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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100,556 | IRIS Software Protocol | 0 | dx.doi.org/10.17504/protocols.io.3byl497wjgo5/v4 | https://www.protocols.io/view/iris-software-protocol-defk3bkw | Leonardo Zilli, Erica Andreose, Salvatore Di Marzo | TITLE: IRIS Software Protocol
AUTHORS: Leonardo Zilli, Erica Andreose, Salvatore Di Marzo
[DESCRIPTION]
We present a step-by-step methodology for tracking the coverage of the IRIS dataset in the OpenCitations Corpus.
The methodology filters the original IRIS dataset and the OpenCitations Meta and Index dumps, produci... | ["[IRIS Dataset Preparation] Make sure that the IRIS dump is present in the work directory.", "[Create iris_in_meta dataset] This step will create a version of the OpenCitations Meta dump that is transformed and filtered according to the elements in the IRIS dump. This new dataset is stored in a parquet format that mak... |
45,239 | Mask-Based Covid-19 testing system using Exhaled Breath Condensate | 4 | null | https://www.protocols.io/view/mask-based-covid-19-testing-system-using-exhaled-b-bqexmtfn | John Daniels | TITLE: Mask-Based Covid-19 testing system using Exhaled Breath Condensate
AUTHORS: John Daniels
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The DiagMetrics (fka Kinaptic) mask-based COVID-19 testing system uses a unique Exhaled Breath Collector (EBC) that converts breath to a liquid bio sample (... | ["Remove release liner from double stick tape on electronics", "Remove release liner from double sided tape on mask", "Pull tab to Activate Battery and Adhere electonics to mask", "Open APP on Smartphone", "Connect to Mask Electronics", "Put mask on and breath normally.", "Continue to breath normally", "Testing is Comp... |
30,800 | Relative viscosity | null | dx.doi.org/10.17504/protocols.io.babqiamw | null | Alison Lovegrove | TITLE: Relative viscosity
AUTHORS: Alison Lovegrove
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Lab protocol for: Relative viscosity measurement in wheat flour using a capillary viscometer.</div><div class = "text-block"><span>based on Saulnier et al. (1995) Journal of Cereal Science, </span><sp... | [] |
20,585 | Protocol for microCT inspection of Gallium particle accelerator targets | null | dx.doi.org/10.17504/protocols.io.ychfst6 | null | Muofhe Tshibalanganda, Anton du Plessis, Stephan le Roux, Paul Papka | TITLE: Protocol for microCT inspection of Gallium particle accelerator targets
AUTHORS: Muofhe Tshibalanganda, Anton du Plessis, Stephan le Roux, Paul Papka
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol described the steps used to inspect the Gallium targets used in particle accelera... | ["[Sample Mounting]\nLoad the sample on a foam (e.g. florist oasis) with prestik at top, but angled towards the flat side by up to 10 degrees. This is to reduce penetration artefacts - perfect vertical is not suggested.", "[Scanning settings]\nThis is using a General Electric VTomex L240 system, but most microCT system... |
84,843 | Best Practices for Ancient Rodent Midden Collection, Processing, and Curation | 1 | dx.doi.org/10.17504/protocols.io.4r3l224q4l1y/v1 | https://www.protocols.click/view/best-practices-for-ancient-rodent-midden-collectio-cw4jxgun | Camille A Holmgren, Angela D Hornsby, Katie M Becklin, Julio L. Betancourt, Francisca P Díaz, Angélica González, Claudio Latorre | TITLE: Best Practices for Ancient Rodent Midden Collection, Processing, and Curation
AUTHORS: Camille A Holmgren, Angela D Hornsby, Katie M Becklin, Julio L. Betancourt, Francisca P Díaz, Angélica González, Claudio Latorre
[DESCRIPTION]
As new midden researchers enter the field and new field campaigns are conducted, s... | ["[Introduction] Although there was some debate early on about the methods and assumptions of midden analysis, as well as differences with purpose of individual studies, the field has largely conformed to similar methods for field collection in the Americas, including subsampling, specimen processing, sorting, identifi... |
null | null | null | dx.doi.org/10.17504/protocols.io.fh6bj9e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><strong>Experiment purpose is to monitor the time-course of a large-scale infection of host cyanobacteria by phage under variable media conditions and obtain samples for proteomic and transcriptomic analysis.</strong></p>
<p> </p>
<p><strong>8 Hourly Timepoints: 0, 2, 4, 6, 8... | [] |
94,312 | Quantitative PCR, 384 well format | 4 | dx.doi.org/10.17504/protocols.io.yxmvm341bl3p/v1 | https://www.protocols.io/view/quantitative-pcr-384-well-format-c8cgzstw | Malu G Tansey | TITLE: Quantitative PCR, 384 well format
AUTHORS: Malu G Tansey
[DESCRIPTION]
Quantitative PCR, 384 well format
[STEPS]
SECTION: Procedure:
2. Place 8-tube PCR strips in PCR tube racks (each single tube runs 1 sample and 1 gene)
SECTION: Procedure:
3. Add 5 µl cDNA to the bottom of each tube, use 20 uL pipetor (keep ... | ["[Procedure:] Place 8-tube PCR strips in PCR tube racks (each single tube runs 1 sample and 1 gene)", "[Procedure:] Add 5 µl cDNA to the bottom of each tube, use 20 uL pipetor (keep on ice)", "[Procedure:] Add 25 µl (duplicates) or 35 µl (triplicates) of Sybr Mastermix to the 8-well tube (keep on ice)", "[Procedure:] ... |
61,620 | In Vitro B-galactosidase and B-hexosaminidase Activity Assay (Total Cell Lysate) | 4 | dx.doi.org/10.17504/protocols.io.kqdg3p8r7l25/v1 | https://www.protocols.io/view/in-vitro-b-galactosidase-and-b-hexosaminidase-acti-b8eurtew | Laura Smith | TITLE: In Vitro B-galactosidase and B-hexosaminidase Activity Assay (Total Cell Lysate)
AUTHORS: Laura Smith
[DESCRIPTION]
Synthetic substrate can be used at acidic pH (pH 4.1) to assess activity of lysosomal hydrolases, β-Galactosidase and β-Hexosaminidase. The substrate is cleaved by β-Galactosidase and β-Hexosamin... | ["[Reagents] Buffers: McIlvaine citrate–phosphate (MV), pH 5.4 \n\nSubstrates: \n- β-Galactosidase: 4-Methylumbelliferyl β-D-galactopyranoside (Sigma M1633)\n- β-hexosaminidase: 4-Methylumbelliferyl N-acetyl-β-D-glucosaminide (Sigma M2133):\n\nStandard:4–methylumbelliferone (MWt. 176) \n\nStopping solution:0.25 M glyci... |
null | null | null | dx.doi.org/10.17504/protocols.io.sdfea3n | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?. | ["Weigh 1 g of agar into flask and add 100 ml H2O.", "Melt the agar by heating in microwave. Keep an eye on it so that it does not boil over. Make certain that all of the agar is melted and that it has come to a rolling boil.", "While agar cools mash up approximately 100 ml of fruit in the beaker.", "When agar is cool... |
99,512 | Protocol to Investigate Factors Impacting Antimicrobial Stewardship (AMS) Implementation Before and During COVID-19 in Two Acute Care Settings to Fight Antimicrobial Resistance | 0 | dx.doi.org/10.17504/protocols.io.yxmvmenj9g3p/v1 | https://www.protocols.io/view/protocol-to-investigate-factors-impacting-antimicr-ddey23fw | Rasha Abdelsalam Elshenawy, Nkiruka Umaru, Zoe Aslanpour | TITLE: Protocol to Investigate Factors Impacting Antimicrobial Stewardship (AMS) Implementation Before and During COVID-19 in Two Acute Care Settings to Fight Antimicrobial Resistance
AUTHORS: Rasha Abdelsalam Elshenawy, Nkiruka Umaru, Zoe Aslanpour
[DESCRIPTION]
This protocol aims to investigate factors affecting the... | ["[Research project] This research project investigates AMS implementation before and during the COVID-19 pandemic. It includes three sequential studies (Figure 2). \n\nSystematic literature review: The first study was undertaken on the published information available in scientific journals and reports to obtain evid... |
39,634 | Modified 1D Native Barcoding genomic DNA protocol from the Temperton Lab (University of Exeter) | 4 | dx.doi.org/10.17504/protocols.io.bixskfne | https://www.protocols.io/view/modified-1d-native-barcoding-genomic-dna-protocol-bixskfne | Michael Henson, Ben Temperton, Cameron Thrash | TITLE: Modified 1D Native Barcoding genomic DNA protocol from the Temperton Lab (University of Exeter)
AUTHORS: Michael Henson, Ben Temperton, Cameron Thrash
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:left">Modified 1D Native Barcoding genomic DNA pro... | ["[DNA Fragmentation]\nLoad 46 μL of genomic DNA into a Covaris g-TUBE.", "[DNA Fragmentation]\nSpin the g-TUBE for 1 minute in an Eppendorf 5424 centrifuge.", "[DNA Fragmentation]\nInvert the tube and spin again for 1 minute.", "[DNA Fragmentation]\nTransfer volume to sterile 1.5 mL Eppendorf DNA LoBind tubes. *Pr... |
99,875 | 0.1M Phosphate Buffer | 1 | dx.doi.org/10.17504/protocols.io.q26g7b7w8lwz/v2 | https://www.protocols.io/view/0-1m-phosphate-buffer-ddsb26an | Allen Institute for Brain Science | TITLE: 0.1M Phosphate Buffer
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
This protocol is used to prepare 0.1M Phosphate Buffer. 0.1M Phosphate Buffer is used in the preparation of Sucrose solutions for cryoprotection.
