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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null | null | null | dx.doi.org/10.17504/protocols.io.uteewje | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
If you only need a small number of semi-synchronized worms or if you simply need to remove yeast or bacterial contaminants, this protocol is easier and less time-consuming than the full-scale egg prep. This procedure is also called ‘spot bleaching’.
[STEPS]
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... | ["Pipette ~20µL of the 2X bleach solution onto the unseeded portion of a new plate.", "Pick approximately 10 gravid adults from the contaminated plate with a metal pick and place into the bleach solution on the clean plate. Try to avoid bringing too much bacteria with the worms. (It is best to pick twice to ensure a go... |
35,994 | Preparation of Binding Buffer (BB) | null | dx.doi.org/10.17504/protocols.io.bfd2ji8e | https://www.protocols.io/view/preparation-of-binding-buffer-bb-bfd2ji8e | Nicola O'Reilly, Svend Kjaer, Maria Greco | TITLE: Preparation of Binding Buffer (BB)
AUTHORS: Nicola O'Reilly, Svend Kjaer, Maria Greco
[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... | ["Please select between the recipes for 2 L + 80 ml Binding buffer BB, 4 L + 160 ml Binding buffer BB and 5 L + 200 ml Binding buffer BB.", "Weigh out and add to a 2 L beaker.\n[GuHCl]", "Add . Stir and heat to to dissolve.\n[freshly drawn milliQ]\n60 °C", "Add , .\n[3M sodium acetate]", "Add . Stir well to mix.\n[Tw... |
null | null | null | dx.doi.org/10.17504/protocols.io.cqjvum | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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17,457 | Sabouroud’s Dextrose Agar | 1 | dx.doi.org/10.17504/protocols.io.81wgb1xznvpk/v1 | https://www.protocols.click/view/sabouroud-s-dextrose-agar-vare2d6 | Amy Gladfelter | TITLE: Sabouroud’s Dextrose Agar
AUTHORS: Amy Gladfelter
[DESCRIPTION]
This media is used to determine lipid dependence of Malassezia species.
[GUIDELINES]
This media is used to determine lipid dependence of Malassezia species.
[STEPS]
1. mycological peptone 10 g
2. glucose 40 g
3. agar 15 g
4. dH2O ... | ["mycological peptone 10 g", "glucose 40 g", "agar 15 g", "dH2O 1 L", "Sterilize by autoclaving."] |
55,190 | Subcutaneous nerve stimulation in canine model of persistent atrial fibrillation | 1 | dx.doi.org/10.17504/protocols.io.bz5wp87e | https://www.protocols.io/view/subcutaneous-nerve-stimulation-in-canine-model-of-bz5wp87e | Takashi Kusayama, Juyi Wan, Yuan Yuan, Xiao Liu, Xiaochun Li, Changyu Shen, Michael C. Fishbein, Thomas H. Everett IV, Peng-Sheng.Chen | TITLE: Subcutaneous nerve stimulation in canine model of persistent atrial fibrillation
AUTHORS: Takashi Kusayama, Juyi Wan, Yuan Yuan, Xiao Liu, Xiaochun Li, Changyu Shen, Michael C. Fishbein, Thomas H. Everett IV, Peng-Sheng.Chen
[DESCRIPTION]
This animal protocol was approved by the Institutional Animal Care and ... | ["[Surgical Procedure] Under isoflurane inhalation general anesthesia, perform left thoracotomy through the 4th intercostal space.", "[Surgical Procedure] Implant a radio transmitter (D70-EEE, Data Sciences International), InterStim II neurostimulator (Medtronic Inc.), and a modified Secura implantable cardioverter def... |
null | null | null | dx.doi.org/10.17504/protocols.io.e8cbhsw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Chemiluminescence Detection System for Horseradish Peroxidase</p>
[BEFORE_START]
<p>1. <strong>Preparation of Working Detection Solution:</strong> Allow the solutions to warm to room temperature before use. For each mini blot membrane (~60cm<sup>2</sup> ), mix 2.0ml of picoL... | [] |
41,712 | Pooled sample testing (VTM/UTM) for SARS-CoV-2 using Magnetic Nanotrap® particles for direct RNA extraction. | 4 | null | https://www.protocols.io/view/pooled-sample-testing-vtm-utm-for-sars-cov-2-using-bkyqkxvw | Anurag Patnaik, Ben Lepene, Robert Barclay | TITLE: Pooled sample testing (VTM/UTM) for SARS-CoV-2 using Magnetic Nanotrap® particles for direct RNA extraction.
AUTHORS: Anurag Patnaik, Ben Lepene, Robert Barclay
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol provides a method for detection of SARS-CoV-2 from pooled Viral ... | ["[Sample preparation]\nPool 8 clinical VTM / UTM samples. Combine from each sample into a or tube.\n500 µl\n5 mL\n15 mL", "[Sample preparation]\nAdd of Magnetic Nanotrap® particles to the sample.\n300 µl", "[Sample preparation]\nIncubate samples with Magnetic Nanotrap® particles at for\n0 Room temperature", "... |
68,388 | Washing Protocol for Intact Proteoform MALDI on Human Pancreas | 1 | dx.doi.org/10.17504/protocols.io.5qpvobe17l4o/v1 | https://www.protocols.io/view/washing-protocol-for-intact-proteoform-maldi-on-hu-ce2ctgaw | Kevin J. Zemaitis, Dusan Velickovic, Ljiljana.PasaTolic | TITLE: Washing Protocol for Intact Proteoform MALDI on Human Pancreas
AUTHORS: Kevin J. Zemaitis, Dusan Velickovic, Ljiljana.PasaTolic
[DESCRIPTION]
Scope:
A detailed protocol entailing the sample washing protocols developed for human pancreas, this includes several timed washing steps for fixing the tissue, removing ... | ["[Preparation] While the tissue is within the vacuum desiccator, pour all necessary solvents and solutions into the Coplin jar. These have a volume of approximately 75 mL and to reduce the variability in extraction fill the jars consistently.", "[Tissue fixation wash] Submerge the tissue section within a Coplin jar fi... |
84,169 | Converting ssDNA oligos to dsDNA with T4 DNA polymerase | 4 | dx.doi.org/10.17504/protocols.io.261ged6xyv47/v2 | https://www.protocols.click/view/converting-ssdna-oligos-to-dsdna-with-t4-dna-polym-cwfhxbj6 | Alex N Nguyen Ba | TITLE: Converting ssDNA oligos to dsDNA with T4 DNA polymerase
AUTHORS: Alex N Nguyen Ba
[DESCRIPTION]
This protocol allows one to convert ssDNA to dsDNA oligos. In principle, one can buy two complementary oligos and anneal them. However, there are a few cases where randomized bases are desired, and therefore compleme... | ["[Primer design] Design your target single-stranded DNA oligo such that the 3' end contains the reverse complement of an extending oligonucleotide. For example, appending \"GTCATAGCTGTTTCCTG\" to the end of your oligo will allow an oligonucleotide matching the M13 Reverse (-27) primer to extend it (5'-CAGGAAACAGCTATGA... |
99,995 | Leica SP8 Confocal Imaging | 1 | dx.doi.org/10.17504/protocols.io.261geo2wdl47/v2 | https://www.protocols.io/view/leica-sp8-confocal-imaging-ddv3268n | Allen Institute for Brain Science | TITLE: Leica SP8 Confocal Imaging
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
This protocol describes the basic setup and scanning using the Leica SP8 confocal microscope of fluorescently-labeled mouse brain tissue sections mounted on positively charged 1” x 3” microscope slides.
Note: Research reported ... | [] |
98,229 | In vivo Ephys: Spike Sorting Protocol | 0 | dx.doi.org/10.17504/protocols.io.8epv5r1b4g1b/v1 | https://www.protocols.io/view/in-vivo-ephys-spike-sorting-protocol-db6v2re6 | Sasha Burwell | TITLE: In vivo Ephys: Spike Sorting Protocol
AUTHORS: Sasha Burwell
[DESCRIPTION]
This protocol details the spike sorting procedures used on the collected electrode recording data.
