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 |
|---|---|---|---|---|---|---|---|
19,725 | CEM (Circular Estimate Method) – Step-by-step Protocol | null | dx.doi.org/10.17504/protocols.io.xhmfj46 | null | Marcelo Josende, Silvana Manske Nunes, Larissa Müller, Marlize Ferreira Cravo, José Marìa Monserrat, Juliane Ventura Lima | TITLE: CEM (Circular Estimate Method) – Step-by-step Protocol
AUTHORS: Marcelo Josende, Silvana Manske Nunes, Larissa Müller, Marlize Ferreira Cravo, José Marìa Monserrat, Juliane Ventura Lima
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol is part of the entitled paper '</span><... | ["Stock the nematode suspension inside a falcon tube according to its total volume (15 or 50 mL falcon tube).", "Prime the pipette tip with the same liquid/medium of the nematode suspension, or with the nematode suspension itself, make five times up and down movement to avoid animal clogging.", "Gently vortex the falco... |
14,815 | Static Glucose-stimulated Insulin Secretion (GSIS) Protocol: Mouse Islets | 1 | dx.doi.org/10.17504/protocols.io.sp7edrn | https://www.protocols.io/view/static-glucose-stimulated-insulin-secretion-gsis-p-sp7edrn | Aliya Spigelman, Jocelyn Manning Fox, Patrick Macdonald | TITLE: Static Glucose-stimulated Insulin Secretion (GSIS) Protocol: Mouse Islets
AUTHORS: Aliya Spigelman, Jocelyn Manning Fox, Patrick Macdonald
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Static glucose stimulated insulin secretion (GSIS) protocol for mouse islets. </div></div>
[STEPS]
?. [Ex... | ["[Experimental Protocol]\nPick islets into 35mm non-tissue cultured coated (NTCC) dish and ‘wash’ islets with of KRBH with low glucose (2.8mM).\n2 mL", "[Experimental Protocol]\nPick islets into new 35mm NTCC dish in of low glucose KRBH and pre-incubate in incubator at 5 % CO2 for .\n2 mL\n37 °C", "[Experimental Pr... |
47,476 | Analysis of Factors Affecting Gelatin Degradation Assay and Countermeasures | 4 | null | https://www.protocols.io/view/analysis-of-factors-affecting-gelatin-degradation-bskuncww | 181830691 | TITLE: Analysis of Factors Affecting Gelatin Degradation Assay and Countermeasures
AUTHORS: 181830691
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:left">Edible gelatin belongs to the animal gelatin category of hydrophilic colloid/edible gelatin, which i... | [] |
91,050 | Photostimulation for optogenetics or uncaging | 1 | null | https://www.protocols.io/view/photostimulation-for-optogenetics-or-uncaging-c46iyzce | enrico.zampese | TITLE: Photostimulation for optogenetics or uncaging
AUTHORS: enrico.zampese
[DESCRIPTION]
Protocol for photostimulation, to be combined with any other electrophysiology/imaging recording approach.
Once the desired patch clamp recording and/or imaging configuration (cell attached, whole cell, perforated patch) is achi... | ["[Preliminary steps] Obtain brain slices of region of interest according to existing protocols", "[Preliminary steps] Identify and patch neurons of interest according to the desired experimental protocol.", "[Preliminary steps] Once a recording on a cell of interest is establish, set up the stimulation protocol.", "[S... |
86,454 | Glucose Tolerance Test | 4 | dx.doi.org/10.17504/protocols.io.261geddodv47/v1 | https://www.protocols.io/view/glucose-tolerance-test-cynwxvfe | Sabina Marciano, Roberta Marongiu | TITLE: Glucose Tolerance Test
AUTHORS: Sabina Marciano, Roberta Marongiu
[DESCRIPTION]
The glucose tolerance test is performed to determine how quickly the glucose is cleared from the blood. It is used to test for diabetes or insulin resistance.
[STEPS]
1. Single cage the mice for 1 week in advance
2. Weight the mic... | ["Single cage the mice for 1 week in advance", "Weight the mice", "Fast mice for 360 min", "After fasting, measure glucose with a glucose meter", "Perform an intraperitoneal injection of 2g / kg body weight of glucose (20% D-glucose stock solution dissolving 2g of glucose in 10ml saline and give 10ul per gram of body w... |
27,131 | Risk factors associated with IgA vasculitis with nephritis (Henoch–Schönlein purpura nephritis) progressing to unfavorable outcomes: a meta-analysis | null | dx.doi.org/10.17504/protocols.io.6q3hdyn | null | Qiu Li | TITLE: Risk factors associated with IgA vasculitis with nephritis (Henoch–Schönlein purpura nephritis) progressing to unfavorable outcomes: a meta-analysis
AUTHORS: Qiu Li
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The aim of this study was to analyze the risk factors associated with unfavorab... | ["literature search: PubMed, Embase, and Web of Science databases were searched for studies, published in English through February 2019. Using basic search terms from combined text and Medica Subject Heading (MeSH) terms. These included a MeSH search using the term ‘Purpura, Schoenlein-Henoch’ and a keyword search usin... |
40,590 | Agarose Gel Electrophoresis-Chem 584 | 1 | dx.doi.org/10.17504/protocols.io.bjvnkn5e | https://www.protocols.io/view/agarose-gel-electrophoresis-chem-584-bjvnkn5e | Ken Christensen, Addgene The Nonprofit Plasmid Repository | TITLE: Agarose Gel Electrophoresis-Chem 584
AUTHORS: Ken Christensen, Addgene The Nonprofit Plasmid Repository
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol is for agarose gel electrophoresis. To see the full abstract and additional resources, visit the </span><a href="https:/... | ["[Pouring a Standard 1% Agarose Gel]\nMeasure of agarose.\n0.6 g\n*Pro-Tip*Agarose gels are commonly used in concentrations of 0.7%-2% depending on the size of bands needed to be separated -see FAQ section of this protocol. Simply adjust the mass of agarose in a given volume to make gels of other agarose concentratio... |
84,106 | Using Amira to manually segment cell bodies in C.Elegans | 1 | null | https://www.protocols.click/view/using-amira-to-manually-segment-cell-bodies-in-c-e-cwdixa4e | Grace Park, Aubrey Weigel, Alyson Petruncio | TITLE: Using Amira to manually segment cell bodies in C.Elegans
AUTHORS: Grace Park, Aubrey Weigel, Alyson Petruncio
[DESCRIPTION]
This protocol describes the techniques used to annotate the cell bodies in C.Elegans. Please reference the Using Amira to manually segment organelles in vEM for machine learning protocol ... | ["[Introduction] This protocol describes the techniques used to annotate the cell bodies in C.Elegans using Amira annotations software. Please reference the Using Amira to manually segment organelles in vEM for machine learning protocol to find details of the annotation techniques and Amira software.", "[Annotation] Fi... |
53,291 | Tissue Culture (tc) PBS | 4 | dx.doi.org/10.17504/protocols.io.byajpscn | https://www.protocols.io/view/tissue-culture-tc-pbs-byajpscn | Jacquelina.Woods | TITLE: Tissue Culture (tc) PBS
AUTHORS: Jacquelina.Woods
[DESCRIPTION]
This method was developed at the FDA’s Center for Food Safety and Applied Nutrition for GenomeTrakr’s pandemic response project, monitoring SARS-CoV-2 variants in wastewater. Protocols developed for this project cover wastewater collection, con... | ["[1X PBS] Dissolve components in deionized or ultrapure water to 1L.", "[1X PBS] 8.0 g", "[1X PBS] 0.2 g", "[1X PBS] Adjust pH 7.5", "[1X PBS] 0.12 g", "[1X PBS] 0.91 g", "[1X PBS] Autoclave 121 °C15 min", "[1X PBS] Store at 2-8 °C", "[10X tc PBS]"] |
92,033 | TFome CRISPRko screens | 4 | null | https://www.protocols.io/view/tfome-crisprko-screens-c549y8z6 | Andrea R Daniel | TITLE: TFome CRISPRko screens
AUTHORS: Andrea R Daniel
[DESCRIPTION]
This protocols describes methods for transcription factor CRISPR knockout screens to reveal cofactors of BATF3 in T cells.
[STEPS]
SECTION: gRNA library construction
1. The Brunello genome-wide KO83 library (four gRNAs per gene) was subset for 1,61... | ["[gRNA library construction] The Brunello genome-wide KO83 library (four gRNAs per gene) was subset for 1,612 TFs45 and IL7R.", "[gRNA library construction] A total of 550 NT gRNAs were included in the library for a total of 7,000 gRNAs (available in Supplementary Table 6 of McCutcheon et al. Nature Genetics, 2023. ht... |
48,207 | Antioxidant activity by DPPH assay: in vitro protocol | 6 | dx.doi.org/10.17504/protocols.io.btbpnimn | https://www.protocols.io/view/antioxidant-activity-by-dpph-assay-in-vitro-protoc-btbpnimn | Adrieli Sachett, Matheus Gallas-Lopes, Greicy M M Conterato, Ana Herrmann, Angelo Piato | TITLE: Antioxidant activity by DPPH assay: in vitro protocol
AUTHORS: Adrieli Sachett, Matheus Gallas-Lopes, Greicy M M Conterato, Ana Herrmann, Angelo Piato
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Considering the role of oxidative stress in the pathology of several diseases and the us... | ["[Preparing the reagents]\nThe first step is to prepare the reagents to be used in this protocol;", "[Preparing the reagents]\n2,2-Diphenyl-1-picrylhydrazyl (DPPH) : 1.1.1 Weigh of DPPH in a piece of aluminum foil; 1.1.2 Add of absolute ethanol to the beaker to dissolve the salt; 1.1.3 Transfer your soluti... |
104,998 | Muconic acid isomers and aromatic compounds analyzed by UHPLC-DAD | 1 | dx.doi.org/10.17504/protocols.io.36wgqjjxyvk5/v3 | https://www.protocols.io/view/muconic-acid-isomers-and-aromatic-compounds-analyz-dise4ebe | Sean P. Woodworth, Stefan J. Haugen, William E. Michener, Kelsey J. Ramirez, Gregg T. Beckham | TITLE: Muconic acid isomers and aromatic compounds analyzed by UHPLC-DAD
AUTHORS: Sean P. Woodworth, Stefan J. Haugen, William E. Michener, Kelsey J. Ramirez, Gregg T. Beckham
[DESCRIPTION]
An analysis method was developed to allow for quantitation of muconic acid isomers (cis, cis and cis, trans) and aromatic compou... | ["[Preparation of Standards] Calibration Curve", "[Analytical Quality Control] Multiple strategies are utilized when performing this analysis to ensure instrument stability and reproducibility.", "[Preparation of Standards] Standards\n\nThis procedure for standard preparation is previously documented in our work publis... |
65,638 | Condor CBD Gummies USA - New Reviews 2022 | 1 | dx.doi.org/10.17504/protocols.io.e6nvwknwwvmk/v1 | https://www.protocols.io/view/condor-cbd-gummies-usa-new-reviews-2022-cccesste | mycondorcbd | TITLE: Condor CBD Gummies USA - New Reviews 2022
AUTHORS: mycondorcbd
[DESCRIPTION]
Condor CBD GummiesEveryone merits the best wellbeing joy, fulfillment, and by and large prosperity! It is actually the case that this isn't not difficult to accomplish with out the assistance of Condor CBD Gummies. These amazing, tac... | [] |
45,749 | CUT&Tag-direct with CUTAC | 1 | dx.doi.org/10.17504/protocols.io.bqwvmxe6 | https://www.protocols.io/view/cut-amp-tag-direct-with-cutac-bqwvmxe6 | Steven Henikoff, Jorja Henikoff, Kami Ahmad | TITLE: CUT&Tag-direct with CUTAC
AUTHORS: Steven Henikoff, Jorja Henikoff, Kami Ahmad
[DESCRIPTION]
<div class = "text-blocks"><div style = "text-align :; float : ;"><img style = "" src = "https://s3.amazonaws.com/protocols-files/files/dryjitfe.jpg" /></div><div class = "text-block"><span>We previously introduced Clea... | ["[ REAGENT SETUP (for up to 16 samples)]\nBinding buffer Mix 200 μL 1M HEPES-KOH pH 7.9*, 100 μL 1M KCl, 10 μL 1M CaCl2 and 10 μL 1M MnCl2, and bring the final volume to 10 mL with dH2O. Store the buffer at 4 °C for up to several months. *HEPES-NaOH pH 7.5 is OK.Wash buffer Mix 1 mL 1 M HEPES pH 7.5, 1.5 mL 5 M NaCl, ... |
62,289 | ViriCan Protocol: PBMC isolation from whole blood | 4 | null | https://www.protocols.io/view/virican-protocol-pbmc-isolation-from-whole-blood-b83rrym6 | Deilson Elgui De Oliveira | TITLE: ViriCan Protocol: PBMC isolation from whole blood
AUTHORS: Deilson Elgui De Oliveira
[DESCRIPTION]
Protocol for isolation of peripheral blood mononuclear cells for downstream applications requiring viable cells or cell pellets to extract DNA or RNA.
