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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51,043 | Sky Islands Collection 2021 | 1 | dx.doi.org/10.17504/protocols.io.bv4bn8sn | https://www.protocols.io/view/sky-islands-collection-2021-bv4bn8sn | Lauren Ponisio | TITLE: Sky Islands Collection 2021
AUTHORS: Lauren Ponisio
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol details the Ponisio Lab's collecting protocol for the 2021 Sky Islands season. </div></div>
[STEPS]
?. [Field station prep]
Prior to collection, it is important to make sure that... | ["[Field station prep]\nPrior to collection, it is important to make sure that the following preparations are made:Shared sampling box:GPSspare batteries flagging tapepin flags spare sharpies, microns etc Shared collection equipment/consumables:sterile, screwtop collection vials for bees non-sterile vials for pan traps... |
42,720 | Spectradyne nCS1: Sample measurement and device maintenence protocol | 1 | dx.doi.org/10.17504/protocols.io.bmx8k7rw | https://www.protocols.io/view/spectradyne-ncs1-sample-measurement-and-device-mai-bmx8k7rw | Bryce Killingsworth, Joshua Welsh, Tim Traynor, Michelle Pleet, Jennifer Jones | TITLE: Spectradyne nCS1: Sample measurement and device maintenence protocol
AUTHORS: Bryce Killingsworth, Joshua Welsh, Tim Traynor, Michelle Pleet, Jennifer Jones
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a generic protocol for using the Spectradyne nCS1 resestive pulse sensing instru... | ["[Preparation of running buffer]\nIf running buffer is more than two weeks old, it must be prepared fresh.", "[Preparation of running buffer]\nDiscard the old running buffer contained in the nCS1 buffer bottles.", "[Preparation of running buffer]\nRinse out the buffer bottles with a small amount of purified/filtered w... |
90,281 | VU TIS Multimodal Molecular Imaging Pipeline for KPMP Biopsy Interrogation | 1 | dx.doi.org/10.17504/protocols.io.kqdg39bbeg25/v2 | https://www.protocols.io/view/vu-tis-multimodal-molecular-imaging-pipeline-for-k-c4ehytb6 | Katerina V Djambazova, Lukasz Migas, Jamie Allen, Martin Dufresne, Madeline E. Colley, N. Heath Patterson, Léonore Tideman, Allison Esselman, Ellie Pingry, Angela R.S. Kruse, Melissa Farrow, Raf Van De Plas, Jeff Spraggins | TITLE: VU TIS Multimodal Molecular Imaging Pipeline for KPMP Biopsy Interrogation
AUTHORS: Katerina V Djambazova, Lukasz Migas, Jamie Allen, Martin Dufresne, Madeline E. Colley, N. Heath Patterson, Léonore Tideman, Allison Esselman, Ellie Pingry, Angela R.S. Kruse, Melissa Farrow, Raf Van De Plas, Jeff Spraggins
[DES... | ["[Sample Interrogation Assays] Autofluorescence Microscopy (AF) is collected on all KPMP tissue sections prior to IMS. AF is also collected on an external reference tissue termed \"BlockQC\".\nAF QC Data Collection Protocol: AFQC Protocol\nAF protocol: AF Microscopy", "[Sample Interrogation Assays] MALDI Imaging Mass ... |
null | null | null | dx.doi.org/10.17504/protocols.io.pp9dmr6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol shows how to dissect the Extensor Digitorum Longus (EDL) muscle and Soleus muscle from a mouse leg. </p>
[BEFORE_START]
<p><strong>Prepare Ringer solution: </strong></p>
<table>
<tbody>
<tr>
<td>
<p><strong>Reagent </strong></p>
</td>
<td>
<p><strong>Concentrat... | [] |
30,664 | Chromatin Immunoprecipitation (ChIP) Assay Protocol | null | dx.doi.org/10.17504/protocols.io.97gh9jw | null | Sam Li | TITLE: Chromatin Immunoprecipitation (ChIP) Assay Protocol
AUTHORS: Sam Li
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. [Chromatin Sample Preparation]
Culture between 1-15 million cells. Collect cells by spinning down at 500xg at 4°C for 5 minutes. Wash cells with PBS at room temperature.
?. [Chromatin ... | ["[Chromatin Sample Preparation]\nCulture between 1-15 million cells. Collect cells by spinning down at 500xg at 4°C for 5 minutes. Wash cells with PBS at room temperature.", "[Chromatin Sample Preparation]\nRemove the PBS and add freshly made basic cell culture media (it should not contain any serum or large molecular... |
33,847 | Superoxide Radical-scavenging Activity | null | dx.doi.org/10.17504/protocols.io.bdaxi2fn | null | Jing Xu | TITLE: Superoxide Radical-scavenging Activity
AUTHORS: Jing Xu
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The superoxide radical scavenging effects were examined [11]. Briefly, extract (1 ml) was added to 1 ml of 50 μM NBT solution and 1 ml of 468 μMNADH, and a 1ml aliquot of 60 μM PMS re... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.uz9ex96 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Carbapenemase producing Enterobacteriaceae (CPE) are becoming a global healthcare concern. Current laboratory methods for the detection of CPE include screening followed by confirmatory phenotypic and genotypic tests. These processes would generally take >/= 72 hours, which coul... | [] |
86,833 | Cell Avidity analysis of murine CD8+ CAR T cells via z-Movi | 4 | dx.doi.org/10.17504/protocols.io.81wgbxx81lpk/v1 | https://www.protocols.io/view/cell-avidity-analysis-of-murine-cd8-car-t-cells-vi-cy2rxyd6 | Andrew R Stevens, Tamer B Shabaneh | TITLE: Cell Avidity analysis of murine CD8+ CAR T cells via z-Movi
AUTHORS: Andrew R Stevens, Tamer B Shabaneh
[DESCRIPTION]
z-Movi is a cell based assay used to assess the avidity of specific immune cells against their targets. Perform this protocol at the end of generating CAR-T cells. For more information see "Retr... | ["[Day -2: Culture target cells (BF194)] Using Trypsin-EDTA (0.05%), passage B16-F10 transduced with pTS194 (BF194) cell culture at a ratio of 1:4 to prepare for experiment day.", "[Day -1: Functionalization of clean, dry z-Movi chip] Functionalize a clean, dry chip with 100 μL Concanavalin A (1 mg/mL) (ConA) for 16-18... |
52,766 | SmartSeq | 2 | dx.doi.org/10.17504/protocols.io.bxr6pm9e | https://www.protocols.io/view/smartseq-bxr6pm9e | cecilia , Suzie Alarcon, Alessandro Sette | TITLE: SmartSeq
AUTHORS: cecilia , Suzie Alarcon, Alessandro Sette
[DESCRIPTION]
This protocol details the collection of methods of SmartSeq, Part 1: SmartSeq and Part 2: Custom QXT.