[STEPS]
SECTION: Spike Sorting Protocol
1. For more information on setting up and using Spyking Circus, see: https://spyking-circus.readt... | ["[Spike Sorting Protocol] For more information on setting up and using Spyking Circus, see: https://spyking-circus.readthedocs.io/en/latest/code/index.html .", "[Spike Sorting Protocol] Make a copy of the continuous.dat data file from your recording into a new “sorted_data” folder.", "[Spike Sorting Protocol] Add a .p... |
null | null | null | dx.doi.org/10.17504/protocols.io.g3tbynn | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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null | null | null | dx.doi.org/10.17504/protocols.io.iqwcdxe | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Protocol for Dephosphorylation of 5´-ends of DNA using CIP in Restriction Enzyme Reaction. Uses the Calf Intestinal Alkaline Phosphatase (CIP - M0290)
[GUIDELINES]
<p><strong>Dephosphorylation of 5' -ends of DNA in Restriction Enzyme Reaction</strong></p>
<ul>
... | [] |
105,734 | Publishing Generic Organ Scaffold as a SPARC Dataset | 0 | dx.doi.org/10.17504/protocols.io.6qpvr8q72lmk/v1 | https://www.protocols.io/view/publishing-generic-organ-scaffold-as-a-sparc-datas-djhe4j3e | Mabelle Lin, Hugh Sorby | TITLE: Publishing Generic Organ Scaffold as a SPARC Dataset
AUTHORS: Mabelle Lin, Hugh Sorby
[DESCRIPTION]
In this protocol, we will demonstrate how to prepare a generic organ scaffold for publication as a SPARC dataset using the Scaffold mapping tools. This protocol will ensure that a generic organ scaffold is made a... | ["Use the latest official version of the Scaffold mapping tools to generate your organ scaffold. Do not use a developer installation to generate a scaffold.", "Use the standard generic organ scaffold workflow to generate organ scaffold files. The workflow is installed by default with the mapping tools MAP Client instal... |
50,017 | Work instruction for preparation of CFPS precursor solutions based on Maltodextrin as Energy source | 1 | null | https://www.protocols.io/view/work-instruction-for-preparation-of-cfps-precursor-bu39nyr6 | Fernando Guzman Chavez, Jim Haseloff | TITLE: Work instruction for preparation of CFPS precursor solutions based on Maltodextrin as Energy source
AUTHORS: Fernando Guzman Chavez, Jim Haseloff
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:justify">This protocol details the procedures for the pr... | ["[Preparing 10x Energy Mix solution]\nThe following protocol describes the preparation of~ 4mL(3.9526 mL) of10x Energy Solution.\n\t\t\t\t\t\t\t .justify:after {\n\t\t\t\t\t\t\t content: \"\";\n\t\t\t\t\t\t\t display:inline-block;\n\t\t\t\t\t\t\t width: 100%;\n\t\t\t\t\t\t\t }\n\t\t\t\t\t\t\tThe energy solu... |
79,009 | QIAamp DNA Extraction Protocol | 1 | null | https://www.protocols.io/view/qiaamp-dna-extraction-protocol-crd9v296 | Vicky Ooi, Lee McMichael, Margaret E. Hunter, Aristide Takoukam Kamla, Janet M. Lanyon | TITLE: QIAamp DNA Extraction Protocol
AUTHORS: Vicky Ooi, Lee McMichael, Margaret E. Hunter, Aristide Takoukam Kamla, Janet M. Lanyon
[DESCRIPTION]
Dugong faecal DNA was extracted using the QIAamp Fast DNA Stool Mini Kit (#51604, Qiagen, Germany). The "Protocol: Isolation of DNA from Stool for Human DNA Analysis" was ... | ["Use a sterile blade to scrape off 220 mg of faecal material from the outside surface of a stool and then transfer it into a 2 mL microcentrifuge tube.", "Transfer the faecal material into a mortar and grind the faeces into powder with liquid nitrogen.", "Add 500 μL of InhibitEX buffer to the mortar containing the fae... |
58,755 | Effectiveness of exercise therapy and self-management education to improve physical activity levels in patients with acute exacerbations of chronic obstructive pulmonary disease: protocol of a systematic review and meta-analysis | 1 | dx.doi.org/10.17504/protocols.io.b5mbq42n | https://www.protocols.io/view/effectiveness-of-exercise-therapy-and-self-managem-b5mbq42n | Koki Yamamoto, Mami Takayama, Tadayoshi Nonoyama, Yusuke Kon, Yoshiki Saimon, Takashi Kitagawa | TITLE: Effectiveness of exercise therapy and self-management education to improve physical activity levels in patients with acute exacerbations of chronic obstructive pulmonary disease: protocol of a systematic review and meta-analysis
AUTHORS: Koki Yamamoto, Mami Takayama, Tadayoshi Nonoyama, Yusuke Kon, Yoshiki Sa... | [] |
34,695 | Dissolved Fe(II/III) colorimetric assay using a plate reader (96-well plate) | null | dx.doi.org/10.17504/protocols.io.bd5fi83n | null | Jian Gong | TITLE: Dissolved Fe(II/III) colorimetric assay using a plate reader (96-well plate)
AUTHORS: Jian Gong
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol describes the adaption of an Iron assay originally described in </span><a href="https://doi.org/10.1016/S0883-2927(99)00097-9" st... | ["Measure absorbance A1: A1 is measured immediately after adding of reagent A to of filtered/filtered-diluted samples or undiluted standard solutions. Mix the mixture well with the pipette by gently pipetting up and down a few times. Load three mixtures onto a 96-well plate to make triplicate measurements on the spe... |
68,673 | Clinical metagenomic sequencing - CSF RNA and DNA Illumina MiSeq | 4 | dx.doi.org/10.17504/protocols.io.j8nlkk7wdl5r/v1 | https://www.protocols.click/view/clinical-metagenomic-sequencing-csf-rna-and-dna-il-cfa9tih6 | Gert Marais, Ziyaad Valley-Omar, Kathleen Bateman, Kate McMullen, Dieter van der Westhuizen, Moepeng Maseko, Suzaan Marais, Diana Hardie, Adrian Brink | TITLE: Clinical metagenomic sequencing - CSF RNA and DNA Illumina MiSeq
AUTHORS: Gert Marais, Ziyaad Valley-Omar, Kathleen Bateman, Kate McMullen, Dieter van der Westhuizen, Moepeng Maseko, Suzaan Marais, Diana Hardie, Adrian Brink
[DESCRIPTION]
This protocol was developed to evaluate unbiased cerebrospinal fluid met... | ["[Nucleic Acid Purification] Perform total nucleic acid extraction using the NUCLISENS easyMAG platform or a similar total nucleic acid extraction platform. \nProcess all samples using appropriate infectious prevention and control protocols relevant to the included samples \nCSF sample input volume of 200-1000ul is ac... |
62,604 | Epik Health Keto Gummies - Reduce Extra Fat And Make Get Healthy! | 3 | dx.doi.org/10.17504/protocols.io.5jyl89686v2w/v1 | https://www.protocols.io/view/epik-health-keto-gummies-reduce-extra-fat-and-make-b9dkr24w | Epik Health Keto Gummies | TITLE: Epik Health Keto Gummies - Reduce Extra Fat And Make Get Healthy!
AUTHORS: Epik Health Keto Gummies
[DESCRIPTION]
Epik Health Keto Gummies
[STEPS] | [] |
86,977 | RNA Slide Preparation Protocol (FFPE) for nanostring DSP - GeoMx - Human Breast samples | 4 | dx.doi.org/10.17504/protocols.io.8epv5xr76g1b/v1 | https://www.protocols.io/view/rna-slide-preparation-protocol-ffpe-for-nanostring-cy69xzh6 | Nicolas Martin | TITLE: RNA Slide Preparation Protocol (FFPE) for nanostring DSP - GeoMx - Human Breast samples
AUTHORS: Nicolas Martin
[DESCRIPTION]
This protocol is designed for RNA slide preparation for formalin-fixed tissue.
[GUIDELINES]
This is the default protocol for slide preparation by Nanostring.
IMPORTANT:
Take care to... | ["Prepare reagents\n\nPrepare the reagents using the dilution instructions (see Table 1).\nUse DEPC- treated water for all dilutions. The actual volume of\nreagents used in the protocol will vary – the volumes to prepare in Table 1 are suggestions.\n\nTable 1: Reagent prep for RNA slide preparation\n\n Reagent ... |
67,381 | NTX Nutrition Keto Gummies : - NTX Nutrition Keto Gummies Scam or Real Weight Loss Results? | 4 | dx.doi.org/10.17504/protocols.io.81wgb6bmqlpk/v1 | https://www.protocols.io/view/ntx-nutrition-keto-gummies-ntx-nutrition-keto-gumm-cd2vs8e6 | NTX Nutrition Keto Gummies | TITLE: NTX Nutrition Keto Gummies : - NTX Nutrition Keto Gummies Scam or Real Weight Loss Results?
AUTHORS: NTX Nutrition Keto Gummies
[DESCRIPTION]
NTX Nutrition Keto Gummies
[STEPS]
1. NTX Nutrition Keto Gummies:-
Product Review: —NTX Nutrition Keto Gummies
Used For: — Weight Loss
... | ["NTX Nutrition Keto Gummies:- \n\n\nProduct Review: —NTX Nutrition Keto Gummies\n\nUsed For: — Weight Loss\n Health Benefits\n Burn extra fats\n Better intestine health & promote digestion\n ... |
null | null | null | dx.doi.org/10.17504/protocols.io.fsvbne6 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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89,273 | A novel laboratory method to simulate climatic stress with successful application to experiments with medically relevant ticks | 4 | dx.doi.org/10.17504/protocols.io.rm7vzyo8rlx1/v5 | https://www.protocols.io/view/a-novel-laboratory-method-to-simulate-climatic-str-c3ezyjf6 | Sang Hyo Kim, Caleb Nielebeck, Lauren Dedmon, Mark Pangilinan, Jahred Quan, William Ota, Javier D. Monzón | TITLE: A novel laboratory method to simulate climatic stress with successful application to experiments with medically relevant ticks
AUTHORS: Sang Hyo Kim, Caleb Nielebeck, Lauren Dedmon, Mark Pangilinan, Jahred Quan, William Ota, Javier D. Monzón
[DESCRIPTION]
This protocol details a novel method to isolate individu... | ["[Set up] Place a single tick with one wooden skewer in each tube and seal with a cap, labelling each tube with an individual identifier", "[Set up] Place six tubes in each airtight container along with a humidity pack, labelling each container", "[Set up] Confirm the humidity in one container of each RH level with th... |
5,278 | Recombining DNA by Gibson Assembly | 1 | dx.doi.org/10.17504/protocols.io.261gee4yg479/v1 | https://www.protocols.io/view/recombining-dna-by-gibson-assembly-hd6b29e | Tobias von der Haar | TITLE: Recombining DNA by Gibson Assembly
AUTHORS: Tobias von der Haar
[DESCRIPTION]
Our protocol for producing recombinant DNA via Gibson Assembly, based on a home-made Gibson Master Mix.
[STEPS]
1.