[GUIDELINES]
Notes:
From Thermofisher (Answer Id: E4470): "... | ["[Blood colection] Collect 4 mL of whole blood in tubes with anticoagulant*", "[PBMC isolation] Centrifuge Room temperature at 400 x g, 30 min,", "[PBMC isolation] Add 3 mL of Histopaque/Ficoll to 15mL conical centrifuge tube", "[PBMC isolation] Carefully layer about 3 mL of whole blood on top of the Histopaque/Ficol... |
52,910 | DNA Maxwell RSC instrument | 4 | null | https://www.protocols.io/view/dna-maxwell-rsc-instrument-bxwnppde | Yin-Tse Huang, Tina | TITLE: DNA Maxwell RSC instrument
AUTHORS: Yin-Tse Huang, Tina
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Maxwell automated nucleotide extraction </div></div>
[STEPS]
?. 先取 或 ，將sample放入研缽加液態氮磨
[plate]
[1.5 ml tube]
?. 加note: 10ul Lyticase = 100U
[Lyticase]
37 °C
?. 加入 等待溶解，並移到離心管
[CTAB]
?. +
... | ["先取 或 ，將sample放入研缽加液態氮磨\n[plate]\n[1.5 ml tube]", "加note: 10ul Lyticase = 100U\n[Lyticase]\n37 °C", "加入 等待溶解，並移到離心管\n[CTAB]", "+\n94 °C\n[Heating]\n[Cooling]", "+ into離心管\n[RNase A]\n[Proteinase K]", "每10～15分鐘搖晃一次\n[加熱]", "Vortex tube 使均勻混合", "Centrifuge: 16000 34, 10 min, 24 10", "加 + 到第一格\n[Lysis buffer]\n[上清液Sample... |
106,662 | Generating Blood-Generating Heart-Forming Organoids from human pluripotent stem cells | 0 | dx.doi.org/10.17504/protocols.io.e6nvw1nkdlmk/v1 | https://www.protocols.io/view/generating-blood-generating-heart-forming-organoid-dkee4tbe | Miriana Dardano, Lika Drakhlis, Robert Zweigerdt | TITLE: Generating Blood-Generating Heart-Forming Organoids from human pluripotent stem cells
AUTHORS: Miriana Dardano, Lika Drakhlis, Robert Zweigerdt
[DESCRIPTION]
Our established human pluripotent stem cell (hPSC)-derived heart-forming organoids (HFOs) recapitulate aspects of heart, vasculature, and foregut co-devel... | ["[Pre-culture] Grow the human pluripotent stem cell (hPSC) lines of interest (in our case hES3 NKX2.5-eGFP1, 2 and HSC_ADCF_SeV-iPS23) on irradiated embryonic mouse fibroblasts in the incubator at 37 °C, 5%CO2. \n\nAt 80% colony confluence, passage the cells and seed either onto fresh irradiated fibroblasts or, to sta... |
54,938 | Native Protein Analysis on TIMSTOF Pro mass spectrometer | 1 | dx.doi.org/10.17504/protocols.io.bzv2p68e | https://www.protocols.io/view/native-protein-analysis-on-timstof-pro-mass-spectr-bzv2p68e | David Roberts | TITLE: Native Protein Analysis on TIMSTOF Pro mass spectrometer
AUTHORS: David Roberts
[DESCRIPTION]
Method described in David Robert et al., https://pubs.acs.org/doi/10.1021/jacs.1c02713
[STEPS]
1. Method for native protein analysis on a TIMSTOF Pro mass spectrometOriginal study by David Robert et al.,
| ["Method for native protein analysis on a TIMSTOF Pro mass spectrometOriginal study by David Robert et al.,"] |
63,058 | Assembly_Template | 5 | null | https://www.protocols.io/view/assembly-template-b9tsr6ne | ann.mccartney | TITLE: Assembly_Template
AUTHORS: ann.mccartney
[DESCRIPTION]
ERGA_Assembly_Strategy
[STEPS]
SECTION: Assembly and Curation
1.
Data Download
SECTION: Assembly and Curation
2. Data cleaning
SECTION: Assembly and Curation
3. Assembly of long reads
2880 min
SECTION: Assembly and Curation
4. Scaffoldi... | ["[Assembly and Curation] Data Download", "[Assembly and Curation] Data cleaning", "[Assembly and Curation] Assembly of long reads\n \n2880 min", "[Assembly and Curation] Scaffolding with HiC", "[Assembly and Curation] Polishing with Illumina", "[Assembly and Curation] QC", "[Assembly and Curation] Curation"] |
40,776 | ELISA for quantification of IL-16 in human serum. | 6 | dx.doi.org/10.17504/protocols.io.bj3gkqjw | https://www.protocols.io/view/elisa-for-quantification-of-il-16-in-human-serum-bj3gkqjw | Angel Justiz-Vaillant | TITLE: ELISA for quantification of IL-16 in human serum.
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 body cells. T... | ["An anti-human IL-16 coating antibody is adsorbed onto microwells by incubation overnight at 4°C.", "Add 50 µl of human serum. Human IL-16 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."... |
32,552 | In situ sequencing for RNA analysis in tissue sections | null | dx.doi.org/10.17504/protocols.io.bb2giqbw | null | Chika Yokota, Daniel Gyllborg, Mats Nilsson | TITLE: In situ sequencing for RNA analysis in tissue sections
AUTHORS: Chika Yokota, Daniel Gyllborg, Mats Nilsson
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">In situ sequencing method for parallel targeted analysis of short RNA fragments in morphologically preserved tissue. This protocol can be... | ["[Tissue section sample preparation]\nFresh frozen tissue samples embedded in OCT compound and stored at -80°C. Tissue is cryosectioned at 10 μm and collected on Superfrost Slides and can be stored at -80°C until fixation and start of procedure.(see Note 9)", "[Tissue section sample preparation]\nSlides are taken from... |
58,007 | LABORATORY PROTOCOLS OF ANAEMIA TESTING USING PORTABLE HEMOCUE, MALARIA SCREENING USING RDT (HRP-2), PROCESSING OF WET PREPARATION, KATO-KATZ AND EXAMINATION OF STOOL SAMPLES, REPORTING OF SOIL-TRANSMITTED HELMINTHES AND FAECAL PARASITES | 4 | dx.doi.org/10.17504/protocols.io.b4vxqw7n | https://www.protocols.io/view/laboratory-protocols-of-anaemia-testing-using-port-b4vxqw7n | Jean Claude Nkurunziza, Aloys Niyongabo, Nicolette Nabukeera-Barungi, Joan Nakayaga Kalyango, Mercy Muwema Mwanja, Ezekiel Mupere, Joaniter I. Nankabirwa | TITLE: LABORATORY PROTOCOLS OF ANAEMIA TESTING USING PORTABLE HEMOCUE, MALARIA SCREENING USING RDT (HRP-2), PROCESSING OF WET PREPARATION, KATO-KATZ AND EXAMINATION OF STOOL SAMPLES, REPORTING OF SOIL-TRANSMITTED HELMINTHES AND FAECAL PARASITES
AUTHORS: Jean Claude Nkurunziza, Aloys Niyongabo, Nicolette Nabukeer... | ["[ANAEMIA TESTING USING PORTABLE HEMOCUE] 1.Switch-on the HemoCue Hb 301 analyser. Check if the vial of HemoCue Hb 301 is empty.", "[ANAEMIA TESTING USING PORTABLE HEMOCUE] Preparation of the patient’s site to prick", "[ANAEMIA TESTING USING PORTABLE HEMOCUE] Open the alcohol swab", "[ANAEMIA TESTING USING PORTABLE HE... |
21,727 | Preparation and enzyme activity of recombinant protein | null | dx.doi.org/10.17504/protocols.io.zf7f3rn | null | Ning Zhang | TITLE: Preparation and enzyme activity of recombinant protein
AUTHORS: Ning Zhang
[STEPS]
?. ligate CTSL sequence with pET28a vector.
?. Grow small culture overnight.
?. Inoculate 1ml overnight culture into 100ml 2xYT media in a 500 ml flask.
