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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55,391 | Single cell CUT&Tag-pro | 4 | dx.doi.org/10.17504/protocols.io.b2b7qarn | https://www.protocols.io/view/single-cell-cut-amp-tag-pro-b2b7qarn | Bingjie Zhang | TITLE: Single cell CUT&Tag-pro
AUTHORS: Bingjie Zhang
[DESCRIPTION]
scCUT&Tag-pro is a multimodal assay for profiling histone modification coupled with the abundance of surface proteins in single cells. It was developed based on CUT&Tag (Kaya-Okur et al., 2019) and scASAP-seq (Eleni Mimitou et al., 2021). Our ap... | ["[Buffer preparation] Staining buffer:\n2% BSA and 0.01% Tween in PBS\n\nIsotonic permeabilization buffer (2 ml)\n40 µl 1M Tris-HCl pH 7.4 (20 mM)\n60 µl 5M NaCl (150 mM)\n6 µl 1M MgCl2 (3 mM) \n20 µl 10% NP-40 (0.1%) \n20 µl 10% Tween-2 (0.1%) \n40 ul 50x Proteinase inhibitor (Roche Complete Protease Inhibitor EDTA-F... |
83,938 | Confirming circRNA expression by qPCR.pdf | 1 | dx.doi.org/10.17504/protocols.io.e6nvwd6nzlmk/v1 | https://www.protocols.click/view/confirming-circrna-expression-by-qpcr-pdf-cv8aw9se | Xianjun Dong | TITLE: Confirming circRNA expression by qPCR.pdf
AUTHORS: Xianjun Dong
[DESCRIPTION]
This protocol delineates a qPCR method to confirm the expression of circRNAs extracted from brain samples.
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.kcdcss6 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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35,953 | Degranulation and cytokine production (functional assay) | 1 | dx.doi.org/10.17504/protocols.io.8epv51me6l1b/v1 | https://www.protocols.io/view/degranulation-and-cytokine-production-functional-a-bfcrjiv6 | Philippa R Kennedy | TITLE: Degranulation and cytokine production (functional assay)
AUTHORS: Philippa R Kennedy
[DESCRIPTION]
Two primary functions of NK cells - their cytotoxcity and ability to produce cytokines, are measured in a flow-based assay that assesses these responses at the single cell level when NK cells are challenged with t... | ["5 x 105 cells/well are added to a U-bottomed 96 well plate. \n\nThese numbers can be decreased to 1 x 105 effector cells/well if the number of effector cells is limited, so long as target numbers are decreased accordingly. \n\nEffector cells can be plated one day in advance in 200 μL R10 and cultured at 37°C 5% CO2 o... |
97,098 | USDA LTAR Common Experiment measurement: Collection of grain yield data using a yield monitor | 1 | dx.doi.org/10.17504/protocols.io.rm7vzjm1rlx1/v1 | https://www.protocols.io/view/usda-ltar-common-experiment-measurement-collection-da3i2gke | Olivia K. Owen, Kenneth A. Sudduth*, Lori J. Abendroth | TITLE: USDA LTAR Common Experiment measurement: Collection of grain yield data using a yield monitor
AUTHORS: Olivia K. Owen, Kenneth A. Sudduth*, Lori J. Abendroth
[DESCRIPTION]
This protocol provides detailed methods for in-field collection of grain yield data using a combine harvester equipped with a yield monitor.... | ["[Harvester Setup and Calibration] Before harvesting, update any monitor software to the newest version available and review your combine manual to ensure the combine is serviced and working properly. Details about maintenance, setup, calibration, and operation can be found there.", "[Harvester Setup and Calibration] ... |
80,512 | My earth-EVAL pilot | 1 | dx.doi.org/10.17504/protocols.io.yxmvm24jbg3p/v1 | https://www.protocols.io/view/my-earth-eval-pilot-csu8wezw | Claudia Teran-Escobar | TITLE: My earth-EVAL pilot
AUTHORS: Claudia Teran-Escobar
[DESCRIPTION]
Background. Certain activities embedded in academic culture (international conferences, field missions) are an important source of greenhouse. Although some institutions and members of the scientific community have started to propose ways to reduc... | ["[Study Description] Common practices in academia such as participating in in-person scientific conferences and field missions are an important source of greenhouse gases and inequalities (Leochico et al., 2021). My earth-EVAL pilot is a study is carried out by a consortium of researchers in social psychology, human g... |
77,106 | EMP 16S Illumina Amplicon Protocol | 1 | dx.doi.org/10.17504/protocols.io.kqdg3dzzl25z/v2 | https://www.protocols.io/view/emp-16s-illumina-amplicon-protocol-cpisvkee | J. Greg Caporaso, Gail Ackermann, Amy Apprill, Markus Bauer, Donna Berg-Lyons, Jason Betley, Noah Fierer, Louise Fraser, Jed A. Fuhrman, Jack A. Gilbert, Niall Gormley, Greg Humphrey, James Huntley, Janet K. Jansson, Rob Knight, Chris L. Lauber, Catherine A. Lozupone, Sean McNally, David M. Needham, Sarah M. Owens, Alm... | TITLE: EMP 16S Illumina Amplicon Protocol
AUTHORS: J. Greg Caporaso, Gail Ackermann, Amy Apprill, Markus Bauer, Donna Berg-Lyons, Jason Betley, Noah Fierer, Louise Fraser, Jed A. Fuhrman, Jack A. Gilbert, Niall Gormley, Greg Humphrey, James Huntley, Janet K. Jansson, Rob Knight, Chris L. Lauber, Catherine A. Lozupone, ... | ["Amplify samples in triplicate, meaning each sample will be amplified in 3 replicate 25-µL PCR reactions.", "Pool triplicate PCR reactions for each sample into a single volume (75 µL).", "Run amplicons from each sample on an agarose gel.", "Quantify amplicons with Quant-iT PicoGreen dsDNA Assay Kit (follow manufacture... |
67,461 | WAS IST Dieatovita und wie wirkt es? | 5 | dx.doi.org/10.17504/protocols.io.dm6gpbprplzp/v1 | https://www.protocols.io/view/was-ist-dieatovita-und-wie-wirkt-es-cd5ds826 | Eaharastcoumer | TITLE: WAS IST Dieatovita und wie wirkt es?
AUTHORS: Eaharastcoumer
[DESCRIPTION]
DIEATOVITA ist ein revolutionäres Medikament, das fettleibigen Menschen hilft, Gewicht zu verlieren und ihren Stoffwechsel zu verändern. Laut der offiziellen Website handelt es sich um eine Mischung aus Pflanzenstoffen, die aus seriöse... | ["SHOP NOW ==> https://healthcare24hrs.com/diaetovita/\n\nDieatovita:DIEATOVITA ist ein revolutionäres Medikament, das fettleibigen Menschen hilft, Gewicht zu verlieren und ihren Stoffwechsel zu verändern. Laut der offiziellen Website handelt es sich um eine Mischung aus Pflanzenstoffen, die aus seriösen Quellen stamme... |
59,756 | Genomic DNA prep with Quick Extract (QE) buffer | 4 | null | https://www.protocols.io/view/genomic-dna-prep-with-quick-extract-qe-buffer-b6kkrcuw | Hannah.Long | TITLE: Genomic DNA prep with Quick Extract (QE) buffer
AUTHORS: Hannah.Long
[DESCRIPTION]
This protocol describes a high throughput extraction method to isolate genomic DNA for screening clones (e.g. from 24 well plate).
There are two options: i) you can split clones onto two plates and extract gDNA from one of th... | ["Grow clones on a multi-well format, e.g. 24-well plate.", "Prepare new matrigel coated plates for passaging clones and label PCR strip tubes corresponding to the position of the clones on the plates. E.g. 1-A1 would refer to plate 1, position A1 on the plate.", "When clones are ready to be split, remove media and add... |
90,895 | CportucalensisOligoMediatedRecombineering | 4 | dx.doi.org/10.17504/protocols.io.eq2lyj1rwlx9/v1 | https://www.protocols.io/view/cportucalensisoligomediatedrecombineering-c4zpyx5n | Lev Tsypin, Dianne K Newman, Allen W Chen, Scott Saunders | TITLE: CportucalensisOligoMediatedRecombineering
AUTHORS: Lev Tsypin, Dianne K Newman, Allen W Chen, Scott Saunders
[DESCRIPTION]
A protocol for introducing translational knockouts via oligo-mediated recombineering in C. portucalensis MBL.
[STEPS]
SECTION: Design oligos for recombineering translational knockouts in C... | ["[Design oligos for recombineering translational knockouts in C. portucalensis MBL (labeled MAGE for Multiplexed Automated Genome Engineering)] Identify where the gene of interest is on the chromosome relative to the origin of replication and determine which strand of DNA will be the lagging strand (the mutating oligo... |
75,948 | Functional Traits in Palms | 1 | dx.doi.org/10.17504/protocols.io.bp2l6935rlqe/v1 | https://www.protocols.io/view/functional-traits-in-palms-cnekvbcw | Colmenares-Trejos, S.L. | TITLE: Functional Traits in Palms
AUTHORS: Colmenares-Trejos, S.L.
[DESCRIPTION]
Protocol to measure functional traits in palms that are strongly associated with growth and survival strategies, which correspond to structural traits, photosynthetic and biochemical traits, and dispersal traits.