SECTION: Preparation of 5x Isothermal Buffer
2. Mix the following to give 1 ml of 5x Isothermal Buffer:
450 μl 5... | ["[Preparation of 5x Isothermal Buffer] Mix the following to give 1 ml of 5x Isothermal Buffer:\n450 μl 50% PEG 8000\n250 μl 2M Tris-HCl pH 7.5\n100 μl 500 mM MgCl2\n50 μl 1M DTT\n100 μl 50 mM NAD\n10 μl each of 100 mM ATP, CTP, GTP and TTP (PCR grade)\n10 μl sterile water", "[Preparation of Gibson Master Mix] Mix the ... |
45,879 | Detection of marbled crayfish Procambarus fallax | 4 | dx.doi.org/10.17504/protocols.io.q26g78199lwz/v1 | https://www.protocols.io/view/detection-of-marbled-crayfish-procambarus-fallax-bq2xmyfn | Alexander Eiler, Eivind Stensrud, Omneya Osman | TITLE: Detection of marbled crayfish Procambarus fallax
AUTHORS: Alexander Eiler, Eivind Stensrud, Omneya Osman
[DESCRIPTION]
Taqman QPCR assay for marbled crayfish Procambarus fallax
[GUIDELINES]
Handling high concentration of positive controls was performed in a post-PCR room which is physically separated fr... | ["[DNA extraction] A tissue of marbled crayfish was extracted with DNeasy blood and tissue extraction kit\nhttps://www.qiagen.com/us/shop/pcr/dneasy-blood-and-tissue-kit/\nThe quality of DNA was checked by nanodrop.", "[DNA extraction] Primers", "[DNA extraction] 2 µL Standard dilution\n\nDNA of marbled crayfish was se... |
104,643 | A CellProfiler computational pipeline to quantify the density of mouse striatal dopaminergic processes | 0 | dx.doi.org/10.17504/protocols.io.x54v92km4l3e/v2 | https://www.protocols.io/view/a-cellprofiler-computational-pipeline-to-quantify-difb4bin | Ebsy Jaimon, Sreeja V Nair, Suzanne R Pfeffer | TITLE: A CellProfiler computational pipeline to quantify the density of mouse striatal dopaminergic processes
AUTHORS: Ebsy Jaimon, Sreeja V Nair, Suzanne R Pfeffer
[DESCRIPTION]
Here, we present a CellProfiler (1) software pipeline to quantify the density and intensity of dopaminergic processes in the mouse striatum.... | ["[A CellProfiler computational pipeline to quantify the density of mouse striatal dopaminergic processes] Batch process images\n \n1. Use the FIJI macro as described in dx.doi.org/10.17504/protocols.io.3byl4bpo8vo5/v1 to Z project the .czi images obtained from Zeiss LSM microscope. Open the images that need to be proc... |
94,307 | SOP for LBP ELISA after DSS-induced injury | 4 | dx.doi.org/10.17504/protocols.io.q26g7pk73gwz/v1 | https://www.protocols.io/view/sop-for-lbp-elisa-after-dss-induced-injury-c8cbzssn | Malu G Tansey | TITLE: SOP for LBP ELISA after DSS-induced injury
AUTHORS: Malu G Tansey
[DESCRIPTION]
SOP for LBP ELISA after DSS-induced injury
[STEPS]
SECTION: Protocol
1. Concentrations of plasma LPS-binding protein (LBP) were examined via Mouse LBP SimpleStep ELISA according to the manufacturer’s protocol (Abcam, #ab269542).
SE... | ["[Protocol] Concentrations of plasma LPS-binding protein (LBP) were examined via Mouse LBP SimpleStep ELISA according to the manufacturer’s protocol (Abcam, #ab269542).", "[Protocol] Plasma samples were prepared at a 1:16,000 dilution.", "[Protocol] Standards, antibody cocktail containing detector and capture antibodi... |
null | null | null | dx.doi.org/10.17504/protocols.io.cwcxav | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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83,506 | Processing and maintenance of Nicotiana benthamiana tissue for phenotypic, histological, and ribonucleic acid analysis | 4 | dx.doi.org/10.17504/protocols.io.261gedpqwv47/v1 | https://www.protocols.io/view/processing-and-maintenance-of-nicotiana-benthamian-cvssw6ee | Brandon G Roy, Marc Fuchs | TITLE: Processing and maintenance of Nicotiana benthamiana tissue for phenotypic, histological, and ribonucleic acid analysis
AUTHORS: Brandon G Roy, Marc Fuchs
[DESCRIPTION]
Nicotiana benthamiana is extensively used as a model herbaceous plant for virus-host interactions and sytems biology research. Here we describe ... | ["[Plant production and growth] Seeds of Nicotiana benthamiana were sown in Cornell LM-2 soil, and seedlings were transplanted after ~14 days into individual pots. Throughout all growth stages, plants were maintained in controlled growth chamber conditions (16:8 light:dark photoperiod, 25 °C, 70% humidity). Plants were... |
42,736 | 反转录cDNA | 4 | null | https://www.protocols.io/view/cdna-bmyqk7vw | 张 雪 | TITLE: 反转录cDNA
AUTHORS: 张 雪
[STEPS]
?. [方法A.Ominiscript kit]
AB110×buffer RT2µl2dNTP mix(5mM) 2µl3oligo-dT primer(10µM)2µl4RNase inhibitor1µl5Ominiscript reverse transcriptase1µl6Template RNA2µg7RNase-free H2Oadd to 20µl
RNase-free枪头
AB110×buffer RT2µl2dNTP mix(5mM) 2µl3oligo-dT primer(10µM)2µl4RNase inhibitor1µl5Omin... | ["[方法A.Ominiscript kit]\nAB110×buffer RT2µl2dNTP mix(5mM) 2µl3oligo-dT primer(10µM)2µl4RNase inhibitor1µl5Ominiscript reverse transcriptase1µl6Template RNA2µg7RNase-free H2Oadd to 20µl\nRNase-free枪头\nAB110×buffer RT2µl2dNTP mix(5mM) 2µl3oligo-dT primer(10µM)2µl4RNase inhibitor1µl5Ominiscript reverse transcriptase1µl6Te... |
20,450 | iPSC gDNA Extraction: For Screening Edited Clones | null | dx.doi.org/10.17504/protocols.io.x8afrse | null | Celeste Karch, Rita Martinez, Jacob Marsh | TITLE: iPSC gDNA Extraction: For Screening Edited Clones
AUTHORS: Celeste Karch, Rita Martinez, Jacob Marsh
[STEPS]
?. Spin 96 well PCR plate at 3800 rpm for at .
?. Pipet off supernatant.
If worried about removing cells, transfer supernatant with multichannel pipet into new PCR plates and store at until DNA extrac... | ["Spin 96 well PCR plate at 3800 rpm for at .", "Pipet off supernatant.\nIf worried about removing cells, transfer supernatant with multichannel pipet into new PCR plates and store at until DNA extraction is complete.", "To cell pellet (often not visible), add QuickExtract DNA Solution (Epicentre Technologies QE090... |
70,693 | The Treadmill-Based Tripping Perturbation | 1 | dx.doi.org/10.17504/protocols.io.ewov1o8k7lr2/v1 | https://www.protocols.io/view/the-treadmill-based-tripping-perturbation-chadt2a6 | Hui-Ting Shih, Robert Gregor, Szu-Ping Lee | TITLE: The Treadmill-Based Tripping Perturbation
AUTHORS: Hui-Ting Shih, Robert Gregor, Szu-Ping Lee
[DESCRIPTION]
The protocol utilized a side-by-side split-belt instrumented treadmill to simulate a trip-like perturbation. Compared to previously published methodologies, this new protocol is focused on delivering the... | ["[The Treadmill-Based Tripping Perturbation] Turn on VICON motion capture system and open “Vicon Nexus\".", "[The Treadmill-Based Tripping Perturbation] Make sure the force platforms are enabled and available.", "[The Treadmill-Based Tripping Perturbation] Turn on Bertec treadmill and open “Bertec treadmill\". A tread... |
73,627 | SARS-CoV-2 RNA extraction with Ceres Nanotrap and Zymo Environ Water | 4 | dx.doi.org/10.17504/protocols.io.14egn26qqg5d/v1 | https://www.protocols.io/view/sars-cov-2-rna-extraction-with-ceres-nanotrap-and-cj53uq8n | Amanda Windsor, kathryn.judy, Tamara Walsky, Padmini Ramachandran, Chris Grim, Maria Hoffmann | TITLE: SARS-CoV-2 RNA extraction with Ceres Nanotrap and Zymo Environ Water
AUTHORS: Amanda Windsor, kathryn.judy, Tamara Walsky, Padmini Ramachandran, Chris Grim, Maria Hoffmann
[DESCRIPTION]
This protocol uses the Ceres Nanotrap® particle-based virus capture and concentration method for 10mL of wastewater followe... | ["[Viral Capture with Nanotrap® Particles] Shake wastewater bottle to mix then let sit 45 s", "[Viral Capture with Nanotrap® Particles] Using a 10mL serological pipette, carefully pipette 10 mL of wastewater into a 15mL conical tube", "[Viral Capture with Nanotrap® Particles] Add 100 µL of Nanotrap® Enhancement Reagent... |
null | null | null | dx.doi.org/10.17504/protocols.io.e7jbhkn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Cryopreservation of cells in 50% glycerol</p>
[STEPS]
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?.
?. | [] |
101,394 | Filter trap assay for the detection of alpha-synuclein aggregation | 1 | dx.doi.org/10.17504/protocols.io.x54v92re4l3e/v1 | https://www.protocols.io/view/filter-trap-assay-for-the-detection-of-alpha-synuc-de9s3h6e | Cole S Sitron, Victoria A Trinkaus, F Ulrich Hartl | TITLE: Filter trap assay for the detection of alpha-synuclein aggregation
AUTHORS: Cole S Sitron, Victoria A Trinkaus, F Ulrich Hartl
[DESCRIPTION]
This protocol describes an assay that detects aggregated alpha-synuclein in cell lysates.
[STEPS]
SECTION: Harvesting cells
1. Prepare lysis buffer and place on ice.
SE... | ["[Harvesting cells] Prepare lysis buffer and place on ice.", "[Harvesting cells] After 1440 min of exposure to PFFs/PBS, wash wells 1X with 1 mL warm PBS.", "[Harvesting cells] Withdraw PBS and treat wells with 300 µL of TrypLE.", "[Harvesting cells] Quench dissociation reagent with 300 µL of 10% FBS and transfer the ... |
null | null | null | dx.doi.org/10.17504/protocols.io.dqy5xv | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
The NEXTflex™ mtDNA-Seq Kit is designed to prepare single or paired-end DNA libraries of mitochondrial DNA (mtDNA) for sequencing using Illumina® platforms. The procedure isolates mitochondrial DNA from genomic DNA (gDNA) by selective digestion of linear nuclear DNA, followed by... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.ejibcke | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol outlines the analysis used to plot KEGG functional annotation.</p>
[BEFORE_START]
Supplemental information available at:<br /><br /><a href="https://figshare.com/articles/The_Human_Skin_dsDNA_Virome_Topographical_and_Temporal_Diversity_Genetic_Enrichment_and_Dy... | [] |
47,875 | Real-Time PCR protocol to screen for SARS-COV-2 variants of concern (B.1.1.7, P.1 and B.1.1.35) | 4 | null | https://www.protocols.io/view/real-time-pcr-protocol-to-screen-for-sars-cov-2-va-bszbnf2n | Camila Romano, Jaqueline De Jesus, Alvina Clara Felix, Anderson V de Paula, Pâmela S Andrade, Franciane M de Oliveira, Darlan Cândido, Nuno Faria, William M de Souza, Ester C Sabino | TITLE: Real-Time PCR protocol to screen for SARS-COV-2 variants of concern (B.1.1.7, P.1 and B.1.1.35)
AUTHORS: Camila Romano, Jaqueline De Jesus, Alvina Clara Felix, Anderson V de Paula, Pâmela S Andrade, Franciane M de Oliveira, Darlan Cândido, Nuno Faria, William M de Souza, Ester C Sabino
[DESCRIPTION]
<div clas... | ["Reconstitute the oligos/probes to 100uM with TE or nuclease-free water. Vortex briefly and allow to sit for about 2 minutes.", "Prepare 10uM working solutions (primers and probes). Suggestion: if the original concentration is 100uM, add 10ul of the reagents in 90ul of ultrapure nuclease-free water.", "The reaction wa... |
42,203 | Autoclave Balch Tube Sterilization | 1 | dx.doi.org/10.17504/protocols.io.bmf3k3qn | https://www.protocols.io/view/autoclave-balch-tube-sterilization-bmf3k3qn | Ada de la Cruz, Catherine Gohar | TITLE: Autoclave Balch Tube Sterilization
AUTHORS: Ada de la Cruz, Catherine Gohar
[STEPS]
?. [BACTERIAL]
Place tubes that need to be sterilized into an autoclave tub.