Note: Research reported in this publication was supported by the National Institute Of... | [] |
37,168 | protocol child 2 18.05 | null | null | https://www.protocols.io/view/protocol-child-2-18-05-bgiqjudw | Mariia Guliakina | TITLE: protocol child 2 18.05
AUTHORS: Mariia Guliakina
[STEPS]
?. {"blocks":[{"key":"144l0","text":"test","type":"unstyled","depth":0,"inlineStyleRanges":[],"entityRanges":[],"data":[]}],"entityMap":[]} | ["{\"blocks\":[{\"key\":\"144l0\",\"text\":\"test\",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[],\"entityRanges\":[],\"data\":[]}],\"entityMap\":[]}"] |
18,023 | ChroDrip - ProteinA/G | null | dx.doi.org/10.17504/protocols.io.vufe6tn | null | David Frommholz, Nadine Stefanczyk, Alexandra Ehl | TITLE: ChroDrip - ProteinA/G
AUTHORS: David Frommholz, Nadine Stefanczyk, Alexandra Ehl
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Purification Guide for the Isolation of Antibodies with ChroDrip Columns by DALEX Biotech.</span></div><div class = "text-block">E... | ["[Load and Wash]\nAdd your sample to the top of the column and let it flow through by gravity.\nFor optimal binding and purity, the pH of the sample should be 7.5 - 8.5 and should contain 150 - 300 mM NaCl. An easy way to achieve this is by adding 1/11 volume 0.5 M Tris, 2 M NaCl (pH 8.0) to your sample.Removal of par... |
22,578 | Small-scale silencing experiment in vegetative Euplotes crassus (provisional) | null | dx.doi.org/10.17504/protocols.io.2asgaee | null | Rachele Cesaroni | TITLE: Small-scale silencing experiment in vegetative Euplotes crassus (provisional)
AUTHORS: Rachele Cesaroni
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. Grow RNAse III deficient E.coli strain HT115 in LB with antibiotic selection o/n at 37°C.
?. Prepare a 1:100 dilution of the bacterial culture, and ... | ["Grow RNAse III deficient E.coli strain HT115 in LB with antibiotic selection o/n at 37°C.", "Prepare a 1:100 dilution of the bacterial culture, and grow it at 37°C until it reaches an OD600 of 0.4.", "Add 0.4 mM IPTG, and induce RNA transcription from the L4440 plasmid in the bacteria o/n at 37°C.", "Collect the bact... |
null | null | null | dx.doi.org/10.17504/protocols.io.cpnvmd | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Guidelines for Primer Design for Restriction Enzyme Cloning (E6901)
[GUIDELINES]
<strong>Introduction<br /></strong><br />Appropriate restriction sites, absent in the target gene, are incorporated in the forward and reverse primers when a target gene is generated by PCR. T... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.rbvd2n6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><strong>Introduction</strong></p>
<p>Despite relevant evidence that supplemental oxygen therapy can be harmful to patients with myocardial injury, the association between hyperoxia and the clinical outcome of such patients has not been evaluated. We assessed whether early hyp... | [] |
96,713 | Stereotaxic α-Syn PFF injection into mouse striatum | 4 | dx.doi.org/10.17504/protocols.io.dm6gp34p1vzp/v1 | https://www.protocols.io/view/stereotaxic-syn-pff-injection-into-mouse-striatum-daph2dj6 | Ramhari Kumbhar, Hanseok Ko, Valina L. Dawson, Ted Dawson, Xiaobo Mao | TITLE: Stereotaxic α-Syn PFF injection into mouse striatum
AUTHORS: Ramhari Kumbhar, Hanseok Ko, Valina L. Dawson, Ted Dawson, Xiaobo Mao
[DESCRIPTION]
For stereotaxic injection of α-Syn PFF into the mouse striatum using 2-3 month old mice. This forked protocol has slight variations in anesthesia solution and injectio... | ["Anesthetize mice with a ketamine cocktail (ketamine 100mg/kg; xylazine 10mg/kg; i.p. or s.c.).", "Shave the animals’ skulls.", "Create a 1.5 cm incision in the scalp after cleaning the scalp with alcohol or betadine swabs.", "Retract the underlying fascia will and drill a hole in the skull.", "Insert a 26 gauge needl... |
59,923 | Water filtration with Zymo Bashing Bead tubes and DNA/RNA Shield reagent for subsequent DNA and RNA extraction from microbial communities | 4 | dx.doi.org/10.17504/protocols.io.eq2lyn6zrvx9/v1 | https://www.protocols.io/view/water-filtration-with-zymo-bashing-bead-tubes-and-b6rtrd6n | Christopher A Hempel | TITLE: Water filtration with Zymo Bashing Bead tubes and DNA/RNA Shield reagent for subsequent DNA and RNA extraction from microbial communities
AUTHORS: Christopher A Hempel
[DESCRIPTION]
Filtration of water samples with Zymo Bashing Bead tubes and DNA/RNA Shield reagent for subsequent DNA and RNA extraction from mic... | ["[Procedure] Sterilize forceps and scissors with burner, then bleach, then EtOH before each filtration", "[Procedure] Filter water sample, make sure to keep the filtration unit closed when opening the wrapping, to hold nothing but the sample over the unit, and to stand as far as possible away from the unit while it is... |
null | null | null | dx.doi.org/10.17504/protocols.io.dyq7vv | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p style="margin: 0in 0in 0pt; line-height: normal;"><span style="color: #3c3c39; font-family: 'Arial',sans-serif; font-size: 10pt;">This is a modified version of the DNA extraction methods published in:<br /> Rowan, R., & Powers, D.A. (1991) Molecular genetic identification... | [] |
73,221 | Fluorescent image acquisition and processing using Axiovert 200M microscope and ImageJ software | 1 | dx.doi.org/10.17504/protocols.io.ewov1o98plr2/v1 | https://www.protocols.io/view/fluorescent-image-acquisition-and-processing-using-cjrdum26 | Electra Brunialti, Alessandro Maria Villa, Paolo Ciana | TITLE: Fluorescent image acquisition and processing using Axiovert 200M microscope and ImageJ software
AUTHORS: Electra Brunialti, Alessandro Maria Villa, Paolo Ciana
[DESCRIPTION]
Fluorescent image acquisition and processing using Axiovert 200M microscope and ImageJ software to analyze morphological and dynamic chang... | ["[Step 1: Acquire live microglia images using Axiovert 200M microscope with dedicated software (AxioVision Rel 4.9, Zeiss)] Insert the cell culture plate in the microscope holder, and set chamber parameters: T 37°C and CO2 5%.", "[Step 1: Acquire live microglia images using Axiovert 200M microscope with dedicated soft... |
null | null | null | dx.doi.org/10.17504/protocols.io.jz7cp9n | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.n6adhae | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The ability to image RNA identity and location with nanoscale precision in intact tissues is of great interest for defining cell types and states in normal and pathological biological settings. Here, we present a strategy for expansion microscopy of RNA. We developed a small-... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.dsr6d5 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This brief protocol shows you how easy it is to get shRNA from demostrated siRNA sequence. With these self-designed shRNA, I've got more than 10 genes knockdown from mammalian cell lines, including mouse embryonic stem cells. Believe it or not, using siRNA sequence from Dharmaco... | [] |
82,118 | Statistical analysis | 1 | dx.doi.org/10.17504/protocols.io.36wgqjxeyvk5/v1 | https://www.protocols.click/view/statistical-analysis-cufewtje | carmela.giachino | TITLE: Statistical analysis
AUTHORS: carmela.giachino
[DESCRIPTION]
Statistics
[STEPS]
SECTION: Statistical Analyses
1. Statistics was carried out using GraphPad Prism Software Version 9 (GraphPad Software, San Diego, California, USA). Significance was calculated using the unpaired, two-tailed Student’s t-test; Two... | ["[Statistical Analyses] Statistics was carried out using GraphPad Prism Software Version 9 (GraphPad Software, San Diego, California, USA). Significance was calculated using the unpaired, two-tailed Student’s t-test; Two-way ANOVA, followed by Bonferroni-post hoc test, as appropriate."] |
7,076 | DNA extraction from frozen whole blood using the DNeasy Blood & Tissue kit (QIAGEN) | 1 | dx.doi.org/10.17504/protocols.io.i6cchaw | https://www.protocols.io/view/dna-extraction-from-frozen-whole-blood-using-the-d-i6cchaw | Luise A. Seeker, Jennifer Fairlie, Sarah L. Underwood, Rachael V. Wilbourn, Rebecca Holland, Daniel H. Nussey | TITLE: DNA extraction from frozen whole blood using the DNeasy Blood & Tissue kit (QIAGEN)
AUTHORS: Luise A. Seeker, Jennifer Fairlie, Sarah L. Underwood, Rachael V. Wilbourn, Rebecca Holland, Daniel H. Nussey
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Even though DNA extraction from whole bloo... | [] |
98,731 | Triparental mating with pSEVA protocol | 0 | dx.doi.org/10.17504/protocols.io.n92ldm4zol5b/v2 | https://www.protocols.io/view/triparental-mating-with-pseva-protocol-dcnj2vcn | Laura Gómez | TITLE: Triparental mating with pSEVA protocol
AUTHORS: Laura Gómez
[DESCRIPTION]
This process involves bacterial conjugation, where a conjugative plasmid found in one bacterial strain facilitates the transfer of a mobilizable plasmid from a second bacterial strain to a third bacterial strain.