?. Incubate in a 37°C shaker until OD600 reaches 0.6 (About 3.5 hours), and ... | ["ligate CTSL sequence with pET28a vector.", "Grow small culture overnight.", "Inoculate 1ml overnight culture into 100ml 2xYT media in a 500 ml flask.", "Incubate in a 37°C shaker until OD600 reaches 0.6 (About 3.5 hours), and then add 100 mM IPTG 100ul and incubate for 3 hr.", "Pellet the bacteria at 6, 000 rpm for 5... |
45,765 | Isolation and Culture of Individual Myofibers and Their Adjacent Muscle Stem Cells from Aged and Adult Skeletal Muscle | 4 | dx.doi.org/10.17504/protocols.io.bqxdmxi6 | https://www.protocols.io/view/isolation-and-culture-of-individual-myofibers-and-bqxdmxi6 | Sören S. Hüttner, Hellen E. Ahrens, Manuel Schmidt, Henriette Henze, Marie Juliane Jung, Svenja C. Schüler, Julia von Maltzahn | TITLE: Isolation and Culture of Individual Myofibers and Their Adjacent Muscle Stem Cells from Aged and Adult Skeletal Muscle
AUTHORS: Sören S. Hüttner, Hellen E. Ahrens, Manuel Schmidt, Henriette Henze, Marie Juliane Jung, Svenja C. Schüler, Julia von Maltzahn
[DESCRIPTION]
<div class = "text-blocks"><div class = "te... | ["[3.1 Dissection and Digestion of the EDL Muscle]\nSacrifice the mouse according to animal welfare regulations (see Note 3).", "[3.1 Dissection and Digestion of the EDL Muscle]\nTransfer the sacrificed mouse to a dissection bench (semi-sterile). Spray the whole mouse and dissection tools with 70% ethanol.", "[3.1 Diss... |
null | null | null | dx.doi.org/10.17504/protocols.io.tmkek4w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Objective: To evaluate the expression of miR-155, nuclear factor kappa B (NF-κB) and soluble intercellular adhesion molecule-1 (sICAM-1) in the peripheral blood of patients with type 2 diabetes mellitus (T2DM) and assess its relationship with diabetic vascular lesions.
Methods... | ["[Sujects] One hundred sixty-five T2DM patients were randomly selected at the endocrinology department of the General Hospital of Tianjin Medical University and Teda International Vascular Hospital from June 2016 to June 2018. The subjects included 90 males and 75 females, and their average age was 61.79±10.55 years. ... |
73,382 | An analytical method for the quantitation (20-8,000 ppb) of Ergot Alkaloids in Wheat grain. | 6 | dx.doi.org/10.17504/protocols.io.6qpvr48k2gmk/v1 | https://www.protocols.io/view/an-analytical-method-for-the-quantitation-20-8-000-cjweupbe | Michelle Mostrom, Kelly Benson, Brett Webb | TITLE: An analytical method for the quantitation (20-8,000 ppb) of Ergot Alkaloids in Wheat grain.
AUTHORS: Michelle Mostrom, Kelly Benson, Brett Webb
[DESCRIPTION]
Ten ergot alkaloids are quantified in wheat and rye grains at concentrations ranging 20-8,000 ppb using HPLC-MS/MS. Briefly, 5 grams of ground sample is m... | ["[Standard Curve:] Prepare serial dilution", "[Standard Curve:] Transfer 50 µL of 500 Parts per Billion (PPB) standard to poly vial for Standard 10", "[Standard Curve:] Make up a 500 PPB solution of 500 PPB each of Ergocornine, Ergocorninine, Ergocristine, Ergocristinine, Ergocryptine, Ergocryptinine, Ergosine, Ergosi... |
97,105 | USDA LTAR Common Experiment measurement: Total phosphorus (TP) and total dissolved phosphorus (TDP) concentration | 1 | dx.doi.org/10.17504/protocols.io.8epv5r7m6g1b/v1 | https://www.protocols.io/view/usda-ltar-common-experiment-measurement-total-phos-da3r2gm6 | Stephen K. Hamilton, Oliva Pisani, John L. Kovar, Robert W. Malone, Amy J. Morrow, Kevin J. Cole | TITLE: USDA LTAR Common Experiment measurement: Total phosphorus (TP) and total dissolved phosphorus (TDP) concentration
AUTHORS: Stephen K. Hamilton, Oliva Pisani, John L. Kovar, Robert W. Malone, Amy J. Morrow, Kevin J. Cole
[DESCRIPTION]
Total dissolved P (TDP) includes organic P (e.g., sugars and phospholipids) an... | ["[Sample collection and filtration] Return samples to the laboratory on ice and filter them on collection day if possible.", "[Sample collection and filtration] To measure TDP, filter samples through a pore size filter to remove particulates before chemical analysis.", "[Sample collection and filtration] If desired,... |
63,250 | Live-cell imaging; cell death assay | 4 | dx.doi.org/10.17504/protocols.io.rm7vzy1d5lx1/v1 | https://www.protocols.io/view/live-cell-imaging-cell-death-assay-b9zsr76e | Minee-Liane Choi | TITLE: Live-cell imaging; cell death assay
AUTHORS: Minee-Liane Choi
[DESCRIPTION]
This protocol contains instructions for examining cell death in live-cell imaging.
[STEPS]
1. Cell death is detected using Propidium iodide (PI, Thermo Fisher Scientific) or SYTOX™ Green (SYTOX, Thermo Fisher Scientific) which is exc... | ["Cell death is detected using Propidium iodide (PI, Thermo Fisher Scientific) or SYTOX™ Green (SYTOX, Thermo Fisher Scientific) which is excluded from viable cells but exhibits red (PI) and green (SYTOX) fluorescence following a loss of membrane integrity and Hoechst 33342 (Hoechst, Thermo Fisher Scientific).", "20 μM... |
76,525 | CRISPR inhibition (CRISPRi) of LINC01876 in hiPSCs and fbNPCs | 4 | dx.doi.org/10.17504/protocols.io.j8nlkwnq6l5r/v1 | https://www.protocols.io/view/crispr-inhibition-crispri-of-linc01876-in-hipscs-a-cnymvfu6 | anita.adami | TITLE: CRISPR inhibition (CRISPRi) of LINC01876 in hiPSCs and fbNPCs
AUTHORS: anita.adami
[DESCRIPTION]
This protocol describes how to perform CRISPRi in hiPSCs and fbNPCs
[STEPS]
SECTION: gRNA design
1. To design the silencing of the expression of LINC01876 in hiPSCs, the protocol detailed in Johansson et al., 2022 ... | ["[gRNA design] To design the silencing of the expression of LINC01876 in hiPSCs, the protocol detailed in Johansson et al., 2022 was adapted. \n\nSingle guide sequences were designed to recognise DNA regions near the transcription start site (TSS) of the chosen locus according to the GPP Portal (Broad Institute).", "[... |
14,864 | Limiting Dilution & Clonal Expansion | null | dx.doi.org/10.17504/protocols.io.srqed5w | null | Synthego | TITLE: Limiting Dilution & Clonal Expansion
AUTHORS: Synthego
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span> CRISPR-Cas9 can be used to generate edited cell pools for a variety of applications. These pools contain a heterogeneous mix of cells, some unedited and some with different genetic al... | ["[Limiting Dilution]\nTransfer 24-well plate containing transfected cells from the humidified CO2 incubator to a biological safety cabinet.", "[Limiting Dilution]\nAspirate medium from cells across all conditions.", "[Limiting Dilution]\nCarefully wash cells with PBS.", "[Limiting Dilution]\nAspirate PBS.", "[Limiting... |
58,915 | Overall protocol for top-down LC-MS/MS of human lung tissue | 1 | dx.doi.org/10.17504/protocols.io.b5sbq6an | https://www.protocols.io/view/overall-protocol-for-top-down-lc-ms-ms-of-human-lu-b5sbq6an | Jeannie Camarillo, Bryon Drown, Neil Kelleher | TITLE: Overall protocol for top-down LC-MS/MS of human lung tissue
AUTHORS: Jeannie Camarillo, Bryon Drown, Neil Kelleher
[DESCRIPTION]
Overview description of the process for acquiring top-down LC-MS/MS data on human lung tissue
[STEPS]
SECTION: Tissue Collection
1. Lung tissue was provided by University of Roche... | ["[Tissue Collection] Lung tissue was provided by University of Rochester Medical Center. Tissue was collected and prepared according to the following:", "[Sample Preparation] Perform LC based Proteomics on adjacent tissue sections:", "[Data Acquisition]", "[Sample Preparation]"] |
null | null | null | dx.doi.org/10.17504/protocols.io.c2fybm | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
MinElute columns can also be used on any vacuum manifold with luer connectors (e.g., QIAvac 24 Plus or QIAvac 6S with Luer Adapters). The following protocol is designed to extract and purify DNA of 70 bp to 4 kb from standard or low-melt agarose gels in TAE or TBE buffer using v... | [] |
28,408 | MojoSort™ Selection Kits Protocol - 4 | null | dx.doi.org/10.17504/protocols.io.7yyhpxw | null | Sam Li | TITLE: MojoSort™ Selection Kits Protocol - 4
AUTHORS: Sam Li
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Product description and procedure summary:</span><span> Target cells are either selected or depleted by incubating the sample with the biotin antibody cockta... | ["Prepare cells from your tissue of interest or blood without lysing erythrocytes. Kits for human samples have been optimized for PBMCs, please prepare the cells using a suitable method.", "In the final wash of your sample preparation, resuspend the cells in MojoSort™ Buffer by adding up to 4mL in a 5 mL (12 x 75 mm) p... |
26,816 | Streptavidin-CBD purification | null | dx.doi.org/10.17504/protocols.io.6e8hbhw | null | Manuela de las Casas | TITLE: Streptavidin-CBD purification
AUTHORS: Manuela de las Casas
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The aim of this protocol is to obtain the purified streptavidin with cellulose binding domains on both sides from the transformed bacteria </span><span style = "font-style:italic;... | ["[Growing the cells]\nFrom the Petri dishes with the bacteria, pick a few colonies with a Digralsky planting handle and resuspend the colonies in liquid LB in an Erlenmeyer flask. It is recommended to set more than one flask, to minimize risks in case one of the flasks goes wrong. Grow a negative control as well (the ... |
53,924 | Botrytis cinerea transformation protocol | 4 | null | https://www.protocols.io/view/botrytis-cinerea-transformation-protocol-bywcpxaw | Paulo Canessa | TITLE: Botrytis cinerea transformation protocol
AUTHORS: Paulo Canessa
[DESCRIPTION]
Botrytis cinerea transformation protocol. Please, acknowledge the work of others.
[STEPS]
SECTION: Day 1: Fungal growth
1. Add 10 ml sterile MiliQ water on top of a well-sporulated Botrytis cinerea plate (7-day old PDA-bean plate).
... | ["[Day 1: Fungal growth] Add 10 ml sterile MiliQ water on top of a well-sporulated Botrytis cinerea plate (7-day old PDA-bean plate).", "[Day 1: Fungal growth] Disaggregate conidia.", "[Day 1: Fungal growth] Collect conidia and filter using Nytex attached to a flask. You can use the spatula to speed up the process.", "... |
21,422 | Sequential smFISH | null | dx.doi.org/10.17504/protocols.io.y6nfzde | null | ZengU19 BICCN Grant | TITLE: Sequential smFISH
AUTHORS: ZengU19 BICCN Grant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">We have developed a multiplexed single molecule FISH protocol for use at the Institute. This protocol was optimized on human tissue, but will work on mouse tissue as well. It was adapted from Lyubim... | ["[Tissue and Sectioning ]\n10-14 um cryosections are taken from fresh-frozen tissue, which are collected on poly-lysinetreated #1 coverslips at room temperature (RT). After 5-10 min at RT, sections are placed at 4°C until sectioning is complete. At that point, proceed immediately to fixation and permeabilization.\n[RT... |
41,372 | Canary VOC testing protocol | 4 | dx.doi.org/10.17504/protocols.io.bkm4ku8w | https://www.protocols.io/view/canary-voc-testing-protocol-bkm4ku8w | Charlie Mize, Raj Reddy, Purav Badani | TITLE: Canary VOC testing protocol
AUTHORS: Charlie Mize, Raj Reddy, Purav Badani
[STEPS]
?.