?. [BACTERIAL]
Fill tub with tap water and add soap solution to help labels come off.
?. [BACTERIAL]
Place autoclave tub with tubes into autoclave and ... | ["[BACTERIAL]\nPlace tubes that need to be sterilized into an autoclave tub.", "[BACTERIAL]\nFill tub with tap water and add soap solution to help labels come off.", "[BACTERIAL]\nPlace autoclave tub with tubes into autoclave and select the \"P12 30 min liquid\" program.", "[DECRIMPING]\nOnce out of autoclave, place th... |
null | null | null | dx.doi.org/10.17504/protocols.io.t3eeqje | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This collection of files contains the raw data and R script for the paper entitled 'The UK Research Excellence Framework and the Matthew Effect: Insights from machine learning.'
Data:
The file balbuena_REF_2014.dta is a Stata 12 file that contains the data for the paper. It ... | ["{\"blocks\":[{\"key\":\"5rpkl\",\"text\":\"Load the RData file using the command Session | Load Workspace. If you wish to import the Stata or Excel files (#1), use the Part I section of the syntax file. Otherwise, go straight to Part II.\",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[],\"entityRanges\":[]... |
59,039 | Seahorse protocol for islets using Xfe24 Analyzer | 1 | dx.doi.org/10.17504/protocols.io.n2bvj63p5lk5/v1 | https://www.protocols.io/view/seahorse-protocol-for-islets-using-xfe24-analyzer-b5v7q69n | Nancy Smith | TITLE: Seahorse protocol for islets using Xfe24 Analyzer
AUTHORS: Nancy Smith
[DESCRIPTION]
Using Agilent's seahorse Xfe Analyzer with the islet capture microplates to assess whole islet bioenergentics in vitro. Agilent Seahorse XFe24 Analyzers measure the oxygen consumption rate (OCR) and extracellular acidification... | ["[Solution Prep - Calibrant Solution] Calibrant Solution (Agilent 100840-000, 500ml) is provided by Agilent and stored at room temperature.", "[Solution Prep - MA media] Use the DMEM (Agilent 103575-100, 500ml) provided by Agilent; stored at 4 oC. Needs to be supplement with 1% Fetal Bovine Serum (FBS, Gibco 12483-020... |
63,344 | What are the ingredients of Tea Burn? | 3 | dx.doi.org/10.17504/protocols.io.kqdg3pbrql25/v1 | https://www.protocols.io/view/what-are-the-ingredients-of-tea-burn-b94qr8vw | TeaBurnsss | TITLE: What are the ingredients of Tea Burn?
AUTHORS: TeaBurnsss
[DESCRIPTION]
Tea Burn
[STEPS] | [] |
55,800 | Singleplex qPCR for SARS-CoV-2 N1 and BRSV | 4 | dx.doi.org/10.17504/protocols.io.b2qyqdxw | https://www.protocols.io/view/singleplex-qpcr-for-sars-cov-2-n1-and-brsv-b2qyqdxw | Chloe Svezia, Anh Nguyen, Jamie VanTassell, Julia Raymond, Marlene K Wolfe, Pengbo Liu, Christine Moe | TITLE: Singleplex qPCR for SARS-CoV-2 N1 and BRSV
AUTHORS: Chloe Svezia, Anh Nguyen, Jamie VanTassell, Julia Raymond, Marlene K Wolfe, Pengbo Liu, Christine Moe
[DESCRIPTION]
This protocol describes the procedure to perform RT-qPCR for the detection of the SARS-CoV-2 N gene and a processing control (BRSV) in... | ["[Preparation] Ensure that assay mix is prepared in advance for both N1 and BRSV assays (primers and probes mixed at appropriate concentrations and stored for future use at -20 °C , see Appendix I for details).", "[Preparation] Ensure that standard curve aliquots have been prepared for SARS-CoV-2 (see Appendix II for ... |
85,356 | Processing human frontal cortex brain tissue for population-scale SQK-LSK114 Oxford Nanopore long-read DNA sequencing SOP | 4 | dx.doi.org/10.17504/protocols.io.kxygx3zzog8j/v1 | https://www.protocols.io/view/processing-human-frontal-cortex-brain-tissue-for-p-cxkkxkuw | Breeana Baker, Laksh Malik, Maysa Abdelhalim, Pilar Alvarez Jerez, Kimberley J Billingsley, on behalf of the CARD Long-read Team | TITLE: Processing human frontal cortex brain tissue for population-scale SQK-LSK114 Oxford Nanopore long-read DNA sequencing SOP
AUTHORS: Breeana Baker, Laksh Malik, Maysa Abdelhalim, Pilar Alvarez Jerez, Kimberley J Billingsley, on behalf of the CARD Long-read Team
[DESCRIPTION]
Processing human frontal cortex brain ... | ["Part 1: Brain Tissue Cutting (~2 hours for 8 samples)", "Add dry ice to an ice bucket.", "Place supplies (sterile weigh boats, razor blades, spatulas, tweezers, labeled empty 2ml Eppendorf Protein LoBind tubes and cooling block) on dry ice and allow to chill for ~ 10 min.\n\nNote: For any metal tools, clean with 70% ... |
65,366 | K3TO Keto Gummies (NEW 2022!) Does It Work Or Just Scam? | 3 | dx.doi.org/10.17504/protocols.io.36wgq71myvk5/v1 | https://www.protocols.io/view/k3to-keto-gummies-new-2022-does-it-work-or-just-sc-cb3wsqpe | Condor CBD Gummies | TITLE: K3TO Keto Gummies (NEW 2022!) Does It Work Or Just Scam?
AUTHORS: Condor CBD Gummies
[DESCRIPTION]
MUST CHECK: *Special Discounted Pricing Available For The First 50 Customers Only! (ORDER Condor CBD Gummies)
[STEPS] | [] |
76,261 | Study Protocol of PISQ-12 Indonesian Version | 1 | dx.doi.org/10.17504/protocols.io.dm6gpjxd5gzp/v1 | https://www.protocols.io/view/study-protocol-of-pisq-12-indonesian-version-cnqdvds6 | Suhair Quzwain, Tyas Priyatini, Aulia Khatib | TITLE: Study Protocol of PISQ-12 Indonesian Version
AUTHORS: Suhair Quzwain, Tyas Priyatini, Aulia Khatib
[DESCRIPTION]
1. Translation Process. We obtained PISQ-12 questionnaire from the English version of Int Urogynecol J Pelvic Floor Disfunct. 2004 May-Jun;15(3):219. We sent an email to Rebecca G. Rogers, MD askin... | [] |
48,164 | Full-UDG treated double-stranded ancient DNA library preparation for Illumina sequencing | 1 | dx.doi.org/10.17504/protocols.io.btacniaw | https://www.protocols.io/view/full-udg-treated-double-stranded-ancient-dna-libra-btacniaw | Franziska Aron, Gunnar Neumann, Guido Brandt | TITLE: Full-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 and Blunt End Repair (aDNA library preparation room)]\nPrepare a mastermix for the blunt end repair calculating . Use a new 1.5 ml LoBind tube to set up the mastermix. ABCD1ReagentStock concentrationFinal concentration1 x Volume [µl]2NEB Buffer 210 x1 x7.53ATP10 mM1 mM7.54BSA20 mg/ml0.1 mg/ml0.385dNTP... |
81,171 | Flaviviruses (West Nile, Zika, Dengue) NS2B/NS3 Fluorescence Dose Response | 1 | null | https://www.protocols.io/view/flaviviruses-west-nile-zika-dengue-ns2b-ns3-fluore-cthtwj6n | Haim Barr, Noa Lahav | TITLE: Flaviviruses (West Nile, Zika, Dengue) NS2B/NS3 Fluorescence Dose Response
AUTHORS: Haim Barr, Noa Lahav
[DESCRIPTION]
This is a functional, biochemical assay used to identify treatments for viral infectious diseases related to viral Flaviviridae infection, (specifically West Nile, Zika, and Dengue) and targets... | ["[Determine which Flavivirus is needed and prepare solutions] Determine which Flavivirus is needed and prepare solutions based on the materials section.\n ReagentStockLoaded into GNFFinal in assay plateunitsDENV NS2B/NS3217000200100nMZIKV NS2B/NS3225000200100nMWNV NS2B/NS3222000200100nMSubstrate10000 105uMAssay bu... |
96,354 | DOH Workshop Protocol Part 3: Library preparation for Rapid Sequencing DNA V14 Barcoding kit (SQK-RBK114.24) with Pronex modification | 0 | dx.doi.org/10.17504/protocols.io.261gedqd7v47/v1 | https://www.protocols.io/view/doh-workshop-protocol-part-3-library-preparation-f-daca2ase | Vesa Qarkaxhija, Bryan Wee, Natalie Ring | TITLE: DOH Workshop Protocol Part 3: Library preparation for Rapid Sequencing DNA V14 Barcoding kit (SQK-RBK114.24) with Pronex modification
AUTHORS: Vesa Qarkaxhija, Bryan Wee, Natalie Ring
[DESCRIPTION]
This protocol performs creation of Nanopore sequencing libraries for the MinION flow cell using the Rapid Barcodi... | ["[DOH Workshop Protocol Part 3] Prepare one 0.2 ml thin-walled PCR tube for each sample from the previous step. Label the top of the tube with the barcode number.", "[DOH Workshop Protocol Part 3] In each 0.2 ml thin-walled PCR tubes:", "[DOH Workshop Protocol Part 3] Pipette an appropriate amount of your sample (1 µL... |
68,487 | Single-Cell Isolation of Human Knee Meniscus | 5 | dx.doi.org/10.17504/protocols.io.n2bvj6k7blk5/v1 | https://www.protocols.io/view/single-cell-isolation-of-human-knee-meniscus-ce5ftg3n | hswahn, Martin Lotz | TITLE: Single-Cell Isolation of Human Knee Meniscus
AUTHORS: hswahn, Martin Lotz
[DESCRIPTION]
This is a protocol that describes the process of isolating single cells from human knee meniscus for scRNA-seq.
