vzb3p4vx1/v2 | https://www.protocols.io/view/modified-promega-wizard-extraction-for-barcoding-m-cq49vyz6 | Stephen Douglas Russell | TITLE: Modified Promega Wizard Extraction for Barcoding Macrofungi
AUTHORS: Stephen Douglas Russell
[DESCRIPTION]
'This protocol is best used when preparing macrofungal specimens for Sanger sequencing or as a secondary extraction protocol for ONT nanopore barcoding.
The quality of a DNA extraction method is a ... | ["Add 600uL of to 1.5mL eppi tubes. One tube for each specimen you are planning an extraction for.", "Place tissue from your specimens into each tube using tweezers. Utilize a piece about the size of a grain of rice. The tissue can be either fresh or dried. Label the tube with the appropriate number. Wipe the tweezer... |
null | null | null | dx.doi.org/10.17504/protocols.io.erpbd5n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Recipe to make 10ml of 2x stock
[GUIDELINES]
<table>
<tbody>
<tr>
<td>1M Tris-HCl pH 6.8</td>
<td>1.0 ml</td>
</tr>
<tr>
<td>SDS</td>
<td>0.4 g</td>
</tr>
<tr>
<td>Glycerol</td>
<td>2.0 ml</td>
</tr>
<tr>
<td>0.5 M EDTA</td>
<td>0.5 ml</td>
</tr>
<tr>
<td>Bromophenol Blue</td>
... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.ch7t9m | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This PCR Protocol is for Taq DNA Polymerase with Standard Taq Buffer (M0273)
[BEFORE_START]
Annealing temperatures should be determined using the <a href="http://tmcalculator.neb.com/#!/" target="_blank">NEB Annealing Temp Calculator</a>.
[GUIDELINES]
<stro... | [] |
76,107 | Resource 2: Fluorescence Detector Setting Incrementation for FCMPASS | 1 | dx.doi.org/10.17504/protocols.io.q26g7yd88gwz/v1 | https://www.protocols.io/view/resource-2-fluorescence-detector-setting-increment-cnjjvckn | Joshua A Welsh, Sean M Cook, Jennifer Jones | TITLE: Resource 2: Fluorescence Detector Setting Incrementation for FCMPASS
AUTHORS: Joshua A Welsh, Sean M Cook, Jennifer Jones
[DESCRIPTION]
Flow cytometry (FCM) is a common extracellular particles (EPs), including viruses and extracellular vesicles (EVs), characterization method. Frameworks such as MIFlowCyt-EV ex... | ["[Sample preparation] Vortex QbSure bottle on a high setting for 5 s.", "[Sample preparation] Pipette 500 µL of DPBS to two FACS tubes. Label one tube 'DPBS\" and the second tube 'Beads'.", "[Sample preparation] Add 3 drops of QbSure beads to the 'Beads' tube and vortex for 5 s.", "[Cytometer Setup] Ensure cytometer i... |
48,131 | 2009 Deep Soil Core Protocol | 5 | null | https://www.protocols.io/view/2009-deep-soil-core-protocol-bs9bnh2n | Test McTester | TITLE: 2009 Deep Soil Core Protocol
AUTHORS: Test McTester
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Describes the method of analyzing Deep Soil Cores</div></div>
[STEPS]
?. Mark cores at top of soil with marker around outside of cylinder, keeping the cores upright not to allow the soil to sl... | ["Mark cores at top of soil with marker around outside of cylinder, keeping the cores upright not to allow the soil to slide up the tube. Measure the overall length of the sample (cm) and enter on data sheet.", "Place piece of tape on side of template and mark segment sizes on it, Lay tube in PVC template and cut tube ... |
102,544 | Platelet adhesion assay for streptococci | 0 | dx.doi.org/10.17504/protocols.io.kqdg328e1v25/v1 | https://www.protocols.io/view/platelet-adhesion-assay-for-streptococci-dgdq3s5w | Samantha King | TITLE: Platelet adhesion assay for streptococci
AUTHORS: Samantha King
[DESCRIPTION]
This protocol describes how to perform adhesion assays examining the interaction between streptococci and fixed platelets.