?. Turn on Basestation. If Basestation is already on because a test has just been completed, leave the Basestation on. Attach disposable sensor cartridge (or Sensor Tray Housing, STH) to Basestation. Device wil run self-te... | ["Turn on Basestation. If Basestation is already on because a test has just been completed, leave the Basestation on. Attach disposable sensor cartridge (or Sensor Tray Housing, STH) to Basestation. Device wil run self-test.", "Testing subject breathes into the breathing tube of the STH at a normal minute ventilatio... |
64,254 | Identification of PKC-regulated phosphosites on LRRK1 by mass spectrometry analysis | 1 | dx.doi.org/10.17504/protocols.io.261gen89dg47/v1 | https://www.protocols.io/view/identification-of-pkc-regulated-phosphosites-on-lr-cay6sfze | Asad Malik, Raja Sekhar Nirujogi, Toan K. Phung, Dario R. Alessi | TITLE: Identification of PKC-regulated phosphosites on LRRK1 by mass spectrometry analysis
AUTHORS: Asad Malik, Raja Sekhar Nirujogi, Toan K. Phung, Dario R. Alessi
[DESCRIPTION]
We describe a non-radioactive, mass spectrometry-based assay that we deploy for identifying novel PKC-regulated sites on LRRK1 that are re... | ["[Preparation of lipid vesicles for PKC activation] Clean a disposable glass culture tube by washing three times with 100% methanol. Allow to air-dry.", "[Preparation of lipid vesicles for PKC activation] Pipette 0.5 µL of Diacylglycerol (stock concentration is 10 mg/mL) and 5 µL of Phosphatidylserine (stock concentra... |
70,694 | Phytolith extraction and counting procedure for modern plant material rich in silica skeletons | 1 | dx.doi.org/10.17504/protocols.io.q26g74mb8gwz/v2 | https://www.protocols.io/view/phytolith-extraction-and-counting-procedure-for-mo-chaet2be | Francesca D’Agostini, Javier Ruiz-Pérez, Marco Madella, Vincent Vadez, Carla Lancelotti | TITLE: Phytolith extraction and counting procedure for modern plant material rich in silica skeletons
AUTHORS: Francesca D’Agostini, Javier Ruiz-Pérez, Marco Madella, Vincent Vadez, Carla Lancelotti
[DESCRIPTION]
Modern plant tissues are often processed for phytolith analysis. They represent a fundamental source of co... | ["[Drying plant material] Collect the tissues of interest from the whole plant. Store each sample in a separate paper bag and put the paper bags in a dryer. Paper bags prevent the formation of fungi and bacterial infection, allowing the evaporation of tissues’ humidity.Collect the tissues of interest from the whole pla... |
48,426 | Efficacy of injection technique education in diabetes with lipohypertrophy: a systematic review and meta-analysis protocol | 3 | dx.doi.org/10.17504/protocols.io.btiinkce | https://www.protocols.io/view/efficacy-of-injection-technique-education-in-diabe-btiinkce | Masahiro Ichikawa, Tomoaki Akiyama, Yasushi Tsujimoto, Keisuke Anan, Tadashi Yamakawa, Yasuo Terauchi | TITLE: Efficacy of injection technique education in diabetes with lipohypertrophy: a systematic review and meta-analysis protocol
AUTHORS: Masahiro Ichikawa, Tomoaki Akiyama, Yasushi Tsujimoto, Keisuke Anan, Tadashi Yamakawa, Yasuo Terauchi
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">1.Introdu... | [] |
65,564 | Scratch-wound assay | 4 | dx.doi.org/10.17504/protocols.io.5qpvob16zl4o/v1 | https://www.protocols.io/view/scratch-wound-assay-cb94sr8w | Goran Tomic | TITLE: Scratch-wound assay
AUTHORS: Goran Tomic
[DESCRIPTION]
This protocol describes the process for setting up a scratch-wound assay analysed by the IncuCyte system.
[STEPS]
1.
Seed cells at a density of 20,000 cells/well (might need optimisation for a particular cell line) in ImageLock 96-well plates. I usually ... | ["Seed cells at a density of 20,000 cells/well (might need optimisation for a particular cell line) in ImageLock 96-well plates. I usually plate replicates in columns as that way you can easily calculate the mean and export from the IncuCyte software directly.", "Incubate overnight (12-16 hours) or until confluent (mak... |
93,349 | L-2 LEECH PROCESSING | 4 | dx.doi.org/10.17504/protocols.io.j8nlkop56v5r/v1 | https://www.protocols.io/view/l-2-leech-processing-c7edzja6 | REDI-NET Consortium | TITLE: L-2 LEECH PROCESSING
AUTHORS: REDI-NET Consortium
[DESCRIPTION]
This protocol details leech processing.
[BEFORE_START]
Pre-cool the Bullet Blender by adding dry ice into the cooling compartment and running the cooling program.
Clean the work surfaces with RNaseZap, then wipe the surfaces with 70% molecula... | ["[2. BIG LEECH BLOOD MEAL COLLECTION AND INNER ORGAN] Add 400 µL 1x PBS and 100 µL ATL-DX buffer in a Thermo Scientific Screw Cap 1.5 mL Micro tube containing 0.1 mm beads from the step 3 in Before You Start.", "[2. BIG LEECH BLOOD MEAL COLLECTION AND INNER ORGAN] Clean forceps with 70% ethanol and Kimwipes before use... |
78,583 | Slide-TCR-Seq v3 (IVT) | 4 | dx.doi.org/10.17504/protocols.io.n92ldp6w8l5b/v1 | https://www.protocols.io/view/slide-tcr-seq-v3-ivt-cqyxvxxn | 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... |
null | null | null | dx.doi.org/10.17504/protocols.io.e3kbgkw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>BioLegend MojoSort™ nanobeads work in commonly used separation columns, based on our internal research as well as validation by external testing by academic labs. This simple protocol consists of following the MojoSort™ protocol to label the cells with pre-diluted MojoSort™ r... | [] |
90,832 | Assocation of serum galectin-3 with survival, cardiovascular disease and kidney function decline in patients with chronic kidney disease: a systematic review | 1 | dx.doi.org/10.17504/protocols.io.kxygx3144g8j/v1 | https://www.protocols.io/view/assocation-of-serum-galectin-3-with-survival-cardi-c4xqyxmw | Ioannis Bellos, Vassiliki Benetou | TITLE: Assocation of serum galectin-3 with survival, cardiovascular disease and kidney function decline in patients with chronic kidney disease: a systematic review
AUTHORS: Ioannis Bellos, Vassiliki Benetou
[DESCRIPTION]
Galectin-3 is a β-galactoside–binding lectin, which is secreted by endothelial cells, vascular sm... | ["Objective To determine the association of serum galectin-3 levels with survival, kidney disease progression and cardiovascular disease in patients with pre-dialysis chronic kidney disease.", "Eligibility criteria The population of the study will consist of adults with diagnosed with chronic kidney disease, without th... |
102,910 | Quantification of fluorescence intensity of antisense constructs within Bodo saltans and its intracellular symbiont | 0 | dx.doi.org/10.17504/protocols.io.6qpvr8pqblmk/v1 | https://www.protocols.io/view/quantification-of-fluorescence-intensity-of-antise-dgq63vze | Marie Held, Mastaneh Ahrar, Gregory DD Hurst, Ewa Chrostek | TITLE: Quantification of fluorescence intensity of antisense constructs within Bodo saltans and its intracellular symbiont
AUTHORS: Marie Held, Mastaneh Ahrar, Gregory DD Hurst, Ewa Chrostek
[DESCRIPTION]
The purpose of this Protocol is to quantify the intensity of fluorescence resulting from antisense molecules withi... | ["[Incubation of B. saltans with antisense molecules] Filter B. saltans culture through 100 and 8 µm filter.", "[Incubation of B. saltans with antisense molecules] Harvest the cells by centrifugation at 1200 × g for 12 mins at 19 °C.", "[Incubation of B. saltans with antisense molecules] Wash the cells with 10-15 ml st... |
62,630 | Slim Mediq Keto Gummies Reviews – How It Work | 1 | dx.doi.org/10.17504/protocols.io.261gen21jg47/v1 | https://www.protocols.io/view/slim-mediq-keto-gummies-reviews-how-it-work-b9eer3be | Slim Science Keto | TITLE: Slim Mediq Keto Gummies Reviews – How It Work
AUTHORS: Slim Science Keto
[DESCRIPTION]
Slim Mediq Keto Gummies Reviews – How It Work
[STEPS]
SECTION: Slim Mediq Keto Gummies Reviews – How It Work Still, you presumably are unhealthy as well, If you're fat. When body fat becomes inordinate, the mortal body... | ["[Slim Mediq Keto Gummies Reviews – How It Work Still, you presumably are unhealthy as well, If you're fat. When body fat becomes inordinate, the mortal body isn't suitable to serve duly, and certain health complications rise, similar as increases in blood sugar, slow metabolism, and the heart and feathers a... |
56,787 | Automated procedure for estimation of methylation levels in MS-HRM analysis | 1 | null | https://www.protocols.io/view/automated-procedure-for-estimation-of-methylation-b3ptqmnn | Sally Samsø Mathiasen, Jan Bińkowski, Tina Kjeldsen, Tomasz K Wojdacz, Lise Lotte Hansen | TITLE: Automated procedure for estimation of methylation levels in MS-HRM analysis
AUTHORS: Sally Samsø Mathiasen, Jan Bińkowski, Tina Kjeldsen, Tomasz K Wojdacz, Lise Lotte Hansen
[DESCRIPTION]