[STEPS]
1. ~1g of tissue from healthy donor knees (Grades 0-1) is collected from the meniscus. For details rega... | ["~1g of tissue from healthy donor knees (Grades 0-1) is collected from the meniscus. For details regarding the tissue harvesting procedure please see \ndx.doi.org/10.17504/protocols.io.6qpvr614zvmk/v1", "Meniscal tissue is washed with Room temperature supplemented with 10% , 1% and 1% .", "The tissue is then fin... |
23,905 | GDSC data set and random forest model scripts | null | dx.doi.org/10.17504/protocols.io.3j9gkr6 | null | Peter Anderson | TITLE: GDSC data set and random forest model scripts
AUTHORS: Peter Anderson
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This location contains the GDSC data set with 145 oncogene mutation statuses and ~1200 chemical descriptors. For instructions how to run binary classification (to predict com... | [] |
48,156 | test 1 | 1 | dx.doi.org/10.17504/protocols.io.bs94nh8w | https://www.protocols.io/view/test-1-bs94nh8w | mar123 | TITLE: test 1
AUTHORS: mar123
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">test</div></div>
[STEPS]
?. test | ["test"] |
61,523 | The effects of robotic assistance on upper limb spatial muscle synergies in healthy people during planar upper-limb training | 1 | dx.doi.org/10.17504/protocols.io.eq2lyn8revx9/v1 | https://www.protocols.io/view/the-effects-of-robotic-assistance-on-upper-limb-sp-b8btrsnn | Adriana Cancrini, Paolo Paolo Baitelli, Matteo Lavit Nicora, Matteo Malosio, Alessandra Laura Giulia Pedrocchi, Alessandro Scano | TITLE: The effects of robotic assistance on upper limb spatial muscle synergies in healthy people during planar upper-limb training
AUTHORS: Adriana Cancrini, Paolo Paolo Baitelli, Matteo Lavit Nicora, Matteo Malosio, Alessandra Laura Giulia Pedrocchi, Alessandro Scano
[DESCRIPTION]
This protocol adopts a stan... | ["[Setup and subject preparation] Subject wears 16 s-EMG electrodes positioned on the following muscles: Erector Spinae (ES), Middle Trapezius (MT), Upper Trapezius (UT), Infraspinatus (IF), Deltoid Anterior (DA), Deltoid Middle (DM), Deltoid Posterior (DP), Pectoralis (PC), Triceps Long Head (TLo), Triceps Lateral Hea... |
48,096 | Chemical Oxygen Demand | 1 | null | https://www.protocols.io/view/chemical-oxygen-demand-bs78nhrw | William Brigman | TITLE: Chemical Oxygen Demand
AUTHORS: William Brigman
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Version 2.0 (COD station 1</span><span style = "vertical-align:super;">st</span><span> lab and analytical trailer)</span></div><div class = "text-block"><span style = ":UNDERLINE;">Developed ... | ["Fill out the COD data sheet, record the sample identification number and COD vial number.", "For samples with moderate to low COD (such as constructed wetlands) use the 1,500 mg/L COD vials.For samples with high COD (such as lagoons) use the 15,000 mg/L COD vials.", "Turn on COD block heater digester (DRB 200-HACH) (... |
73,585 | Fascial manipulation® for musculoskeletal disorders: a scoping review | 1 | dx.doi.org/10.17504/protocols.io.dm6gpjz68gzp/v1 | https://www.protocols.io/view/fascial-manipulation-for-musculoskeletal-disorders-cj4ruqv6 | Yuichi Isaji, Daisuke Sasaki, Yusuke Kon, Takashi Kitagawa | TITLE: Fascial manipulation® for musculoskeletal disorders: a scoping review
AUTHORS: Yuichi Isaji, Daisuke Sasaki, Yusuke Kon, Takashi Kitagawa
[DESCRIPTION]
Objective: The purpose of this scoping review is to synthesize all available literature on the effects/mechanisms of myofascial manipulation interventions and a... | [] |
43,714 | Predicting Tankyrase Binders | 5 | dx.doi.org/10.17504/protocols.io.bnxamfie | https://www.protocols.io/view/predicting-tankyrase-binders-bnxamfie | Katie Pollock, Michael Ranes, Ian Collins, Sebastian Guettler | TITLE: Predicting Tankyrase Binders
AUTHORS: Katie Pollock, Michael Ranes, Ian Collins, Sebastian Guettler
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol is part of a collection: </span><a href="https://www.protocols.io/private/DA5F6F33163011EBAE360A58A9FEAC2A" style = "text-dec... | ["[Predicting Tankyrase Binders]\nScreen your protein of interest for potential TBMs. In an initial step, a search for Arg and Gly spaced 6 amino acids apart (i.e., with four amino acids in between, RxxxxG) will suffice. See step 4 below for atypical TBMs.", "[Predicting Tankyrase Binders]\nUsing UniProt (http://www.un... |
68,009 | Histological image quantification of picrosirius red stained skeletal muscle sections | 1 | dx.doi.org/10.17504/protocols.io.81wgb6j1olpk/v1 | https://www.protocols.io/view/histological-image-quantification-of-picrosirius-r-cenhtdb6 | John Hildyard, Emma Foster, Dominic Wells, Richard Piercy | TITLE: Histological image quantification of picrosirius red stained skeletal muscle sections
AUTHORS: John Hildyard, Emma Foster, Dominic Wells, Richard Piercy
[DESCRIPTION]
Picrosirius Red (PSR) staining of skeletal muscle tissue sections permits histological evaluation of muscle fibrosis: muscle fibres are stained a... | ["[PSR staining] Prepare solutions and reagents (see materials)", "[PSR staining] Remove slides* from -80 and allow to equilibrate to room temperature.\nNote: for best results stain slides in large batches (~24 slides or more) -staining is comparable between batches but most consistent within batches\n\n*see materials"... |
62,218 | Availability of Open Citations from Open Journals in Crossref - Protocol | 1 | dx.doi.org/10.17504/protocols.io.kxygxz7ywv8j/v2 | https://www.protocols.io/view/availability-of-open-citations-from-open-journals-b8zirx4e | Davide Brembilla, Chiara Catizone, Giulia Venditti | TITLE: Availability of Open Citations from Open Journals in Crossref - Protocol
AUTHORS: Davide Brembilla, Chiara Catizone, Giulia Venditti
[DESCRIPTION]
This protocol is for the research about the availability of Open Citations from Open Journals in Crossref.
The goal is to find out how many papers from DOAJ journ... | ["[Data Gathering] We download the DOAJ public data dump containing article metadata in tar.gz format.\nThe dump is structured as a single directory of the form doaj_article_data_[date generated] where are listed files with names of the form article_batch_[number].json. Each file contains up to 100,000 records for a to... |
41,709 | User Protocol for SaliCoV Detection Kit | 4 | dx.doi.org/10.17504/protocols.io.bkymkxu6 | https://www.protocols.io/view/user-protocol-for-salicov-detection-kit-bkymkxu6 | huan.jia , patthara | TITLE: User Protocol for SaliCoV Detection Kit
AUTHORS: huan.jia , patthara
[STEPS]
?. Turn on 'Ninja Eyes' device, put a white paper on cassette loading tray. Wait for device to warm up till user interface is lighted up.
?. Transfer test individual's saliva sample from saliva collection tube to Reagent A bottle with... | ["Turn on 'Ninja Eyes' device, put a white paper on cassette loading tray. Wait for device to warm up till user interface is lighted up.", "Transfer test individual's saliva sample from saliva collection tube to Reagent A bottle with provided Small, Clear 100 uL Fixed Volume Pipette.\n[Reagent A is stored at 4°C before... |
68,531 | URA3 PCR | 4 | null | https://www.protocols.io/view/ura3-pcr-ce6tthen | Brian Teague | TITLE: URA3 PCR
AUTHORS: Brian Teague
[DESCRIPTION]
The polymerase chaine reaction (PCR) amplifies linear DNA using a DNA polymerase enzyme and a pair of short single-stranded DNA "primers." This protocol is for amplifying the URA3 gene from the YTK74 plasmid and adding the homology sequences needed for homology-d... | ["Check that the thermocycler is programmed and holding at 98°C. The thermocycler program we're using is the following:", "Grab an ice bucket and fill it with ice. If you don't have an ice bucket, a beaker will work in a pinch.", "If necessary, dilute the primers to a concentration of 10 micromolar (µM) in . (Make 10... |
75,433 | DNA Extraction | 1 | dx.doi.org/10.17504/protocols.io.81wgby4m1vpk/v1 | https://www.protocols.io/view/dna-extraction-cmwhu7b6 | izabel.stohel@pnnl.gov | TITLE: DNA Extraction
AUTHORS: izabel.stohel@pnnl.gov
[DESCRIPTION]
A list of all protocols used, from Zymo Research with slight modification. Additionally, protocols for measurement of purity and concentration are listed as well.