In the method from our l... | ["[Insertion of he suicide plasmid by three partner conjugation] Inoculate cultures of strains:\n \nDONOR CC118λpir pSEVA Gm (10 μg/ml)\n \nHELPER E. coli 1047 pRK2013 Km (50 μg/ml) \n \nRECEIVER C. rodenti... |
40,215 | Ethanol precipitation of nucleic acids (microcentrifuge tubes) | 1 | null | https://www.protocols.io/view/ethanol-precipitation-of-nucleic-acids-microcentri-bjhxkj7n | Heather Etchevers | TITLE: Ethanol precipitation of nucleic acids (microcentrifuge tubes)
AUTHORS: Heather Etchevers
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This is a classic technique out of the molecular biologist's playbook of the 1980s, </span><span style = "font-weight:bold;font-style:italic;">Molecu... | ["[Salting-out]\nAdd 1/10 volume of 3M sodium acetate, pH 5.2 (or 1/2 volume of 5M ammonium acetate) relative to initial volume A. Mix.", "[Salting-out]\nAdd 2.5 volumes of 100% ethanol relative to the volume in Step 1. (= 2.5 * 1.1 *A)", "[Salting-out]\nMix and freeze overnight at -20°C. (My original comment on OWW: ... |
27,806 | SMARTerV4 (1x) Amplification for single-cell or single-nuclei RNASeq Protocol | null | dx.doi.org/10.17504/protocols.io.7d6hi9e | null | ZengU19 BRAIN grant | TITLE: SMARTerV4 (1x) Amplification for single-cell or single-nuclei RNASeq Protocol
AUTHORS: ZengU19 BRAIN grant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol to generate full-length cDNA from single cells, or nuclei, using Takara SMARTer V4.</div></div>
[STEPS] | [] |
70,550 | The role of artificial contact materials in experimental use-wear studies - "artificial vs. natural experiment" | 1 | dx.doi.org/10.17504/protocols.io.eq2lyn91pvx9/v2 | https://www.protocols.io/view/the-role-of-artificial-contact-materials-in-experi-cg5wty7e | Lisa Schunk, Walter Gneisinger, Ivan Calandra, Joao Marreiros | TITLE: The role of artificial contact materials in experimental use-wear studies - "artificial vs. natural experiment"
AUTHORS: Lisa Schunk, Walter Gneisinger, Ivan Calandra, Joao Marreiros
[DESCRIPTION]
The sequential "artificial vs. natural experiment" described here aimed at investigating use-wear formatio... | ["[Sample preparation] Standardised tools \n\n12 x 60 ° \n12 x 60 °", "[Sample preparation] Raw material \n\nBaltic flint: \nSouthern Sweden (secondary deposit):\n \n\nSilicified schist: \nBalver Höhle (secondary deposit) \n \nBuhlen (secondary deposit)", "[Sample preparation] Blanks\n\nRaw material nodules (step #... |
28,162 | Beyond Persuasion: Evidence Type Affects Impressions of a Message Source | null | dx.doi.org/10.17504/protocols.io.7rahm2e | null | Jenna Clark, Melanie C. Green, Joseph J. P. Simons | TITLE: Beyond Persuasion: Evidence Type Affects Impressions of a Message Source
AUTHORS: Jenna Clark, Melanie C. Green, Joseph J. P. Simons
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Persuasion research often focuses on how source characteristics affect attitude change in response to a message;... | ["[Study 1a]\nParticipants accessed the survey online via Qualtrics.They were asked to read a vignette in which the target solicits advice on a topic and the source provides an argument that is either narrative or statistical, and rate this vignette on multiple dimensions.Participants then completed competence and warm... |
83,405 | DNA Barcoding Protocol for Darwin Tree of Life at The Natural History Museum of London | 4 | dx.doi.org/10.17504/protocols.io.8epv5x7qjg1b/v1 | https://www.protocols.click/view/dna-barcoding-protocol-for-darwin-tree-of-life-at-cvpmw5k6 | Jordan Beasley | TITLE: DNA Barcoding Protocol for Darwin Tree of Life at The Natural History Museum of London
AUTHORS: Jordan Beasley
[DESCRIPTION]
This protocol outlines the DNA barcoding process at the Natural History Museum of London (NHM) for the Darwin Tree of Life project (DToL). DNA barcoding is used as part of the species ide... | ["[DNA Extraction] Spin down the sample plate and inspect to check no tissue/sample is stuck in the lids of the sealing caps.", "[DNA Extraction] Remove the caps and remove the ethanol. Use a single channel pipette for very small samples and take care to ensure the sample is not aspirated into the tip and removed with ... |
79,526 | Soluble and insoluble A-SYN fractionation | 1 | dx.doi.org/10.17504/protocols.io.rm7vzbrn2vx1/v1 | https://www.protocols.io/view/soluble-and-insoluble-a-syn-fractionation-crwev7be | michela.deleidi, Hariam Raji, Federico Bertoli | TITLE: Soluble and insoluble A-SYN fractionation
AUTHORS: michela.deleidi, Hariam Raji, Federico Bertoli
[DESCRIPTION]
Soluble/insoluble alpha-synuclein fractionation is a technique used to separate different forms of the alpha-synuclein protein based on their solubility properties.
[STEPS]
SECTION: Soluble and ins... | ["[Soluble and insoluble A-SYN fractionation] Perform extraction and detection of Triton-soluble (T-sol) and Triton-insoluble (T-insol) alpha-synuclein as described in Stojkovska and Mazzulli(2021).", "[Soluble and insoluble A-SYN fractionation] Lyse individual organoids in 1% Triton X-100 extraction buffer supplemente... |
68,051 | Electron microscope sample preparation technique_V2 | 4 | dx.doi.org/10.17504/protocols.io.14egn75zmv5d/v1 | https://www.protocols.io/view/electron-microscope-sample-preparation-technique-v-cepttdnn | Wai Kit Lam (Leo) | TITLE: Electron microscope sample preparation technique_V2
AUTHORS: Wai Kit Lam (Leo)
[DESCRIPTION]
There are eight main steps in preparing EM sample, including fixation, en bloc staining, agarose embedding, dehydration, infiltration, resin embedding, resin-embedded sample trimming and ultrathin sectioning.
This EM... | ["[Fixation] Aspirate cell culture media then fix cells with pre-warmed phosphate-buffered 4% Paraformaldehyde (PFA) at Room temperature for 60 min.", "[Fixation] Wash cells twice with 0.1 Molarity (M) sodium-cacodylate (NaCac) pH 7.4 buffer.", "[Fixation] Post-fix the sample with 2.5 1498 glutaraldehyde in 0.1 Molarit... |
89,412 | Troubleshooting guide for DDNS | 3 | dx.doi.org/10.17504/protocols.io.yxmvm3w25l3p/v1 | https://www.protocols.io/view/troubleshooting-guide-for-ddns-c3jcykiw | Joyce Akello, Alex Shaw, Catherine Troman, Erika Bujaki, Manasi Majumdar, Aine.OToole, c.ansley, Zoe Vance, rachel.colquhoun, Andrew Rambaut, Javier Martin, Nick Grassly | TITLE: Troubleshooting guide for DDNS
AUTHORS: Joyce Akello, Alex Shaw, Catherine Troman, Erika Bujaki, Manasi Majumdar, Aine.OToole, c.ansley, Zoe Vance, rachel.colquhoun, Andrew Rambaut, Javier Martin, Nick Grassly
[DESCRIPTION]
This document provides general guidance for troubleshooting problems encountered in the... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.drv565 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<span class="cit-title">This protocols is from:<br /></span><span class="cit-auth cit-auth-type-author">Linlin Yin</span><span class="cit-sep cit-sep-separator">, et al.</span><span class="cit-auth cit-auth-type-author"> (2015) <a href="http://www.genetics.org/content/200/2/431.... | [] |
37,678 | Guide RNA Library Transduction of Cas9 Cancer Cell Lines | 1 | dx.doi.org/10.17504/protocols.io.bg2njyde | https://www.protocols.io/view/guide-rna-library-transduction-of-cas9-cancer-cell-bg2njyde | Verity Goodwin, Emily Souster, Charlotte Beaver, Adam Jackson, Rizwan Ansari, Mathew Garnett, Fiona Behan | TITLE: Guide RNA Library Transduction of Cas9 Cancer Cell Lines
AUTHORS: Verity Goodwin, Emily Souster, Charlotte Beaver, Adam Jackson, Rizwan Ansari, Mathew Garnett, Fiona Behan
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is for the whole-genome CRISPR screening of stably expressi... | ["[Day 1: Transduction]\nDetach and collect cas9 cells as per protocol \"Passaging adherent cancer cell lines\" steps 1-8 found here: https://protocols.io/view/passaging-adherent-cancer-cell-lines-bgtbjwin.html", "[Day 1: Transduction]\nDilute the gRNA library if required, in complete media. The defrosted library shoul... |
82,027 | MR imaging of the mouse hindlimb musculature (T2 weighted and T2 map) | 4 | dx.doi.org/10.17504/protocols.io.261ge4z1ov47/v2 | https://www.protocols.io/view/mr-imaging-of-the-mouse-hindlimb-musculature-t2-we-cucjwsun | Emily Waters | TITLE: MR imaging of the mouse hindlimb musculature (T2 weighted and T2 map)
AUTHORS: Emily Waters
[DESCRIPTION]
This is a procedure for imaging the musculature in the hind limb of a mouse. The protocol was designed for imaging of edema in mouse models of muscular damage, but could be adapted to other applications.
[... | ["[Prepare mouse for imaging] Place mouse in an induction chamber and induce anesthesia using 3% isoflurane and 1 L/min O2. The induction chamber should be placed on a warm water circulating blanket set at 37ºC to maintain the mouse's body temperature. Use a charcoal canister to collect waste gases from the induction c... |
69,087 | Measurement of vaginal temperatures in cows using the Thermochron iButton® and CIDR | 4 | dx.doi.org/10.17504/protocols.io.n2bvj65kblk5/v1 | https://www.protocols.io/view/measurement-of-vaginal-temperatures-in-cows-using-cfp7tmrn | Laura M. Jensen, Serdal Dikmen, Camila J Cuellar, Peter J Hansen | TITLE: Measurement of vaginal temperatures in cows using the Thermochron iButton® and CIDR
AUTHORS: Laura M. Jensen, Serdal Dikmen, Camila J Cuellar, Peter J Hansen
[DESCRIPTION]
A protocol for measurement of vaginal temperature in female cattle using the iButton datalogger and CIDR intravaginal device is described.