[GUIDELINES]
Planning the layout of your plate prior to starting the experiment is helpful. The platelets are... | ["[Basics] The volumes of all washes are 120 µl of PBS", "[Basics] Everything is diluted and made in PBS pH 7.4", "[Basics] Binding of each strain or condition is performed in triplicate and each strain has a control of binding to BSA.", "[Preparation of plate] Aspirate liquid from platelet coated wells", "[Preparation... |
72,964 | Golgi immunopurification (Golgi-IP) for subcellular lipid profiling | 1 | dx.doi.org/10.17504/protocols.io.5qpvor3dbv4o/v1 | https://www.protocols.io/view/golgi-immunopurification-golgi-ip-for-subcellular-cjhcuj2w | Wentao Dong, Eshaan S Rawat, Monther Abu-Remaileh | TITLE: Golgi immunopurification (Golgi-IP) for subcellular lipid profiling
AUTHORS: Wentao Dong, Eshaan S Rawat, Monther Abu-Remaileh
[DESCRIPTION]
The Golgi is a membrane-bound organelle that is central to protein and lipid processing, sorting and secretion in the cell. Despite its critical cellular function, there h... | ["[Preparation of homogenizers and sample tubes] Wash the glass vessel homogenizer with MilliQ Water, 10 times each. Wash the tissue grinder homogenizer thoroughly with DI Water and MilliQ Water, especially the gap between the white parts, don’t touch the part that goes into the glass vessel. Then dry upside-down using... |
null | null | null | dx.doi.org/10.17504/protocols.io.p2xdqfn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol was developed to use common wet lab device (Real Time PCR machine) to detect viral genome release and native viral particle conversion. We used temperature ramping for inducing genome uncoating and fluorescent probes for RNA/DNA and/or proteins, to detect genome... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.kkqcuvw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Preparation of insect specimens for morphological studies classically employs chaotropic salts which can cause disruption of important structures. Also, extraction of nucleic acids for genetic studies leads to destruction of the specimen. Thus, in this paper is proposed a new... | [] |
63,412 | Vissentials Max BHB Canada:-Updated Results 2022 | Canada | Does It Works Or Scam? | 3 | dx.doi.org/10.17504/protocols.io.yxmvmnqxng3p/v1 | https://www.protocols.io/view/vissentials-max-bhb-canada-updated-results-2022-ca-b96ur9ew | vissenmax | TITLE: Vissentials Max BHB Canada:-Updated Results 2022 | Canada | Does It Works Or Scam?
AUTHORS: vissenmax
[DESCRIPTION]
Vissentials Max BHB Reviews, Canada: Obesity issues are fatal, and if you have an obese body, it may provide you multiple negative effects if you do not get rid of it in time. If you have an obe... | [] |
69,781 | Astrocyte extraction from brain organoids | 4 | dx.doi.org/10.17504/protocols.io.261ge364wl47/v2 | https://www.protocols.io/view/astrocyte-extraction-from-brain-organoids-cgdvts66 | gustavo.parfitt | TITLE: Astrocyte extraction from brain organoids
AUTHORS: gustavo.parfitt
[DESCRIPTION]
Protocol for astrocyte extraction from brain organoids.
[STEPS]
1. Coat a 6 well plate coat with gelatin 0.1% or 1:100
2. Collect 10-20 spheres and place in a 6 well plate (day 40+ spheres)
3. Wash in PBS twice
4. Aspirat... | ["Coat a 6 well plate coat with gelatin 0.1% or 1:100", "Collect 10-20 spheres and place in a 6 well plate (day 40+ spheres)", "Wash in PBS twice", "Aspirate the PBS", "Add 1 mL of for 5 min", "Triturate using glass a pipette (2-3 up and down)", "Transfer the cells and tissue (even the chunks, the trituration is... |
89,887 | Purificación PCR desde Gel | 4 | dx.doi.org/10.17504/protocols.io.n2bvj3zrnlk5/v1 | https://www.protocols.io/view/purificaci-n-pcr-desde-gel-c3z7yp9n | Diego Antonio Márquez | TITLE: Purificación PCR desde Gel
AUTHORS: Diego Antonio Márquez
[DESCRIPTION]
Método para purificar productos de PCR de hasta 1000 pb
[STEPS]
SECTION: Electroforesis