D6010 is used when there are only a handful of samples and we use tubes, with the cor... | ["The filter may be discarded and the eluted DNA is now in the 1.5mL microcentrifuge tube", "[Measuring Concentration and Purity with Nanodrop] Select dsDNA and follow the prompts from the Nanodrop.", "[DNA Extraction Protocol by Hand: Quick DNA Fecal/Soil Microbe Miniprep Kit D6010] Print Labels for 1.5mL tubes (“Mone... |
101,867 | 12S rRNA-Gene Metabarcoding Library Prep: Dual-PCR Method | 1 | dx.doi.org/10.17504/protocols.io.4r3l2q9k3l1y/v1 | https://www.protocols.io/view/12s-rrna-gene-metabarcoding-library-prep-dual-pcr-dfqj3mun | Andreas Novotny | TITLE: 12S rRNA-Gene Metabarcoding Library Prep: Dual-PCR Method
AUTHORS: Andreas Novotny
[DESCRIPTION]
This protocol is used for eDNA metabarcoding of the mitochondrial 12S rRNA gene (Miya et al 2015) using Pair-End Illumina Miseq Sequencing. This protocol was implemented as part of the Urban Ocean Biodiversity proje... | ["[Preparations] Ensure that the laboratory is appropriately configured and that staff has appropriate training. See \"Guidelines\" for more information. Pay attention to the separation of pre and post-PCR spaces and equipment.", "[Triplicate PCR Amplification (1st PCR)] Preparations\n\n \n\n Reagents:\n (Or equal)\n ... |
null | null | null | dx.doi.org/10.17504/protocols.io.kttcwnn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div title="Page 8">
<div>
<div>
<ol style="list-style-type: none;" start="21">
<li>
<p>The royal python (<em>Python regius</em>) is commonly bred in captivity. To have a successful breeding, accurate monitoring of the reproductive activity is necessary. The use of non-invasive ... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.nkfdctn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>A modified TOTO-1 iodide labeling protocol to enable visualization of nucleic acid loading efficiency, as a means to verify that nucleic acid constructs are entering the cells. With additional cleanup steps to decrease background staining. A convenient assay to use in conjunc... | [] |
20,157 | U Mass - Glucose | null | dx.doi.org/10.17504/protocols.io.xw5fpg6 | null | Jason Kim | TITLE: U Mass - Glucose
AUTHORS: Jason Kim
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">This experiment measures blood or plasma glucose concentration using Analox GM9 Glucose Analyzer or GM7 Micro-Stat Rapid Multi-... | ["Check waste and fill glucose reagent reservoir.", "Prepare ~0.1ml of standard solution (~144 mg/dl).", "Press “Enter”, and then “No” to cycle the Analox Analyzer.", "When cycling is finished, wait for reading to return to ~0 mg/dl (±1mg/dl).", "Enter calibration mode.", "Using precision pipet, inject 10 µl of standa... |
90,471 | C-SOP-501: Normalisation and Pooling of DNA Libraries for Illumina Whole Genome Sequencing | 4 | null | https://www.protocols.io/view/c-sop-501-normalisation-and-pooling-of-dna-librari-c4kfyutn | Mihir Kekre, Ben Pascoe | TITLE: C-SOP-501: Normalisation and Pooling of DNA Libraries for Illumina Whole Genome Sequencing
AUTHORS: Mihir Kekre, Ben Pascoe
[DESCRIPTION]
Normalisation in next-generation sequencing (NGS) is the process of equalising the concentration of multiple DNA libraries for the purpose of multiplexing. Multiplexing helps... | ["[Before Starting] Prior to initiating this protocol, ensure that all active workbenches are cleaned with 80% ethanol, all relevant personal protective clothing is worn and the work area is prepared according to local GLP guidelines for molecular methods.", "[Before Starting] Ensure that you have all of the following ... |
44,448 | BSCI:414--Lab 11:Confirming Cloning of spike(RBD)-SUMO/pET28 | 1 | null | https://www.protocols.io/view/bsci-414-lab-11-confirming-cloning-of-spike-rbd-su-bpm8mk9w | Harley King | TITLE: BSCI:414--Lab 11:Confirming Cloning of spike(RBD)-SUMO/pET28
AUTHORS: Harley King
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">We've amplified our target genes (SARS-CoV-2 spike and spike (RBD) and SUMO) with primers. Then we purified and performed Gibson Assembly. After transformatio... | ["[Create Alignment with Chromatograms]\nOpen the \"F20_spike(RBD)-SUMO/pET28\" plasmid from our BSCI:414 plasmids folder. Make a copy into a new folder under \"BSCI:414 Lab 11\".", "[Create Alignment with Chromatograms]\nDownload the 4 sequence chromatograms from our class folder onto your computer.BSCI414>Files>Lab R... |
null | null | null | dx.doi.org/10.17504/protocols.io.qz6dx9e | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
80,990 | Isolation of Nuclei from Adult Human Brain Tissue for 10x Genomics Platform | 1 | dx.doi.org/10.17504/protocols.io.yxmvmkerng3p/v2 | https://www.protocols.io/view/isolation-of-nuclei-from-adult-human-brain-tissue-ctb6wire | Allen Institute for Brain Science | TITLE: Isolation of Nuclei from Adult Human Brain Tissue for 10x Genomics Platform
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
Isolation of nuclei from frozen adult human brain tissue or thawed and microdissected brain tissue sections for RNA-seq analysis.
Note: Research reported in this publication was... | [] |
55,211 | PRESTO-Tango Assay | 4 | dx.doi.org/10.17504/protocols.io.bz6jp9cn | https://www.protocols.io/view/presto-tango-assay-bz6jp9cn | Abigail Cornwell | TITLE: PRESTO-Tango Assay
AUTHORS: Abigail Cornwell
[DESCRIPTION]
PRESTO-Tango Assay protocol for assessing GPR68 activation by benzodiazepines at acidic pH.
[BEFORE_START]
Acidic media preparation (modified from Pera et al.): Rehydrate VWR Traceable pH/ORP meter (10539-802) in pH4.0 solution at least 30 minutes bef... | ["[Based on Kroeze, Wesley K., et al. "PRESTO-Tango as an open-source resource for interrogation of the druggable human GPCRome." Nature structural & molecular biology 22.5 (2015): 362-369.] Day 1: Plated 400,000 HTLA cells/2mL of media in each well of a 6-well dish by bulk preparing 13mL media + 2.6x10^6... |
null | null | null | dx.doi.org/10.17504/protocols.io.qx8dxrw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol describes how to use a short-term cold shock to render Aiptasia aposymbiotic.</p>
<p>After the cold shock it includes two possibilities to proceed one faster one with usage of DCMU and a slower and more gentle one with only keeping the animals in the dark.</p>
... | [] |
41,058 | Soil thin-layer chromatography | 4 | dx.doi.org/10.17504/protocols.io.bkcaksse | https://www.protocols.io/view/soil-thin-layer-chromatography-bkcaksse | Andreea S | TITLE: Soil thin-layer chromatography
AUTHORS: Andreea S
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">In order to get a relative estimation of the diffusion of our neuropeptide in the soil we can use a soil thin-layer chromatography. In this experiment, developed by Helling & Turner in 1968, a t... | ["Preparation of the soil samples. Several soil samples are collected from potato fields in the area of Groningen & Numansdorp, the Netherlands. The soil from Groningen is predominantly sand whereas the soil from Numansdorp is clay.", "After collection of the soil samples, they are air-dried and sieved through a siev... |
null | null | null | dx.doi.org/10.17504/protocols.io.jzvcp66 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><strong>Background: </strong>The field of cancer cure is flooded with various newer technologies ranging from advanced form of surgeries to new drugs to novel forms of radiotherapy techniques. While the newer forms of radiotherapy i.e., Intensity modulated radiotherapy (IMRT)... | [] |
88,087 | Cognitive and Math Performance and Body Mass Index (BMI) Assessment in Children | 1 | dx.doi.org/10.17504/protocols.io.n2bvj39knlk5/v1 | https://www.protocols.io/view/cognitive-and-math-performance-and-body-mass-index-cz9xx97n | Felipe FC Barradas Cordeiro, João Bento-Torres | TITLE: Cognitive and Math Performance and Body Mass Index (BMI) Assessment in Children
AUTHORS: Felipe FC Barradas Cordeiro, João Bento-Torres
[DESCRIPTION]
Summary of the Study
The assessment sessions took place during class hours in which the children usually study, in a schoolroom reserved for the study procedure... | ["[Assessment of BMI (Body Mass Index)] Measure the height", "[Assessment of BMI (Body Mass Index)] Measure the weight", "[Assessment of BMI (Body Mass Index)] Calculate BMI by dividing body weight, in kilograms, by height, in meters squared.", "[Assessment of BMI (Body Mass Index)] Classify children according to BMI p... |
null | null | null | dx.doi.org/10.17504/protocols.io.ke2ctge | null | null | TITLE: No Title
AUTHORS:
[STEPS] | [] |
68,749 | Scanning electron microscopy protocol | 1 | dx.doi.org/10.17504/protocols.io.j8nlkk796l5r/v1 | https://www.protocols.io/view/scanning-electron-microscopy-protocol-cfdmti46 | Rene Flores Clavo, Francisco Breno S. Teófilo | TITLE: Scanning electron microscopy protocol
AUTHORS: Rene Flores Clavo, Francisco Breno S. Teófilo
[DESCRIPTION]
This protocol briefly summarizes the basic steps of a scanning electron microscopy processing. The methods adopted for fixation, post-fixation, dehydration, drying in a critical point chamber, sputter coa... | ["[MATERIAL SELECTION] 1 mm2 samples were selected in the colony.", "[FIXATION] Samples were fixed in a solution of 2.5 % volume and 0.1 Molarity (M) buffer pH 7.3) , at Room temperature, for 240 min.", "[POST-FIXATION] Samples was then post-fixed with 1 % volume osmium tetroxide in 0.1 Molarity (M) buffer, pH 7.... |