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.quqdwvw | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?. | [] |
76,224 | Cell line information | 1 | dx.doi.org/10.17504/protocols.io.rm7vz82o8vx1/v3 | https://www.protocols.io/view/cell-line-information-cnn8vdhw | Philippa R Kennedy, Melissa Khaw | TITLE: Cell line information
AUTHORS: Philippa R Kennedy, Melissa Khaw
[DESCRIPTION]
An amalgamation of cell line data in the lab. Its origin and standard culture conditions.
[STEPS]
SECTION: Overview
1. All cells are maintained in humidified incubators at 37°C, 5% CO2, unless otherwise specified.
All cells are ro... | ["[Overview] All cells are maintained in humidified incubators at 37°C, 5% CO2, unless otherwise specified. \n\nAll cells are routinely tested for mycoplasma infection using a PCR-based test (Universal Mycoplasma Detection Kit, ATCC Cat. No. 30-1012K)\n\nDates of purchase are provided. Aliquots of purchased cells lines... |
null | null | null | dx.doi.org/10.17504/protocols.io.e6abhae | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol is designed for high sensitivity miRNA library generation for the Illumina sequencing platform. Our protocol and the enhanced reagent kit enables the discovery and profiling of small RNAs from a variety of sources including FFPE, exosome, serum, and whole blood.... | [] |
98,236 | VTA Surgery Protocol | 0 | dx.doi.org/10.17504/protocols.io.yxmvmexzng3p/v1 | https://www.protocols.io/view/vta-surgery-protocol-db642rgw | Sasha Burwell | TITLE: VTA Surgery Protocol
AUTHORS: Sasha Burwell
[DESCRIPTION]
This protocol details the VTA surgery procedures used to infect VTA dopamine neurons with virus and implant various cannulas and fibers intracranially.
[STEPS]
SECTION: Setup:
1. Wipe down the whole surgical area and the stereotax (Kopf Model 1900) with... | ["[Setup:] Wipe down the whole surgical area and the stereotax (Kopf Model 1900) with 100% ethanol.", "[Setup:] Prep your sterile surface with \n\nsurgical tools (scissors, fine forceps, graefe forceps), \nsurgical Eyespears, \nsterile cotton gauze pads, \nsterile cotton tipped applicators, \na scalpel, \nand something... |
107,776 | DNAMA VSVC Guidebook | 0 | null | https://www.protocols.io/view/dnama-vsvc-guidebook-dmg843zw | Harte Singer, Joshua Birkebak, Alden Dirks, Jessica Williams, Scott Ostuni | TITLE: DNAMA VSVC Guidebook
AUTHORS: Harte Singer, Joshua Birkebak, Alden Dirks, Jessica Williams, Scott Ostuni
[DESCRIPTION]
A guidebook for learning how to analyze and validate fungal nrITS barcode data generated by Oxford Nanopore Technologies (ONT) MinION sequencing platform using free software and platforms.