[GUIDELINES]
Collected t... | ["[Photosynthetic and biochemical traits] Physiological and biochemical measurements are potential indicators of palm responses to light. These are rapid light response curves (RLC), total chlorophyll content (ChlT mmol*g-1), and chlorophyll a/b ratio (Chlab).", "[Photosynthetic and biochemical traits] Rapid light resp... |
null | null | null | dx.doi.org/10.17504/protocols.io.kk3cuyn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Dextran sodium sulfate (DSS) i<em>s </em>commonly used in mouse studies to induce a very reproducible<br />colitis that effectively mimics the clinical and histological features of human inflammatory bowel disease (IBD)<br />patients, especially ulcerative colitis. However, t... | [] |
91,988 | Immunofluorescent labelling of paraffin brain tissue sections | 4 | dx.doi.org/10.17504/protocols.io.5qpvo3wdzv4o/v1 | https://www.protocols.io/view/immunofluorescent-labelling-of-paraffin-brain-tiss-c53uy8nw | Birger Victor Dieriks, Helen Murray | TITLE: Immunofluorescent labelling of paraffin brain tissue sections
AUTHORS: Birger Victor Dieriks, Helen Murray
[DESCRIPTION]
This immunofluorescence protocol permits the labelling of multiple antibodies on one paraffin tissue section. This protocol details the potential variations that detect the protein of interes... | ["[Slide preparation] Label slides with a Statmark pen or a pencil.\n \nAlways include the proper controls for any fluorescent labelling. Control sections where the primary antibody was omitted should show no immunoreactivity.", "[Dewaxing] Immediately following hotplate incubation, sections were submerged in \n30 min ... |
103,170 | Open field test | 0 | dx.doi.org/10.17504/protocols.io.x54v923m4l3e/v1 | https://www.protocols.io/view/open-field-test-dgza3x2e | Chuyu Chen | TITLE: Open field test
AUTHORS: Chuyu Chen
[DESCRIPTION]
The open field test was developed to test locomotor activity.
[STEPS]
1. Mice were put in a 56 ×56 cm open-field arenas in noise-canceling boxes, illuminated by dim red lights
2. The 20-minute-long session started recoding when mice were placed in the center of... | ["Mice were put in a 56 ×56 cm open-field arenas in noise-canceling boxes, illuminated by dim red lights", "The 20-minute-long session started recoding when mice were placed in the center of the arena.", "Locomotor activity was analyzed by the LimeLight 5 (Actimetrics) software and reported as distance traveled."] |
null | null | null | dx.doi.org/10.17504/protocols.io.fw8bphw | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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28,536 | Influenza A H3 virus TaqMan assay | null | dx.doi.org/10.17504/protocols.io.74yhqxw | null | Ian Mackay, Judy Northill | TITLE: Influenza A H3 virus TaqMan assay
AUTHORS: Ian Mackay, Judy Northill
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This test is a modification to the World Health Organization's influenza A H3 TaqMan documented in 'WHO information for molecular diagnosis of influenza virus - update 1' (see ... | ["[Oligonucleotides]\nAB1Name5'-3' SEQUENCE2H3hFor1GGTACGGYTTCAGGCAT3H3hRev1TCAATCTGATGGAATTTCTCGTTG4H3h-1144dProbe6FAM-CTGCTGCTTGTCCTCTTCCCT-BHQ1New primers were designed to improve assay performance. http://www.who.int/entity/influenza/gisrs_laboratory/molecular_diagnosis_influenza_virus_humans_update_201403rev201505... |
38,267 | Primer Design for Restriction Enzyme Cloning (E6901) | 1 | dx.doi.org/10.17504/protocols.io.bhk3j4yn | https://www.protocols.io/view/primer-design-for-restriction-enzyme-cloning-e6901-bhk3j4yn | New England Biolabs | TITLE: Primer Design for Restriction Enzyme Cloning (E6901)
AUTHORS: New England Biolabs
[DESCRIPTION]
Guidelines for Primer Design for Restriction Enzyme Cloning (E6901).
[GUIDELINES]
Introduction
Appropriate restriction sites, absent in the target gene, are incorporated in the forward and reverse primers when a... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.icbcasn | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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70,096 | Immunoprecipitation protocol | 4 | dx.doi.org/10.17504/protocols.io.bp2l694zzlqe/v1 | https://www.protocols.io/view/immunoprecipitation-protocol-cgpqtvmw | Chuyu Chen | TITLE: Immunoprecipitation protocol
AUTHORS: Chuyu Chen
[DESCRIPTION]
Immunoprecipitation procedure for brain tissue material
[STEPS]
1. Add 750ug tissue in 1ml IP buffer and antibody, incubate 4°C 2hrs on tube rotator
2. Prepare ProteinA/G beads 30ul/sample. Pool all beads in one tube to perform wash
3. Centrifuge 4... | ["Add 750ug tissue in 1ml IP buffer and antibody, incubate 4°C 2hrs on tube rotator", "Prepare ProteinA/G beads 30ul/sample. Pool all beads in one tube to perform wash", "Centrifuge 4°C 13000g 30sec, remove supernatant", "Resuspend beads with 80ul PBS/sample. Centrifuge again at 13000g for 30sec.", "Repeat wash 3 times... |
null | null | null | dx.doi.org/10.17504/protocols.io.dsp6dm | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
The reduction approach to assess virus production and the prokaryotic mortality by viral lysis stops new infection by reducing total virus abundance (and thus virus–host contacts). This allows for easy enumeration of viruses that originate from lysis of already infected cells du... | [] |
80,198 | Exercises on a balancе cushion to influence of lumbar vertebral syndrome | 1 | dx.doi.org/10.17504/protocols.io.n2bvj8mebgk5/v1 | https://www.protocols.io/view/exercises-on-a-balanc-cushion-to-influence-of-lumb-csjewcje | Krasimira KZ Zlatkova, Yuliyan Zlatkov | TITLE: Exercises on a balancе cushion to influence of lumbar vertebral syndrome
AUTHORS: Krasimira KZ Zlatkova, Yuliyan Zlatkov
[DESCRIPTION]
Background: The pain in the lumbar region is common. One of the causes of low back pain is lumbar vertebral syndrome. There is a wide range of options for treating low back pain... | ["[Research] We evaluate the condition of each patient by examining the degree of pain (according to the VAS), the mobility of lumbar spine ( Schober test and lateral slope) and the presence of neurological symptoms (with Straight leg raise test).", "[Research] Each patients performs exercises on a balance cushion for... |
47,512 | Polymer-brushes-immersed-in-solvent-molecules | 1 | dx.doi.org/10.17504/protocols.io.bsmync7w | https://www.protocols.io/view/polymer-brushes-immersed-in-solvent-molecules-bsmync7w | Mike Edwards | TITLE: Polymer-brushes-immersed-in-solvent-molecules
AUTHORS: Mike Edwards
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">By means of density functional theory (DFT), influence of solvent molecules on polymer brushes is investigated. Osmotic pressure of solvent molecules gives rise to a stronger ... | [] |
62,286 | Power Keto Gummy - It 100% Effective & Real Ingredients? | 3 | dx.doi.org/10.17504/protocols.io.e6nvwko5dvmk/v1 | https://www.protocols.io/view/power-keto-gummy-it-100-effective-amp-real-ingredi-b83nryme | H Douglas Morris | TITLE: Power Keto Gummy - It 100% Effective & Real Ingredients?
AUTHORS: H Douglas Morris
[DESCRIPTION]
Some health plan providers may even offer a perk that has nothing to do with medical services but can be inviting, such as discounts on sporting goods or apparel.
[STEPS] | [] |
21,637 | Vandy – Chronic Catheterization of carotid artery and jugular vein | null | dx.doi.org/10.17504/protocols.io.zddf226 | null | Bingle Bracy | TITLE: Vandy – Chronic Catheterization of carotid artery and jugular vein
AUTHORS: Bingle Bracy
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">Study of the unstressed mouse requires prior implantation of catheters in ... | ["Preparation:1. Anesthetize mouse. Bevel catheters to correct lengths*, fill with 200U heparinized saline and plug. 2. Surgery must be conducted in a disinfected area that promotes asepsis. 3. Prepare the animal by removing hair from the surgical site. Perform this procedure in an area separate from where the surgery ... |
52,391 | Study Protocol: Assessment of Racial/Ethnic Disparities in the Timeliness and Comprehensiveness of Surgery for Colorectal Cancer | 1 | dx.doi.org/10.17504/protocols.io.bxefpjbn | https://www.protocols.io/view/study-protocol-assessment-of-racial-ethnic-dispari-bxefpjbn | rhow , Vidhya Gunaseelan, mbicket | TITLE: Study Protocol: Assessment of Racial/Ethnic Disparities in the Timeliness and Comprehensiveness of Surgery for Colorectal Cancer
AUTHORS: rhow , Vidhya Gunaseelan, mbicket
[DESCRIPTION]
This retrospective cohort study will investigate the timeliness of surgery based on the racial/ethnic group of patients who ... | ["[Brief Rationale and Hypothesis] Although disparities in access to healthcare are widely recognized as a critical issue in the United States, it is often difficult to identify these disparities and their subsequent impact due to their multifactorial nature. One manifestation of imbalances in access to care for surgic... |
null | null | null | dx.doi.org/10.17504/protocols.io.kixcufn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol provides the procedure to generate gene calls on your contigs using Prodigal. </p>
[STEPS]
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28,552 | DNase I treatment in solution (after RNA extraction) | null | dx.doi.org/10.17504/protocols.io.75ghq3w | null | Ben Kuipers | TITLE: DNase I treatment in solution (after RNA extraction)
AUTHORS: Ben Kuipers
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a protocol used for the Dnase treatment after RNA isolation with the RNeasy mini kit. Protocol is based on the RNase-Free DNase Set and the RNeasy Mini Handbook 10... | ["DNase I Stock solution was made from the Promega Maxwell 16 LEV SimplyRNA kit DNase by adding 275 µL nuclease free water to the lyophilized DNase I.", "Prepare a mastermix of 5 µL Buffer RDD (RNase-Free DNase Set) + 1.25 µL DNase I stock (Promega Maxwell 16 LEV simplyRNA kit) + eluted sample. Make the volume up to 5... |
99,076 | Generation of Immunodeficient Mice Bearing Human Immune Systems by the Engraftment of Hematopoietic Stem Cells | 4 | dx.doi.org/10.17504/protocols.io.36wgq4q43vk5/v3 | https://www.protocols.io/view/generation-of-immunodeficient-mice-bearing-human-i-dczc2x2w | Suheyla Hasgur, Ken Edwin Aryee, Leonard D. Shultz, Dale L. Greiner, and Michael A. Brehm | TITLE: Generation of Immunodeficient Mice Bearing Human Immune Systems by the Engraftment of Hematopoietic Stem Cells
AUTHORS: Suheyla Hasgur, Ken Edwin Aryee, Leonard D. Shultz, Dale L. Greiner, and Michael A. Brehm
[DESCRIPTION]
Immunodeficient mice are being used as recipients of human hematopoietic stem cells (HSC... | ["[Methods] Preparation of umbilical cord blood (UCB)", "[Methods] Allow histopaque and RPMI supplemented with 0.5% BSA to warm to room temperature.", "[Methods] Transfer UBC to 50 mL conical tubes (30 mls per tube).", "[Methods] Add hespan to each tube of UBC to a final concentration of 20% per volume and mix gently."... |
32,722 | Bioflux Analyses: Modelling | null | dx.doi.org/10.17504/protocols.io.bb7sirne | null | Tobias Weise, Bettina Boettcher, Slavena Vylkova | TITLE: Bioflux Analyses: Modelling
AUTHORS: Tobias Weise, Bettina Boettcher, Slavena Vylkova
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Biofilm formation under shear flow conditions was monitored using the Bioflux1000 device (Fluxion Biosciences, Inc.). In short, Candida albicans overnight cult... | ["[Modelling Approach]\nThe modelling presented here uses a simple ODE model fitted to the individual Bioflux Ipix time series data sets (Fig. 1-A) in order to estimate the height as well as the time point of maximum observable growth (Fig. 2-B). Table 1 contains symbols and abbreviations used within the modelling appr... |
104,804 | Competent Transformation | 0 | dx.doi.org/10.17504/protocols.io.5jyl82w47l2w/v1 | https://www.protocols.io/view/competent-transformation-dikc4csw | Miquel Estévez-Gay | TITLE: Competent Transformation
AUTHORS: Miquel Estévez-Gay
[DESCRIPTION]
Transform a Plasmid into previously obtained Competent E.coli Cells.