Testing for disease-related DNA methylation changes provides clinically relevant information in personalized patient care. M... | ["[DATA IMPORT] MS-HRM data preparation for the analyses (when using Light Cycler system – other PCR systems may require adjusting of the data format)", "[DATA IMPORT] Normalize the HRM curves using the Gene Scanning software (we recommend default settings for the normalization).", "[DATA IMPORT] Generate difference pl... |
39,323 | BGISEQ-500 （DNBSEQ-G50）WGS library construction | 1 | dx.doi.org/10.17504/protocols.io.bim3kc8n | https://www.protocols.io/view/bgiseq-500-dnbseq-g50-wgs-library-construction-bim3kc8n | Jie Huang, Xinming Liang, Yuankai Xuan, Chunyu Geng, Yuxiang Li, Haorong Lu, Shoufang Qu, Xianglin Mei, Hongbo Chen, Ting Yu, Nan Sun, Junhua Rao, Jiahao Wang, Wenwei Zhang, Ying Chen, Sha Liao, Hui Jiang, Xin Liu, Zhaopeng Yang, Feng Mu, Shangxian Gao | TITLE: BGISEQ-500 （DNBSEQ-G50）WGS library construction
AUTHORS: Jie Huang, Xinming Liang, Yuankai Xuan, Chunyu Geng, Yuxiang Li, Haorong Lu, Shoufang Qu, Xianglin Mei, Hongbo Chen, Ting Yu, Nan Sun, Junhua Rao, Jiahao Wang, Wenwei Zhang, Ying Chen, Sha Liao, Hui Jiang, Xin Liu, Zhaopeng Yang, Feng Mu, Shangxian Gao
[D... | ["[Overview]", "[DNA fragmentation]\n1) Input genomic DNA sampleGenomic DNA Sample Recommendation AB1Nucleic Acid\n*High-quality genomic DNA\n2Molecular Weight\n>23k bp\n3Amount\n1μg\n4Concentration\n≥12.5ng/μL\n5Purity\nOD260/OD280=1.8~2.0\n*High-quality genomic DNA should be free of salt or organics. It could run... |
48,282 | General Field Plot Sampling Protocol for DNA-based analyses (2018-2020) | 4 | dx.doi.org/10.17504/protocols.io.btd2ni8e | https://www.protocols.io/view/general-field-plot-sampling-protocol-for-dna-based-btd2ni8e | Lori Phillips | TITLE: General Field Plot Sampling Protocol for DNA-based analyses (2018-2020)
AUTHORS: Lori Phillips
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">General field plot sampling protocol for DNA-based analyses (2018-2020)</div></div>
[STEPS]
?. [General Field Sampling Workflow]
Clean the soil probe... | ["[General Field Sampling Workflow]\nClean the soil probe out by taking a discard sample.In the new plot, take a full depth core on the edge of the plot and discard that sample.If using a truck-mounted soil probe, ensure the liner is clean as per the above instructions.", "[General Field Sampling Workflow]\nIf manual s... |
52,091 | Long read genome assembly | 5 | null | https://www.protocols.io/view/long-read-genome-assembly-bw43pgyn | Scott Ferguson, Ashley Jones, Justin Borevitz | TITLE: Long read genome assembly
AUTHORS: Scott Ferguson, Ashley Jones, Justin Borevitz
[DESCRIPTION]
With the introduction of long-read, third generation sequencing (e.g. Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio) and associated bioinformatics tools, we can now affordably assemble complex... | ["[Data Input] De novo genome assembly works best if long-read sequencing has been performed. For best results, optimise a high-molecular weight DNA extraction, for example we use: High-molecular weight DNA extraction, clean-up and size selection for long-read sequencing (https://journals.plos.org/plosone/article?id=10... |
71,458 | Quantifying and Checking Genomic DNA | 1 | null | https://www.protocols.io/view/quantifying-and-checking-genomic-dna-ch2at8ae | Carlos Goller, Carly Sjogren | TITLE: Quantifying and Checking Genomic DNA
AUTHORS: Carlos Goller, Carly Sjogren
[DESCRIPTION]
Overview and Goals
Your bacterial isolate has been grown on agar plates, lysed open and genomic DNA has been isolated for sequencing. Next, we need to quantify our DNA yield and assess its integrity. For this, we will use t... | ["[Activity 1:Quantification of DNA with the Nanodrop Spectrophotometer] Based on the NanoDrop ND-1000 Spectrophotometer Protocol.\n \n\nBefore starting, watch this 10-minute video: NanoDrop Microvolume Quantitation of Nucleic Acids", "[Activity 1:Quantification of DNA with the Nanodrop Spectrophotometer] Initializing"... |
null | null | null | dx.doi.org/10.17504/protocols.io.rx7d7rn | null | null | TITLE: No Title
AUTHORS:
[STEPS] | [] |
69,893 | Transfer of plasmid DNA to Rhodobacter sphaeroides via Conjugal mating | 4 | dx.doi.org/10.17504/protocols.io.ewov1oydolr2/v1 | https://www.protocols.io/view/transfer-of-plasmid-dna-to-rhodobacter-sphaeroides-cghdtt26 | Jaya K Yakha, laible, Deborah K Hanson, Rosemarie Wilton | TITLE: Transfer of plasmid DNA to Rhodobacter sphaeroides via Conjugal mating
AUTHORS: Jaya K Yakha, laible, Deborah K Hanson, Rosemarie Wilton
[DESCRIPTION]
Rhodobacter is not capable of being transformed with pure, double-stranded DNA containing sites for endogenous restriction enzymes. The most efficient way of t... | ["In a sterile microfuge tube mix 1ml of the recipient host strain with 35 ul of donor S17-1(pXYZ) culture and spin for about 30 s at max speed. Decant the supernatant.", "Two days prior to the conjugation, inoculate 25 ml of GYCC with desired host strain and grow at 33 °C with shaking at 125 rpm. If culture becomes to... |
40,416 | Quantification of thiobarbituric acid reactive species (TBARS) optimized for zebrafish brain tissue | 6 | dx.doi.org/10.17504/protocols.io.bjp8kmrw | https://www.protocols.io/view/quantification-of-thiobarbituric-acid-reactive-spe-bjp8kmrw | Adrieli Sachett, Matheus Gallas-Lopes, Greicy M M Conterato, Radharani , Ana Herrmann, Angelo Piato | TITLE: Quantification of thiobarbituric acid reactive species (TBARS) optimized for zebrafish brain tissue
AUTHORS: Adrieli Sachett, Matheus Gallas-Lopes, Greicy M M Conterato, Radharani , Ana Herrmann, Angelo Piato
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Zebrafish are increasingly used as a... | ["[Preparing the reagents]\nThe first step is to prepare the reagents to be used in the quantification of thiobarbituric acid reactive species (TBARS) in the samples;", "[Preparing the reagents]\nTrichloroacetic acid (TCA) 20% + Thiobarbituric acid (TBA) 0.5%: this reagent should be prepared on the day of the biochemi... |
null | null | null | dx.doi.org/10.17504/protocols.io.j6rcrd6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Backgrounds and aims: The association of melanosis coli with the development of</p>
<p>colorectal polyps remains uncertain.</p>
<p> </p>
<p>Methods: From a total of 18263 patients who had received colonoscopy in our hospital,</p>
<p>219 with melanosis coli cases and 438 contr... | [] |
28,595 | Endometrium dissociation with collagenase | null | dx.doi.org/10.17504/protocols.io.76thren | null | Roser Vento-Tormo, Regina Hoo | TITLE: Endometrium dissociation with collagenase
AUTHORS: Roser Vento-Tormo, Regina Hoo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol describe the tissue dissociation procedures from human endometrium and pregnancy endometrium samples. This protocol is adapted from</span><span ... | ["[Tissue dissociation and digestion]\nNote: Flash-frozen tissue with isopentane for Spatial Transcriptomics work. {optional} Note: If tissue is going to be transported, do it with preservation solution (HypoThermosol® FRS) at . Store sample for fixing in formalin (RNA Scope) & nuclei sequencing (flash-frozen) {option... |
34,741 | Culturing Chlorella Vulgaris and Desmodesmus Quadricauda | null | dx.doi.org/10.17504/protocols.io.bd6vi9e6 | null | Jakub Nedbal | TITLE: Culturing Chlorella Vulgaris and Desmodesmus Quadricauda
AUTHORS: Jakub Nedbal
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol describes the steps required for maintaining a healthy culture of </span><span style = "font-style:italic;">Chlorella vulgaris</span><span> and </... | ["[Peparatory Steps]\nWarm-up ½ SŠ Growth Medium (0.5g/l) to room temperature.Leave it outside of a fridge for at least an hour, or leave it in a 37 °C water bath for 10 minutes or so.", "[Peparatory Steps]\nPre-label Erlenmeyer flasks with the culture type, date, own initials, passage number or other pieces of informa... |
79,058 | SOP25v2_TGD_Immunoprecipitation | 4 | dx.doi.org/10.17504/protocols.io.6qpvr4y3ogmk/v1 | https://www.protocols.io/view/sop25v2-tgd-immunoprecipitation-crfsv3ne | Alina Pollner, Varsha Rajesh | TITLE: SOP25v2_TGD_Immunoprecipitation
AUTHORS: Alina Pollner, Varsha Rajesh
[DESCRIPTION]
This protocol describes how to perform immunoprecipitation in protein lysates with the intention of sending the samples for mass spectrometry.
The main concept is described below:
1) To pull down a specific protein in a lysat... | ["[Preparation of Lysate] This protocol has only been validated with adherent cells. \n\nThe first step is to calculate how many cells you will need to lyse to get the protein concentration you need for Mass spectrometry. It is recommended that every immunoprecipitation (IP) has a starting input of 1 mg of protein. The... |
58,911 | AutoFCD | 3 | null | https://www.protocols.io/view/autofcd-b5r7q59n | Jiajie Mo | TITLE: AutoFCD
AUTHORS: Jiajie Mo
[DESCRIPTION]
We construct an integrated platform that can accurately detect FCD and automatically establish trajectory planning for minimally invasive treatment.