[S... | [] |
84,629 | Saturation Mutagenesis-Reinforced Functional Assays (SMuRF) for alpha-dystroglycan glycosylation enzymes (using FKRP and LARGE1 as examples) | 4 | dx.doi.org/10.17504/protocols.io.8epv5x1yjg1b/v1 | https://www.protocols.io/view/saturation-mutagenesis-reinforced-functional-assay-cwvvxe66 | Kaiyue Ma, Shushu Huang, Jenny Xu, Angela Lek, Monkol Lek | TITLE: Saturation Mutagenesis-Reinforced Functional Assays (SMuRF) for alpha-dystroglycan glycosylation enzymes (using FKRP and LARGE1 as examples)
AUTHORS: Kaiyue Ma, Shushu Huang, Jenny Xu, Angela Lek, Monkol Lek
[DESCRIPTION]
Interpretation of disease-causing genetic variants remains a challenge in the field of ... | ["[Create FKRP-KO and LARGE1-KO cell lines via CRISPR RNP nucleofection] Prepare RNP complexes in", "[Create FKRP-KO and LARGE1-KO cell lines via CRISPR RNP nucleofection] Transfer the mixed samples to the wells of the 16-well Nucleocuvette Strips\nPerform nucleofection with \nUse EN-138 for HAP1; CA-137 for MB135", ... |
37,565 | High-molecular weight DNA extraction and small fragment removal of Ascochyta lentis | 1 | dx.doi.org/10.17504/protocols.io.bgw5jxg6 | https://www.protocols.io/view/high-molecular-weight-dna-extraction-and-small-fra-bgw5jxg6 | Johannes Wolfram Debler, Ashley Jones, Ramawatar Nagar, Anna Sharp, Benjamin Schwessinger | TITLE: High-molecular weight DNA extraction and small fragment removal of Ascochyta lentis
AUTHORS: Johannes Wolfram Debler, Ashley Jones, Ramawatar Nagar, Anna Sharp, Benjamin Schwessinger
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:left"><span>Extract... | ["[PREPARATION]\nPrepare about 500 mg of fungal mycelia grown in liquid media (YEG, 0.5% Yeast Extract, 5% Glucose). Remove media by filtering through a sterile milk filter disk. Wash mycelia with Milli-Q water while on the filter and keep frozen in liquid nitrogen.", "[PREPARATION]\nSet a water bath to 55°C. This will... |
null | null | null | dx.doi.org/10.17504/protocols.io.fnnbmde | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The aim of this protocol is to describe how to do a very reproducible upshift of a nitrogen-limited yeast culture to nitrogen non-limited conditions. In order to do this with enough cells to make inefficient analysis (ie RATEseq) feasible, we start in the chemostat for high-c... | [] |
27,619 | The laboratory protocol: Agrobacterium tumefaciens-mediated transformation of a hevein-like gene into asparagus leads to stem wilt resistance | null | dx.doi.org/10.17504/protocols.io.68bhhsn | null | Helong Chen | TITLE: The laboratory protocol: Agrobacterium tumefaciens-mediated transformation of a hevein-like gene into asparagus leads to stem wilt resistance
AUTHORS: Helong Chen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The laboratory protocol's aim is to develop a genetic transformation system ... | ["Glufosinate （PPT）Resistance Observation A total of 20 units of 0.6 cm2 blocks of asparagus embryos were placed in different concentrations of transformation media (0, 5, 10, 20, 40, and 80 mg/l PPT), and the survival rate of asparagus embryos was recorded after 20 days.", "Construction of Vector (1) The fragments cl... |
54,152 | Hybridization and Immobilization | 4 | dx.doi.org/10.17504/protocols.io.by5gpy3w | https://www.protocols.io/view/hybridization-and-immobilization-by5gpy3w | Chia-Hsien Shih | TITLE: Hybridization and Immobilization
AUTHORS: Chia-Hsien Shih
[DESCRIPTION]
This protocol is to assemble GotCha with circular probe, immobilization probe and magnetic beads.
[STEPS]
SECTION: Preparation
1. Dilute immobilization probe into 10µM
SECTION: Protocol of Hybridization
2. Add 4.5 µL of 1µM circular probe... | ["[Preparation] Dilute immobilization probe into 10µM", "[Protocol of Hybridization] Add 4.5 µL of 1µM circular probe", "[Protocol of Hybridization] Add 9 µLof 10X pH 7.4 PBS buffer", "[Protocol of Hybridization] Add 0.9 µL of 10µM immobilization probe", "[Protocol of Hybridization] Add 75.6 µL RNase-free water", "[Pro... |
109,145 | Vector Digestion and Purification | 0 | dx.doi.org/10.17504/protocols.io.261ge5dyog47/v2 | https://www.protocols.io/view/vector-digestion-and-purification-dntz5ep6 | Carolina Lopez | TITLE: Vector Digestion and Purification
AUTHORS: Carolina Lopez
[DESCRIPTION]
Protocol for plasmid digestion and purification
[STEPS]
SECTION: Isolate Digested Vector:
1. 1. Digest Vector with New England Biolabs Restriction Enzymes:
2. Incubate for 120 min at 37 °C.
3. Add 10 µL of 6x loading buffer to reaction a... | ["[Isolate Digested Vector:] 1. Digest Vector with New England Biolabs Restriction Enzymes:\n \n2. Incubate for 120 min at 37 °C.\n3. Add 10 µL of 6x loading buffer to reaction and vortex briefly to mix.\n4. Make 1% low melt-agarose gel.\n a) Mix 1 g of Agar with 100 mL of TAE Buffer.\n b) Microwave to bo... |
60,675 | Maternal Lines Protocol | 3 | null | https://www.protocols.io/view/maternal-lines-protocol-b7hbrj2n | Meghan Duffy, Rebecca Bilich | TITLE: Maternal Lines Protocol
AUTHORS: Meghan Duffy, Rebecca Bilich
[DESCRIPTION]
This a protocol to set up and maintain Daphnia maternal lines for clones that will be used in experiments.