1. Para un gel estandar, diluir 0.75 g de Agarosa de Bajo Punto de Fusión en 50 mL de Agua destilada junto con 1 mL de Buffer TAE 50X en una botella... | ["[Electroforesis] Para un gel estandar, diluir 0.75 g de Agarosa de Bajo Punto de Fusión en 50 mL de Agua destilada junto con 1 mL de Buffer TAE 50X en una botella Schott", "[Electroforesis] Calentar en microondas a maxima potencia entre 30 y 90 segundos, hasta que la solución se vuelva transparente y no se observen r... |
64,229 | Expression and purification of recombinant MM4 reverse transcriptase (RT) | 4 | dx.doi.org/10.17504/protocols.io.8epv59objg1b/v1 | https://www.protocols.io/view/expression-and-purification-of-recombinant-mm4-rev-caydsfs6 | Diana A Tapia-Sidas, Brenda Vargas-Hernández, José Abrahán Ramírez-Pool, Leandro A Nuñez-Muñoz, Berenice Calderón-Pérez, Rogelio González-González, Luis Gabriel Brieba, Rosalía Lira-Carmona, Eduardo Ferat-Osorio, Constantino López-Macías, Roberto Ruiz-Medrano, Beatriz Xoconostle-Cazares | TITLE: Expression and purification of recombinant MM4 reverse transcriptase (RT)
AUTHORS: Diana A Tapia-Sidas, Brenda Vargas-Hernández, José Abrahán Ramírez-Pool, Leandro A Nuñez-Muñoz, Berenice Calderón-Pérez, Rogelio González-González, Luis Gabriel Brieba, Rosalía Lira-Carmona, Eduardo Ferat-Osorio... | ["[Preparation of RT expression cells] Transformation of chemically competent BL21 (DE3) cells with pKJE7 plasmid.", "[Preparation of RT expression cells] Add 1 µL consisting of the pKJE7 plasmid from the to 50 µL . Mix the cells gently and incubate on ice for \n 20 min .", "[Preparation of RT expression cells]... |
98,476 | Direct Detection of poliovirus and Nanopore Sequencing (DDNS) - Stool | 4 | dx.doi.org/10.17504/protocols.io.rm7vzbyyxvx1/v3 | https://www.protocols.io/view/direct-detection-of-poliovirus-and-nanopore-sequen-dcek2tcw | 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... |
94,895 | Single-cell RNA-seq | 1 | dx.doi.org/10.17504/protocols.io.eq2lyjy5mlx9/v1 | https://www.protocols.io/view/single-cell-rna-seq-c8wpzxdn | patricia.garcia | TITLE: Single-cell RNA-seq
AUTHORS: patricia.garcia
[DESCRIPTION]
Harvesting and performing single-cell RNA-seq.
[STEPS]
SECTION: Harvesting cells for single-cell RNA-sequencing
1. Samples were trypsinised or scraped from the culture surface and placed in a 15mL conical tube.
SECTION: Harvesting cells for single-cell... | ["[Harvesting cells for single-cell RNA-sequencing] Samples were trypsinised or scraped from the culture surface and placed in a 15mL conical tube.", "[Harvesting cells for single-cell RNA-sequencing] Tubes were centrifuged at 800g in a refrigerated centrifuge for 5 minutes, and the culture media was decanted.", "[Harv... |
null | null | null | dx.doi.org/10.17504/protocols.io.c24ygv | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
References to 'DNA Extraction of Viruses using Wizard Prep Columns' protocol<br /><br />Needed:<br /><ul><li>Filters</li><li>Forceps (bleached)</li><li>Aluminum foil squares</li><li>50cc tube</li><li>Resuspension buffer (0.1M EDTA - 0.2M MgCl2 - 0.2M Ascorbate Buffer)</li><li>Ste... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.nundeve | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>It is not always possible to isolate microalgae immediately after sample collection, for example on long cruises where no proper conditions are available (lack of culture chamber, sterile hoods) or on trips to remote locations. Therefore it is desirable to be able to preserve... | [] |
89,818 | Two-step method for isolation of inactivated CD4+ T-cells from human blood mononuclear cells | 4 | dx.doi.org/10.17504/protocols.io.36wgq3mxolk5/v1 | https://www.protocols.io/view/two-step-method-for-isolation-of-inactivated-cd4-t-c3x2ypqe | Anna Esman, Michael Vinokurov | TITLE: Two-step method for isolation of inactivated CD4+ T-cells from human blood mononuclear cells
AUTHORS: Anna Esman, Michael Vinokurov
[DESCRIPTION]
1. Obtaining human CD4+ T cells
2. Obtaining CD4+ inactivated cells
using
1.