[STEPS]
1. Melt in ice and aliquot of 100μL competent E-coli DH5α or BL21(DE3) .
2. Preheat 500 µL LB or SOC medium (37ºC).
3. Add 50-100μg DNA into competent cells and mi... | ["Melt in ice and aliquot of 100μL competent E-coli DH5α or BL21(DE3) .", "Preheat 500 µL LB or SOC medium (37ºC).", "Add 50-100μg DNA into competent cells and mix softly. This is usually 1-2µl from minipreps. \nI recommend using 10µl if the DNA comes from PCR and/or DpnI digestion.", "Incubate 20 min in ice.", "Incuba... |
87,649 | Sputum Sample Processing for Single Cell Isolation and Live Recovery for Single Cell RNA Sequencing | 4 | dx.doi.org/10.17504/protocols.io.j8nlko9k5v5r/v1 | https://www.protocols.io/view/sputum-sample-processing-for-single-cell-isolation-czt9x6r6 | Jason D Limberis, Alina Nalyvayko, Michele Tomasicchio, Shameem Jaumdally, anil pooran, Keertan Dheda, john.metcalfe | TITLE: Sputum Sample Processing for Single Cell Isolation and Live Recovery for Single Cell RNA Sequencing
AUTHORS: Jason D Limberis, Alina Nalyvayko, Michele Tomasicchio, Shameem Jaumdally, anil pooran, Keertan Dheda, john.metcalfe
[DESCRIPTION]
Processing of clinical sputum samples for single live cell isolation for... | ["[Sputum collection] Collect an induced sputum, preferably 5 mL or more in volume, and process as below as soon as possible.", "[Bulk RNA sequencing] Using a wide bore tip (or cut the bottom of a 1000 µL) draw up ~200 µL sputum. If the sample is too viscous for a pipette, use a syringe needle instead.", "[Bulk RNA seq... |
46,569 | Semi-Automated Extraction of Viral RNA using the Omega Bio-tek Mag-Bind Viral DNA/RNA 96 Kit for SARS-CoV-2 Detection | 4 | dx.doi.org/10.17504/protocols.io.brqhm5t6 | https://www.protocols.io/view/semi-automated-extraction-of-viral-rna-using-the-o-brqhm5t6 | Lisa Marotz, Pedro Belda-Ferre, Mark Zeller, Catelyn Anderson, Sydney Morgan, Rob Knight, Kristian Andersen | TITLE: Semi-Automated Extraction of Viral RNA using the Omega Bio-tek Mag-Bind Viral DNA/RNA 96 Kit for SARS-CoV-2 Detection
AUTHORS: Lisa Marotz, Pedro Belda-Ferre, Mark Zeller, Catelyn Anderson, Sydney Morgan, Rob Knight, Kristian Andersen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The purpos... | ["[Sample Collection]\nNasopharyngeal (NP) swabs are collected by licensed personnel by sampling the posterior nasopharynx through both nares using an individually-wrapped and sterilized swab, according to CDC instructions for nasopharyngeal swab collection. The swab is then inserted into a 5 mL sample tube containing ... |
70,188 | Quick DNA Extraction for Fungal Barcoding (X-Amp) | 4 | dx.doi.org/10.17504/protocols.io.4r3l2oy2pv1y/v4 | https://www.protocols.io/view/quick-dna-extraction-for-fungal-barcoding-x-amp-cgsktwcw | Stephen Douglas Russell | TITLE: Quick DNA Extraction for Fungal Barcoding (X-Amp)
AUTHORS: Stephen Douglas Russell
[DESCRIPTION]
Below you will find a simple and fast two-step DNA extraction protocol that works well with many different groups of fungi. This protocol can be utilized in preparation for DNA barcoding of fungi utilizing Oxf... | ["[Initial Preparation] Begin by laying out (96) 0.2mL cells on a 96-well PCR plate rack. This can be done in a plate or strip format. \n\nEven though it costs more, I prefer to use 8-strips with individual caps as they are easier to work with. Only a single sample cell needs to be open at a time, individual rows can b... |
23,381 | Cyclic Immunofluoresence Staining Protocol (OHSU) | 1 | dx.doi.org/10.17504/protocols.io.23vggn6 | https://www.protocols.io/view/cyclic-immunofluoresence-staining-protocol-ohsu-23vggn6 | Jenny Eng, Koei Chin, Zhi Hu | TITLE: Cyclic Immunofluoresence Staining Protocol (OHSU)
AUTHORS: Jenny Eng, Koei Chin, Zhi Hu
[DESCRIPTION]
Cyclic immunofluorescence protocol, including tissue processing and staining, image acquisition and fluorophore bleaching.
[STEPS]
SECTION: Tissue Preparation
1. For phospho-protein preservation, fix tissu... | ["[Tissue Preparation] For phospho-protein preservation, fix tissues in formalin at 4 degrees C for 12-24 hours. Use a standard histopathological protocol for clearing, dehydration and paraffin processing and embedding. Cut 4-5 um sections of formalin-fixed parrafin-embedded tissues and place on Tanner Adhesive Slides ... |
18,185 | Impact of miR-223-3p and miR-2909 on inflammatory factors IL-6, IL-1, and TNF-, and the TLR4/TLR2/NF-B/STAT3 signaling pathway induced by lipopolysaccharide in human adipose stem cells | null | dx.doi.org/10.17504/protocols.io.vzhe736 | null | Juan Wu | TITLE: Impact of miR-223-3p and miR-2909 on inflammatory factors IL-6, IL-1, and TNF-, and the TLR4/TLR2/NF-B/STAT3 signaling pathway induced by lipopolysaccharide in human adipose stem cells
AUTHORS: Juan Wu
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">In the current study, we successfully es... | ["1.\tEstablish an acute inflammation model of adipose stem cells", "1.\tCells were routinely grown in medium under 5% CO2 incubator at 37 °C. For the experiments, cell suspension with a density of approximately 1 105 /mL was uniformly seeded in a 96-well plate (100 L per well). The cells were incubated in a 5% CO2 ... |
null | null | null | dx.doi.org/10.17504/protocols.io.j2icqce | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol will introduce a workflow for quality control and pre-processing of metagenomic sequence reads using FastQC for visualization and FastX Toolkit for editing the fastq files. </p>
[GUIDELINES]
<p><a href="http://hannonlab.cshl.edu/fastx_toolkit/index.html" target... | [] |
50,308 | Mechanistic Assays (Part 7 of Safety and Efficacy of Imatinib for Preserving Beta-Cell Function in New-onset Type 1 Diabetes Mellitus) | 1 | dx.doi.org/10.17504/protocols.io.bvdcn22w | https://www.protocols.io/view/mechanistic-assays-part-7-of-safety-and-efficacy-o-bvdcn22w | Stephen.Gitelman , Jeffrey A. Bluestone | TITLE: Mechanistic Assays (Part 7 of Safety and Efficacy of Imatinib for Preserving Beta-Cell Function in New-onset Type 1 Diabetes Mellitus)
AUTHORS: Stephen.Gitelman , Jeffrey A. Bluestone
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is Part 7 of "Safety and Efficacy of Imatinib for Preser... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.gycbxsw | 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... | [] |
102,839 | SCRMshaw: supervised cis-regulatory module prediction for insect genomes | 0 | dx.doi.org/10.17504/protocols.io.e6nvw1129lmk/v2 | https://www.protocols.io/view/scrmshaw-supervised-cis-regulatory-module-predicti-dgnx3vfn | Hasiba Asma, Luna Liu, Marc S. Halfon | TITLE: SCRMshaw: supervised cis-regulatory module prediction for insect genomes
AUTHORS: Hasiba Asma, Luna Liu, Marc S. Halfon
[DESCRIPTION]
As the number of sequenced insect genomes continues to grow, there is a pressing need for rapid and accurate annotation of their regulatory component. SCRMshaw is a computational... | ["[Create Project directory] Create a Project Directory and subdirectories", "[Create Project directory] Under the project directory create subdirectories for saving input and output files respectively, for training data, and for scripts", "[Install SCRMshaw] From the project directory, clone the SCRMshaw_HD software f... |
96,036 | CellTitre Glo 2.0 Viability Assay | 0 | dx.doi.org/10.17504/protocols.io.yxmvm3815l3p/v1 | https://www.protocols.io/view/celltitre-glo-2-0-viability-assay-c92cz8aw | aasirvatham | TITLE: CellTitre Glo 2.0 Viability Assay
AUTHORS: aasirvatham
[DESCRIPTION]
The purpose of this experiment is to investigate the effects of forskolin-mediated cAMP activation on the viability of LPS-treated Schwann cells. The immortalized rat RT4-D6P2T (ATCC #CRL-2768) and S16 (ATCC #CRL-2941) cell lines were cultured... | ["[To perform one CellTitre-Glo Viability Assay:] Aseptically culture immortalized rat RT4-D6P2T Schwann cells (ATCC, Cat #CRL-2768, Manassas, VA) or S16 Schwann cells (ATCC, Cat #CRL-2941, Manassas, VA) in Dulbecco’s Modified Eagle Medium (DMEM) (ATCC, Cat #30-2002, Manassas, VA) supplemented with 10% fetal bovine ser... |
null | null | null | dx.doi.org/10.17504/protocols.io.i3ecgje | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Below is a protocol for logging in and submitting a RELION GPU job to Comet GPU nodes at the San Diego Supercomputer Center.</p>
[STEPS]
?.