88,928 | C-SOP-101: Bacterial Genomic DNA Isolation using the Nexttec 1-step Kit (96-plate format) | 4 | null | https://www.protocols.io/view/c-sop-101-bacterial-genomic-dna-isolation-using-th-c238ygrw | Mihir Kekre, Ben Pascoe | TITLE: C-SOP-101: Bacterial Genomic DNA Isolation using the Nexttec 1-step Kit (96-plate format)
AUTHORS: Mihir Kekre, Ben Pascoe
[DESCRIPTION]
This protocol describes an easy, convenient and rapid method of genomic DNA isolation and purification from Gram (+) and (-) bacterial broth suspensions. The workflow, dubbed ... | ["[Before Starting] Create an organised bench space by clearing away all clutter in order to maximize work efficiency. Avoid movements that will expose sterile materials to airborne contaminants.", "[Preparation of the Overnight Bacterial Suspension]", "[Before Starting] Treat all isolates and cultures as infectious. L... |
32,126 | Measurement of Symbiodiniaceae cell density in Exaiptasia diaphana tentacles | null | dx.doi.org/10.17504/protocols.io.bbk6ikze | null | giada tortorelli, Roy Belderok, Simon Davy, Geoff McFadden, Madeleine van Oppen | TITLE: Measurement of Symbiodiniaceae cell density in Exaiptasia diaphana tentacles
AUTHORS: giada tortorelli, Roy Belderok, Simon Davy, Geoff McFadden, Madeleine van Oppen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>To monitor Symbiodiniaceae uptake and measure their colonization rate in ... | ["SAMPLING & FIXING TENTACLES (DAY 1)", "Anaesthetize the anemone by submersion in the MgCl2 solution for about in the dark.", "Gently move the anaesthetized anemone on a watchglass on the microscope, and try to have as less liquid as possible on the watchglass (this will facilitate tentacles excision).With the micros... |
45,822 | Quantification of plant hormones by standard addition method | 1 | dx.doi.org/10.17504/protocols.io.bqy6mxze | https://www.protocols.io/view/quantification-of-plant-hormones-by-standard-addit-bqy6mxze | Takuyu Hashiguchi, Masatsugu Hashiguchi, Hidenori Tanaka, Koki Fukushima, Takahiro Gondo, Ryo Akashi | TITLE: Quantification of plant hormones by standard addition method
AUTHORS: Takuyu Hashiguchi, Masatsugu Hashiguchi, Hidenori Tanaka, Koki Fukushima, Takahiro Gondo, Ryo Akashi
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Phytohormones are essential signaling molecules in multiple plant processe... | ["Plant tissues of interest such as leaves, roots, and stems are disrupted in liquid nitrogen using a homogenizer (e.g. TissueLyzer II, QIAGEN).", "Collect 50 mg of the tissue and extract with 1 ml of cold 50 % acetonitrile. Prepare the tissues for both a sample and standards. For example, when you make a calibration ... |
85,081 | TelePi: Assembly, Installation and Customization Guide | 1 | dx.doi.org/10.17504/protocols.io.3byl4jp22lo5/v1 | https://www.protocols.click/view/telepi-assembly-installation-and-customization-gui-cxbzxip6 | Almoatazbellah Youssef, Andreas Rosenwald, Mathias T. Rosenfeldt | TITLE: TelePi: Assembly, Installation and Customization Guide
AUTHORS: Almoatazbellah Youssef, Andreas Rosenwald, Mathias T. Rosenfeldt
[DESCRIPTION]
Telepathology facilitates histological diagnoses through sharing expertise between pathologists, with added benefits in terms of teaching and potential research collabor... | ["[Hardware Assembly] Unpack the Raspberry Pi High Quality Camera (HQ Camera) and the mounting bracket. Use the supplied M2 screws and nuts to attach the HQ Camera to the bracket.", "[Installing the Raspberry Pi Operating System] Download and install the official Raspberry Pi Imager program. For this guide, we are assu... |
60,059 | World's Best Cup of Coffee | 4 | null | https://www.protocols.io/view/world-39-s-best-cup-of-coffee-b6v3re8n | timothy.propst | TITLE: World's Best Cup of Coffee
AUTHORS: timothy.propst
[DESCRIPTION]
Basic instructions on how to create a cup of coffee.
[BEFORE_START]
Make sure to utilize filtered water for best flavor results.
[GUIDELINES]
Follow instructions carefully.
[STEPS]
1. Measure your coffee. The standard ratio is approximate... | ["Measure your coffee. The standard ratio is approximately 2 tablespoons of coffee per 6 ounces of water. Don’t be afraid to add a few extra beans to be on the safe side – you can more approximately measure out your coffee using a scale after it’s ground.\n \n1600 mg \n177 mL water", "Prepare the water.", "Pour. Sat... |
23,139 | Calibrating 10-AU fluorometer to quantify extracted chl-a | null | dx.doi.org/10.17504/protocols.io.2ubgesn | null | Shelby Whitehead, Samantha Coy, Steven Wilhelm | TITLE: Calibrating 10-AU fluorometer to quantify extracted chl-a
AUTHORS: Shelby Whitehead, Samantha Coy, Steven Wilhelm
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This method is for use for calibrating the 10-AU flurometer using chl-a extracts. The method also provides guidelines for extractin... | ["[Chlorophyll Extraction]\nExtract chlorophyll from of gound spinach with of 90% acetone at overnight.\n1 g\n5 ml\n-20 °C", "[Spectrophotometry]\nUse the Biomate 5 spectrophotometer to measure the adsorption of extracted chlorophyll by adding to a quartz cuvette. Make sure the cuvette is in the correct position... |
36,623 | SPARC Cat - Sham Control Chronic Cat 3, Day 14 | 1 | dx.doi.org/10.17504/protocols.io.bfzpjp5n | https://www.protocols.io/view/sparc-cat-sham-control-chronic-cat-3-day-14-bfzpjp5n | Brett Hanzlicek, Anna Rietsch, Margot Damaser | TITLE: SPARC Cat - Sham Control Chronic Cat 3, Day 14
AUTHORS: Brett Hanzlicek, Anna Rietsch, Margot Damaser
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a procedure for a sham control chronic cat experiment (Day 14) for cystotomy (bladder surgery). The cystotomy is performed with... | ["[Transport Cat]\nTransport cat from housing site to surgery site.", "[Animal Prep and catheter placement]\nAnimal is anesthetized and abdomen is shaved by the vet team. The cat is then moved into the surgery room and attached to monitors by the vet team.", "[Animal Prep and catheter placement]\nDrape animal and perf... |
null | null | null | dx.doi.org/10.17504/protocols.io.e2cbgaw | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
<p>Reagent List:</p>
<p><br />- Sterile PBS<br />- Cell culture medium (IMDM supplemented with 10% FBS)<br />- Sterile plastic petri dishes<br />- RBC Lysis Buffer (Cat. No. 420301)<br />- Anti-mouse CD3ε, clone 145-2C11 (LEAF™ format, Cat. No. 100314)<br />- Anti-mouse CD28, clo... | [] |
79,723 | Multiplex Genotyping PCR for the KPC Pancreatic Cancer Mouse Model | 4 | dx.doi.org/10.17504/protocols.io.eq2ly7bxrlx9/v1 | https://www.protocols.io/view/multiplex-genotyping-pcr-for-the-kpc-pancreatic-ca-cr4jv8un | Shou Kitahara, Shounak Ranabhor, Thae Su Thu, Neha Ramesh, Chang-il Hwang | TITLE: Multiplex Genotyping PCR for the KPC Pancreatic Cancer Mouse Model
AUTHORS: Shou Kitahara, Shounak Ranabhor, Thae Su Thu, Neha Ramesh, Chang-il Hwang
[DESCRIPTION]
Genetically engineered mouse model (GEMM) is one of the most important pre-clinical models in cancer research. In pancreatic cancer research, Kras+/... | ["[Crude genomic DNA isolation] Prepare Lysis Buffer (Recipe for 10 mL)\n●0.0121 g Tris-HCl pH 8.0\n●0.0373 g KCl\n●12.5 µl 2M MgCl2\n●45 µL NP-40 \n●45 µL Tween-20\n●9.9 mL Ultrapure Distilled Water (DW)", "[Crude genomic DNA isolation] Add 3 µl Proteinase K (20 mg/mL) to 1 mL of Lysis buffer prior to use (Store in -2... |
19,921 | U Mass - Albumin | null | dx.doi.org/10.17504/protocols.io.xprfmm6 | null | Jason Kim | TITLE: U Mass - Albumin
AUTHORS: Jason Kim
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span><span style = "font-weight:bold;"> </span></div><div class = "text-block">
This experiment involves a spectrophotometric measurement using Roche Cobas Clinical ... | ["Perform daily quality control assessment of instrumentation before analysis.", "Load each sample into a specialized micro-sample cup for the clinical chemistry analyzer.", "Select Albumin test on display and run the analysis.", "Collect and analyze the data."] |
69,748 | PCR | 1 | dx.doi.org/10.17504/protocols.io.bp2l694n1lqe/v1 | https://www.protocols.io/view/pcr-cgcutsww | Ana Belem García González, Jair Alexis Gardea Sáenz, Irán Alessandra Chaparro Rodríguez, Georgina Diego | TITLE: PCR
AUTHORS: Ana Belem García González, Jair Alexis Gardea Sáenz, Irán Alessandra Chaparro Rodríguez, Georgina Diego
[DESCRIPTION]
50 µL volume PCR protocol
[STEPS]
SECTION: RECOVERY IDT SEQUENCES
1. Centrifuge the tubes with the sequences for one minute at 3,000 g x m in the centrifuge
SECTION: RECOVERY IDT S... | ["[RECOVERY IDT SEQUENCES] Centrifuge the tubes with the sequences for one minute at 3,000 g x m in the centrifuge", "[RECOVERY IDT SEQUENCES] Centrifuge for 5 seconds in the microcentrifuge", "[RECOVERY IDT SEQUENCES] Add nuclease-free water needed to have a final concentration of 10 ng/uL.", "[RECOVERY IDT SEQUENCES]... |
103,275 | Welcome & Onboarding | 0 | dx.doi.org/10.17504/protocols.io.14egn6m6zl5d/v1 | https://www.protocols.io/view/welcome-amp-onboarding-dg4j3yun | Andy Alexander, Emma Cimino | TITLE: Welcome & Onboarding
AUTHORS: Andy Alexander, Emma Cimino
[DESCRIPTION]
Must knows for onboarding at UCSB and in the Alexander laboratory.