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.ja4cigw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol is to annotate the tetraploid coffee long read transcriptome. </p>
[GUIDELINES]
<p><strong>Warning</strong></p>
<p>BLAST output format should be type 5 (.xml).</p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
79,152 | Reproductive Tissue Collection (Mammals): Post-mortem Sampling | 1 | dx.doi.org/10.17504/protocols.io.q26g7yrb3gwz/v2 | https://www.protocols.io/view/reproductive-tissue-collection-mammals-post-mortem-criqv4dw | sanaz.arenivas, Barbara Durrant, comizzolip, mhouck, Jacquelyn Mountcastle, Budhan Pukazhenthi, phil.purdy | TITLE: Reproductive Tissue Collection (Mammals): Post-mortem Sampling
AUTHORS: sanaz.arenivas, Barbara Durrant, comizzolip, mhouck, Jacquelyn Mountcastle, Budhan Pukazhenthi, phil.purdy
[DESCRIPTION]
Version date: April 2023
The following protocol illustrates how to collect and ship living reproductive tissue from a ... | ["[Preparation] Pre-chill icepacks in the freezer the day before planning to collect and ship samples (testicular tissues only).", "[Preparation] Record all information about the species and individual, including a picture of the animal for identification and GPS location where the animal was found.", "[Preparation] Pr... |
66,529 | Preparing 10x PCR buffer | 4 | null | https://www.protocols.io/view/preparing-10x-pcr-buffer-cc79szr6 | Nadine Mowoh, Stephane Fadanka | TITLE: Preparing 10x PCR buffer
AUTHORS: Nadine Mowoh, Stephane Fadanka
[DESCRIPTION]
10X ThermoPol Reaction Buffer is optimized for use with Vent® and Deep Vent® DNA Polymerases. This buffer also provides superior reaction conditions for other thermophilic DNA polymerases, includingTaqDNA Polymerase, OpenVent as w... | ["[Preparing reagent stocks] Before preparing the 10x PCR buffer, prepare 1M and initial stocks of the different chemicals that would be used.\n\n \n\n \n\n\nPrepare 10 mL of 1 M concentration of each of the chemical stocks by weighing the salt powders as indicated in the table 1 below:\nWeigh out the salts as indicate... |
51,279 | Processamento de actígrafos pós-coleta - ActTrust | 1 | dx.doi.org/10.17504/protocols.io.bwbppamn | https://www.protocols.io/view/processamento-de-act-grafos-p-s-coleta-acttrust-bwbppamn | Daniel Vartanian | TITLE: Processamento de actígrafos pós-coleta - ActTrust
AUTHORS: Daniel Vartanian
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Este protocolo faz parte do processo de coleta de dados actigráficos do Grupo Interdisciplinar de Pesquisa em Sono (GIPSO). Ele foi desenhado para os actígrafos pr... | ["[Kanban]\nAdicione o cartão da tarefa no quadro de trabalho do seu projeto (somente para projetos que usam Kanban)\nAbra o quadro de trabalho de seu projeto e adicione um cartão chamado Realizar o processamento de actígrafos pós-coleta na lista Em andamento.No cartão, adicione uma etiqueta chamada Processamento e os ... |
null | null | null | dx.doi.org/10.17504/protocols.io.fa3bign | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Quality impact results is the universal first step for all sequencing methods. Sequencing results distrputed in FASTQ format.</p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
73,682 | protocols.io academic and non-profit contract | 1 | dx.doi.org/10.17504/protocols.io.e6nvwk5j7vmk/v3 | https://www.protocols.io/view/protocols-io-academic-and-non-profit-contract-cj7surne | protocols.io team | TITLE: protocols.io academic and non-profit contract
AUTHORS: protocols.io team
[DESCRIPTION]
Template Contract
This contract is hereby made between the UNIVERSITY/ORGANIZATION (Univ) and ZappyLab, Inc. (DBA “protocols.io”).
DATE:December 13, 2021START DATE:December 27, 2021END DATE:December 26, 2022DESCRIPTION OF S... | ["[Activation] Within thirty (30) days from the Start Date, Univ will provide to protocols.io a list of IP addresses for on-campus user notification about free Premium workspaces.", "[Activation] Within two (2) weeks from the Start Date, protocols.io will enable free Premium workspaces accounts to be created by any Uni... |
28,017 | Antibiotic Stocks | null | dx.doi.org/10.17504/protocols.io.7krhkv6 | null | Alba Balletbó | TITLE: Antibiotic Stocks
AUTHORS: Alba Balletbó
[STEPS]
?. Unless otherwise indicated, the antibiotic powder can be dissolved in dH20. Addgene recommends making 1000X stock solutions and storing aliquots at -20ºC. ABC1AntibioticRecomended Stock ConcentrationRecomended Working Concentration2Ampicillin100 mg/mL100 µg/m... | ["Unless otherwise indicated, the antibiotic powder can be dissolved in dH20. Addgene recommends making 1000X stock solutions and storing aliquots at -20ºC. ABC1AntibioticRecomended Stock ConcentrationRecomended Working Concentration2Ampicillin100 mg/mL100 µg/mL3Chloramphenicol25 mg/mL(dissolve in EtOH)25 µg/mL4Gentam... |
null | null | null | dx.doi.org/10.17504/protocols.io.h95b986 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Please contact Dr. Steven Wilhelm (wilhelm@utk.edu) for additional information regarding this protocol.</p>
[STEPS]
?.
?.
?.
?.
?.
?. | [] |
39,927 | DNeasy Protocol | 3 | dx.doi.org/10.17504/protocols.io.bi8xkhxn | https://www.protocols.io/view/dneasy-protocol-bi8xkhxn | John E Gorzynski | TITLE: DNeasy Protocol
AUTHORS: John E Gorzynski
[STEPS] | [] |
31,264 | How to plant Mimulus guttatus | null | dx.doi.org/10.17504/protocols.io.bar8id9w | null | David Lowry, Acer VanWallendael | TITLE: How to plant Mimulus guttatus
AUTHORS: David Lowry, Acer VanWallendael
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a video of how to plant Mimulus guttatus seeds. </div></div>
[STEPS] | [] |
20,563 | UC Davis - Alanine transaminase | null | dx.doi.org/10.17504/protocols.io.ybtfsnn | null | Peter Havel | TITLE: UC Davis - Alanine transaminase
AUTHORS: Peter Havel
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span></div><div class = "text-block">
Alanine transaminase (ALT) also known as alanine aminotransferase or (sGPT) is a metabolic enzyme expressed pr... | ["Add 10 μl of each sample or standard (in duplicate) to the microplate wells.IMPORTANT: Make sure not to add any bubbles to the wells when dispensing reagents, this will interfere with reading in the platereader.", "Add 50 μl of ALT Reagent Solution to the wells. Cover wells with the adhesive film and incubate at 37°C... |
42,967 | Scoring systems for the prediction of choledocholithiasis: systematic review and meta-analysis (protocol) | 1 | dx.doi.org/10.17504/protocols.io.bm7xk9pn | https://www.protocols.io/view/scoring-systems-for-the-prediction-of-choledocholi-bm7xk9pn | Jun Watanabe, Takanori Sano, Takeshi Kanno, Kotani Kazuhiko, Atsushi Masamune, Yuki Kataoka | TITLE: Scoring systems for the prediction of choledocholithiasis: systematic review and meta-analysis (protocol)
AUTHORS: Jun Watanabe, Takanori Sano, Takeshi Kanno, Kotani Kazuhiko, Atsushi Masamune, Yuki Kataoka
[STEPS] | [] |
86,858 | Sanger Tree of Life HMW DNA Extraction: Manual MagAttract | 4 | dx.doi.org/10.17504/protocols.io.6qpvr33novmk/v1 | https://www.protocols.io/view/sanger-tree-of-life-hmw-dna-extraction-manual-maga-cy3ixyke | Caroline Howard, Michelle Strickland, Robin Moll, Clare Cornwell, Michelle Smith | TITLE: Sanger Tree of Life HMW DNA Extraction: Manual MagAttract
AUTHORS: Caroline Howard, Michelle Strickland, Robin Moll, Clare Cornwell, Michelle Smith
[DESCRIPTION]
This protocol describes the manual extraction of HMW DNA from multiple different tissue samples from a variety of species, excluding plants and fungi,... | ["[Sample Lysis] Prepare a lysis buffer master mix:\n Phosphate buffered solution (PBS)200 µLProteinase K20 µLRNase A4 µLBuffer AL150 µL", "[Sample Lysis] For samples which have been prepared by cryoPREP:\na) Transfer 25 mg sample into a 2 mL microcentrifuge tube, then hold on dry ice to keep the sample frozen.\nb) Wh... |
47,173 | Sanger sequencing of a part of the SARS-CoV-2 spike protein | 3 | dx.doi.org/10.17504/protocols.io.bsbdnai6 | https://www.protocols.io/view/sanger-sequencing-of-a-part-of-the-sars-cov-2-spik-bsbdnai6 | Tue Sparholt Jørgensen | TITLE: Sanger sequencing of a part of the SARS-CoV-2 spike protein
AUTHORS: Tue Sparholt Jørgensen
[STEPS] | [] |
23,200 | Quantitative RT-PCR using the TaqMan® Gene Expression Assays on StepOnePlus™ Real-Time PCR System | null | dx.doi.org/10.17504/protocols.io.2v8ge9w | null | Lisa-Maria Rosenthal, Giang Tong, Katharina Schmitt | TITLE: Quantitative RT-PCR using the TaqMan® Gene Expression Assays on StepOnePlus™ Real-Time PCR System
AUTHORS: Lisa-Maria Rosenthal, Giang Tong, Katharina Schmitt
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Quantitative RT-PCR using the TaqMan® Gene Expressi... | ["Primers ABCD1Primers2GeneGene Assay IDGeneGene Assay ID3RBM3Hs00943160_g1CIRPHs00989762_g14IL-6Hs00174131_m1MCP-1 (Ccl2)Hs00234140_m15iNOSHs01075529_m1GAPDHHs02786624_g1P\nABCD1Primers2GeneGene Assay IDGeneGene Assay ID3RBM3Hs00943160_g1CIRPHs00989762_g14IL-6Hs00174131_m1MCP-1 (Ccl2)Hs00234140_m15iNOSHs01075529_m1GA... |
95,833 | DNA Extraction with ZymoBIOMICS MiniPrep Kit | 0 | dx.doi.org/10.17504/protocols.io.81wgbxjn1lpk/v1 | https://www.protocols.io/view/dna-extraction-with-zymobiomics-miniprep-kit-c9tzz6p6 | Carlos Goller | TITLE: DNA Extraction with ZymoBIOMICS MiniPrep Kit
AUTHORS: Carlos Goller
[DESCRIPTION]
DNA extraction of bacterial DNA Using ZymoBIOMICS‱ DNA Miniprep Kit (D4300) using lysis tubes with DNA/RNA Shield.
[STEPS]
SECTION: D
1. Add to a ZR BashingBead‱ Lysis Tubes (0.1 & 0.5 mm). Add750 µL ZymoBIOMICS‱ Lysis Solution... | ["[D] Add to a ZR BashingBead‱ Lysis Tubes (0.1 & 0.5 mm). Add750 µL ZymoBIOMICS‱ Lysis Solution to the tube and cap tightly. Note: For samples stored and lysed in Lysis Tubes, do not add ZymoBIOMICS‱ Lysis Solution and proceed to Step 2.", "[D] Obtain DNA/RNA Shield Lysis Tubes with samples/swab heads from instru... |
null | null | null | dx.doi.org/10.17504/protocols.io.k3ecyje | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><strong>Objective</strong> To correlate the value of lactate in fetal scalp blood at delivery and the outcomes of the offspring at four years of age.</p>
<p><strong>Methods:</strong> Cases where scalp blood lactate was taken within sixty minutes before delivery were identifie... | [] |
99,600 | Sensor Guided Needle Entry Procedures: A Scoping Review of Advancements to the Veress Needle & selected Needle Entry Techniquesnique Advancements | 0 | dx.doi.org/10.17504/protocols.io.bp2l621jkgqe/v1 | https://www.protocols.io/view/sensor-guided-needle-entry-procedures-a-scoping-re-ddhq235w | Chimwemwe Miti, Richard Scott, Hermes Gadelha-Bloomfield | TITLE: Sensor Guided Needle Entry Procedures: A Scoping Review of Advancements to the Veress Needle & selected Needle Entry Techniquesnique Advancements
AUTHORS: Chimwemwe Miti, Richard Scott, Hermes Gadelha-Bloomfield
[DESCRIPTION]
Primary entry during minimally invasive abdominal surgery remains the one step ass... | ["[Eligibility Criteria] Studies in English", "[Eligibility Criteria] Publication period 1992- May 2024", "[Eligibility Criteria] Articles with full text available", "[Eligibility Criteria] Human subjects"] |
35,746 | A-Tailing with Taq Polymerase | 1 | dx.doi.org/10.17504/protocols.io.be6ajhae | https://www.protocols.io/view/a-tailing-with-taq-polymerase-be6ajhae | New England Biolabs | TITLE: A-Tailing with Taq Polymerase
AUTHORS: New England Biolabs
[DESCRIPTION]
This protocol can be used to add As to the blunt-ends of DNA fragments that have been amplified using a high-fidelity polymerase (such as Q5® High Fidelity DNA Polymerase).