2.
3.
4.
5.
6.
and magnetic tube separator.
[STEPS]
SECTION: Neg... | ["[Negative depletion of inactivated CD4+ T-cells] Preparing buffers for operations\n• Buffer 1: supplemented with 0.1% bovine serum albumin (BSA), pH 7.4 \n• Buffer 2: with 0.1% BSA and 0.6% sodium citrate or 2 millimolar (mM) EDTA.", "[Negative depletion of CD4+ T-cells] Preparation of PBMC (peripheral blood ... |
86,859 | Sanger Tree of Life HMW DNA Extraction: Manual Plant MagAttract v.1 | 4 | dx.doi.org/10.17504/protocols.io.n92ldmmx9l5b/v1 | https://www.protocols.io/view/sanger-tree-of-life-hmw-dna-extraction-manual-plan-cy3jxykn | Maja Todorovic, Caroline Howard | TITLE: Sanger Tree of Life HMW DNA Extraction: Manual Plant MagAttract v.1
AUTHORS: Maja Todorovic, Caroline Howard
[DESCRIPTION]
This protocol describes the manual extraction of HMW DNA from plant or fungi tissue samples from a variety of species intended for long-read sequencing using the Qiagen MagAttract HMW DNA e... | ["[Sample lysis] Transfer 50 mg of cryogenically homogenised plant/fungi tissue from each sample to 2 mL microcentrifuge tubes and place on dry ice to keep the samples frozen.", "[Sample lysis] Add 374 µL of the lysis buffer master mix to each sample, then homogenise sample and mastermix by gently pipetting 10 times wi... |
21,855 | aCGH results extraction from TIFF file | null | dx.doi.org/10.17504/protocols.io.zj7f4rn | null | Hendrik F van Essen | TITLE: aCGH results extraction from TIFF file
AUTHORS: Hendrik F van Essen
[STEPS]
?. Copy TIFF file to “output folder”
?. Open “Feature Extraction” (Fe) program
?. File -> ‘Add extraction set’
?. Select TIFF files in "output folder"
?. Select under ‘project properties’ tab the correct grid name* 4x44K* 2x105K* 4x180k... | ["Copy TIFF file to “output folder”", "Open “Feature Extraction” (Fe) program", "File -> ‘Add extraction set’", "Select TIFF files in \"output folder\"", "Select under ‘project properties’ tab\tthe correct grid name* 4x44K* 2x105K* 4x180k", "Under Project select ‘Start extracting’"] |
64,054 | Reproducibility of the reporting of post-operative anterior cruciate ligament reconstruction rehabilitation programmes: a scoping review | 1 | dx.doi.org/10.17504/protocols.io.261gen8nyg47/v1 | https://www.protocols.io/view/reproducibility-of-the-reporting-of-post-operative-caswsefe | Sebastiano Nutarelli, Nicol Van Dyk, Chad Cook, Gabriele Severini, Catherine Blake, Eamonn Delahunt | TITLE: Reproducibility of the reporting of post-operative anterior cruciate ligament reconstruction rehabilitation programmes: a scoping review
AUTHORS: Sebastiano Nutarelli, Nicol Van Dyk, Chad Cook, Gabriele Severini, Catherine Blake, Eamonn Delahunt
[DESCRIPTION]
Rupture of the anterior cruciate ligament (ACL), the... | ["[Protocol and Registration] The authors developed the protocol and made it public by registering it on protocols.io.", "[Research Question] Our scoping review aims to evaluate the reproducibility of reporting of post-operative physical therapy rehabilitation programmes in published studies describing surgical interve... |
99,117 | DNA Extraction: Zymo Research Quick-DNA Fecal/Soil Microbe Midiprep Kit (Cat #: D6110) | 0 | dx.doi.org/10.17504/protocols.io.3byl49b2ogo5/v1 | https://www.protocols.io/view/dna-extraction-zymo-research-quick-dna-fecal-soil-dc2m2yc6 | Jenna Brown, Mirayana Marcelino Barros, Tiago Pereira, Alejandro De Santiago Perez, Hunter Powell | TITLE: DNA Extraction: Zymo Research Quick-DNA Fecal/Soil Microbe Midiprep Kit (Cat #: D6110)