[STEPS]
SECTION: Welcome to the Alexander lab!🙂 Please complete the following steps to get started:
1. IACUC researcher training checklist:
Email IACUC
PI: Andy Alexa... | ["[Welcome to the Alexander lab!🙂 Please complete the following steps to get started:] IACUC researcher training checklist:\n\nEmail IACUC\nPI: Andy Alexander, Protocol: 986\nSkim through our protocol: you will NOT be quizzed on the it by us or IACUC, but just read the beginning to get a gist of our research and every... |
20,453 | Prediction of pneumoconiosis by serum and urinary biomarkers in workers exposed to asbestos-contaminated minerals | null | dx.doi.org/10.17504/protocols.io.x8dfrs6 | null | Hsiao-Yu Yang | TITLE: Prediction of pneumoconiosis by serum and urinary biomarkers in workers exposed to asbestos-contaminated minerals
AUTHORS: Hsiao-Yu Yang
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Prediction of pneumoconiosis by serum and urinary biomarkers in workers ex... | ["[Dataset preparation]\nDownload the dataset and store at \"C:\\r\".", "[Required software]\nThis protocol requires R-3.5.2 for Windows (32/64 bit) (https://cran.r-project.org/bin/windows/base/)", "[Dataset preparation]", "[Dataset preparation]\nDownload the file of “PLoS One Excel Main Raw Datafile.csv”. Store at “C:... |
101,328 | Cluster Counting | 0 | dx.doi.org/10.17504/protocols.io.5jyl8224rl2w/v1 | https://www.protocols.io/view/cluster-counting-de7q3hmw | daniel.dautan daniel, Per Svenningsson | TITLE: Cluster Counting
AUTHORS: daniel.dautan daniel, Per Svenningsson
[DESCRIPTION]
Used for counting clusters labeled for pSer129 alpha-synuclein in mouse upper gastrointestinal tract (intestine). Sections should be stained, mounted, and imaged with high resolution (2048 x 2048 scanning).
[STEPS]
1. Stain structur... | ["Stain structures for pSer129 and scan with high-resolution (pixel size of 6.25µm).", "Import the images into ImageJ.", "Adjust signal intensity to a standardized threshold of 95%. (All thresholds, exposure settings, and laser intensities were applied consistently across all scans).", "Convert to grayscale.", "Employ ... |
38,683 | A Randomised Controlled Trial to Evaluate the Administration of the Health Improvement Card as a Health Promotion Tool: A Physiotherapist-led Community-based Initiative | 1 | dx.doi.org/10.17504/protocols.io.bhz3j78n | https://www.protocols.io/view/a-randomised-controlled-trial-to-evaluate-the-admi-bhz3j78n | Yiwen Bai, Xubo Wu, Raymond Tsang, Ruisheng Yun, Yan LU, Elizabeth Dean, Alice YM Jones | TITLE: A Randomised Controlled Trial to Evaluate the Administration of the Health Improvement Card as a Health Promotion Tool: A Physiotherapist-led Community-based Initiative
AUTHORS: Yiwen Bai, Xubo Wu, Raymond Tsang, Ruisheng Yun, Yan LU, Elizabeth Dean, Alice YM Jones
[DESCRIPTION]
<div class = "text-blocks"><div ... | ["Adults between 50-90 years of age were recruited through information sessions, posters and pamphlets provided by 3 community centres affiliated with a university involved in this study", "Interested subjects were screened for inclusion and exclusion criteria.", "Eligible participants were randomly allocated to either... |
23,161 | Risk Assessment and Increasing Safety in Dementia – RAISe-Dementia study | null | dx.doi.org/10.17504/protocols.io.2uzgex6 | null | Juanita Hoe, Gill Livingston, Sergi Costafreda, Nomi Weberloff, Gianluca Biao, Helen Souris, Emily van de Pol | TITLE: Risk Assessment and Increasing Safety in Dementia – RAISe-Dementia study
AUTHORS: Juanita Hoe, Gill Livingston, Sergi Costafreda, Nomi Weberloff, Gianluca Biao, Helen Souris, Emily van de Pol
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:justify">A... | [] |
49,780 | DNA Extract was from filter paper stored at room temperature | 1 | dx.doi.org/10.17504/protocols.io.buuunwww | https://www.protocols.io/view/dna-extract-was-from-filter-paper-stored-at-room-t-buuunwww | Katie Izenour, Anwar Kalalah, Fayez Salib, Sarah Zohdy | TITLE: DNA Extract was from filter paper stored at room temperature
AUTHORS: Katie Izenour, Anwar Kalalah, Fayez Salib, Sarah Zohdy
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Preservation of samples requiring cold-chain storage is an often unavoidable challenge especially when doing laborator... | ["[Whole blood collection from animal]\nUsing a sterile syringe and needle, collect of whole blood from animal's forelimb. Immediately express the contents of the syringe into a new, clean EDTA tube and invert several times to mix.\n1 mL", "[Whole blood storage]\nIF EXTRACTING DNA ON THE SAME DAY AS BLOOD COLLECTION ... |
60,146 | Phenol Chloroform DNA Extraction Optimized for HMW gDNA from Coccidioides spp. | 4 | null | https://www.protocols.io/view/phenol-chloroform-dna-extraction-optimized-for-hmw-b6ysrfwe | mitchellbryant , Heather Mead, Bridget M. Barker, Austin Blackmon | TITLE: Phenol Chloroform DNA Extraction Optimized for HMW gDNA from Coccidioides spp.
AUTHORS: mitchellbryant , Heather Mead, Bridget M. Barker, Austin Blackmon
[DESCRIPTION]
Coccidioides spp. are fungal pathogens present in the arid soil of the American Southwest.This group of pathogenic fungi are responsible for c... | ["[Fungal Lysis Buffer] Lysis Buffer (prepare in sterile 50 ml falcon tube while in hood)\n •\t30 ml Mol. Biol grade water\n •\t5 ml 3M NaOAc at pH 6.0\n •\t2.5 ml 10% SDS\n •\t10 ml 0.5 M EDTA at pH 8.0\n •\t2.5 ml 1M Tris HCl at pH 7.5\n •\tPrepare stock in small batches with mol. bio. grade water or purchase premade... |
22,335 | Ultra-freeze media | null | dx.doi.org/10.17504/protocols.io.z27f8hn | null | David Shis, L. F. Gibson, J. T. Khoury | TITLE: Ultra-freeze media
AUTHORS: David Shis, L. F. Gibson, J. T. Khoury
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This is a recipe for an "ultra-freeze" meda recipe. Taken stock from Gibson </span><span style = "font-style:italic;">et al. </span><span>This recipe enables the quicker re... | ["[100mL recipe]\nMix Together the following reagentsTryptone Soya brothGlucose Skim milk powder Glycerol\n3 g\n0 g\n2 g\n4 g", "[100mL recipe]\nAutoclave for 30 minutes", "[100mL recipe]\nSolution should be turbid, heterogeneous. Store at RT", "[Using Ultra-freeze media]\nThe paper suggests growing up a lawn but I hav... |
68,260 | Ligation | 4 | null | https://www.protocols.io/view/ligation-cewctfaw | Brian Teague | TITLE: Ligation
AUTHORS: Brian Teague
[DESCRIPTION]
A DNA ligase is an enzyme that forms phosphodiester bonds -- it can "glue" together two pieces of DNA. The ligase we're using comes from the T4 bacteriophage virus.
Why do we need to do a ligation anyway? Remember, we're going to use a Cas9 protein to "cut" your ... | ["[Ligation] Dilute the annealed oligonucleotides in to make 100 µL of working stock at a final concentration of 200 nanomolar (nM)", "[Ligation] In the PCR tube, mix in order:\n4 µL \n2 µL of the L2-01 DNA plasmid backbone\n 2 µL of the diluted annealed oligos\n1 µL \n1 µL", "[Ligation] Flick the tube several t... |
null | null | null | dx.doi.org/10.17504/protocols.io.jjdcki6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div>
<p>The corms and leaves of elephant foot yams (<em>Amorphophallus paeoniifolius</em> (Dennst.) Nicolson) are important foods in the local diet in many Asian regions. The crop has high productivity and wide agroecological adaptation and exhibits suitability for the agrofore... | [] |
69,592 | Lentivirus production for primary neuron transduction | 4 | dx.doi.org/10.17504/protocols.io.kqdg39eo1g25/v1 | https://www.protocols.io/view/lentivirus-production-for-primary-neuron-transduct-cf7ytrpw | Miguel Da Silva Padilha, Irina Dudanova, Itika Saha, F. Ulrich Hartl, Mark S. Hipp | TITLE: Lentivirus production for primary neuron transduction
AUTHORS: Miguel Da Silva Padilha, Irina Dudanova, Itika Saha, F. Ulrich Hartl, Mark S. Hipp
[DESCRIPTION]
This protocol describes the production of lentiviruses to transduce mouse primary neurons and has to be performed in a biosafety level 2 laboratory
[ST... | ["Expand HEK293T cells (LentiX 293T cell line, Takara) for lentiviral packaging to 70-85% confluency in DMEM Glutamax (+4.5 g/L D-glucose, - pyruvate) supplemented with 10% Fetal Bovine Serum (FBS)(Sigma), 1% G418 (Gibco), 1% Non-Essential Amino Acids (Thermo Fisher) and 1% HEPES (Biomol).", "For lentiviral production,... |
45,061 | Quick Protocol for Oligonucleotide Cleanup Using the Monarch® PCR & DNA Cleanup Kit (5 ?g) (NEB #T1030) | 1 | dx.doi.org/10.17504/protocols.io.bp9dmr26 | https://www.protocols.io/view/quick-protocol-for-oligonucleotide-cleanup-using-t-bp9dmr26 | New England Biolabs | TITLE: Quick Protocol for Oligonucleotide Cleanup Using the Monarch® PCR & DNA Cleanup Kit (5 ?g) (NEB #T1030)
AUTHORS: New England Biolabs
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Quick Protocol for Oligonucleotide Cleanup Using the Monarch® PCR & DNA Cleanup Kit (5 μg) (</span><a hre... | ["Add 100 μl DNA Cleanup Binding Buffer to the 50 μl sample.\n[DNA Cleanup Binding Buffer]\nWe recommend a sample volume of 50 μl. For smaller samples, adjust the volume with nuclease-free water.", "Add 300 μl ethanol (≥ 95%). Mix well by pipetting up and down or flicking the tube. Do not vortex.\n[Ethanol (≥ 95%)]", "... |
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