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.uieeube | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Pacific Halibut (Hippoglossus stenolepis) support culturally and economically important fisheries in the Gulf of Alaska, though recent decreases in mean size-at-age have substantially reduced fishery yields, generating concerns among stakeholders and resource managers. Among the... | ["[Spatial Analyses - R Script File] {\"blocks\":[{\"key\":\"esunh\",\"text\":\"# This script file includes code necessary to construct a delta GAM (generalized additive model) for estimating spatial overlap between Pacific Halibut and Arrowtooth Flounder in the Gulf of Alaska. The methods used were modified from Hunsi... |
57,989 | The Summary of Treatment Protocol in motivational psychotherapy | 1 | dx.doi.org/10.17504/protocols.io.b4vdqw26 | https://www.protocols.io/view/the-summary-of-treatment-protocol-in-motivational-b4vdqw26 | Hosein Sahebdel, Mohammad Tahan | TITLE: The Summary of Treatment Protocol in motivational psychotherapy
AUTHORS: Hosein Sahebdel, Mohammad Tahan
[DESCRIPTION]
Reviewing the history of theories associated with psychotherapy establishes that motivational psychotherapy (MPT) has been centered on environmental mind, lies, selfishness, and rich mind, wh... | ["Rapport> \tRapport, providing introductory acquaintance, having discussion about the purpose of the therapy, building trust.", "Describing> \tHelping clients to describe themselves by emphasizing incompatible aspects of their personality, this description includes all the characteristics of clients, including cogniti... |
7,985 | Killing wolves to prevent predation on livestock may protect one farm but harm neighbors: Variables and Sample STATA code for survival analytics | 1 | dx.doi.org/10.17504/protocols.io.j2rcqd6 | https://www.protocols.io/view/killing-wolves-to-prevent-predation-on-livestock-m-j2rcqd6 | Francisco Santiago-Ávila, Adrian Treves | TITLE: Killing wolves to prevent predation on livestock may protect one farm but harm neighbors: Variables and Sample STATA code for survival analytics
AUTHORS: Francisco Santiago-Ávila, Adrian Treves
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Here, we make available basic sample code for the ... | ["[VARIABLES USED (and description):]\nID_TRS_yr --> identifier for each area-year combination (please see study for more information)Interv_dich --> intervention type (lethal, non-lethal)wolves_killed --> number of wolves killedInterv_dummy --> dummy variable for intervention type (0 if ‘non-lethal’, 1 if ‘lethal’)Del... |
20,697 | Miltenyi MACS Bead Isolation | null | dx.doi.org/10.17504/protocols.io.yfzftp6 | null | Dannielle Moore, Andre G Loxton | TITLE: Miltenyi MACS Bead Isolation
AUTHORS: Dannielle Moore, Andre G Loxton
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol includes the step-by-step used for isolation of a cell popultation of interest using MACS bead technology. The kits used for this protocol were obtained from Mil... | ["Isolated PBMCs washed in 10mL 1x at 400xg for at\n{\"blocks\":[{\"key\":\"1k48s\",\"text\":\"Isolation of human peripheral blood mononuclear cells (PBMCs) using the Ficoll density gradient method. \",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[],\"entityRanges\":[],\"data\":{}}],\"entityMap\":{}}\n[(Ro... |
null | null | null | dx.doi.org/10.17504/protocols.io.dpg5jv | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol is for the separation of free virus particles from sediments. It is from:<br /><br />Danovaro, R., and M. Middelboe. 2010. Separation of free virus particles from sediments in aquatic systems, p. 74–81. In S. W. Wilhelm, M. G. Weinbauer, and C. A. Suttle [eds.], Ma... | [] |
62,116 | Fun Drops CBD Gummies | Reclaim Your Stamina And Increase Inches Stay active With Fun Drops CBD Gummies Male Enhancement | 3 | dx.doi.org/10.17504/protocols.io.5qpvobqzbl4o/v1 | https://www.protocols.io/view/fun-drops-cbd-gummies-reclaim-your-stamina-and-inc-b8wcrxaw | Fun Drops CBD Gummies | TITLE: Fun Drops CBD Gummies | Reclaim Your Stamina And Increase Inches Stay active With Fun Drops CBD Gummies Male Enhancement
AUTHORS: Fun Drops CBD Gummies
[DESCRIPTION]
Fun Drops CBD Gummies
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.c7vzn5 | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
Original protocol written by Yasmine Graf.
[STEPS]
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null | null | null | dx.doi.org/10.17504/protocols.io.ejkbckw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocols outlines our definitions of core operational protein families (OPFs), potential auxiliary metabolic genes (AMGs), sharing of genes across anatomical sites, and Bray-Curtis dissimilarity of the OPFs by anatomical site. Based on methods from the following publicatio... | [] |
62,607 | Epik Health Keto Gummies Reviews! | 3 | dx.doi.org/10.17504/protocols.io.q26g74dn9gwz/v1 | https://www.protocols.io/view/epik-health-keto-gummies-reviews-b9dpr25n | Epik Health Keto Gummies | TITLE: Epik Health Keto Gummies Reviews!
AUTHORS: Epik Health Keto Gummies
[DESCRIPTION]
Epik Health Keto Gummies Reviews!
[STEPS] | [] |
20,914 | UC Davis - HDL Protocol | null | dx.doi.org/10.17504/protocols.io.ynsfvee | null | Peter Havel | TITLE: UC Davis - HDL Protocol
AUTHORS: Peter Havel
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">LDL and VLDL are separated from HDL using a precipitation reagent. Then the HDL fraction is measured for either TC or... | ["Add 25µl 2X precipitation buffer to 25µl of sample using a positive displacement pipet.", "Vortex and let sit at RT for 10 minutes.", "Centrifuge at 2000×g for 10 minutes at 4°C.", "Pipet supernatant into new tube, this is the HDL fraction.", "Add 5 µl of calibrator and sample to each well.IMPORTANT: Make sure not to... |
42,675 | Rqtl_code | 3 | dx.doi.org/10.17504/protocols.io.bmwtk7en | https://www.protocols.io/view/rqtl-code-bmwtk7en | Anna Miller | TITLE: Rqtl_code
AUTHORS: Anna Miller
[STEPS] | [] |
91,596 | SM buffer for making phage dilutions | 4 | dx.doi.org/10.17504/protocols.io.bp2l6xykrlqe/v1 | https://www.protocols.io/view/sm-buffer-for-making-phage-dilutions-c5pky5kw | HANNAH ZHU | TITLE: SM buffer for making phage dilutions
AUTHORS: HANNAH ZHU
[DESCRIPTION]
How to make sm buffer for phage dilutions
[STEPS]
1. Dissolve following components in 300 mL of MilliQ water:
2. Adjust pH to 7.4 – 7.5 with HCl
3. Top up the volume to 400 mL with MilliQ water
4. Autoclave at 121 °C for 15 min
5. ... | ["Dissolve following components in 300 mL of MilliQ water:", "Adjust pH to 7.4 – 7.5 with HCl", "Top up the volume to 400 mL with MilliQ water", "Autoclave at 121 °C for 15 min", "Cool down to room temperature", "Filter-sterilise through 0.22 µm membrane", "Store at room temperature"] |
80,836 | Data storage and security | 1 | dx.doi.org/10.17504/protocols.io.yxmvm269ng3p/v1 | https://www.protocols.io/view/data-storage-and-security-cs7cwhiw | Kajiru Gad Kilonzo, Stefanie J. Krauth, Jo Halliday, Clive Kelly, Stefan Siebert, Gloria Temu, Christopher Bunn, Nateiya M Yongolo, Sally Wyke, Emma McIntosh, Blandina Mmbaga | TITLE: Data storage and security
AUTHORS: Kajiru Gad Kilonzo, Stefanie J. Krauth, Jo Halliday, Clive Kelly, Stefan Siebert, Gloria Temu, Christopher Bunn, Nateiya M Yongolo, Sally Wyke, Emma McIntosh, Blandina Mmbaga
[DESCRIPTION]
This protocol details data storage and security.