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null | null | null | dx.doi.org/10.17504/protocols.io.dbb2im | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Drosophila Tissue Processing for Paraffin Embedding<br />modified by the Baehrecke Lab from published protocols by Ristifo and White, 1991 (Pubmed ID 1936557) and Muro et al., 2006 (Pubmed ID 16887831)
[BEFORE_START]
Collect white pre-pupae, raised at 25 degrees Celsi... | [] |
47,354 | TEST: Ultra Turrax Tube Drive | 1 | null | https://www.protocols.io/view/test-ultra-turrax-tube-drive-bsg2nbye | Nannie | TITLE: TEST: Ultra Turrax Tube Drive
AUTHORS: Nannie
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Evaluation of tubes for the Ultra-Turrax Tube Drive instrument from IKA</span></div><div class = "text-block">Date: 10th February 2021 + 17th February 2021</div><di... | ["rs on the instrument (second 30s run).Steel10+5 on the instrument (second 30s run)."] |
94,348 | Assessment of autophagic flux assay in the adult Drosophila brain | 4 | dx.doi.org/10.17504/protocols.io.bp2l6x661lqe/v1 | https://www.protocols.io/view/assessment-of-autophagic-flux-assay-in-the-adult-d-c8dkzs4w | Mel Feany | TITLE: Assessment of autophagic flux assay in the adult Drosophila brain
AUTHORS: Mel Feany
[DESCRIPTION]
Transgenic flies expressing GFP-mCherry-Atg8a (obtained from the Bloomington Drosophila Stock Center)
under the control of the neuronal nSyb-GAL4 driver are used for assaying autophagic flux.
[STEPS]
1. Trans... | ["Transgenic flies expressing GFP-mCherry-Atg8a (obtained from the Bloomington Drosophila Stock Center) under the control of the neuronal nSyb-GAL4 driver are used for assaying autophagic flux", "Brains from 10-day-old animals are dissected in ice-cold 1X PBS", "The dissected brain are transferred to a glass slide", ... |
49,703 | HTAPP_Dissociation of human primary colorectal cancer resection specimens into single cell suspension for single cell RNA-seq | 1 | dx.doi.org/10.17504/protocols.io.busfnwbn | https://www.protocols.io/view/htapp-dissociation-of-human-primary-colorectal-can-busfnwbn | Karin Pelka, Jonathan H Chen, Matan Hofree, Tabea Moll, Max Goder-Reiser, SusannahPhillips, Anise Applebaum, Danielle Dionne, Will Ge, Julia Waldman, Toni Delorey, Mike Cuoco, Moshe Biton, Moshe Sade-Feldman, Judit Jané-Valbuena, Ana Anderson, Vijay Kuchroo, Andrew Aguirre, Orit Rozenblatt-Rosen, Tatyana Sharova, Genev... | TITLE: HTAPP_Dissociation of human primary colorectal cancer resection specimens into single cell suspension for single cell RNA-seq
AUTHORS: Karin Pelka, Jonathan H Chen, Matan Hofree, Tabea Moll, Max Goder-Reiser, SusannahPhillips, Anise Applebaum, Danielle Dionne, Will Ge, Julia Waldman, Toni Delorey, Mike Cuoco, Mo... | ["[Sample Description and Allocation]\nReport sample information.\nSample ID:Time specimen out:Time start tissue triage:Other assays tissue is allocated to:", "[Sample Description and Allocation]\nSample allocation: Transfer resection specimen into a Petri dish kept on ice. Take a picture of the specimen alongside a ru... |
30,133 | LyGo protocol collection | 2 | dx.doi.org/10.17504/protocols.io.9nvh5e6 | https://www.protocols.io/view/lygo-protocol-collection-9nvh5e6 | Kristoffer Bach Falkenberg, Maja Rennig, Cristina Hernandez Rollan, Andreas Birk Bertelsen, Morten Norholm | TITLE: LyGo protocol collection
AUTHORS: Kristoffer Bach Falkenberg, Maja Rennig, Cristina Hernandez Rollan, Andreas Birk Bertelsen, Morten Norholm
[STEPS] | [] |
86,456 | Protein Extraction from Dental Enamel | 1 | dx.doi.org/10.17504/protocols.io.8epv5j8n4l1b/v2 | https://www.protocols.io/view/protein-extraction-from-dental-enamel-cynyxvfw | simon.daled, Alexandra Burnett | TITLE: Protein Extraction from Dental Enamel
AUTHORS: simon.daled, Alexandra Burnett
[DESCRIPTION]
This protocol details a method for extracting proteins from ~5mg of powdered dental enamel for proteomic analysis by LC-MS/MS. This procedure includes the use of alkylating and reducing agents, a sample cleanup step, and... | ["[Sample acquisition] Place your tooth on a fresh piece of weighing paper on a clean worktop. \nUsing a small drill bit, gently abrade the surface of the tooth crown to remove powdered enamel and collect it on the weighing paper.", "[Sample acquisition] Carefully tip the powdered enamel into a protein lo-bind Eppendor... |
88,443 | Measurement of biogenic silica from plankton | 6 | dx.doi.org/10.17504/protocols.io.8epv5jjzjl1b/v3 | https://www.protocols.io/view/measurement-of-biogenic-silica-from-plankton-c2k3ycyn | Ying-Yu Hu, Nuwanthi Samarasinghe, Zoe V. Finkel | TITLE: Measurement of biogenic silica from plankton
AUTHORS: Ying-Yu Hu, Nuwanthi Samarasinghe, Zoe V. Finkel
[DESCRIPTION]
Here, we present a method for measuring biogenic silica from plankton. Biogenic silica is digested using a wet-alkaline method, in which 2 M sodium carbonate is used to hydrate and depolymerize a... | ["[Sample collection] Estimation:\nThe low limit of detection is approximately 0.6 uM silicate in the molybdate method. For siliceous plankton, sample requires no less than 4 ug PON (particulate organic nitrogen) per filter when using a 50 mL volumetric flask, or 2 ug PON per filter when using a 25 mL volumetric flask.... |
null | null | null | dx.doi.org/10.17504/protocols.io.dy47yv | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Generation of DNA fragments by DNase digestion involves digesting DNA for a range of times, then picking the time that gives optimal-sized DNA fragments (typically 1000–4000 bp).
[STEPS]
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72,733 | Goga Lab RT-qPCR protocol: QuantStudio6 Machine | 4 | null | https://www.protocols.io/view/goga-lab-rt-qpcr-protocol-quantstudio6-machine-ci95uh86 | Jeremy.williams | TITLE: Goga Lab RT-qPCR protocol: QuantStudio6 Machine
AUTHORS: Jeremy.williams
[DESCRIPTION]
Guidelines for preparing RT-qPCR samples for QuantStudio 6 located in HSW7 lab space.
[BEFORE_START]
*Thaw on ice (leave time!) and keep all reagents on ice through preparation. Prepare the plate on ice.
[GUIDELINES]
*star... | ["[Prior to plate preparation:] Dilute stock IDT primers to 100uM (see note in Guidelines).", "Use 'GogaLab-RTqPCR-Preparation' Excel spreadsheet to input your sample number and calculate reagent volumes.", "[Prepare your plate:] Mix *total reagent volumes required* (see spreadsheet, green) for DI and PowerUP", "[Prepa... |
79,918 | Live-cell imaging | 1 | dx.doi.org/10.17504/protocols.io.36wgqjk1xvk5/v1 | https://www.protocols.io/view/live-cell-imaging-csanwade | michela.deleidi, María José Pérez J. | TITLE: Live-cell imaging
AUTHORS: michela.deleidi, María José Pérez J.
[DESCRIPTION]
Live-cell imaging is a technique to visualize dynamic cellular processes in living biological samples.
[STEPS]
SECTION: 1. Cell Preparation
1. Wash cells 1x with OptiMEM (Gibco).
SECTION: 1. Cell Preparation
2. Incubate cells with 1... | ["[1. Cell Preparation] Wash cells 1x with OptiMEM (Gibco).", "[1. Cell Preparation] Incubate cells with 100nM MitoTracker red CMH2Xros (Thermo Fisher Scientific) in OptiMEM at 37 °C for 30 min", "[1. Cell Preparation] Wash cells with OptiMEM once, and keep cells in the same medium for imaging", "[2. Imaging] Images we... |
41,136 | ELISA for quantification of IL-19 in human serum or plasma. | 6 | dx.doi.org/10.17504/protocols.io.bkeqktdw | https://www.protocols.io/view/elisa-for-quantification-of-il-19-in-human-serum-bkeqktdw | Angel Justiz-Vaillant | TITLE: ELISA for quantification of IL-19 in human serum or plasma.