... | [] |
54,607 | In vitro transcription of guide RNAs and 5'-triphosphate removal | 1 | dx.doi.org/10.17504/protocols.io.n2bvjyp5vk5w/v13 | https://www.protocols.io/view/in-vitro-transcription-of-guide-rnas-and-5-triphos-bzjpp4mn | Mark Dewitt, Julia Wong, Beeke Wienert, Moritz F Schlapansky | TITLE: In vitro transcription of guide RNAs and 5'-triphosphate removal
AUTHORS: Mark Dewitt, Julia Wong, Beeke Wienert, Moritz F Schlapansky
[DESCRIPTION]
sgRNA template assembly, in vitro T7 transcription, and sgRNA column cleanup to remove 5'-triphosphate groups
[GUIDELINES]
The primers used are: one long, variab... | ["[Design sgRNA and order PCR oligos.] Add the desired protospacer sequence to the T7FwdVarV2 oligo and order the oligo from your favorite oligonucleotide supplier. There are many programs available for protospacer design that attempt to optimize on- and/or off-target activity. Which program is most useful depends upon... |
12,969 | 18S and 16S rRNA genes amplicon generation for eukaryotic and prokaryotic metabarcoding | null | dx.doi.org/10.17504/protocols.io.qwhdxb6 | null | Adriana Alberti, Julie Poulain, Stefan Engelen, Karine Labadie, Sarah Romac, Isabel Ferrera, Guillaume Albini, Jean-Marc Aury, Caroline Belser, Alexis Bertrand, Corinne Cruaud, Corinne Da Silva, Carole Dossat, Frédéric Gavory, Shahinaz Gas, Julie Guy, Maud Haquelle, E'krame Jacoby, Olivier Jaillon, Arnaud Lemainque, E... | TITLE: 18S and 16S rRNA genes amplicon generation for eukaryotic and prokaryotic metabarcoding
AUTHORS: Adriana Alberti, Julie Poulain, Stefan Engelen, Karine Labadie, Sarah Romac, Isabel Ferrera, Guillaume Albini, Jean-Marc Aury, Caroline Belser, Alexis Bertrand, Corinne Cruaud, Corinne Da Silva, Carole Dossat, Frédé... | ["Please select from the following two cases: 1. Eukaryotic 18S rRNA gene amplicon generation (Method ID: 18S_PCR)2. Prokaryotic 16S rRNA gene amplicon generation (Method ID: 16S_PCR)", "[18S_PCR]\nFor generation of 18S barcodes, perform PCR amplifications with the Phusion High Fidelity PCR Master Mix with GC buffer (T... |
85,246 | Parse Evercode Fixation Protocol v2.1.1 for cells or nuclei -- University of Minnesota TMCs | 1 | dx.doi.org/10.17504/protocols.io.x54v9pj9qg3e/v1 | https://www.protocols.io/view/parse-evercode-fixation-protocol-v2-1-1-for-cells-cxg6xjze | Parse Biosciences, Laura J Niedernhofer, David A Bernlohr | TITLE: Parse Evercode Fixation Protocol v2.1.1 for cells or nuclei -- University of Minnesota TMCs
AUTHORS: Parse Biosciences, Laura J Niedernhofer, David A Bernlohr
[DESCRIPTION]
https://www.parsebiosciences.com/products/evercode-whole-transcriptome
Fixation for Parse Evercode sc/snRNAseq
Includes details for both ... | [] |
87,461 | Quantitative Immunoblotting Analysis of LRRK2 Signalling Pathway | 4 | dx.doi.org/10.17504/protocols.io.ewov14znkvr2/v2 | https://www.protocols.io/view/quantitative-immunoblotting-analysis-of-lrrk2-sign-czndx5a6 | Francesca Tonelli, Dario Alessi | TITLE: Quantitative Immunoblotting Analysis of LRRK2 Signalling Pathway
AUTHORS: Francesca Tonelli, Dario Alessi
[DESCRIPTION]
Accurate, quantitative analysis of protein expression and modifications (such as phosphorylation) is critical when studying cell signalling. Here we describe our method for efficient immunoblo... | ["[Preparation of lysates] Please choose the relevant method for preparation of lysate: \nPreparation of lysates from cultured cells\nPreparation of lysates from mouse tissues", "[Preparation of lysates] Quickly wash cells in the tissue culture dish by carefully pouring Room temperature that the cells are currently gro... |
null | null | null | dx.doi.org/10.17504/protocols.io.tppemmn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Sample collection and culture
Aquatic plant samples were collected from habitats across the USA and a sediment sample from Australia (Tables S1.1, S1.2). Limnias melicerta and L. ceratophylli were identified and isolated from rehydrated sediments or by removing a piece of vegeta... | [] |
40,719 | Visualisation of bacteria around roots | 4 | dx.doi.org/10.17504/protocols.io.bjzpkp5n | https://www.protocols.io/view/visualisation-of-bacteria-around-roots-bjzpkp5n | Andreea S | TITLE: Visualisation of bacteria around roots
AUTHORS: Andreea S
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is carried out to observe the growth of the bacterial biofilm along with the roots in the rhizosphere. In the paper by Bennett, R. and Lynch, J (1981), they inoculated the p... | ["[Removal of roots and bacterial counts]\nCarefully remove the roots from the soil.", "[Removal of roots and bacterial counts]\nDivide the roots into three portions: a) 0 to 2 cm from the tip; b) 2 to 4 cm from the tip; and c) 4 cm from the tip to the seed.", "[Removal of roots and bacterial counts]\nPlace each sample... |
108,075 | The perfect slice - Cutting bread made easy | 0 | null | https://www.protocols.io/view/the-perfect-slice-cutting-bread-made-easy-dmsj46cn | Bread Pitt, Rye-an Reynolds, Crumbelina Jolie, Elon Crust | TITLE: The perfect slice - Cutting bread made easy
AUTHORS: Bread Pitt, Rye-an Reynolds, Crumbelina Jolie, Elon Crust
[DESCRIPTION]
Bread cutting, while seemingly simple, is an art that embodies both precision and mindfulness. "Cutting bread is the simplest form of precision, where a steady hand meets the resistance ... | ["[Prepare to cut] Gather Your Tools: a serrated bread knife (aka \"Loaf Saber\"), a sturdy wooden cutting board, a nice loaf of bread, and a piece of cloth for crum control", "[Prepare to cut] Make sure your bread is at room temperature. Warm bread will squish under pressure, like a marshmallow in a vice. If you’re de... |
65,655 | OMS Atlas OCT Spatial Mapping | 1 | null | https://www.protocols.io/view/oms-atlas-oct-spatial-mapping-cccxssxn | Brett Johnson, Danielle Galipeau, George Thomas | TITLE: OMS Atlas OCT Spatial Mapping
AUTHORS: Brett Johnson, Danielle Galipeau, George Thomas
[DESCRIPTION]
This protocol describes the procedure by which the OMS Atlas serially sections an OCT block, prepares the resulting slides and samples, and then distributes the specimens for downstream analysis.
[BEFORE_S... | ["[Preparation] Verify the identity of the OCT block to be cut against written request for sectioning.", "[Preparation] Remove OCT block from -80 °C freezer and acclimate to cryostat (-20 °C ) for minimum of 180 min.", "[Preparation] Label all slides and cryotubes with a unique BEMS ID and Part#, corresponding to the w... |
55,789 | Quantification of SARS-CoV-2 variant mutations (HV69-70, E484K/N501Y, del156-157/R158G, and Del143-145) in settled solids using digital RT-PCR | 1 | dx.doi.org/10.17504/protocols.io.b2qmqdu6 | https://www.protocols.io/view/quantification-of-sars-cov-2-variant-mutations-hv6-b2qmqdu6 | Bridgette Hughes, Bradley J. White, Marlene K. Wolfe, Krista Wigginton, Alexandria B B Boehm | TITLE: Quantification of SARS-CoV-2 variant mutations (HV69-70, E484K/N501Y, del156-157/R158G, and Del143-145) in settled solids using digital RT-PCR
AUTHORS: Bridgette Hughes, Bradley J. White, Marlene K. Wolfe, Krista Wigginton, Alexandria B B Boehm
[DESCRIPTION]
This process instruction describes the steps for q... | ["[Preparation] Retrieve all kit components from the One-Step RT-ddPCR advanced kit for probes from the -20 °C freezer and thaw the components on ice.", "[Preparation] Retrieve ddPCR positive control aliquots (50 copies per uL gRNA) from the -80 °C freezer and thaw on ice", "[Preparation] For re-running frozen plates o... |
null | null | null | dx.doi.org/10.17504/protocols.io.ds66hd | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This is a collection of protocols from:<br /><span class="cit-title"><span class="cit-auth cit-auth-type-author">Paix A</span><span class="cit-sep cit-sep-separator">,</span><span class="cit-auth cit-auth-type-author"> Folkmann A</span><span class="cit-sep cit-sep-separator">,</... | [] |
89,657 | A novel method for the isolation of single cells mimicking circulating tumour cells adhered on Smart Bio Surface slides by Laser Capture Microdissection | 4 | null | https://www.protocols.io/view/a-novel-method-for-the-isolation-of-single-cells-m-c3szynf6 | Grazia Visci, Doron Tolomeo, Angelo Lonoce, Aram Arshadi, Lorenzo Bascetta, Gianluca Trotta, Margot van Riel, Joris Robert Vermeesch, Roberta Carbone, Clelia Tiziana Storlazzi | TITLE: A novel method for the isolation of single cells mimicking circulating tumour cells adhered on Smart Bio Surface slides by Laser Capture Microdissection
AUTHORS: Grazia Visci, Doron Tolomeo, Angelo Lonoce, Aram Arshadi, Lorenzo Bascetta, Gianluca Trotta, Margot van Riel, Joris Robert Vermeesch, Roberta Carbone, ... | ["[Preparation of spiked-in samples] Collect healthy donor blood, after discarding the first 3 mL of the blood draw to minimize keratinocyte contamination.", "[Preparation of spiked-in samples] Process blood samples with red blood cell lysis through ammonium chloride buffer.\n\nAmmonium chloride buffer\n NH4Cl 0.... |
null | null | null | dx.doi.org/10.17504/protocols.io.g4xbyxn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p style="text-align: center;"><img style="display: block; margin-left: auto; margin-right: auto;" src="https://s3.amazonaws.com/pr-journal/hnnfjtn.png" width="100" height="90" data-src="https://s3.amazonaws.com/pr-journal/hnnfjtn.png" data-ofn="nehirarma-üst-Tr.png" /> </p>
<p... | [] |
45,238 | Radiolabeled lipid extraction protocol | 4 | null | https://www.protocols.io/view/radiolabeled-lipid-extraction-protocol-bqewmtfe | Elizabeth Fozo | TITLE: Radiolabeled lipid extraction protocol
AUTHORS: Elizabeth Fozo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Radiolabeled - Lipid Extraction Protocol for </span><span style = "font-style:italic;">Enterococcus faecalis</span></div></div>
[STEPS]
?. [Radiolabeled - Lipid Extraction Pro... | ["[Radiolabeled - Lipid Extraction Protocol for Enterococcus faecalis]\nGrow a large culture of cells (suggest 35 mL per condition) in the lab as normal.", "[Radiolabeled - Lipid Extraction Protocol for Enterococcus faecalis]\nOnce cells have reached mid-log, harvest 5mL of culture (no fatty acid added yet!) and place ... |
83,290 | Catalepsy test (Bar test) | 1 | dx.doi.org/10.17504/protocols.io.36wgq3ryolk5/v1 | https://www.protocols.click/view/catalepsy-test-bar-test-cvj2w4qe | Chuyu Chen | TITLE: Catalepsy test (Bar test)
AUTHORS: Chuyu Chen
[DESCRIPTION]
The catalepsy test (bar test) was developed to test motor coordination and motor impairments.