[STEPS]
SECTION: Data storage and secu... | ["[Data storage and security] The database will be hosted on a web-based application designed to allow researchers to upload, view and manage data.", "[Data storage and security] An Open Data Kit (ODK) platform(32) will be deployed for this purpose. Community and hospital survey data will be collected on ODK-programmed... |
20,626 | Case - Heavy Water Assays by GC-mass spectrometry | null | dx.doi.org/10.17504/protocols.io.ydsfs6e | null | Henri Brunengraber | TITLE: Case - Heavy Water Assays by GC-mass spectrometry
AUTHORS: Henri Brunengraber
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block"><span>Heavy water can be used as a tracer for estimating metabolic rates (</span><spa... | ["1. Quantitation by ²H²O Standard Curve:2. Standards are made from deuterium oxide (Aldrich 617385) 3. Pipette 10μl of plasma or standard into Eppendorf4. ²H²O standards a. Blank (MQ H²O) b. 0.1% D²O in (MQ H²O) c. 0.5% D²O in (MQ H²O) d. 0.10% D²O in (MQ H²O) e. 1.5% D²O in (MQ H²O) f. 2.0% ... |
103,027 | AAV Injection and Tissue Preparation | 0 | dx.doi.org/10.17504/protocols.io.14egn6wkql5d/v1 | https://www.protocols.io/view/aav-injection-and-tissue-preparation-dgut3wwn | Justin T Savage | TITLE: AAV Injection and Tissue Preparation
AUTHORS: Justin T Savage
[DESCRIPTION]
This protocol provides guidelines for injection of AAVs into the cortex and striatum of young and adult mice. For post-injection tissue processing, the protocol for perfusing mice and preparing brain tissue for sectioning is also inclu... | ["[Perfusion of Animals and Tissue Processing] A) Setup/Preparation", "[Perfusion of Animals and Tissue Processing] 1. Thaw out 4% PFA at least 30mins prior to perfusion. Estimate 15-25ml/animal (P21 depending on size). Check if there is thawed 4% PFA that is not expired in the 4C fridge before thawing out new tubes", ... |
96,294 | Reconditioning PCR for removal of PCR bubbles in Illumina librarys | 0 | dx.doi.org/10.17504/protocols.io.x54v9p9ypg3e/v1 | https://www.protocols.io/view/reconditioning-pcr-for-removal-of-pcr-bubbles-in-i-daae2abe | Dominik Buchner | TITLE: Reconditioning PCR for removal of PCR bubbles in Illumina librarys
AUTHORS: Dominik Buchner
[DESCRIPTION]
This protocol describes how to remove partly single-stranded PCR products ("PCR bubbles") from Illumina libraries. For more information about this phenomenon please see this explanation from Illumina. For m... | ["[Quality control] Perform a quality control of your library. PCR bubbles may look different depending on the method used for quality control. See below and example of the Fragment Analyzer, Bioanalyzer and an agarose gel.", "[Library concentration (optional)] Concentrate your library by reducing the volume down to 10... |
38,924 | 5: User-friendly protocol: SABER RNA FISH in cells | 1 | null | https://www.protocols.io/view/5-user-friendly-protocol-saber-rna-fish-in-cells-bh9kj94w | Jocelyn Y. Kishi, Sylvain W. Lapan, Brian J Beliveau, Emma R. West, Allen Zhu, Hiroshi M. Sasaki, Sinem Saka, Yu Wang, Constance L Cepko, Peng Yin | TITLE: 5: User-friendly protocol: SABER RNA FISH in cells
AUTHORS: Jocelyn Y. Kishi, Sylvain W. Lapan, Brian J Beliveau, Emma R. West, Allen Zhu, Hiroshi M. Sasaki, Sinem Saka, Yu Wang, Constance L Cepko, Peng Yin
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the SABER RNA ... | ["[Preparing the slide]\nSeed 8-well Ibidi chamber slides (Cat #80827) with cells and grow in tissue culture incubator (typically with ) to desired confluency.\n37 °C\n[CO2]\nNotes: You may need to adjust the deposition protocol (e.g. what concentration of cells, how long to let them grow on the slide) in order to ach... |
99,155 | DNA Extraction from Sterivex Filters - Qiagen Blood and Tissue Kit | 1 | null | https://www.protocols.io/view/dna-extraction-from-sterivex-filters-qiagen-blood-dc3t2ynn | Colleen Kellogg | TITLE: DNA Extraction from Sterivex Filters - Qiagen Blood and Tissue Kit
AUTHORS: Colleen Kellogg
[DESCRIPTION]
Draft!