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Interleukins (IL) are a type of cytokine first thought to be expressed by leukocytes alone but have later been found to be produced by many other bod... | ["An anti-human IL-19 coating antibody is adsorbed onto microwells by incubation overnight at 4°C.", "Add 50 µl of human serum. Human IL-19 present in the serum sample binds to antibodies adsorbed to the microwells.", "The microplate is blocked with 3% non-fat milk-PBS buffer and later wash to remove unbound proteins."... |
90,618 | Comprehensive analysis methods for developmental GC exposed zebrafish | 3 | dx.doi.org/10.17504/protocols.io.kxygx9ooog8j/v3 | https://www.protocols.io/view/comprehensive-analysis-methods-for-developmental-g-c4q2yvye | Min-Kyeung Choi, Alex Cook, Helen Eachus, Anna Tochwin, Sara Kuntz, Soojin Ryu | TITLE: Comprehensive analysis methods for developmental GC exposed zebrafish
AUTHORS: Min-Kyeung Choi, Alex Cook, Helen Eachus, Anna Tochwin, Sara Kuntz, Soojin Ryu
[DESCRIPTION]
This protocol describes methods for the molecular, behavioral, and bioinformatic analyses of GC-exposed zebrafish. All procedures were used ... | [] |
51,601 | Early mobilization for acute heart failure: a systematic review and meta-analysis protocol | 1 | dx.doi.org/10.17504/protocols.io.bwmrpc56 | https://www.protocols.io/view/early-mobilization-for-acute-heart-failure-a-syste-bwmrpc56 | Masatsugu Okamura, Yuki Kataoka, Shunsuke Taito, Takashi Fujiwara, Atsushi Ide, Hideyuki Oritsu, Masashi Shimizu, Yoshitaka Shimizu, Ryoko Someya, Masaaki Konishi | TITLE: Early mobilization for acute heart failure: a systematic review and meta-analysis protocol
AUTHORS: Masatsugu Okamura, Yuki Kataoka, Shunsuke Taito, Takashi Fujiwara, Atsushi Ide, Hideyuki Oritsu, Masashi Shimizu, Yoshitaka Shimizu, Ryoko Someya, Masaaki Konishi
[DESCRIPTION]
<div class = "text-blocks... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.hgzb3x6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div>
<p>This protocol is from 'Flower Ca<sup>2+</sup> channel in CME and ADBE' of Yao CK et al.</p>
<div>
<div>
<p> </p>
<p>Please see the manuscript for the full method details.</p>
</div>
</div>
</div>
[BEFORE_START]
<p>You'll need: </p>
<p> </p>
<p><strong>0 mM Ca<sup>2+</s... | [] |
47,313 | Human in vitro Parkin ubiquitin E3 ligase assay | 4 | dx.doi.org/10.17504/protocols.io.bsfrnbm6 | https://www.protocols.io/view/human-in-vitro-parkin-ubiquitin-e3-ligase-assay-bsfrnbm6 | Michael Stevens, Miratul M. K. Muqit | TITLE: Human in vitro Parkin ubiquitin E3 ligase assay
AUTHORS: Michael Stevens, Miratul M. K. Muqit
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Mutations in PARK2 encoding Parkin are causal for early-onset Parkinson’s disease. Parkin is a ubiquitin E3 ligase and is activated by the PINK1 kinase... | ["[Preamble]\nThe set of reactions performed are where Parkin is phosphorylated by wt MBPTcPINK1, kinase inactive (KI) MBP-TcPINK1, and no MBP-TcPINK1, with all reactions performed in duplicate.", "[Preamble]\nand are required per reaction.\n[kinase master mix]\n[ubiquitylation master mix]", "[Preamble]\nThe volume of... |
90,642 | Human primary fibroblast culture | 4 | dx.doi.org/10.17504/protocols.io.36wgq3edklk5/v1 | https://www.protocols.io/view/human-primary-fibroblast-culture-c4rsyv6e | Ching-Chieh Chou, Judith Frydman | TITLE: Human primary fibroblast culture
AUTHORS: Ching-Chieh Chou, Judith Frydman
[DESCRIPTION]
This is a protocol for human primary fibroblast culture.
[STEPS]
SECTION: Preparing culture medium
1. Fibroblast medium @4°C lasts for 1 month. A total of 500 mL:
435 ml DMEM (High glucose, GlutaMAX) (Thermo Fisher Scienti... | ["[Preparing culture medium] Fibroblast medium @4°C lasts for 1 month. A total of 500 mL:\n435 ml DMEM (High glucose, GlutaMAX) (Thermo Fisher Scientific) \n50 ml Fetal bovine serum (FBS) (Thermo Fisher Scientific)\n5 ml Penicillin-Streptomycin (Thermo Fisher Scientific) \n5 ml MEM NEAA (100X; Thermo Fisher Scientific)... |
29,384 | Protocols for selective injection of tracer into the gastric mucosa and the gastric muscle of rat | 1 | dx.doi.org/10.17504/protocols.io.yxmvmxko9l3p/v1 | https://www.protocols.io/view/protocols-for-selective-injection-of-tracer-into-t-8xghxjw | John Furness, Martin Stebbing | TITLE: Protocols for selective injection of tracer into the gastric mucosa and the gastric muscle of rat
AUTHORS: John Furness, Martin Stebbing
[DESCRIPTION]
This protocol is for injection of neural tracers into the wall of the stomach to identify neurons innervating various tissues in the gastric wall including the g... | ["Sprague Dawley rats (RRID: RGD_10395233) of 200-500 g, both sexes, are used. They are fasted overnight and operated in the morning.", "The rat is anesthetized with a mixture of medetomidine (0.5 mg/kg) and ketamine (75 mg/kg), given intraperitoneally, using a 27 gauge needle. Carprofen (5 mg/kg) analgesic injection i... |
41,040 | Mitogenome Assembly from NGS Genome Skimming Data | 5 | dx.doi.org/10.17504/protocols.io.bkbqksmw | https://www.protocols.io/view/mitogenome-assembly-from-ngs-genome-skimming-data-bkbqksmw | Avery Hiley | TITLE: Mitogenome Assembly from NGS Genome Skimming Data
AUTHORS: Avery Hiley
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol provides thorough instructions for how to assemble and annotate full mitochondrial genomes from NGS genome skimming data (specifically paired-end, FASTQ, gzippe... | ["[I. Download Programs and Dependencies]\nOpen up the App Store (macOS), and search for Xcode (macOS). Download Xcode Version 12.1. Minimize the App Store window. Proceed to step 3 while the Xcode download is in progress, because this may take some time.", "[III. Simple Stats with SeqKit]\nOptionally, follow along wit... |
null | null | null | dx.doi.org/10.17504/protocols.io.dpa5id | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
For <a href="https://www.protocols.io/view/One-step-growth-curves-for-Cellulophaga-phages-ddh235" target="_blank">One-step growth curves for Cellulophaga phages</a> protocol and <a href="https://www.protocols.io/view/Transcriptomics-During-One-Step-Growth-Curves-for-dem3c5" targ... | [] |
44,181 | Reproducibility for Thistlethwaite et al. 2020 | 5 | dx.doi.org/10.17504/protocols.io.bpdvmi66 | https://www.protocols.io/view/reproducibility-for-thistlethwaite-et-al-2020-bpdvmi66 | Lillian Thistlethwaite, xiqi.li2 , Varduhipetrosyan | TITLE: Reproducibility for Thistlethwaite et al. 2020
AUTHORS: Lillian Thistlethwaite, xiqi.li2 , Varduhipetrosyan
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">We consider the following algorithmic problem that arises in transcriptomics, metabolomics and other fields: given a weighted graph and ... | ["[Prepare dataset]\nThe CTD R package version 1.0.0 was used.", "[Fig 1: Plot individual metabolomics profiles onto biochemical pathway maps.]\nThe CTDext R package version 1.0.0 was used. The CTDext R package holds many pre-computed files necessary to reproduce some results from Thistlethwaite et al. 2020, as well as... |
57,464 | HyDrop Bead Generation & PCR Barcoding v1.0 | 1 | dx.doi.org/10.17504/protocols.io.b4cyqsxw | https://www.protocols.io/view/hydrop-bead-generation-amp-pcr-barcoding-v1-0-b4cyqsxw | Florian De Rop, Suresh Poovathingal, Stein Aerts | TITLE: HyDrop Bead Generation & PCR Barcoding v1.0
AUTHORS: Florian De Rop, Suresh Poovathingal, Stein Aerts
[DESCRIPTION]
Protocol for producing dissolvable barcoded hydrogel beads used in HyDrop experiments.
[STEPS]
SECTION: Hydrogel bead generation
1.
Hydrogel bead generation
Here, we will create an emulsi... | ["[Hydrogel bead generation] Hydrogel bead generation\nHere, we will create an emulsion of acrylamide monomers in a carrier oil containing TEMED. The monomer droplets will polymerise and form hydrogel beads. Ideally, you have a bead stock of around 3 mL of beads before you barcode, but 2 mL can work as well. It is best... |
30,015 | Steps to Create FASTQ of CCS Overlapping Genomic SSR - CCS ROI | null | dx.doi.org/10.17504/protocols.io.9i7h4hn | null | Gregory Harhay | TITLE: Steps to Create FASTQ of CCS Overlapping Genomic SSR - CCS ROI
AUTHORS: Gregory Harhay
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The virulence and pathogenicity of bacterial pathogens are related to their adaptability to changing environments. One process enabling adaptation i... | ["[Software Requirements]\nFor those without Matlab licences, Matlab code can be run in CodeOcean at this Matlab Compute CapsuleGeneious was used to as wrapper to for running sequence mappers, phobos, and sequence", "[Download Genome and BAM Alignment of nine CCS libraries to CP018802 (H somni) from NCBI]\nGenome a... |
36,024 | Preparation of 0.1M Tris HCl, pH 6.4 | null | dx.doi.org/10.17504/protocols.io.bfeyjjfw | https://www.protocols.io/view/preparation-of-0-1m-tris-hcl-ph-6-4-bfeyjjfw | Nicola O'Reilly | TITLE: Preparation of 0.1M Tris HCl, pH 6.4
AUTHORS: Nicola O'Reilly
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Purpose of examination / Clinical relevance</span></div><div class = "text-block">At the end of 2019, several pneumonia cases were reported in Wuhan,... | ["Please select between the recipes for 1 L 0.1M Tris HCl pH 6.4 and 5 L 0.1M Tris HCl pH 6.4.\nWork in fume hood!", "Weigh out and add to a 1 L beaker.\n[Tris HCl]", "Measure out and add to the beaker.\n[milliQ water]", "Add a magnetic flea and place on a magnetic stirring plate to mix the solution.", "Add a newly c... |
51,652 | Generation of knock-in and knock-out CRISPR/Cas9 editing in mammalian cells | 4 | dx.doi.org/10.17504/protocols.io.5jyl85x89l2w/v1 | https://www.protocols.io/view/generation-of-knock-in-and-knock-out-crispr-cas9-e-bwpcpdiw | Michael Hanna, Pietro De Camilli | TITLE: Generation of knock-in and knock-out CRISPR/Cas9 editing in mammalian cells
AUTHORS: Michael Hanna, Pietro De Camilli
[DESCRIPTION]
This protocol is to help with the generation of knock-in and knock-out genomically edited mammalian cells lines using CRISPR/Cas9.