[STEPS]
2. The time during which each mouse maintained the position was recorded up to a maximum of 3 minutes for three trials
1. Mice were gently removed fr... | ["The time during which each mouse maintained the position was recorded up to a maximum of 3 minutes for three trials", "Mice were gently removed from their home cage by their tail and their forepaws were placed over a horizontal bar, 0.2 cm in diameter and fixed at a height of 4 cm above the working surface.", "Averag... |
null | null | null | dx.doi.org/10.17504/protocols.io.dzt76m | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
For use in <a href="https://www.protocols.io/view/Viral-and-bacterial-isolates-propagation-and-prepa-dzs76d" target="_blank">Viral and bacterial isolates, propagation and preparation of stocks</a>.
[STEPS]
?.
?.
?.
?. | [] |
27,069 | BCA Assay for protein quantification | null | dx.doi.org/10.17504/protocols.io.6n5hdg6 | null | Karina Conkrite | TITLE: BCA Assay for protein quantification
AUTHORS: Karina Conkrite
[STEPS]
?. Use provided 0.2% BSA for creating a standard curve: Dilute amount necessary for the assay 1:2 using lysis buffer
?. Label tubes (1.5 mL Eppendorf) for standards. Final Conc ug/mL Volume 0.1% BSA Volume buffer Standard (ug) ... | ["Use provided 0.2% BSA for creating a standard curve: Dilute amount necessary for the assay 1:2 using lysis buffer", "Label tubes (1.5 mL Eppendorf) for standards. Final Conc ug/mL\t\tVolume 0.1% BSA\t\tVolume buffer Standard (ug)\t Volume 0.1% BSA (uL) Volume buffer(uL) 0\t ... |
86,295 | Mouse Behavior - Open Field and T-Maze | 4 | dx.doi.org/10.17504/protocols.io.eq2lyj7rqlx9/v1 | https://www.protocols.io/view/mouse-behavior-open-field-and-t-maze-cyhxxt7n | Robert Edwards, Shweta Jain | TITLE: Mouse Behavior - Open Field and T-Maze
AUTHORS: Robert Edwards, Shweta Jain
[DESCRIPTION]
This protocol describes two behavioral tasks for mice. The first is the Open Field Test, which is used to asses motor behavior, and the second is the T-Maze, which is used to assess spatial learning.
[STEPS]
SECTION: Open... | ["[Open Field Behavior] On each behavior day, bring mice in their home cages to the behavioral area. Blind experimenter to all test variables (e.g. genotype, drug condition, etc.).", "[Open Field Behavior] On days 1 and 2, habituate mice to an open field chamber (clear acrylic cylinder, 25 cm diameter) by placing them ... |
27,733 | UC Davis - Basic Adipocyte Culture Protocol | null | dx.doi.org/10.17504/protocols.io.7bvhin6 | null | K.C. Kent Lloyd | TITLE: UC Davis - Basic Adipocyte Culture Protocol
AUTHORS: K.C. Kent Lloyd
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">Basic Adipocyte Culture Protocol</div></div>
[STEPS]
?. Day Before Preparation: Make phosphat... | ["Day Before Preparation: Make phosphate-hepes buffer (instructions posted on chem shelf or last page of this document). Prepare and autoclave supplies: Nalgene incubation jars (30 ml for mice--Fisher 02-925-1a), nytex filters (250 um PGC 34-1800-03, 450 um for subcutaneous depot PGC 34-1800-09), long needles (+6—Fish... |
69,014 | Loading Syringes to Inject into Microfluidics Device | 1 | dx.doi.org/10.17504/protocols.io.e6nvwkxy2vmk/v1 | https://www.protocols.io/view/loading-syringes-to-inject-into-microfluidics-devi-cfmwtk7e | freeman.lan | TITLE: Loading Syringes to Inject into Microfluidics Device
AUTHORS: freeman.lan
[DESCRIPTION]
Protocol for loading syringes with small amounts of liquid sample for injection into droplet microfluidic devices.
[STEPS]
SECTION: Preparing Syringes
1. Take out a syringe
Add 27g needle to the syringe
SECTION: Prep... | ["[Preparing Syringes] Take out a syringe \n \nAdd 27g needle to the syringe", "[Preparing Syringes] Use the needle and syringe to draw out approximately 200 µL of", "[Preparing Syringes] Cut approximately 20 centimeters of with a razor and attach it to the needle tip.", "[Loading the Syringe] Push the syringe so tha... |
35,629 | Pillowcase & rubber band DIY face mask | null | dx.doi.org/10.17504/protocols.io.be2mjgc6 | null | Jernej Turnsek | TITLE: Pillowcase & rubber band DIY face mask
AUTHORS: Jernej Turnsek
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:left">This protocol describes a very simple way to make a face mask at home using a cotton pillowcase, a (coffee) filter, 2 rubber bands, a... | ["[Assemble]\nBegin with a ~14 inch x ~20 inch (~36 cm x ~51 cm) pillowcase piece, a coffee filter, and 2 rubber bands.", "[Assemble]\nFold twice along the longer edge; sandwich a coffee filter between layers of fabric.Tip: alternative (more effective) DIY filter options (source):1/ HEPA vacuum filters and bags (make s... |
84,586 | A pragmatic approach to neuropsychological assessment for clinical treatment in smoking cessation. | 1 | dx.doi.org/10.17504/protocols.io.e6nvwd9rzlmk/v1 | https://www.protocols.click/view/a-pragmatic-approach-to-neuropsychological-assessm-cwuixeue | Raquel Martín-Ríos | TITLE: A pragmatic approach to neuropsychological assessment for clinical treatment in smoking cessation.