[STEPS]
1. Clean-up the amplified DNA from the PCR components ... | ["Clean-up the amplified DNA from the PCR components", "Set-up the reaction by adding the following components:", "Incubate the reaction at 72 °C for 20 min."] |
62,797 | Coverage of DOAJ journals' citations through OpenCitations - Protocol | 1 | dx.doi.org/10.17504/protocols.io.n92ldz598v5b/v4 | https://www.protocols.io/view/coverage-of-doaj-journals-39-citations-through-ope-b9jmr4k6 | Constance Dami, Alessandro Bertozzi, Chiara Manca, Umut Kucuk | TITLE: Coverage of DOAJ journals' citations through OpenCitations - Protocol
AUTHORS: Constance Dami, Alessandro Bertozzi, Chiara Manca, Umut Kucuk
[DESCRIPTION]
This is the protocol for the research of the coverage of DOAJ journals' citations through OpenCitations.
Our goal is to find out:
about the covera... | ["[Data Gathering: DOAJ] Collecting data from DOAJ: we download data about journals and articles from the DOAJ website, and then refine it excluding all information that we are not interested in.\n\nThe following outputs are expected from this step:", "[Data Gathering: DOAJ] From the DOAJ dump we create doi.json by run... |
36,724 | LC-MS/MS Untargeted Metabolomics Data Acquisition | 1 | dx.doi.org/10.17504/protocols.io.bf4ujqww | https://www.protocols.io/view/lc-ms-ms-untargeted-metabolomics-data-acquisition-bf4ujqww | Kevin Contrepois | TITLE: LC-MS/MS Untargeted Metabolomics Data Acquisition
AUTHORS: Kevin Contrepois
[DESCRIPTION]
Scope:
To describe the procedure to acquire metabolomics data using our broad spectrum plateform.
Expected outcome/data:
Metabolite extracts are analyzed four times using HILIC and RPLC in positive and negative ionization... | ["Untargeted metabolomics was performed using a combination of HILIC- and RPLC-MS methods.", "Metabolic extracts were analyzed four times using HILIC and RPLC separation in both positive and negative ionization modes.", "Data were acquired on a Thermo Q Exactive HF mass spectrometer for HILIC (Thermo Fisher Scientific,... |
28,872 | Sanger sequencing | null | dx.doi.org/10.17504/protocols.io.8fghtjw | null | iGEM Dusseldorf | TITLE: Sanger sequencing
AUTHORS: iGEM Dusseldorf
[STEPS]
?. Label 1.5 mL tubes with barcodes from sequencing company
?. . Add template (400 to 500 ng), primer and water (10 uL total volume, details below) AB1uL per Reaction2Template400-500ng310 uM Primer2.54Waterfill up with water5Total Volume10.0
AB1uL per Reaction... | ["Label 1.5 mL tubes with barcodes from sequencing company", ". Add template (400 to 500 ng), primer and water (10 uL total volume, details below) AB1uL per Reaction2Template400-500ng310 uM Primer2.54Waterfill up with water5Total Volume10.0\nAB1uL per Reaction2Template400-500ng310 uM Primer2.54Waterfill up with water5... |
44,969 | LRRK2RCKW single molecule kinesin motility assays | 4 | dx.doi.org/10.17504/protocols.io.ewov14qykvr2/v1 | https://www.protocols.io/view/lrrk2rckw-single-molecule-kinesin-motility-assays-bp6hmrb6 | John Salogiannis | TITLE: LRRK2RCKW single molecule kinesin motility assays
AUTHORS: John Salogiannis
[DESCRIPTION]
This protocol is about LRRK2RCKW single molecule kinesin motility assays.
[BEFORE_START]
Please take notice of the buffer preparation in section 'Materials'.
Make sure that you have labeled taxol-stabilized microtubule... | ["[Create microscope slides:] Adhere Biotin-PEG-functionalized coverslips (Microsurfaces) to a microscope slide using double-sided scotch tape, creating 4 channels per slide.", "[Prepare LRRK2:] Prepare a 1 micromolar (µM) solution of LRRK2RCKW in a cold LRRK2 buffer. Centrifuge through a 0.1 μm PVDF filter to remove a... |
90,958 | How to grow wheat in controlled and semi-controlled environment | 1 | dx.doi.org/10.17504/protocols.io.6qpvr37jbvmk/v1 | https://www.protocols.io/view/how-to-grow-wheat-in-controlled-and-semi-controlle-c43nyyme | James Simmonds, Isabel Faci, Valentina Buffagni, Cristobal Uauy | TITLE: How to grow wheat in controlled and semi-controlled environment
AUTHORS: James Simmonds, Isabel Faci, Valentina Buffagni, Cristobal Uauy
[DESCRIPTION]
This protocol explains how to germinate and grow wheat, as well as how to harvest and store the grain. This is one of many ways of doing this, but we provide thi... | ["[Germinating Wheat Grains] Grains are usually germinated on filter paper before transferring them into soil as this provides a more uniform and successful germination than sowing them directly in the soil (which can be done by placing the grain 3-5 cm under the surface of the soil and ensure it is well watered).", "[... |
67,273 | BASIC PROTOCOL 1: Species Prescreening | 5 | dx.doi.org/10.17504/protocols.io.j8nlkkqj5l5r/v1 | https://www.protocols.io/view/basic-protocol-1-species-prescreening-cdxhs7j6 | miriam.goldman , chunyu.zhao | TITLE: BASIC PROTOCOL 1: Species Prescreening
AUTHORS: miriam.goldman , chunyu.zhao
[DESCRIPTION]
Reference-based metagenotyping depends crucially on the choice and customization of reference database. Therefore, a typical MIDAS2 workflow starts with a species prescreening step for each metagenome, which enables cu... | ["Install MIDAS2 (See Support Protocol 1)", "Create a work folder containing the FASTQ files (here example input files are downloaded from Zenodo)", "Initialize a local copy of a MIDAS Reference Database (MIDASDB). Here the SCG data from the UHGG MIDASDB is downloaded:", "Run the single-sample species analysis to ident... |
100,784 | FFPE Blocking and Sectioning - UMN TMCs | 0 | dx.doi.org/10.17504/protocols.io.yxmvme3d9g3p/v1 | https://www.protocols.io/view/ffpe-blocking-and-sectioning-umn-tmcs-denq3ddw | Colleen Forster, HT(ASCP)QIHC, David A Bernlohr, Laura J Niedernhofer | TITLE: FFPE Blocking and Sectioning - UMN TMCs
AUTHORS: Colleen Forster, HT(ASCP)QIHC, David A Bernlohr, Laura J Niedernhofer
[DESCRIPTION]
FFPE Blocking and Sectioning protocol from BLS Histology at the University of Minnesota.
[STEPS]
SECTION: FFPE Blocking
1. Specimen Preparation:
The tissues for processin... | ["[FFPE Blocking] Specimen Preparation: \n\nThe tissues for processing should be well fixed, rinsed in running tap and placed into 80%\nalcohol. The suggested fixation is perfusion with 4% paraformaldehyde, fresh tissue dropped\ninto 4% paraformaldehyde or 10% formalin for 24-48 hours or alcohol fixed tissues.\nTo impr... |
null | null | null | dx.doi.org/10.17504/protocols.io.q2jdycn | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?. | [] |
72,366 | 城市微生物相調查計畫—採集土壤教學 | 1 | dx.doi.org/10.17504/protocols.io.n92ldpyj9l5b/v3 | https://www.protocols.io/view/protocol-ciwnufde | Hsin-Mao Wu | TITLE: 城市微生物相調查計畫—採集土壤教學
AUTHORS: Hsin-Mao Wu
[DESCRIPTION]
吳昕懋
[STEPS]
SECTION: 採土與iNaturalist紀錄教學
1. 移除表土，取距離土表5~7公分之處的土，裝入塑膠夾鏈袋中
SECTION: 採土與iNaturalist紀錄教學
2. 將塑膠袋中的土均勻混合，倒入採集罐之中，並且將鏟子清潔乾淨。
SECTION: 採土與iNaturalist紀錄教學
3. 在採集紀錄紙上勾選採樣地點、採樣種類，以及填寫日期、城市、鄉鎮、地點、採集者等資訊
SECTION: 採土與iNaturalist紀錄教學
4... | ["[採土與iNaturalist紀錄教學] 移除表土，取距離土表5~7公分之處的土，裝入塑膠夾鏈袋中", "[採土與iNaturalist紀錄教學] 將塑膠袋中的土均勻混合，倒入採集罐之中，並且將鏟子清潔乾淨。", "[採土與iNaturalist紀錄教學] 在採集紀錄紙上勾選採樣地點、採樣種類，以及填寫日期、城市、鄉鎮、地點、採集者等資訊", "[採土與iNaturalist紀錄教學] 最後拍兩張照片", "[採土與iNaturalist紀錄教學] 接著打開iNaturalist app", "[採土與iNaturalist紀錄教學] 如圖所示，點選右下角的加號", "[採土與iNaturalist紀錄教學] 如下圖所示接著需選... |
49,418 | Targeted Sequencing by Sanger to Recover Key Mutations in Illumina SARS-CoV-2 Whole-genome Sequences | 4 | null | https://www.protocols.io/view/targeted-sequencing-by-sanger-to-recover-key-mutat-buhint4e | Lavanya Singh, Pius M. Brzoska, Ugochukwu J. Anyaneji, James Emmanuel San, Tulio De Oliveira | TITLE: Targeted Sequencing by Sanger to Recover Key Mutations in Illumina SARS-CoV-2 Whole-genome Sequences
AUTHORS: Lavanya Singh, Pius M. Brzoska, Ugochukwu J. Anyaneji, James Emmanuel San, Tulio De Oliveira
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The Spike (S) gene of SARS-CoV-2 demons... | ["[Abstract]\nIn a 96-well plate, add 10 μl of master mix to each sample and no-template control (NTC) well.", "[Sanger Sequencing]\nOne-step RT-PCR", "[Abstract]\nAdd 10 μl of extracted RNA to each sample well. Mix gently by pipetting", "[Abstract]", "[Abstract]", "On ice, prepare a master mix containing the componen... |
45,711 | Coronavirus Lateral Flow Assay (LFA) operation protocol v2 | 4 | dx.doi.org/10.17504/protocols.io.bqvpmw5n | https://www.protocols.io/view/coronavirus-lateral-flow-assay-lfa-operation-proto-bqvpmw5n | peijun he | TITLE: Coronavirus Lateral Flow Assay (LFA) operation protocol v2
AUTHORS: peijun he
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Coronavirus Lateral Flow Assay (LFA) operation protocol</div></div>
[STEPS]
?. Place ELISA plate on lid so that angled towards you.