AUTHORS: Jenna Brown, Mirayana Marcelino Barros, Tiago Pereira, Alejandro De Santiago Perez, Hunter Powell
[DESCRIPTION]
DNA Extraction: Zymo Research Quick-DNA Fecal/Soil Microbe Midiprep Kit (Cat #: D6110); kit and protocol... | ["[DNA Extraction: Zymo Research Quick-DNA Fecal/Soil Microbe Midiprep Kit (Cat #: D6110)] Add 5 g of soil sample to the bead/filter of a ZR Bashing Bead Lysis/Filtration Tube (50 mL w/ 0.5 mm Beads; Cat #: S6010).", "[DNA Extraction: Zymo Research Quick-DNA Fecal/Soil Microbe Midiprep Kit (Cat #: D6110)] Add 6 mL of B... |
100,091 | Cobia PCR of sex-specific markers | 0 | dx.doi.org/10.17504/protocols.io.4r3l2q7r3l1y/v1 | https://www.protocols.io/view/cobia-pcr-of-sex-specific-markers-ddy327yn | Zhi Weng Josiah Poon | TITLE: Cobia PCR of sex-specific markers
AUTHORS: Zhi Weng Josiah Poon
[DESCRIPTION]
PCR for sex-specific markers in Cobia (Rachycentron canadum)
[STEPS]
SECTION: Brazil population (Taq PCR Core Kit (QIAGEN))
2. (cephx1_1)
20 μL reaction containing:
- 2.08 µL of 10X Taq Buffer
- 0.42 µl of dNTPs (10 µM)
- 0.67 μL o... | ["[Brazil population (Taq PCR Core Kit (QIAGEN))] (cephx1_1)\n20 μL reaction containing:\n- 2.08 µL of 10X Taq Buffer \n- 0.42 µl of dNTPs (10 µM) \n- 0.67 μL of each primer (10 µM)\n- 0.17 μL of Taq DNA polymerase (5 units/μL) \n- 35 ng of extracted DNA\n- made up to final volume with nuclease-free water\n\nThermal cy... |
51,747 | Chemical Fixation and embedding of cultured cells for Transmission Electron Microscopy | 1 | null | https://www.protocols.io/view/chemical-fixation-and-embedding-of-cultured-cells-bwsbpean | Marta Orlando | TITLE: Chemical Fixation and embedding of cultured cells for Transmission Electron Microscopy
AUTHORS: Marta Orlando
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol can be followed to fix primary cultured neurons (or cells in general) and embed them in epoxy resin. Later ultrathin sect... | ["Fix for 1 hr at RT in 1.25% glutaraldehyde in 66mM sodium cacodylate buffer", "Wash 3 times with 0.1 M sodium cacodylate buffer", "Postfix 1 hr in 1% OsO4 (optional: for better contrast add 1.5% K4Fe(CN)6 to the osmium solution) in 0.1M sodium cacodylate buffer", "Wash 3x10' with 0.1 M sodium cacodylate buffer", "Was... |
105,237 | Poly-ornithine/laminin substrate for neural cell culture | 0 | dx.doi.org/10.17504/protocols.io.dm6gpz2mplzp/v1 | https://www.protocols.io/view/poly-ornithine-laminin-substrate-for-neural-cell-c-dizv4f66 | Gist Croft, Regine Tipon | TITLE: Poly-ornithine/laminin substrate for neural cell culture
AUTHORS: Gist Croft, Regine Tipon
[DESCRIPTION]
This protocol is used to create adhesive and bioactive substrate for neural cell types, low to high density nuerons, astrocytes, or organoids. It is based on standard methods but includes several optimizat... | ["[Preparing Reagents] Filter sterilize and store at 4 degrees for 3 months", "[Preparing Reagents] Dissolve unopened vial of Poly-Ornithine in Borate Buffer at 1mg/ml (P-Orn)", "[Preparing Reagents] Pretreatment for coverslips:", "Add Laminin in L15+ NaBicarbonate solution: final 10ug laminin/ml, same volume and incub... |
62,786 | Processing of pediatric bronchoalveolar lavage samples for single cell analysis | 4 | dx.doi.org/10.17504/protocols.io.36wgq4b9ovk5/v2 | https://www.protocols.io/view/processing-of-pediatric-bronchoalveolar-lavage-sam-b9jar4ie | Shivanthan Shanthikumar, Richard Saffery, Sarath C. Ranganathan, Melanie R Neeland | TITLE: Processing of pediatric bronchoalveolar lavage samples for single cell analysis