AUTHORS: Raquel Martín-Ríos
[DESCRIPTION]
Smoking is a psycho-organic disorder characterised by a compulsive urge to smoke despite the negative effects of such abuse. Such addictive behaviour constitutes one of th... | ["[Objective] Promote a protocol for assessing executive functioning in chronic smokers based on a selection of neuropsychological tasks that assess the executive functions of inhibition, updating and change/flexibility.", "[Objective] Based on previous research, we designed a protocol to assess executive function in s... |
44,808 | RNA Integrity Check | 4 | null | https://www.protocols.io/view/rna-integrity-check-bpzgmp3w | Elizabeth Fozo | TITLE: RNA Integrity Check
AUTHORS: Elizabeth Fozo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">RNA Integrity Check: Modification of Protocol from Qiagen</div></div>
[STEPS]
?. [RNA Integrity Check]
Determine the concentration of RNA; ideally want to run approximately of RNA on the gel (should... | ["[RNA Integrity Check]\nDetermine the concentration of RNA; ideally want to run approximately of RNA on the gel (should be about of your sample)\n1 µg\n1 µl", "[RNA Integrity Check]\nSpray gel tray, comb, damns, and a small flask with RNAse Zap.", "[RNA Integrity Check]\nFor small gels, melt 0.3 grams of RNA ONLY ... |
79,670 | Reto F1016B.201.01 | 1 | dx.doi.org/10.17504/protocols.io.x54v9d42zg3e/v1 | https://www.protocols.io/view/reto-f1016b-201-01-cr2wv8fe | Natalia Gámez, Diego Zazueta Acosta | TITLE: Reto F1016B.201.01
AUTHORS: Natalia Gámez, Diego Zazueta Acosta
[DESCRIPTION]
-Armar un circuito RC
-Medir el tiempo de carga del capacitor
-Obtener mediciones e importarlas a matlab para compararlas con nuestro modelo matematico simulado
[STEPS]
SECTION: Traducir el valor de las resistencias
1. Se necesita... | ["[Traducir el valor de las resistencias] Se necesita traducir los Ohms (Ω) que nos dan cierta combinacion de colores en las resistencias para así saber cual debemos utilizar. \nPuedes encontrar una imagen en internet que te diga cuanto vale cada banda de color, en nuestro caso utilizamos el siguiente sitio web:\nhttps... |
null | null | null | dx.doi.org/10.17504/protocols.io.ez2bf8e | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
<p><strong>Application Notes </strong></p>
<p> </p>
<p>1. Activated cell populations can be prepared from in vivo-stimulated tissues or from in vitro-stimulated cultures (e.g., antigen-specific activation or mitogen-induced). For cytokine and chemokine detection, it is critical t... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.mcbc2sn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Preparation of yeast-malt-sucrose-agar, that is used as solid media for growing <em>Zt.</em> This is called 'YMA' in Bruce McDonald lab, althoug the same acronym is used also for different media.<br /><br />Have a look for example: Zain, M. E., et al. 'Influence of growth me... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.dmz475 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?. | [] |
70,338 | Live-cell imaging: Mitochondria membrane potential | 1 | dx.doi.org/10.17504/protocols.io.e6nvwj997lmk/v1 | https://www.protocols.io/view/live-cell-imaging-mitochondria-membrane-potential-cgxatxie | gurvir.virdi, mineechoi | TITLE: Live-cell imaging: Mitochondria membrane potential
AUTHORS: gurvir.virdi, mineechoi
[DESCRIPTION]
Mitochondrial membrane potential is the electrogenic potential between the inner membrane and matrix of mitochondria which, in combination with the mitochondrial pH gradient, provides the force to drive protons int... | ["Cells were washed 2x with HBSS (Invitrogen)", "They are then incubated w 25 nM tetramethylrhodamine methyl ester (TMRM, Thermo Fisher Scientific) in HBSS for 40 min at Room temperature.", "After 40 minutes, confocal microscope imaging is performed in the presence of TMRM (in HBSS); the 560 nm laser was used to excite... |
null | null | null | dx.doi.org/10.17504/protocols.io.j9dcr26 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Diet-induced obesity by administration of a western-type diet high in fat and sugar to mice may result in an elevation of plasma total and LDL-cholesterol levels, triglycerides and the levels of the liver enzymes alkaline phosphatases and aspartate (AST) and alanine aminotran... | [] |
75,343 | High Throughput Ligand Interaction Profiler | 5 | dx.doi.org/10.17504/protocols.io.4r3l27njqg1y/v1 | https://www.protocols.io/view/high-throughput-ligand-interaction-profiler-cmtpu6mn | Akshay Uttarkar, Shreyagirish09, Vidya Niranjan | TITLE: High Throughput Ligand Interaction Profiler
AUTHORS: Akshay Uttarkar, Shreyagirish09, Vidya Niranjan
[DESCRIPTION]
High Throughput Ligand Interaction Profiler (HT-LIP) is a web-based tool that runs on Google Colab, which allows users to predict ligand-protein interactions. HT-LIP can be used to screen large ch... | ["[Prepare the Google Drive] In your Google Drive home directory, create a new folder called “data”. Inside this folder, add 3 files.\n(a) protein: in PDB format\n(b) ligand: in SDF format\n(c) reference ligand: in PDB format\n\nFor example, the data folder created here, have files with the following names :\n(a) prote... |
null | null | null | dx.doi.org/10.17504/protocols.io.ew8bfhw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol describes how the parasitic flatworms (S. solidus) were cultured in the lab for:<br /><br /><em><span style="color: #222222; font-family: arial, sans-serif; font-size: 12.8px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; li... | [] |
101,115 | Purification of GST-WIPI1/WIPI2d/WIPI3/WIPI4 | 0 | dx.doi.org/10.17504/protocols.io.n2bvjnnqxgk5/v1 | https://www.protocols.io/view/purification-of-gst-wipi1-wipi2d-wipi3-wipi4-dey33fyn | Elias Adriaenssens | TITLE: Purification of GST-WIPI1/WIPI2d/WIPI3/WIPI4
AUTHORS: Elias Adriaenssens
[DESCRIPTION]
This protocol details the purification of GST-tagged WIPI1/2d/3/4.
[STEPS]
SECTION: Purification procedure
1. To purify GST-WIPI1/GST-WIPI2/GST-WIPI3/GST-WIPI4, we express the GST-tagged WIPI1/2d/3/4 from a pCAG backbone enc... | ["[Purification procedure] To purify GST-WIPI1/GST-WIPI2/GST-WIPI3/GST-WIPI4, we express the GST-tagged WIPI1/2d/3/4 from a pCAG backbone encoding GST-TEV-WIPI1/2/3/4 (available from Addgene).", "[Purification procedure] Store the proteins at -80 °C.", "[Purification procedure] Wash the beads twice with wash buffer, on... |
90,814 | CRISPR knock-in (endogenous tagging) | 1 | dx.doi.org/10.17504/protocols.io.e6nvwdmqwlmk/v1 | https://www.protocols.io/view/crispr-knock-in-endogenous-tagging-c4w6yxhe | Leonardo A Parra-Rivas | TITLE: CRISPR knock-in (endogenous tagging)
AUTHORS: Leonardo A Parra-Rivas
[DESCRIPTION]
CRISPR knock-in (endogenous tagging)
[STEPS]
SECTION: Plasmid construction
1.
For the C-terminus knock-in experiment, the sgRNAs and the homology-independent donor templates were generated
following strategies similar to tho... | ["[Plasmid construction] For the C-terminus knock-in experiment, the sgRNAs and the homology-independent donor templates were generated\nfollowing strategies similar to those described previously \n \nBriefly, the coding sequence of SNCA1 –the gene encoding α-syn at exon 6 was targeted by a sgRNA, and the oScarlet tag ... |
96,723 | ECIS Data Analysis for Stimulation of Human Pulmonary Microvascular Endothelial Cells (HPMECs) with Human Serum | 4 | dx.doi.org/10.17504/protocols.io.bp2l69erklqe/v5 | https://www.protocols.io/view/ecis-data-analysis-for-stimulation-of-human-pulmon-dapt2dnn | Michael Bokoch | TITLE: ECIS Data Analysis for Stimulation of Human Pulmonary Microvascular Endothelial Cells (HPMECs) with Human Serum
AUTHORS: Michael Bokoch
[DESCRIPTION]
Sera from patients in our UCSF Liver Transplant Biobank are used to stimulate human pulmonary microvascular endothelial cells (HPMECs) grown to confluency on ECIS... | ["[ECIS Data Analysis for HPMEC stimulation by Liver Biobank Sera] Determine Difference in Area-under-the-Curve (Normalized Resistance at 4000 Hz)\nTo be calculated after recording full ECIS curve after stimulation with human serum from liver transplant (LT) patients.\n\nGoal: To calculate the difference in AUC between... |
101,020 | Whole genome sequencing of H5N1 from dairy products with tiled 250bp amplicons | 0 | dx.doi.org/10.17504/protocols.io.kqdg322kpv25/v1 | https://www.protocols.io/view/whole-genome-sequencing-of-h5n1-from-dairy-product-dev43e8w | William C. Vuyk, Andrew Lail, Isla Emmen, Nura Hassan, Patrick Barros Tiburcio, Christina Newman, Nicholas R. Minor, Nancy Wilson, Thomas Friedrich, David O'Connor | TITLE: Whole genome sequencing of H5N1 from dairy products with tiled 250bp amplicons
AUTHORS: William C. Vuyk, Andrew Lail, Isla Emmen, Nura Hassan, Patrick Barros Tiburcio, Christina Newman, Nicholas R. Minor, Nancy Wilson, Thomas Friedrich, David O'Connor
[DESCRIPTION]
Here we present a new short tiled amplicon sc... | ["[Obtaining primer pools] Navigate to the oPools primer pools product page on IDT.", "[Obtaining primer pools] To order, upload the file attached to this protocol. There should be 178 valid sequences. Order at a concentration of 50pmol/oligo.", "[Obtaining primer pools] Purchase AVRL_H5N1_250bpAmpWGS_Pool1 and AVRL_... |
67,571 | Centriflaken: an automated data analysis pipeline for assembly and in silico analyses of food-borne pathogens from metagenomic samples | 5 | dx.doi.org/10.17504/protocols.io.kxygxzdbwv8j/v4 | https://www.protocols.io/view/centriflaken-an-automated-data-analysis-pipeline-f-cd8ts9wn | Kranti Konganti, Vishal Thovarai, Meghan Maguire, Julie A. Kase, Narjol Gonzalez-Escalona | TITLE: Centriflaken: an automated data analysis pipeline for assembly and in silico analyses of food-borne pathogens from metagenomic samples
AUTHORS: Kranti Konganti, Vishal Thovarai, Meghan Maguire, Julie A. Kase, Narjol Gonzalez-Escalona
[DESCRIPTION]
Rapid and comprehensive analysis of metagenomic data from any sa... | ["[Step 1] Create an account and Login:\n\nIf you do not already have an account on GalaxyTrakr, please create one by visiting this URL: https://account.galaxytrakr.org/Account/Register", "[Step 1] Once your account is activated, login by visiting https://galaxytrakr.org.", "[Step 2] Create a new history:\n \n\n \n\n\n... |
109,190 | FUNDIS DNA Extraction, PCR, Oxford Nanopore Technologies MinION Sequencing and data analysis. | 0 | null | https://www.protocols.io/view/fundis-dna-extraction-pcr-oxford-nanopore-technolo-dnve5e3e | Harte Singer, Stephen Douglas Russell | TITLE: FUNDIS DNA Extraction, PCR, Oxford Nanopore Technologies MinION Sequencing and data analysis.
AUTHORS: Harte Singer, Stephen Douglas Russell
[DESCRIPTION]
Generating DNA barcode sequences from fungal samples using the Oxford Nanopore Technologies MinION platform. Some methods adapted from Stephen D. Russell's ... | [] |
58,358 | Welcome | 3 | null | https://www.protocols.io/view/welcome-b48wqzxe | Elena L. Peredo | TITLE: Welcome
AUTHORS: Elena L. Peredo
[DESCRIPTION]
This is the welcome page for ScenGen Workspace
[STEPS] | [] |
59,117 | Preparing Indexed Primer Plates (IDT Ultramers) for the Illumina MiSeq - Nextera Dual Indices | 4 | dx.doi.org/10.17504/protocols.io.3byl4bq1jvo5/v1 | https://www.protocols.io/view/preparing-indexed-primer-plates-idt-ultramers-for-b5ymq7u6 | André M Comeau, Alessi Kwawukume | TITLE: Preparing Indexed Primer Plates (IDT Ultramers) for the Illumina MiSeq - Nextera Dual Indices
AUTHORS: André M Comeau, Alessi Kwawukume
[DESCRIPTION]
The preparation of diluted IDT working primer stocks of Illumina Dual Index primers for use in IMR PCR preps.