[BEFORE_START]
Read background information, MIOP and BePOP-OBON information under the "Guidelines" tab.
[GUIDELINES]
MIOP: Minimum Information about an Omics Protocol
AUTHORS
RELATED PROTOC... | ["[PREPARATION - must be done in Clean Room 1 or Clean Room 2]", "[PREPARATION - must be done in Clean Room 1 or Clean Room 2] Set aside ATL buffer, AL buffer, proteinase K, RNase A and anhydrous ethanol. \nPut the ATL and AL buffers in the incubator to eliminate any precipitate that may be in the solution. \nThere is ... |
49,674 | Maturation of Spinal Motor Neurons Derived from Human Embryonic Stem Cells | 1 | dx.doi.org/10.17504/protocols.io.burinv4e | https://www.protocols.io/view/maturation-of-spinal-motor-neurons-derived-from-hu-burinv4e | Tomonori Takazawa, Gist F. Croft, Mackenzie W. Amoroso, Lorenz Studer, Hynek Wichterle, Amy B. MacDermott | TITLE: Maturation of Spinal Motor Neurons Derived from Human Embryonic Stem Cells
AUTHORS: Tomonori Takazawa, Gist F. Croft, Mackenzie W. Amoroso, Lorenz Studer, Hynek Wichterle, Amy B. MacDermott
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Our understanding of motor neuron biology in humans is ... | ["[ESC Culture]\nGrow a human embryonic stem cell line with a motor neuron reporter (BAC-Hb9::GFP) under standard pluripotency maintenance conditions: on irradiated CF-1 mouse embryonic fibroblast feeder cells (0.015 M cells/cm2, GlobalStem) seeded on gelatinized (Millipore) tissue culture plastic.", "[ESC Culture]\nFe... |
null | null | null | dx.doi.org/10.17504/protocols.io.g9ebz3e | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.kj3cuqn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Protocol for making 0.5 YTSS Agar Plates (1.5%). </p>
[STEPS]
?.
?.
?.
?. | [] |
108,692 | Prepare Tris Buffer for Meat identification Protocol | 0 | dx.doi.org/10.17504/protocols.io.kqdg32z1zv25/v1 | https://www.protocols.io/view/prepare-tris-buffer-for-meat-identification-protoc-dndu5a6w | openbioscience Adrian | TITLE: Prepare Tris Buffer for Meat identification Protocol
AUTHORS: openbioscience Adrian
[DESCRIPTION]
Buffer protocol for meat identification experiment
[BEFORE_START]
Make sure you adjust the pH to the same temperature for the reaction in which the buffer is used.
[STEPS]
SECTION: Prepare Tris Buffer for Meat id... | ["[Prepare Tris Buffer for Meat identification Protocol. Prepare (50 ml) of 0.04 mol/L Tris HCl (pH 7.75)] Measure and add 0.24 g of Tris\n\nCalculation for weight:\nMW for TRIS Hydrochloride (C4H11NO3 ·HCl) 121.14 mol/Liter, (Hydrochloric HCl Acid, MW: 36.46 g/mol)\n0.04 M TRIS TRIS Hydrochloride: m=CMV =0.04mol/L... |
98,057 | Small volume viral RNA extraction using MagMAX Viral RNA Isolation Kit | 0 | dx.doi.org/10.17504/protocols.io.81wgbzpyogpk/v1 | https://www.protocols.io/view/small-volume-viral-rna-extraction-using-magmax-vir-dbzh2p36 | Erika Bujaki, Joyce Akello, Alex Shaw, Catherine Troman, khurshida, arshady, alammu, Nick Grassly, Javier Martin | TITLE: Small volume viral RNA extraction using MagMAX Viral RNA Isolation Kit
AUTHORS: Erika Bujaki, Joyce Akello, Alex Shaw, Catherine Troman, khurshida, arshady, alammu, Nick Grassly, Javier Martin
[DESCRIPTION]
This protocol describes the viral nucleic acid recovery and purification from stool suspensions. The met... | ["[Reagent Preparation] Wash Solution 1", "[Reagent Preparation] Add indicated volume of 100% Isopropanol to the bottle of Wash Solution 1 Concentrate.", "[Reagent Preparation] Mix well by inverting at least 5 times and mark bottle to indicate that the alcohol was added.", "[Reagent Preparation] Wash Solution 2", "[Rea... |
107,757 | Basic Maintenance Protocol for Human Induced Pluripotent Stem Cells (hiPSCs) Introduction | 4 | dx.doi.org/10.17504/protocols.io.81wgbx1q1lpk/v3 | https://www.protocols.io/view/basic-maintenance-protocol-for-human-induced-pluri-dmgm43u6 | William J Buchser, Mallory Wright, purva patel, Jason Waligorski, Colin Kremitzki | TITLE: Basic Maintenance Protocol for Human Induced Pluripotent Stem Cells (hiPSCs) Introduction
AUTHORS: William J Buchser, Mallory Wright, purva patel, Jason Waligorski, Colin Kremitzki
[DESCRIPTION]
This protocol details the maintenance of human induced pluripotent stem cells (hiPSCs), covering thawing, passaging, ... | ["[Thawing iPSCs] Quickly thaw the frozen vial of iPSCs in a water bath at 37°C. Gently agitate the vial in the water bath until the cells are just thawed (usually takes about 1-2 minutes).", "[Thawing iPSCs] Using a 10 mL serological pipette, add 9 mL of media into a 15 mL conical tube.", "[Thawing iPSCs] Using a 5 mL... |