AUTHORS: Shivanthan Shanthikumar, Richard Saffery, Sarath C. Ranganathan, Melanie R Neeland
[DESCRIPTION]
This protocol describes the collection, processing, cryopreservation and thawing of pediatric bronchoalveolar lavage (BAL) s... | ["[COLLECTION OF 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 BAL.] For guidelines on how to safely perform bronchoscopy and lavage in children, please see:", "[COLLECTION OF BAL.] ... |
null | null | null | dx.doi.org/10.17504/protocols.io.c3ayid | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Modified after Glöckner et al. 1999
[GUIDELINES]
Needed:<br />
<ul>
<li>PFA Fixative</li>
<li>Water sample</li>
<li>Formaldehyde (optional)</li>
<li>Moistened support filter (0.45 µm pore size, cellulos nitrate, 47 mm diameter)</li>
<li>Membrane filter (0.2 µm pore size, w... | [] |
57,801 | Electroporation of hPSCs | 4 | dx.doi.org/10.17504/protocols.io.b4phqvj6 | https://www.protocols.io/view/electroporation-of-hpscs-b4phqvj6 | Hanqin Li, Oriol Busquets, Steven Poser, Dirk Hockemeyer, Frank Soldner | TITLE: Electroporation of hPSCs
AUTHORS: Hanqin Li, Oriol Busquets, Steven Poser, Dirk Hockemeyer, Frank Soldner
[DESCRIPTION]
This protocol describes the standard procedure for the delivery of plasmids into human pluripotent stem cells (hPSCs) using electroporation.
Protocol Overview
A. Preparation of MEFs-culture... | ["[A. Preparation of MEFs-cultured hPSCs for electroporation] Incubate the hPSC cultures (on MEF feeders) in hPSC medium containing 10 µM Y-27632 (1:1000 dilution of stock) for at least two hours (overnight works as well) before electroporation. Two to three near confluent 6-well plates should provide sufficient cells ... |
31,114 | Lipids in microalgae: Quantitation by acid-dichromate method in microtiter plate | 1 | null | https://www.protocols.io/view/lipids-in-microalgae-quantitation-by-acid-dichroma-bamiic4e | Yingyu Hu, Zoe V Finkel | TITLE: Lipids in microalgae: Quantitation by acid-dichromate method in microtiter plate
AUTHORS: Yingyu Hu, Zoe V Finkel
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a protocol for quantitating total lipids in microalgae. </div><div class = "text-block">The acid-dichromate method is widel... | ["[Preparation of Standard]\nPrepare glyceryl tripalmitate (GTP) primary standard solution (around 1 mg/ml)", "[Preparation of Standard]\nPrepare working standards:", "[Preparation of acid-dichromate reagent]\nEstimate the total volume of potassium dichromate required:Number of standards and standard blanks: 12Number ... |
37,896 | UT Southwestern - Staining Melanoma Cells for Flow Cytometry | 4 | null | https://www.protocols.io/view/ut-southwestern-staining-melanoma-cells-for-flow-c-bg9gjz3w | Arin Aurora, Sean Morrison | TITLE: UT Southwestern - Staining Melanoma Cells for Flow Cytometry
AUTHORS: Arin Aurora, Sean Morrison
[STEPS]
?. [STAINING CELLS FOR FLOW CYTOMETRY]
Adjust staining volume and antibody concentration to the number of cells. Concentrations listed are for 5x106 cells in a 50ml reaction. Do not exceed 106 cells/10ml.- m... | ["[STAINING CELLS FOR FLOW CYTOMETRY]\nAdjust staining volume and antibody concentration to the number of cells. Concentrations listed are for 5x106 cells in a 50ml reaction. Do not exceed 106 cells/10ml.- mLin APC: Ter119 (1/100), CD31(1/100), CD45(1/200) - HLA FITC: HLA-ABC (1/5)", "[STAINING CELLS FOR FLOW CYTOMETRY... |