[BEFORE_START]
Knock-out mammalian cell lines
Ge... | ["[Knock-out mammalian cell lines - Choosing a gRNA for editing endogenous locus of gene of interest] All gRNA sequences used in these protocols were identified using the publicly available CRISPR/Cas9\ngRNA design program CHOPCHOP (https://chopchop.cbu.uib.no/). For the generation of SHIP164\nknock-out cells, a gRNA d... |
63,125 | Nurses’, patients’, and informal caregivers’ attitudes toward aggression in psychiatric hospitals: a comparative survey study | 1 | dx.doi.org/10.17504/protocols.io.j8nlkk62wl5r/v1 | https://www.protocols.io/view/nurses-patients-and-informal-caregivers-attitudes-b9vvr666 | Maritta A Välimäki, Joyce Y Lam, Daniel Bressington, Teris Cheung, Wai Kit Wong, Po Yee Ivy Cheng, Chi Fai Ng, Tony Ng, Chun Pong Yam, Glendy Ip, Lee Paul, Tella Lantta | TITLE: Nurses’, patients’, and informal caregivers’ attitudes toward aggression in psychiatric hospitals: a comparative survey study
AUTHORS: Maritta A Välimäki, Joyce Y Lam, Daniel Bressington, Teris Cheung, Wai Kit Wong, Po Yee Ivy Cheng, Chi Fai Ng, Tony Ng, Chun Pong Yam, Glendy Ip, Lee Paul, Tella Lant... | [] |
57,898 | Provasoli Enriched Seawater (PES) medium solution | 6 | dx.doi.org/10.17504/protocols.io.rm7vzyyo5lx1/v1 | https://www.protocols.io/view/provasoli-enriched-seawater-pes-medium-solution-b4siqwce | Anton Kuech | TITLE: Provasoli Enriched Seawater (PES) medium solution
AUTHORS: Anton Kuech
[DESCRIPTION]
This protocol outlines the steps required to prepare Provasoli Enriched Seawater (PES) medium in accordance with the method by Provasoli (1966).
[BEFORE_START]
It is important to follow the order of chemicals added as shown... | ["[Primary solution] 6000 mL", "[Primary solution] Add 23.4 g (or 30 g Tris buffer)", "[Primary solution] Add 1500 mL P II-solution", "[P II solution] 5000 mL", "[Primary solution] Add 1500 mL Fe-solution", "[Fe-solution] 5000 mL", "[Primary solution] Add 21 g", "[Primary solution] Add 2.12 g", "[Primary solution... |
70,204 | Determining biofilm growth amount (dry weight) | 4 | dx.doi.org/10.17504/protocols.io.5jyl8jny9g2w/v1 | https://www.protocols.io/view/determining-biofilm-growth-amount-dry-weight-cgs4twgw | Weizhuo.Chen, An.Huang | TITLE: Determining biofilm growth amount (dry weight)
AUTHORS: Weizhuo.Chen, An.Huang
[DESCRIPTION]
This protocol will help determine the amount of biofilm grown on carriers.
[STEPS]
SECTION: IPTG induction
1. Escherichia coli grown overnight was diluted by LB to OD600=0.4-0.6.
SECTION: IPTG induction
2. IPTG was a... | ["[IPTG induction] Escherichia coli grown overnight was diluted by LB to OD600=0.4-0.6.", "[IPTG induction] IPTG was added to cell culture to 1mM IPTG finally, and incubated 3h at 171 rpm, 37℃ in orbital shaking incubator.", "[Sample preparation] For each bottle:\n(1) The total mass of thirty Moving Bed Biofilm Reactor... |
67,372 | CUT&RUN Chromatin Profiling of Human Kidney Tissue | 1 | dx.doi.org/10.17504/protocols.io.bp2l615o1vqe/v1 | https://www.protocols.io/view/cut-amp-run-chromatin-profiling-of-human-kidney-ti-cd2ks8cw | Lynn Robbins, Jeannine M Basta, Michelle Pherson, Sabine Dietmann, Michael Rauchman | TITLE: CUT&RUN Chromatin Profiling of Human Kidney Tissue
AUTHORS: Lynn Robbins, Jeannine M Basta, Michelle Pherson, Sabine Dietmann, Michael Rauchman
[DESCRIPTION]
Histone post-translational modifications are key epigenetic features that define gene regulatory elements in the genome. Identifying changes in ... | ["[Antibody Buffer Prep and ConA Bead Activation] The day of the experiment, add protease inhibitors (PIs) to 1X concentration in 5 mL of Wash Buffer and leave at Room temperature . Store the remaining Wash Buffer at 4 °C for Day 2.", "[Antibody Buffer Prep and ConA Bead Activation] Make the Antibody Buffer (100 µL/s... |
66,991 | FAST DiI Injection Protocol from Neural Tracing in Porcine SAN | 1 | dx.doi.org/10.17504/protocols.io.4r3l2okqqv1y/v1 | https://www.protocols.io/view/fast-dii-injection-protocol-from-neural-tracing-in-cdnps5dn | Donald Hoover, Peter Hanna, Zixi Jack Cheng | TITLE: FAST DiI Injection Protocol from Neural Tracing in Porcine SAN
AUTHORS: Donald Hoover, Peter Hanna, Zixi Jack Cheng
[DESCRIPTION]
Protocol for injecting FAST DiI into the sinoatrial node of porcine test subjects for neural tracing purposes.
[STEPS]
SECTION: Injection of FAST DiI
1. Sedated, anesthetized... | ["[Injection of FAST DiI] Sedated, anesthetized, and intubated pig (induction: ketamine 10 mg/kg IM/midazolam 1 mg/ kg IM, maintenance: isoflurane 1-2% inhalation).", "[Injection of FAST DiI] Performed right unilateral thoracotomy by dividing the pectoral muscle.", "[Injection of FAST DiI] Made a small incision in the ... |
44,826 | CK111 comp cells electroporation | 4 | null | https://www.protocols.io/view/ck111-comp-cells-electroporation-bpz2mp8e | Elizabeth Fozo | TITLE: CK111 comp cells electroporation
AUTHORS: Elizabeth Fozo
[STEPS]
?. [How to generate competent CK111/pCF10-101 cells for transformation]
In 10 mL BHI with 100 µg/mL erythromycin, start an overnight culture of EC1000 containing your plasmid of interest.
?. [How to generate competent CK111/pCF10-101 cells for tra... | ["[How to generate competent CK111/pCF10-101 cells for transformation]\nIn 10 mL BHI with 100 µg/mL erythromycin, start an overnight culture of EC1000 containing your plasmid of interest.", "[How to generate competent CK111/pCF10-101 cells for transformation]\nIn 10 mL BHI with 1 mg/mL spectinomycin, start an overnight... |
29,146 | Miracle Prep for Plasmid Isolation | null | dx.doi.org/10.17504/protocols.io.8p2hvqe | null | Blake Flood | TITLE: Miracle Prep for Plasmid Isolation
AUTHORS: Blake Flood
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Based on:</div><div class = "text-block"><a href="https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0160509" style = "text-decoration:underline;color:blue;cursor:pointer;"><... | ["[Grow bacteria containing plasmid]\nAllow to grow overnight at .\n37 °C", "[Isolate Plasmid]\nSpin culture\nCentrifuge: 4000 34\n4 °C", "[Isolate Plasmid]\nRemove supt. Resuspend cells in Buffer P1..\n2 ml", "[Isolate Plasmid]\nBuffer P2 (invert 3-4 times)\n2 ml", "[Isolate Plasmid]\nIncubate @\n37 Room temperature... |
26,156 | Make liquid Superbroth for bacteria | null | dx.doi.org/10.17504/protocols.io.5skg6cw | null | Cancer Research UK / Wellcome Gurdon Institute media kitchen | TITLE: Make liquid Superbroth for bacteria
AUTHORS: Cancer Research UK / Wellcome Gurdon Institute media kitchen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Prepare Superbroth.</div><div class = "text-block">Superbroth is a liquid medium to feed bacteria.</div></div>
[STEPS]
?.
?. ABCD1Ingredi... | ["ABCD1Ingredients Quantity2Bacto-tryptone 72g3Yeast\n Extract144g4Glycerol24ml5Double\n distilled H2Oupto 5.4L\nABCD1Ingredients Quantity2Bacto-tryptone 72g3Yeast\n Extract144g4Glycerol24ml5Double\n distilled H2Oupto 5.4L", "A1Before starting ensure six 1L bottles have been\n sterilised.2Fill a 5.4L \n be... |
19,441 | Preparation of nasopharyngeal samples for immunofluorescence assay | null | dx.doi.org/10.17504/protocols.io.w8rfhv6 | null | Maria Lucia Silva, Flavia Escremim de Paula, Talita Gagliardi, Eurico Arruda | TITLE: Preparation of nasopharyngeal samples for immunofluorescence assay
AUTHORS: Maria Lucia Silva, Flavia Escremim de Paula, Talita Gagliardi, Eurico Arruda
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. Add the nasopharyngeal sample into a conical tube.