97,153 | GeoMx Digital Spatial Profiler (DSP) Protocol - University of Minnesota TMCs | 0 | dx.doi.org/10.17504/protocols.io.8epv5r7k6g1b/v1 | https://www.protocols.io/view/geomx-digital-spatial-profiler-dsp-protocol-univer-da492gz6 | Laura J Niedernhofer, David A Bernlohr | TITLE: GeoMx Digital Spatial Profiler (DSP) Protocol - University of Minnesota TMCs
AUTHORS: Laura J Niedernhofer, David A Bernlohr
[DESCRIPTION]
The nanoString GeoMx‱ Digital Spatial Profiler (DSP) is a platform that allows high-plex profiling at the protein and RNA level, providing spatial and temporal assessment o... | ["[Slide Preparation] GeoMx DSP Manual Slide Preparation User Manual", "[ROI Acquisition] GeoMx DSP Instrument User Manual", "[Library Preparation] GeoMx DSP NGS Readout User Manual", "[FASTQ Generation] BCL data from Illumina sequencer is demultiplexed and converted into FASTQ format using bcl2fastq version 2.20.0"] |
101,703 | Xpert MTB/RIF Ultra testing from tongue swabs – Diluted SR method | 0 | dx.doi.org/10.17504/protocols.io.14egn69nyl5d/v1 | https://www.protocols.io/view/xpert-mtb-rif-ultra-testing-from-tongue-swabs-dilu-dfjf3kjn | Charlotte Ahls, Anura David, Gayatri Shankar Chilambi, Adithya Cattamanchi, Margaretha de Vos, Kelsey Heard, Karen Heichman, Adam Penn-Nicholson, Lesley Scott, Amy E Steadman, Lindsey Turnbull, David Alland | TITLE: Xpert MTB/RIF Ultra testing from tongue swabs – Diluted SR method
AUTHORS: Charlotte Ahls, Anura David, Gayatri Shankar Chilambi, Adithya Cattamanchi, Margaretha de Vos, Kelsey Heard, Karen Heichman, Adam Penn-Nicholson, Lesley Scott, Amy E Steadman, Lindsey Turnbull, David Alland
[DESCRIPTION]
This standard op... | ["[Preparation of diluted 66% SR:PB] Dilute SR in a 2:1 ratio with PB, daily in a biosafety cabinet.\nPlease use step 2 for testing of smaller batches of samples, and step 3 for testing of larger batches (up to 16 samples) or standardized daily preparation of diluted SR buffer", "[Preparation of diluted 66% SR:PB] Meth... |
null | null | null | dx.doi.org/10.17504/protocols.io.rhfd33n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>A real-time PCR to detect Orientia tsutsugamushi DNA. This method has been adapted from a publication by Jiang et al 2004, and the oligonucleotides have been modified and a different PCR kit used.</p>
[GUIDELINES]
<ul>
<li>If using a different brand or model of real-time th... | [] |
44,775 | Trajectories of Glucocorticoid-Therapy After Initiation in Early (or Methotrexate-Naive) Rheumatoid Arthritis: Protocol for a Systematic Review, Meta-Analysis and Meta-Regression of Observational Cohort Studies | 1 | null | https://www.protocols.io/view/trajectories-of-glucocorticoid-therapy-after-initi-bpyfmptn | Andriko Palmowski, Frank Buttgereit | TITLE: Trajectories of Glucocorticoid-Therapy After Initiation in Early (or Methotrexate-Naive) Rheumatoid Arthritis: Protocol for a Systematic Review, Meta-Analysis and Meta-Regression of Observational Cohort Studies
AUTHORS: Andriko Palmowski, Frank Buttgereit
[STEPS]
?. [Objective]
To assess real-world trajector... | ["[Objective]\nTo assess real-world trajectories of glucocorticoid-therapy initiated as part of early rheumatoid arthritis (RA) treatment.", "[Eligibility]\nObservational cohort studies (CS) published between Jan 01, 2005 and now. Studies must enroll early (or methotrexate-naive) RA patients and report on those startin... |
22,705 | Transfection of construct containing kinetoplastid Blastocrithidia sp. p57 UTR's in Diplonema papillatum using AMAXA Nucleofactor apparatus. | null | dx.doi.org/10.17504/protocols.io.2ergbd6 | null | Binnypreet Kaur | TITLE: Transfection of construct containing kinetoplastid Blastocrithidia sp. p57 UTR's in Diplonema papillatum using AMAXA Nucleofactor apparatus.
AUTHORS: Binnypreet Kaur
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Transfection of construct containing kinetoplastid </span><span style = "... | [] |
36,726 | LC-MS/MS Untargeted Metabolomics Data Processing | 1 | dx.doi.org/10.17504/protocols.io.bf4wjqxe | https://www.protocols.io/view/lc-ms-ms-untargeted-metabolomics-data-processing-bf4wjqxe | Kevin Contrepois | TITLE: LC-MS/MS Untargeted Metabolomics Data Processing
AUTHORS: Kevin Contrepois
[DESCRIPTION]
Scope:
To describe the procedure to process untargeted metabolomics data.