86,424 | Nuclei Isolation for 10x Chromium single-nuclei RNA sequencing | 4 | dx.doi.org/10.17504/protocols.io.bp2l6xx4klqe/v1 | https://www.protocols.io/view/nuclei-isolation-for-10x-chromium-single-nuclei-rn-cymyxu7w | Chiara Pavan, Clare Parish | TITLE: Nuclei Isolation for 10x Chromium single-nuclei RNA sequencing
AUTHORS: Chiara Pavan, Clare Parish
[DESCRIPTION]
Single-nucleus RNA sequencing (sn-RNA seq) enables the profiling of nuclear gene expression in isolated cells. Herein, we present a step-wise protocol for single nuclei isolation from a fresh-frozen ... | ["[Preparation of reagents and materials] Prepare ~50 mLof ice-cold PBS and store it on ice\nPrepare 8 mLof ice-cold lysis buffer containing 0.2U/ul of RNase inhibitor by adding 40 µL of RNase inhibitor to 8 mLof Nuclei EZ-prep\nPrepare 10 mLof ice-cold wash buffer containing 1%BSA and 0.2U/ul of RNase inhibitor by add... |
null | null | null | dx.doi.org/10.17504/protocols.io.fqhbmt6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Protocol for preparing biological samples fro isotopic analysis by column chemistry.</p>
[STEPS]
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.ipqcdmw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><em>Diatraea</em> spp. (Lepidoptera: Crambidae) are a group of insects considered as an agriculture pest in many economically relevant crops such as sugarcane, sorghum, corn and rice. Currently, identification is based on the male genitalia. However, the availability of speci... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.e37bgrn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>ACUITYAdvanced Biotin Free HRP<br />Polymer Detection System for Immunohistochemistry</p>
[GUIDELINES]
<p><img id="s-mce-img" class="s-mce-img" src="https://s3.amazonaws.com/pr-journal/dutecje.jpg" data-src="https://s3.amazonaws.com/pr-journal/dusecje.jpg" data-ofn="acuity1.... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.ex7bfrn | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
<strong>Reagent List:</strong><br />
<ul>
<li> Sterile PBS</li>
<li> Cell culture medium (RPMI 1640 supplemented with 10% FBS)</li>
<li> Sterile 12-well plate</li>
<li> RBC Lysis Buffer (Cat. No. 420301)</li>
<li> Anti-mouse CD3ε, clone 145-2C11 (LEAF™ format, Cat. No. 100314)</l... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.n6zdhf6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Details of envrionmental sampling methodology of different production locations within a broiler production enterprise.</p>
<p>Specific details regarding the sampling methodology and samples collected are provided.</p>
[BEFORE_START]
<p><strong>Sampling Equipment</strong></p... | [] |
21,574 | Two-step protocol: Preparation and extrusion of phospholipid liposomes | null | dx.doi.org/10.17504/protocols.io.zbef2je | null | James Collins, James R. Collins, Krista Longnecker, Helen F. Fredricks, Benjamin A. S. Van Mooy | TITLE: Two-step protocol: Preparation and extrusion of phospholipid liposomes
AUTHORS: James Collins, James R. Collins, Krista Longnecker, Helen F. Fredricks, Benjamin A. S. Van Mooy
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The protocols in this collection were original created by </... | [] |
57,351 | Sigma GeneElute total RNA extraction from fungal tissue | 4 | dx.doi.org/10.17504/protocols.io.14egn7znyv5d/v1 | https://www.protocols.io/view/sigma-geneelute-total-rna-extraction-from-fungal-t-b39fqr3n | Alexander J Bradshaw | TITLE: Sigma GeneElute total RNA extraction from fungal tissue
AUTHORS: Alexander J Bradshaw
[DESCRIPTION]
RNA extraction from fungal tissue using the Sigma GeneElute total RNA kit.