?. Only in samples with much mucus, drop N-L-Ace... | ["Add the nasopharyngeal sample into a conical tube.", "Only in samples with much mucus, drop N-L-Acetyl-Cysteine (maximum 1ml) into the tube and homogenize by vortex.", "Centrifuge the tube for 10 minutes at 4oC and 300 x g.", "Discard the supernatant.", "Homogenize the pellet of cells with phosphate-buffered saline... |
76,048 | A protocol to prevent plastic contamination during sample collection of cadaveric tissues | 4 | dx.doi.org/10.17504/protocols.io.bp2l69rkzlqe/v1 | https://www.protocols.io/view/a-protocol-to-prevent-plastic-contamination-during-cnhqvb5w | Kara Coffman-Rea, Alvise Vianello, Karen E. Samonds | TITLE: A protocol to prevent plastic contamination during sample collection of cadaveric tissues
AUTHORS: Kara Coffman-Rea, Alvise Vianello, Karen E. Samonds
[DESCRIPTION]
Research on microplastic pollution and its effects on atmospheric, aquatic, and terrestrial environments has grown rapidly as potential risks for h... | ["[Sterilization of tools] Rinse dissection trays, scalpel handles, forceps, hemostats, stainless steel biopsy punch, and glass syringes with particle-free ethanol.", "[Sterilization of tools] Rinse tools with particle-free water 3 times.", "[Sterilization of tools] Rinse dissection trays, scalpel handles, forceps, hem... |
89,766 | Unbiased Stereology (MBF Bioscience, StereoInvestigator Software) | 5 | dx.doi.org/10.17504/protocols.io.36wgq3m83lk5/v1 | https://www.protocols.io/view/unbiased-stereology-mbf-bioscience-stereoinvestiga-c3weypbe | Jhodi Webster, Ashley Harms | TITLE: Unbiased Stereology (MBF Bioscience, StereoInvestigator Software)
AUTHORS: Jhodi Webster, Ashley Harms
[DESCRIPTION]
This protocol allows for unbiased stereo logical assessment of neurons and other cells in specific brain regions using StereoInvestigator Software.
[STEPS]
SECTION: WORKFLOW
1. Create a map of ... | ["[WORKFLOW] Create a map of your slide using the stereology worksheet and make note of the estimated population and total markers counted", "[WORKFLOW] Set slide properly on the microscope.", "[WORKFLOW] Click on Probes > Optical Fractionator Workflow > Start a new subject\nLabel subject/study\nExisting sample in conf... |
null | null | null | dx.doi.org/10.17504/protocols.io.ektbcwn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Stellaris® RNA FISH protocol for fresh frozen mouse brain
[BEFORE_START]
<p align="LEFT">Reagents and Equipment</p>
<p align="LEFT">Reagents and Consumables:</p>
<p align="LEFT">a) TE buffer (10 mM Tris-HCl, 1 mM EDTA, pH 8.0)</p>
<p align="LEFT">b) 20% Electron Microscopy Grad... | [] |
92,278 | Guide to Generating International Chemical Identifier (InChI) Label for Isotopically Labelled Compounds | 1 | dx.doi.org/10.17504/protocols.io.rm7vzx9nrgx1/v1 | https://www.protocols.io/view/guide-to-generating-international-chemical-identif-c6cwzaxe | Roland C. Wilhelm | TITLE: Guide to Generating International Chemical Identifier (InChI) Label for Isotopically Labelled Compounds
AUTHORS: Roland C. Wilhelm
[DESCRIPTION]
This protocol was written to support the article by Simpson et al., 2024 entitled: MISIP: A data standard for the reuse and reproducibility of any stable isotope probi... | ["[Generating International Chemical Identifier (InChI) Label] The InChI label is a machine-readable format that specifies the exact position of all atoms in a molecule, including the isotope number (at the end of the label). The label is a stable identifier supported by the IUPAC. The InChI label is the required forma... |
null | null | null | dx.doi.org/10.17504/protocols.io.g27byhn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>How I created a BLAST app for Cyverse.</p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
28,188 | Enzymatic PCR Cleanup Protocol (NEB #M0525) | null | dx.doi.org/10.17504/protocols.io.7r4hm8w | https://www.protocols.io/view/enzymatic-pcr-cleanup-protocol-neb-m0525-7r4hm8w | New England Biolabs | TITLE: Enzymatic PCR Cleanup Protocol (NEB #M0525)
AUTHORS: New England Biolabs
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><ul style = "list-style-type:disc;"><li style = "counter-reset:ol0;list-style-type:disc;">Rapid and irreversible heat inactivation eliminates unwanted activity</li><li sty... | ["Add of Quick CIP (NEB #M0525) to of PCR product.\n1 µl\n5 µl\nNote that 0.5 μl of Exo I (NEB #M0293) and 1 μl of rSAP (NEB #M0371) can be used in the same volume.", "Incubate the mix at the for .\n37 °C", "Inactivate both enzymes at for .\n80 °C", "PCR products are ready for downstream application."] |
95,735 | Triparental mating with pSEVA protocol | 0 | dx.doi.org/10.17504/protocols.io.n92ldm4zol5b/v1 | https://www.protocols.io/view/triparental-mating-with-pseva-protocol-c9qxz5xn | Laura Gómez | TITLE: Triparental mating with pSEVA protocol
AUTHORS: Laura Gómez
[DESCRIPTION]
This process involves bacterial conjugation, where a conjugative plasmid found in one bacterial strain facilitates the transfer of a mobilizable plasmid from a second bacterial strain to a third bacterial strain.
In the method from our l... | ["[Insertion of he suicide plasmid by three partner conjugation] Inoculate cultures of strains:\n \nDONOR CC118λpir pSEVA Gm (10 μg/ml)\n \nHELPER E. coli 1047 pRK2013 Km (50 μg/ml) \n \nRECEIVER C. rodenti... |
null | null | null | dx.doi.org/10.17504/protocols.io.pasdiee | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The thermocoagulation model is a type of focal cerebral ischemia with craniectomy. It represents an opportunity to study permanent ischemic brain lesions with good reproducibility and low mortality</p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
40,881 | Counting particles and EVs on Astrios EQ with spike in reference beads | 1 | dx.doi.org/10.17504/protocols.io.bj6rkrd6 | https://www.protocols.io/view/counting-particles-and-evs-on-astrios-eq-with-spik-bj6rkrd6 | Aizea Morales-Kastresana, Joshua Welsh, Jennifer Jones | TITLE: Counting particles and EVs on Astrios EQ with spike in reference beads
AUTHORS: Aizea Morales-Kastresana, Joshua Welsh, Jennifer Jones
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">There are different methods to quantify the particle count in a solution. Common counting methods are resistiv... | ["Prepare a stock of 200 nm polystyrene reference beads by diluting 50 µL of Fluosphere beads in 50 ml of DPBS (1000-fold dilution) and keep this solution as a ‘Big Stock’. Determine the particle concentration of the beads in the ‘Big Stock’using NTA or any other method.\nCompanies provide an estimated concentration of... |
63,696 | Qiagen All-Prep DNA/RNA Mini Kit | 1 | null | https://www.protocols.io/view/qiagen-all-prep-dna-rna-mini-kit-cafqsbmw | George Testo | TITLE: Qiagen All-Prep DNA/RNA Mini Kit
AUTHORS: George Testo
[DESCRIPTION]
The AllPrep DNA/RNA Mini Kit is designed to purify genomic DNA and total RNA simultaneously from a single biological sample. Lysate is first passed through an AllPrep DNA spin column to selectively isolate DNA and then through an RNeasy spin ... | ["[Homogenization] Add 600 µL of to Lysing Matrix E tubes.", "[Homogenization] Place the entire tissue or a portion into Lysing Matrix E tubes for homogenization.", "[Homogenization] For Swab(s): pick up with tweezers and cut with surgical scissors sterilized in a Germinator 500. Place the cut end of a single swab in... |
42,166 | In silico and RT-qPCR analysis of the 8q22.2 region in muscle invasive bladder cancer | 5 | dx.doi.org/10.17504/protocols.io.bmewk3fe | https://www.protocols.io/view/in-silico-and-rt-qpcr-analysis-of-the-8q22-2-regio-bmewk3fe | Daniel Uysal, Philipp Erben | TITLE: In silico and RT-qPCR analysis of the 8q22.2 region in muscle invasive bladder cancer
AUTHORS: Daniel Uysal, Philipp Erben
[STEPS]
?. [data download]
Access cBioPortal (https://www.cbioportal.org/) and select the Bladder Cancer (TCGA, Cell 2017) study.
?. [Data download ]
?. [data download]
Select genomic profi... | ["[data download]\nAccess cBioPortal (https://www.cbioportal.org/) and select the Bladder Cancer (TCGA, Cell 2017) study.", "[Data download ]", "[data download]\nSelect genomic profiles to putative copy-number alterations from GISTIC and mRNA expression z-Scores relative to diploid samples (z-score 1,2,3). Select case ... |
null | null | null | dx.doi.org/10.17504/protocols.io.f55bq86 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol was used to express a nourseothricin (<em>nou</em>/<em>nat</em>) resistance gene and a gene encoding a silaffin precursor TpSil3p-APEX2 fusion protein in <em>Thalassiosira pseudonana </em>(<em>Tp</em>) strain <a href="https://ncma.bigelow.org/ccmp1335?___SID=U#.... | [] |
89,437 | DToL Specimen Vouchering Standard Operating Procedure: Lepidoptera (V.1) | 1 | dx.doi.org/10.17504/protocols.io.dm6gp3o35vzp/v1 | https://www.protocols.io/view/dtol-specimen-vouchering-standard-operating-proced-c3j5ykq6 | Dominic Phillips, Geoff Martin, Inez Januszczak | TITLE: DToL Specimen Vouchering Standard Operating Procedure: Lepidoptera (V.1)
AUTHORS: Dominic Phillips, Geoff Martin, Inez Januszczak
[DESCRIPTION]
This Standard Operating Procedure (SOP) contains guidance on how to voucher Lepidoptera specimens submitted to the Darwin Tree of Life (DToL) project. The guidance spec... | [] |
77,214 | General procedure for long-term cryopreservation of Yeast | 4 | null | https://www.protocols.io/view/general-procedure-for-long-term-cryopreservation-o-cpm6vk9e | Andreas Sagen | TITLE: General procedure for long-term cryopreservation of Yeast
AUTHORS: Andreas Sagen
[DESCRIPTION]
A simple and generalized procedure for freezing yeast cells.