?. Vortex conjugate to mix (gold p... | ["Place ELISA plate on lid so that angled towards you.", "Vortex conjugate to mix (gold particles settle out) and pipette into front of first well (A1).\n1 µl", "Pipette into first well of next row (B1).\n[PBS]", "Add of sample (follow the sample preparation protocol for sample preparation) to conjugateand mix by pi... |
52,071 | PCR protocol to identify an equine mutation associated with Warmblood Fragile Foal Syndrome(WFFS) | 4 | dx.doi.org/10.17504/protocols.io.bw4fpgtn | https://www.protocols.io/view/pcr-protocol-to-identify-an-equine-mutation-associ-bw4fpgtn | gerald.barry , Sharon Flanagan, Áine Rowe, Vivienne Duggan, Erin Markle, Maureen O’Brien | TITLE: PCR protocol to identify an equine mutation associated with Warmblood Fragile Foal Syndrome(WFFS)
AUTHORS: gerald.barry , Sharon Flanagan, Áine Rowe, Vivienne Duggan, Erin Markle, Maureen O’Brien
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Warmblood Fragile Foal syndrome (WFFS) is an auto... | ["[DNA extraction]\nHair strands (10 per extraction) are cut at a maximum length of 1 cm, including the follicular tag.", "[DNA extraction]\nThe hair is placed into a 1.5 ml Rnase, DNase-free micro-centrifuge tube followed by 300 µl of ATL Buffer, 20 µl of Proteinase K and 20ul of a 1 M DTT solution.", "[DNA extraction... |
17,460 | Tween 60-esculin Agar (TE slant) | 1 | dx.doi.org/10.17504/protocols.io.yxmvm73e5v3p/v1 | https://www.protocols.click/view/tween-60-esculin-agar-te-slant-vaue2ew | Amy Gladfelter | TITLE: Tween 60-esculin Agar (TE slant)
AUTHORS: Amy Gladfelter
[DESCRIPTION]
This media is used to determine ability of Malassezia species to hydrolyzeesculin and utilize Tween 60.
[GUIDELINES]
This media is used to determine ability of Malassezia species to hydrolyze esculin and utilize Tween 60.
[STEPS]
1. pepton... | ["peptone 10 g", "glucose 10 g", "yeast extract 2 g", "ferric ammonium citrate 0.5 g", "esculin 1 g", "agar 15 g", "Tween 60 5 mL", "dH2O 1 L", "Sterilize by autoclaving."] |
50,771 | Libraries construction for HPV targeted NGS | 4 | dx.doi.org/10.17504/protocols.io.bvttn6nn | https://www.protocols.io/view/libraries-construction-for-hpv-targeted-ngs-bvttn6nn | monia.ardhaoui | TITLE: Libraries construction for HPV targeted NGS
AUTHORS: monia.ardhaoui
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol allow the construction of libraries for targeted NGS. Customized primers were designed and indexes were used to permit a one run sequencing.</div></div>
[STEPS]
... | ["A first PCR with PGMY09/11primers was performed using 50μl mixture containing 3mM MgCl2, 10 μmol of each primer, 1.5 mM of dNTP (dATP, dCTP, TTP, dGTP), 5μl of the Taq DNA polymerase buffer, 1U of Taq DNA Polymerase, and 10 μl of DNA preparation was aliquoted. The PCR cycling parameters were composed of a 10 minutes ... |
92,645 | Stereotaxic Injections and Implants | 4 | dx.doi.org/10.17504/protocols.io.8epv5xdw4g1b/v1 | https://www.protocols.io/view/stereotaxic-injections-and-implants-c6qdzds6 | Jonathan Tang | TITLE: Stereotaxic Injections and Implants
AUTHORS: Jonathan Tang
[DESCRIPTION]
Methods for Stereotaxic injections and implants from Tang et al 2023.
[STEPS]
SECTION: VTA AAV Viral Steriotaxic Injections
1. Using a standard mouse surgical suite (see references for example), 750nl of rAAV.EF1a.DIO.hChR2(H134R).eYFP... | ["[VTA AAV Viral Steriotaxic Injections] Using a standard mouse surgical suite (see references for example), 750nl of rAAV.EF1a.DIO.hChR2(H134R).eYFP or rAAV.EF1a.DIO.eYFP (3-4 x 10^12 vg/ml,\nAAV5, University of North Carolina Vector Core; 1-2 x 10^13 vg/ml, AAV1,\nAddgene, 27056-AAV1 and 20298-AAV1) were injected int... |
81,229 | Periplasmic Bacterial Expression and Purification of Elastin-like Polymers - high pH | 1 | null | https://www.protocols.io/view/periplasmic-bacterial-expression-and-purification-ctjmwkk6 | Eva Rose Balog | TITLE: Periplasmic Bacterial Expression and Purification of Elastin-like Polymers - high pH
AUTHORS: Eva Rose Balog
[DESCRIPTION]
This protocol describes the expression and purification procedures used in the Balog lab at the University of New England for producing recombinant elastin-like polymers (ELPs) in E. coli. ... | ["[Transformation] In a pre-chilled Eppendorf tube, mix 10-100 ng plasmid (typically 1-2 μL of mini-prep DNA) with 50-100 μL BL21(DE3) competent cells on ice. Let sit on ice for 30 min.", "[Transformation] Heat shock at 42 ºC in a water bath for 1 min.", "[Transformation] Allow cells to recover on ice for 2-3 min.", "[... |
31,408 | AAV Purification by Iodixanol Gradient Ultracentrifugation | null | dx.doi.org/10.17504/protocols.io.bawqifdw | null | Addgene the nonprofit plasmid repository | TITLE: AAV Purification by Iodixanol Gradient Ultracentrifugation
AUTHORS: Addgene the nonprofit plasmid repository
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol goes through AAV purification by Iodixanol gradient ultracentrifugation. To see the full abstract and additional res... | ["[Procedure]\nPreparation and loading of the iodixanol gradient:15% iodixanol step: mix of 60% iodixanol and of 1 M NaCl/PBS-MK buffer25% iodixanol step: mix of 60% iodixanol and of 1x PBS-MK buffer and 30 μL of phenol red40% iodixanol step: mix of 60% iodixanol and of 1x PBS-MK buffer60% iodixanol step: mix of... |
69,670 | Setting a sequencing run with a nanopore MinION and the Rapid Sequencing gDNA kit (SQK-RAD004) | 4 | dx.doi.org/10.17504/protocols.io.4r3l2oy53v1y/v4 | https://www.protocols.io/view/setting-a-sequencing-run-with-a-nanopore-minion-an-cgaetsbe | Narjol Gonzalez-Escalona | TITLE: Setting a sequencing run with a nanopore MinION and the Rapid Sequencing gDNA kit (SQK-RAD004)
AUTHORS: Narjol Gonzalez-Escalona
[DESCRIPTION]
This protocol is to help in setting up a MinION sequencing run using the rapid sequencing kit from Nanopore (SQK-RAD004). It contains all steps and material need for a s... | ["[Preparation of the DNA Library:] Thaw all reagents in box 1 and 2 of the RAD004 kit.", "[Preparation of the DNA Library:] Take a flow cell from 4-8 °C and leave it at room temperature (RT).", "[Preparation of the DNA Library:] Prepare the DNA to a concentration of 400 ng total in 7.5 µL, or a concentration of 54 ng... |
55,606 | Fluorescence microscope (Zeiss) | 1 | dx.doi.org/10.17504/protocols.io.b2iwqcfe | https://www.protocols.io/view/fluorescence-microscope-zeiss-b2iwqcfe | x.chu | TITLE: Fluorescence microscope (Zeiss)
AUTHORS: x.chu
[DESCRIPTION]
How to operate the fluorescence microscope in the lab. Beware of safety hazards: This instrument uses led radiation. Do not stare at the operating lamp for a prolonged period of time in fluorescence mode.
[STEPS]
SECTION: Microscope layout
1.
S... | ["[Microscope layout]", "[Operating microscope] Turn on the white light intensity and shutter", "[Operating microscope] Turn on the zoom controller", "[Operating microscope] Turn on the LED, if using fluorescent mode", "[Operating microscope] Turn on the software on the computer: Pylon viewer", "[Operating microscope] ... |
78,694 | Quality control assessment for microbial genomes: GalaxyTrakr MicroRunQC workflow | 1 | dx.doi.org/10.17504/protocols.io.5jyl8mj16g2w/v4 | https://www.protocols.io/view/quality-control-assessment-for-microbial-genomes-g-cq4evyte | Ruth Timme, Yesha Shrestha, Tina.Pfefer, Paul Morin, Maria Balkey, Errol Strain | TITLE: Quality control assessment for microbial genomes: GalaxyTrakr MicroRunQC workflow
AUTHORS: Ruth Timme, Yesha Shrestha, Tina.Pfefer, Paul Morin, Maria Balkey, Errol Strain
[DESCRIPTION]
PURPOSE: Step-by-step instructions for checking WGS sequence quality for bacterial pathogens. The MicroRunQC workflow, impleme... | ["[Account set up] Create a GalaxyTrakr account here: https://account.galaxytrakr.org/Account/Register", "[Account set up] Log into your GalaxyTrakr account: https://galaxytrakr.org", "[Create a new history] Create a new history. \n\nWe recommend creating a new history for each new MiSeq Run and including the flow-cell... |
42,270 | Half-UDG treated double-stranded ancient DNA library preparation for Illumina sequencing | 1 | dx.doi.org/10.17504/protocols.io.bmh6k39e | https://www.protocols.io/view/half-udg-treated-double-stranded-ancient-dna-libra-bmh6k39e | Franziska Aron, Gunnar Neumann, Guido Brandt | TITLE: Half-UDG treated double-stranded ancient DNA library preparation for Illumina sequencing
AUTHORS: Franziska Aron, Gunnar Neumann, Guido Brandt
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol for the preparation of double-stranded genomic libraries for Illumina sequencing, optimised f... | ["[UDG Treatment (aDNA library preparation room)]\nPrepare a mastermix for the UDG (USER enzyme) treatment calculating . Use a new 1.5 ml LoBind tube to set up the mastermix. ABCD1ReagentStock concentrationFinal concentration1x Volume [µl]2Buffer Tango10 x1.2 x63ATP10 mM1.2 mM64BSA20 mg/ml0.2 mg/ml0.55dNTPs25 mM each... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.