[STEPS]
SECTION: Tissue and workspace preparation
2. Flash Freeze tissue in Liquid Nitrogen (LN2).
SECTION: Tissue and workspace prepa... | ["[Tissue and workspace preparation] Flash Freeze tissue in Liquid Nitrogen (LN2).", "[Tissue and workspace preparation] Grind Fungal Tissue to a fine powder with a mortar and pestle with LN2, be careful to not allow the tissue to thaw during this Process.", "[Tissue and workspace preparation] At this point frozen grou... |
57,560 | Library construction for human placenta bulk RNAseq | 4 | dx.doi.org/10.17504/protocols.io.b4fyqtpw | https://www.protocols.io/view/library-construction-for-human-placenta-bulk-rnase-b4fyqtpw | Scott Lindsay-Hewett | TITLE: Library construction for human placenta bulk RNAseq
AUTHORS: Scott Lindsay-Hewett
[DESCRIPTION]
This protocol describes the generation of stranded RNA-seq libraries from placenta total RNA. Since RNA quality can be an issue with total RNA isolated from placental tissue, it is advisable to enrich mRNA using a ... | ["[DNA removal] To remove any possible contaminating DNA prior to ribodepletion, follow Ambion's protocol (Publication # 1906M, Revision E) for their DNA-free DNase Treatment and Removal Reagents.\n\n \n \n\nQuantitate DNase-treated total RNA using Qubit RNA Broad Range Assay.", "[Ribodepletion and library constructio... |
49,749 | Fungal isolate identification using ITS-LSU regions | 1 | dx.doi.org/10.17504/protocols.io.butvnwn6 | https://www.protocols.io/view/fungal-isolate-identification-using-its-lsu-region-butvnwn6 | Cassie Ettinger | TITLE: Fungal isolate identification using ITS-LSU regions
AUTHORS: Cassie Ettinger
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol was written as a companion to the </span><a href="https://peerj.com/articles/960/" style = "text-decoration:underline;color:blue;cursor:pointer;"><s... | ["[Process Sanger sequences following the ‘Swabs to Genome’ workflow using Seqtrace]\nIf on undergraduate computer in the Eisen lab, you can type in ‘seqtrace’ into ‘terminal’ to start. Otherwise you may need to type 'python seqtrace.py'\nFollow directions here on how to install and use Seqtrace: https://peerj.com/arti... |
33,323 | create protocol bug test 2 | 1 | null | https://www.protocols.io/view/create-protocol-bug-test-2-bcsjiwcn | null | TITLE: create protocol bug test 2
AUTHORS:
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.iijcccn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><strong>Objective:</strong> To evaluate the comparative efficacy and safety of antiplatelet agents, vitamin K antagonist (VKA) and non-VKA oral anticoagulants (NOACs) in patients with atrial fibrillation (AF) undergoing percutaneous coronary intervention (PCI).</p>
<p><strong... | [] |
44,003 | Vivarium Population Spenser: Fertility protocol | 5 | dx.doi.org/10.17504/protocols.io.bn8bmhsn | https://www.protocols.io/view/vivarium-population-spenser-fertility-protocol-bn8bmhsn | Camila Rangel Smith | TITLE: Vivarium Population Spenser: Fertility protocol
AUTHORS: Camila Rangel Smith
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Description of the steps followed by Vivarium Population Spenser library when running the Fertility module. </div></div>
[STEPS]
?. Divide the annual fertility rates f... | ["Divide the annual fertility rates for that local authority by the number of time steps existing in a year.", "For each time step:", "Select all women in the sample that appear as \"alive\" and haven't had a child in at least one year.", "For these selected women, get the fertility rate given their age, ethnicity and... |
37,905 | Quick Protocol for DNA Cleanup and Concentration Using the Monarch® PCR & DNA Cleanup Kit (5 μg) (NEB #T1030) | 1 | dx.doi.org/10.17504/protocols.io.bg9rjz56 | https://www.protocols.io/view/quick-protocol-for-dna-cleanup-and-concentration-u-bg9rjz56 | New England Biolabs | TITLE: Quick Protocol for DNA Cleanup and Concentration Using the Monarch® PCR & DNA Cleanup Kit (5 μg) (NEB #T1030)
AUTHORS: New England Biolabs
[DESCRIPTION]
This is the "quick" version of Monarch® PCR & DNA Cleanup Kit (5 μg) Protocol (NEB #T1030) DNA Cleanup and Concentration. For the full protocol, please cli... | ["Dilute sample with DNA Cleanup Binding Buffer according to the table below. Mix well by pipetting up and down or flicking the tube. Do not vortex. \n Sample Type Ratio of Binding Buffer: Sample Example dsDNA > 2 kb (plasmids, gDNA) 2:1 200 μl: 100 μl dsDNA < 2 kb (some amplicons, fragments) 5:1 500 μl: 100 μl... |
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