[STEPS]
SECTION: 50% Glycerol solution
1. Fill a 200 mL Duran bottle with 100 mL PBS
Materials:
SECTION: 50% Glycerol solution
2. Transfer 100 mL 100% ... | ["[50% Glycerol solution] Fill a 200 mL Duran bottle with 100 mL PBS\n\nMaterials:", "[50% Glycerol solution] Transfer 100 mL 100% Glycerol to Duran bottle\n\nMaterials:", "[50% Glycerol solution] Sterilize by autoclave at 121 °C for 15 min", "Incubate a 20 mL batch of Yeast overnight", "Aliquot saturated culture into ... |
null | null | null | dx.doi.org/10.17504/protocols.io.jv9cn96 | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
<p>Glassware should be acid-washed and rinsed well with dH<sub>2</sub>O before use. If unable to measure small quantities accurately, either scale up the recipe or prepare stock solutions of the individual compounds.</p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.fmhbk36 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Growth Medium used for Alternaria Solani cultivation</p>
<p> </p>
<p>First described: Nirenberg 1981</p>
[STEPS]
?.
?.
?.
?. | [] |
64,376 | XP Nutrition Keto Gummies Reviews – Complete Ripoff or Keto Pills That Work?Real Scam Complaints or Legit Diet Pills? | 1 | dx.doi.org/10.17504/protocols.io.5jyl89qodv2w/v1 | https://www.protocols.io/view/xp-nutrition-keto-gummies-reviews-complete-ripoff-ca4ysgxw | fateh | TITLE: XP Nutrition Keto Gummies Reviews – Complete Ripoff or Keto Pills That Work?Real Scam Complaints or Legit Diet Pills?
AUTHORS: fateh
[DESCRIPTION]
If you do not know how to lose weight fast, let me help you. This article will discuss XP Nutrition Keto Gummies, which is a natural and effective supplement that ... | ["XP Nutrition Keto GummiesXP Nutrition Keto Gummies - According to the product’s official website, the XP Nutrition Keto Gummies are taking America by storm with the way they help people get rid of their unwanted fat. They contain Beta-Hydroxybutyrate (BHB), and BHB is getting released in the body when on the ketogeni... |
94,237 | Stedehouder, J. and Roberts, B.M. et al. (2024) Rapid modulation of striatal cholinergic interneurons and dopamine release by satellite astrocytes | 2 | dx.doi.org/10.17504/protocols.io.dm6gp3k25vzp/v1 | https://www.protocols.io/view/stedehouder-j-and-roberts-b-m-et-al-2024-rapid-mod-c795zr86 | Jeff Stedehouder, Bradley M. Roberts, Shinil Raina, Alan K. L. Liu, Laura Parkkinen, Dorly Verdier, Arlette Kolta, Stephanie J Cragg | TITLE: Stedehouder, J. and Roberts, B.M. et al. (2024) Rapid modulation of striatal cholinergic interneurons and dopamine release by satellite astrocytes
AUTHORS: Jeff Stedehouder, Bradley M. Roberts, Shinil Raina, Alan K. L. Liu, Laura Parkkinen, Dorly Verdier, Arlette Kolta, Stephanie J Cragg
[DESCRIPTION]
This col... | [] |
24,714 | Transformation of Diplonema papillatum using V5+NeoR construct | null | dx.doi.org/10.17504/protocols.io.4digs4e | null | Binnypreet Kaur, Drahomíra Faktorová, Julius Lukes | TITLE: Transformation of Diplonema papillatum using V5+NeoR construct
AUTHORS: Binnypreet Kaur, Drahomíra Faktorová, Julius Lukes
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>p57-V5+Neo</span><span style = "vertical-align:super;">R </span><span>plasmid contains V5-tagged aminoglycoside 3'-p... | ["p57-V5+NeoR plasmid contains V5-tagged aminoglycoside 3'-phosphotransferase gene (APT; conferring resistance to neomycin) flanked by partial regulatory sequences derived from the hexokinase gene of the kinetoplastid Blastocrithidia (strain p57).", "This 1779 bp long sequence is surrounded by SwaI restriction sides an... |
102,475 | Sonication of α-synuclein Fibrils for injection into the mouse brain | 1 | dx.doi.org/10.17504/protocols.io.14egn337zl5d/v3 | https://www.protocols.io/view/sonication-of-synuclein-fibrils-for-injection-int-dgbj3skn | Vijay Singh, Marta Castellana-Cruz, Nunilo Cremades, Laura Volpicelli-Daley | TITLE: Sonication of α-synuclein Fibrils for injection into the mouse brain
AUTHORS: Vijay Singh, Marta Castellana-Cruz, Nunilo Cremades, Laura Volpicelli-Daley
[DESCRIPTION]
Animal models that accurately recapitulate the accumulation of alpha-synuclein (α-syn) inclusions, progressive neurodegeneration of the nigrost... | ["[Sonicating α-synuclein Fibrils (PFFs)] After the temperature inside Q700 Sonicator water reservoir is equilibrated to 10 °C, thaw and pipette 25-22 µL PFFs stored at -80 °C and transfer to polystyrene sonication tube (Active Motif, Cat No. 53071) inside a biosafety cabinet. Screw the cap of the polystyrene sonicatio... |
101,127 | Purification of FUNDC1-GST | 0 | dx.doi.org/10.17504/protocols.io.14egn66nyl5d/v1 | https://www.protocols.io/view/purification-of-fundc1-gst-dezf3f3n | Elias Adriaenssens | TITLE: Purification of FUNDC1-GST
AUTHORS: Elias Adriaenssens
[DESCRIPTION]
This protocol details the purification of FUNDC1-GST.
[STEPS]
SECTION: Purification - FUNDC1-GST
1. To purify FUNDC1-GST, fuse the cytosol-exposed domain of FUNDC1 (1-50aa) to a C-terminal GST-tag through cloning into a pET-DUET1 vector (avai... | ["[Purification - FUNDC1-GST] To purify FUNDC1-GST, fuse the cytosol-exposed domain of FUNDC1 (1-50aa) to a C-terminal GST-tag through cloning into a pET-DUET1 vector (available on Addgene).", "[Purification - FUNDC1-GST] Introduce the point mutants by in vitro mutagenesis to generate FUNDC1 Y18A/L21A (ΔLIR)(available ... |
52,238 | Homology modeling with trRosetta | 5 | dx.doi.org/10.17504/protocols.io.bw9nph5e | https://www.protocols.io/view/homology-modeling-with-trrosetta-bw9nph5e | Chris Berndsen | TITLE: Homology modeling with trRosetta
AUTHORS: Chris Berndsen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol for homology modeling using trRosetta written for students in Biochemistry I at James Madison University. </div></div>
[STEPS]
?. [Setting up modeling]
Navigate to the trRosetta ... | ["[Setting up modeling]\nNavigate to the trRosetta homepage.", "[Setting up modeling]\nInput your sequence in FASTA format. The first list should start with > as shown in the example below.", "[Setting up modeling]\nEnter your email address and give a target name.\nIt is always a good idea to include target name or ide... |
null | null | null | dx.doi.org/10.17504/protocols.io.crdv25 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol consists of an IgG purification step followed by covalent cross-linking of the IgG to the Protein A/G solid support. For IgG that has been previously purified, proceed directly to the cross-linking protocol.
[GUIDELINES]
<strong>Overview</strong><br /><br /><stron... | [] |
46,863 | 16s rDNA sequencing reaction and precipitation protocol | 4 | dx.doi.org/10.17504/protocols.io.brzpm75n | https://www.protocols.io/view/16s-rdna-sequencing-reaction-and-precipitation-pro-brzpm75n | Rene Flores Clavo, Cristian Daniel Asmat Ortega, Nataly Ruiz Quinones | TITLE: 16s rDNA sequencing reaction and precipitation protocol
AUTHORS: Rene Flores Clavo, Cristian Daniel Asmat Ortega, Nataly Ruiz Quinones
[STEPS]
?. [Sequencing reaction ]
Consider a total volume of 10 µl
?. [Sequencing reaction ]
Add 6 µl of water for PCR
?. [Sequencing reaction ]
Add 2 µl of save money buffer
?... | ["[Sequencing reaction ]\nConsider a total volume of 10 µl", "[Sequencing reaction ]\nAdd 6 µl of water for PCR", "[Sequencing reaction ]\nAdd 2 µl of save money buffer", "[Sequencing reaction ]\nAdd 1 µl of DNA (10 - 20 ng/µl)", "[Sequencing reaction ]\nAdd 0.5 µl of primer", "[Sequencing reaction ]\nAdd 0.5 µl of Byg... |
26,045 | Calibration Protocol - Particle Standard Curve with Microspheres | null | dx.doi.org/10.17504/protocols.io.5n5g5g6 | null | Jacob Beal, Traci Haddock-Angelli, Markus Gershater, Vishal Sanchania, Russell Buckley-Taylor, Geoff Baldwin, Natalie Farny, Richard Tennant, Paul Rutten | TITLE: Calibration Protocol - Particle Standard Curve with Microspheres
AUTHORS: Jacob Beal, Traci Haddock-Angelli, Markus Gershater, Vishal Sanchania, Russell Buckley-Taylor, Geoff Baldwin, Natalie Farny, Richard Tennant, Paul Rutten
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>You will pr... | ["[Prepare the Microsphere Stock Solution]\nObtain the tube labeled “Silica Beads” from the Measurement Kit and vortex vigorously for 30 seconds.\nMicrospheres should NOT be stored at 0°C or below, as freezing affects the properties of the microspheres. If you believe your microspheres may have been frozen, please cont... |
53,157 | Wastewater Sequencing using the EasySeq™ RC-PCR SARS CoV-2 (Nimagen) V1.0 | 4 | null | https://www.protocols.io/view/wastewater-sequencing-using-the-easyseq-rc-pcr-sar-bx6dpra6 | Aaron Jeffries, Steve Paterson, Matthew Loose, Ronny van Aerle | TITLE: Wastewater Sequencing using the EasySeq™ RC-PCR SARS CoV-2 (Nimagen) V1.0
AUTHORS: Aaron Jeffries, Steve Paterson, Matthew Loose, Ronny van Aerle
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This SOP describes the procedure for generating cDNA libraries from SARS-CoV-2 viral nucleic ... | ["[Cleanup of RNA extract]\nAim: Reduction of any PCR inhibitors and potential concentration of RNA. Starting volume is 20 µl but this can be increased if further concentration is required (although for the latter tests on whether inhibitors are also concentrated have not been undertaken).Notes: Use either AMPure RNA X... |
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