[STEPS]
SECTION: Order Primers
1. Use our Excel tem... | ["[Order Primers] Use our Excel template ( ) to copy existing 16S/18S/ITS primers or to design your own custom gene primers with the proper Illumina indices and Nextera adapter orientations. We order IDT “Ultramers” for such long primers (~80-90 nt) as their coupling efficiency is one of the highest available (critical... |
105,357 | Sterilizing and Preparing Seeds for Laboratory Use | 0 | dx.doi.org/10.17504/protocols.io.81wgbz933gpk/v1 | https://www.protocols.io/view/sterilizing-and-preparing-seeds-for-laboratory-use-di5m4g46 | Gabriela Paredes | TITLE: Sterilizing and Preparing Seeds for Laboratory Use
AUTHORS: Gabriela Paredes
[DESCRIPTION]
Sterilizing seeds is a critical step in many plant biology and microbiology experiments to ensure that the seeds are free from contaminants such as bacteria, fungi, and other microorganisms. This protocol outlines the ste... | ["[Prepare the Bleach Solution:] Prepare a 25% bleach solution by mixing 250 ml of commercial bleach with 750 ml of sterile distilled water to obtain a total of 1000 ml of the solution.\nEnsure that the solution is prepared in a sterile container.", "[Sterilize the Seeds:] Place the counted seeds into an autoclaved Erl... |
null | null | null | dx.doi.org/10.17504/protocols.io.cdgs3v | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocols is to be performed with the Quick Ligation Reaction Buffer. Please see the NEB website for more information.
[STEPS]
?.
?.
?.
?.
?. | [] |
30,656 | Immunocytochemistry Staining Protocol | null | dx.doi.org/10.17504/protocols.io.968h9hw | null | Sam Li | TITLE: Immunocytochemistry Staining Protocol
AUTHORS: Sam Li
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. [Sterilization (for 12-well plates with coverslips):]
Transfer a single cover slip into a 12-well plate. Then add 1 mL of 70% Ethanol into a well for 20 minutes at room temperature.
?. [Sterilizatio... | ["[Sterilization (for 12-well plates with coverslips):]\nTransfer a single cover slip into a 12-well plate. Then add 1 mL of 70% Ethanol into a well for 20 minutes at room temperature.", "[Sterilization (for 12-well plates with coverslips):]\nWash quickly three times with PBS.", "[Poly-Lysine Coating for 12-Well Plates... |
60,293 | Preparation of Biological Tissues for Serial Block Face Scanning Electron Microscopy (SBEM) | 1 | dx.doi.org/10.17504/protocols.io.36wgq7je5vk5/v2 | https://www.protocols.io/view/preparation-of-biological-tissues-for-serial-block-b65drg26 | Thomas J. Deerinck, Eric A. Bushong, Mark H. Ellisman, Andrea Thor | TITLE: Preparation of Biological Tissues for Serial Block Face Scanning Electron Microscopy (SBEM)
AUTHORS: Thomas J. Deerinck, Eric A. Bushong, Mark H. Ellisman, Andrea Thor
[DESCRIPTION]
This protocol was designed to enhance signal for backscatter electron imaging of epoxy embedded mammalian tissue at low accelerati... | ["Animals are anesthetized and perfused with normal Ringer’s solution (see protocol for Ringer's solution) containing xylocaine (0.2 mg/ml) and heparin (20 units/ml) for 2 minutes at 35°C followed by 0.15M cacodylate buffer (Product No. 18851, Ted Pella Inc.) pH 7.4 containing 2.5% glutaraldehyde (Product No: 18426, Te... |
46,313 | Scintillation Count of radiolabeled whole cell | 4 | null | https://www.protocols.io/view/scintillation-count-of-radiolabeled-whole-cell-brghm3t6 | Elizabeth Fozo | TITLE: Scintillation Count of radiolabeled whole cell
AUTHORS: Elizabeth Fozo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Scintillation Count of radiolabeled whole cell</div></div>
[STEPS]
?. [Steps]
Grow OG1RF to mid log phase in BHI.
?. [Steps]
Harvest 5mL of cells.
?. [Steps]
Wash twice in 1... | ["[Steps]\nGrow OG1RF to mid log phase in BHI.", "[Steps]\nHarvest 5mL of cells.", "[Steps]\nWash twice in 1X davis salts without glucose.", "[Steps]\nRe-suspend in 5mL 1X davis salt without glucose with 10mg/mL BSA.", "[Steps]\nIncubate at 37oC for 30 minutes as starvation treatment.", "[Steps]\nMove to hot room.", "[... |
41,626 | NuFaction SARS-CoV2 Antigen Test Protocol | 1 | dx.doi.org/10.17504/protocols.io.bkv2kw8e | https://www.protocols.io/view/nufaction-sars-cov2-antigen-test-protocol-bkv2kw8e | Don Cooper, Timothy Wandell, ben | TITLE: NuFaction SARS-CoV2 Antigen Test Protocol
AUTHORS: Don Cooper, Timothy Wandell, ben
[STEPS]
?. [Saliva Specimen Collection]
Remove the device with onbaord diagnostic flow assay from packaging.
?. [Mobile Assay Application]
For iOS iPad and iPhone devices newer than 2018 use the following procedure. To scan th... | ["[Saliva Specimen Collection]\nRemove the device with onbaord diagnostic flow assay from packaging.", "[Mobile Assay Application]\nFor iOS iPad and iPhone devices newer than 2018 use the following procedure. To scan the result of the developed test open the Safari browser on the iPad or iPhone device and navigate to ... |
88,722 | Ex vivo Brain Slice Preparation for electrophysiology and 2PLSM recordings | 1 | null | https://www.protocols.io/view/ex-vivo-brain-slice-preparation-for-electrophysiol-c2vsye6e | taylor.panczyk | TITLE: Ex vivo Brain Slice Preparation for electrophysiology and 2PLSM recordings
AUTHORS: taylor.panczyk
[DESCRIPTION]
In this protocol we detail the steps to obtain brain slices containing the pedunculopontine nucleus (PPN) for ex vivo electrophysiology and 2PLSM recordings. We perform parasagital slices with a 20º ... | ["[Prepare Bubbling Solution] On the experiment day prepare the working aCSF and slicing solution in a 1:10 dilution from stock solutions", "[Prepare Bubbling Solution] Place slicing solution in -20 °C freezer for 30-40 minutes.", "[Prepare Bubbling Solution] Then place the slicing solution in a large Styrofoam contain... |
29,347 | ACUITYAdvanced Protocol | null | dx.doi.org/10.17504/protocols.io.8wbhxan | null | Sam Li | TITLE: ACUITYAdvanced Protocol
AUTHORS: Sam Li
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. [Peptide Exchange:]
ACUITYAdvanced system is recommended for use on formalin fixed paraffin embedded sections.
?. [Peptide Exchange:]
Positively charged slides recommended to securely adhere tissue.
?. [Peptide E... | ["[Peptide Exchange:]\nACUITYAdvanced system is recommended for use on formalin fixed paraffin embedded sections.", "[Peptide Exchange:]\nPositively charged slides recommended to securely adhere tissue.", "[Peptide Exchange:]\nParaffin embedded sections must be de-paraffinized with xylene and rehydrated with a graded s... |
26,321 | Progeny test for generating single copy homozygous transgenic lines in Arabidopsis thaliana. | null | dx.doi.org/10.17504/protocols.io.5xrg7m6 | null | Akila Wijerathna-Yapa | TITLE: Progeny test for generating single copy homozygous transgenic lines in Arabidopsis thaliana.
AUTHORS: Akila Wijerathna-Yapa
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The regenerated transgenic plants (T0) seeds were sown onto Murashige and Skoog Agar (MSA) plates containing 100µg/ml Car... | ["Plants should grow for ~4 weeks, until primary bolts appear. Then, primary bolts should be clipped to allow for the emergence of multiple secondary inflorescences.", "When secondary inflorescences are 1 -10 cm tall (6 - 8 days after clipping) the plants can be transformed. Plan transformation at this stage.", "Two ... |
23,993 | Neuropathy Phentoyping Protocols - Transmission Electron Microscopy | null | dx.doi.org/10.17504/protocols.io.3nzgmf6 | null | Eva Feldman | TITLE: Neuropathy Phentoyping Protocols - Transmission Electron Microscopy
AUTHORS: Eva Feldman
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span></div><div class = "text-block"><span style = "font-weight:bold;">Phenotyping of Rodents for the Presence o... | ["Fixation Tissue (fixed) Following intracardiac perfusion, dissect tissue of interest into 3 mm cubes, postfix in 4% para, 2.5% glutaraldehyde 4-12 hours, 4ºC Tissue (fresh) Quickly dissect tissue of interest into 3 mm cubes and fix by immersion in 4% para, 2.5% glutaraldehyde at 4ºC, at least 12 hours, replace fix wi... |
98,444 | CODA (part 2): calculate registration on low-resolution tissue images | HuBMAP | JHU-TMC | 0 | dx.doi.org/10.17504/protocols.io.kxygxym3dl8j/v2 | https://www.protocols.io/view/coda-part-2-calculate-registration-on-low-resoluti-dcdk2s4w | Kyu Sang Han, Pei-Hsun Wu, Joel Sunshine, Ashley Kiemen, Sashank Reddy, Denis Wirtz | TITLE: CODA (part 2): calculate registration on low-resolution tissue images | HuBMAP | JHU-TMC
AUTHORS: Kyu Sang Han, Pei-Hsun Wu, Joel Sunshine, Ashley Kiemen, Sashank Reddy, Denis Wirtz
[DESCRIPTION]
CODA workflow part 2. Calculate registration on low-resolution tissue images
[STEPS]
SECTION: Calculating the tissu... | ["[Calculating the tissue space] For most images, a resolution of 1x should be sufficient. If the 1x results are not well registered, or registration of small tissues (such as needle biopsies) is desired, try calculating registration at a higher resolution such as 2x or 4x.", "[Calculating the tissue space] The quality... |
44,809 | Recombineering | 4 | null | https://www.protocols.io/view/recombineering-bpzhmp36 | Elizabeth Fozo | TITLE: Recombineering
AUTHORS: Elizabeth Fozo
[STEPS]
?. [Template]
Prepare a PCR product. Typically, 200-600 ng/transformation. See note below. If using a plasmid template, may have to digest using DpnI or another enzyme to remove the additional plasmid
?. [Template]
Following purification, combine PCR products and e... | ["[Template]\nPrepare a PCR product. Typically, 200-600 ng/transformation. See note below. If using a plasmid template, may have to digest using DpnI or another enzyme to remove the additional plasmid", "[Template]\nFollowing purification, combine PCR products and ethanol precipitate. Resuspend products in water\nI usu... |
null | null | null | dx.doi.org/10.17504/protocols.io.iutcewn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>These were developed to measure potential microbial activity for uptake of acetate and bicarbonate by microbes in venting hydrothermal fluids. The protocol was designed for Axial Seamount diffusely venting fluids, but can be applied to other fluid systems (e.g. cold, oxic flu... | [] |
22,162 | Electrotransformation of Clostridium species | null | dx.doi.org/10.17504/protocols.io.zvsf66e | null | Chin Yee Tan | TITLE: Electrotransformation of Clostridium species
AUTHORS: Chin Yee Tan
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">A brief protocol for electrotransformation of Clostridium species</div></div>
[STEPS]
?. Inoculate with overnight.
[BHI-supplemented broth]
[stock culture]
?. Use the overnig... | ["Inoculate with overnight.\n[BHI-supplemented broth]\n[stock culture]", "Use the overnight culture to inoculate to a starting density of OD 0.02.\n[BHI-supplemented broth]", "Harvest early-exponential phase culture (OD 0.2 to 0.25) by centrifugation by 12,000g x at.", "Wash once in .\n[SML electroporation buffer]... |
63,917 | Pure strength cbd gummies canada - You plan to recuperate just as truly feel over and above anyone's expectations previously! However when you are encountering steady medical conditions, it tends to be hard to feel your ideal. This is the reason you re | 1 | dx.doi.org/10.17504/protocols.io.3byl4bdmjvo5/v1 | https://www.protocols.io/view/pure-strength-cbd-gummies-canada-you-plan-to-recup-canmsdc6 | Natures cbd Gummies | TITLE: Pure strength cbd gummies canada - You plan to recuperate just as truly feel over and above anyone's expectations previously! However when you are encountering steady medical conditions, it tends to be hard to feel your ideal. This is the reason you re
AUTHORS: Natures cbd Gummies
[DESCRIPTION]
"Pure stren... | ["Pure strength cbd gummies Canada", "Soothes Your Stress And Anxiety And Tension Quick", "Fantastic For Easing Discomfort/ Body Pains", "Helps In Reducing Back And Neck Pain Rapid", "Lowers Tightness And Swelling", "Excellent For Assisting You Move A Lot More", "Calms Any Kind Of Concerns Or Anxieties You Have", "Aids... |
100,755 | T4 Ligation | 0 | dx.doi.org/10.17504/protocols.io.q26g71po8gwz/v1 | https://www.protocols.io/view/t4-ligation-demt3c6n | Carolina Lopez | TITLE: T4 Ligation
AUTHORS: Carolina Lopez
[DESCRIPTION]
Protocol for DNA ligation using T4 ligase
[STEPS]
SECTION: T4 Ligation Protocol (Thermofisher, 15224041):
2. 1. For initial reaction, Mix:
X and Y should be calculated for 3 Insert:1 vector molar ratio
Example of Molar Ratio calculation for 3000bp vector wi... | ["[T4 Ligation Protocol (Thermofisher, 15224041):] 1. For initial reaction, Mix: \n \nX and Y should be calculated for 3 Insert:1 vector molar ratio\n\nExample of Molar Ratio calculation for 3000bp vector with 500bp PCR product insert:\n\n \n\n\n2. Incubate at room temperature for 15 min.\n3. Transform Product into E. ... |
78,727 | Characterization of the VKORC1 and CYP2C9 genotypes | 1 | dx.doi.org/10.17504/protocols.io.kxygx9edzg8j/v4 | https://www.protocols.io/view/characterization-of-the-vkorc1-and-cyp2c9-genotype-cq5fvy3n | Mirsada Causevic, Edin Begic | TITLE: Characterization of the VKORC1 and CYP2C9 genotypes
AUTHORS: Mirsada Causevic, Edin Begic
[DESCRIPTION]
Vitamin K antagonists (e.g. warfarin) are anticoagulants which represent widely prescribed drugs for prevention and treatment of thromboembolic disorders.
Warfarin's molecular target is vitamin K epoxide re... | ["[Genomic DNA extraction] Patients' whole blood was collected in ethylenediaminetetraacetic acid (EDTA)-containing tubes and stored at -20°C until use. Genomic DNA extraction from the human whole blood, that is, leukocytes, was carried out according to the protocol described by Subbarayan PR and colleagues (doi: 10.21... |
44,550 | Expressão de scPPx 1 | 1 | null | https://www.protocols.io/view/express-o-de-scppx-1-bpremm3e | Mariana Jacques | TITLE: Expressão de scPPx 1
AUTHORS: Mariana Jacques
[STEPS]
?. [:]
Tampão C -60 mM Tris HCl pH 7,5, 6 mM MgCl2, Glicerol 30%.Tampão B- 60 mM Tris HCl pH 7,5, 6 mM MgCl2, 250 mM ImidazolTampão de Lise - ? mM Tris HCl pH 7,5, 200 mM NaCl, 5% GlicerolTampão A- 60 mM Tris HCl pH 7,5, 6 mM MgCl2, 10 mM Imidazol.
?. [:]
... | ["[:]\nTampão C -60 mM Tris HCl pH 7,5, 6 mM MgCl2, Glicerol 30%.Tampão B- 60 mM Tris HCl pH 7,5, 6 mM MgCl2, 250 mM ImidazolTampão de Lise - ? mM Tris HCl pH 7,5, 200 mM NaCl, 5% GlicerolTampão A- 60 mM Tris HCl pH 7,5, 6 mM MgCl2, 10 mM Imidazol.", "[:]\nCultura em 5mLCultura em 1 L", "[:]\nCrescer até 0,6 - 0,8 DO ... |
16,664 | Single-cell analysis of functional heterogeneity in DNA repair capacity | null | dx.doi.org/10.17504/protocols.io.uhyet7w | null | Jay Hesselberth, Amanda Richer | TITLE: Single-cell analysis of functional heterogeneity in DNA repair capacity
AUTHORS: Jay Hesselberth, Amanda Richer
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Methods to measure heterogeneity among cells are rapidly transforming our understanding of biology but are currently limited to stati... | ["[10x Kit Changes - GEM generation]\nFollow the 10x protocol (CG00052 Rev F / CG000075 Rev C) for GEM generation with the following changes:1. Using the cell suspension volume calculator table, subtract 5 µl from the Volume of Nuclease-free Water.2. Add 5 µl of 20x hairpin solution per sample to the MM after you have... |
null | null | null | dx.doi.org/10.17504/protocols.io.g8wbzxe | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol is suitable for rapidly generating extracts of fungal cells for gel electrophoresis or western blots. It was optimised for complete extraction of difficult-to-solubilise proteins. This protocol was originally described in <a href="http://journals.plos.org/ploson... | [] |
40,762 | ELISA for quantification of IL-2 in human serum. | 6 | dx.doi.org/10.17504/protocols.io.bj22kqge | https://www.protocols.io/view/elisa-for-quantification-of-il-2-in-human-serum-bj22kqge | Angel Justiz-Vaillant | TITLE: ELISA for quantification of IL-2 in human serum.
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>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... | ["An anti-human IL-2 coating antibody is adsorbed onto microwells by incubation overnight at 4°C.", "Add 50 µl of human serum. Human IL-2 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 wasth o remove unbound proteins.",... |
86,206 | Generation of stable cell lines using viral infection | 4 | dx.doi.org/10.17504/protocols.io.261ged38yv47/v1 | https://www.protocols.io/view/generation-of-stable-cell-lines-using-viral-infect-cye6xthe | Louise Uoselis | TITLE: Generation of stable cell lines using viral infection
AUTHORS: Louise Uoselis
[DESCRIPTION]
Protocol for generation and precipitation of retrovirus, and infection of HeLa cells to generate stable cell lines.
[STEPS]
SECTION: Day 1
1. Seed HEK293T cells into a 10cm tissue culture plate (6.1 million cells/plate)... | ["[Day 1] Seed HEK293T cells into a 10cm tissue culture plate (6.1 million cells/plate), seeding one plate per construct you are generating virus for.", "[Day 2] Transfect cells with viral and helper vectors using lipofectamine LTX. In a 15mL falcon tube, combine the following:\n \n Reagent Amount ... |
93,932 | Denaturation analysis of α-synuclein fibrils | 4 | dx.doi.org/10.17504/protocols.io.kxygx3bmdg8j/v1 | https://www.protocols.io/view/denaturation-analysis-of-synuclein-fibrils-c7ykzpuw | Arpine Sokratian | TITLE: Denaturation analysis of α-synuclein fibrils
AUTHORS: Arpine Sokratian
[DESCRIPTION]
This protocol details the specific parameters used to accurately measure the denaturation sensitivity of α-synuclein fibrils. Essential parts of this protocol describe the evaluation of sonicated fibrils to ensure the reproduci... | ["[Preparation of α-synuclein sonicated fibrils] Follow the protocol to prepare the batch of sonicated fibrils. If the samples have been prepared earlier and kept at -80, thaw down in a water bath. Then, perform a quality control check to ensure the size distribution and concentration are corresponding to values outlin... |
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