Expected outcome/data:
Metabolomics dataset is processed using commercial software and custom R scripts. Metabolite annotation was performed using a... | ["Data from each mode were independently analyzed using Progenesis QI software (v2.3) (Nonlinear Dynamics, Durham, NC).", "Metabolic features from blanks and those that didn’t show sufficient linearity upon dilution in QC samples (r < 0.6) were discarded.", "Only metabolic features present in >2/3 of the samples were k... |
null | null | null | dx.doi.org/10.17504/protocols.io.q3rdym6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol describes the basic steps for a reciprocal best hit BLAST. It will show you how to download sequences from NCBI, creating BLAST databases, and how to blast.</p>
[GUIDELINES]
<p>I recommend running this protocol in a docker container, so you don't have to worry ... | [] |
78,528 | ENVIRONMENTAL AND FAMILY HISTORY QUESTIONNAIRE | 1 | dx.doi.org/10.17504/protocols.io.5jyl8j8drg2w/v1 | https://www.protocols.io/view/environmental-and-family-history-questionnaire-cqw8vxhw | null | TITLE: ENVIRONMENTAL AND FAMILY HISTORY QUESTIONNAIRE
AUTHORS:
[DESCRIPTION]
The protocol details the environmental & family history questionnaire_self administered by subjects.
[STEPS] | [] |
38,493 | Rine Lab Reopening SOP | 3 | null | https://www.protocols.io/view/rine-lab-reopening-sop-bht5j6q6 | Rine Lab | TITLE: Rine Lab Reopening SOP
AUTHORS: Rine Lab
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a living document that should reflect our current understanding of best practices. It is subject to change and will evolve as the situation changes and our understanding evolves.</div><div class =... | [] |
36,238 | shRNA Selection and Quality Control for Cancer Target Gene Validation | 1 | null | https://www.protocols.io/view/shrna-selection-and-quality-control-for-cancer-tar-bfmnjk5e | Adhana Asfaw, Brenton Paolella, Francisca Vazquez | TITLE: shRNA Selection and Quality Control for Cancer Target Gene Validation
AUTHORS: Adhana Asfaw, Brenton Paolella, Francisca Vazquez
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Proper design of shRNA sequences can be challenging, requiring empirical testing of up to 10-20 shRNA sequence... | ["[1. shRNA Selection and Evaluation: Genes with high-quality shRNAs tested in RNAi Data ]\nFor genes that were profiled in the RNAi datasets, we can use the shRNA quality estimates calculated using DEMETER2 to identify high-quality shRNAs (5).", "[1. shRNA Selection and Evaluation: Genes with high-quality shRNAs teste... |
null | null | null | dx.doi.org/10.17504/protocols.io.dmi44d | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Reference: Fuhrman et al, 1988. <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC202673/" target="_blank">Extraction from Natural Planktonic Microorganisms of DNA Suitable for Molecular Biological Studies</a>. AEM 54(6), 1426‐1429
[GUIDEL... | [] |
45,782 | Correlation of eccentric quadriceps torque with knee pain, physical function and extension lag in Indian women with grade ≤ II knee osteoarthritis | 3 | dx.doi.org/10.17504/protocols.io.bqxwmxpe | https://www.protocols.io/view/correlation-of-eccentric-quadriceps-torque-with-kn-bqxwmxpe | Masood Khan | TITLE: Correlation of eccentric quadriceps torque with knee pain, physical function and extension lag in Indian women with grade ≤ II knee osteoarthritis
AUTHORS: Masood Khan
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.cp2vqd | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Protocol for non-radioactive phosphorylation with T4 PNK 3' phosphatase minus.
[STEPS]
?.
?.
?. | [] |
54,383 | (NANOPORE MENU) Protocols for SARS-CoV-2 Bioinformatic Analysis and Database Submission | 2 | null | https://www.protocols.io/view/nanopore-menu-protocols-for-sars-cov-2-bioinforma-bzcpp2vn | Technical Outreach and Assistance for States Team | TITLE: (NANOPORE MENU) Protocols for SARS-CoV-2 Bioinformatic Analysis and Database Submission
AUTHORS: Technical Outreach and Assistance for States Team
[DESCRIPTION]
This collection of protocols covers library preparation and sequencing on Oxford Nanopore platforms as well as bioinformatic analysis and submission o... | [] |
67,458 | Nordic CBD Gummies Australia Reviews - Nordic CBD Gummies Australia Chemist Warehouse in 2022 | 3 | dx.doi.org/10.17504/protocols.io.6qpvr6jozvmk/v1 | https://www.protocols.io/view/nordic-cbd-gummies-australia-reviews-nordic-cbd-gu-cd5as82e | znfdbzldf | TITLE: Nordic CBD Gummies Australia Reviews - Nordic CBD Gummies Australia Chemist Warehouse in 2022
AUTHORS: znfdbzldf
[DESCRIPTION]
Nordic CBD Gummies Australia Reviews:- A strong body and an ordinary mind are we need nowadays. Notwithstanding, this ongoing truth is stacked down with standard activities that could... | [] |
18,917 | RNA isolation and cDNA synthesis from the marine ichthyosporean Sphaeroforma arctica | null | dx.doi.org/10.17504/protocols.io.wqdfds6 | null | Sebastián Najle | TITLE: RNA isolation and cDNA synthesis from the marine ichthyosporean Sphaeroforma arctica
AUTHORS: Sebastián Najle
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:justify"><span>This protocol describes the steps for isolation of total RNA for cDNA synthes... | ["[Collect cells by centrifugation]\nRemove the cells from the culture flasks with aid of a cell scraper (Nunc).Transfer cells to a 15 ml centrifuge tube. Pellet cells by centrifugation at 4500 xg for 5 min at .Carefully remove supernatant by pipetting. Be cautious not to perturb the pellet, to avoid loosing material.... |
45,427 | Sterilization of ISE | 4 | null | https://www.protocols.io/view/sterilization-of-ise-bqktmuwn | Elizabeth Fozo | TITLE: Sterilization of ISE
AUTHORS: Elizabeth Fozo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Sterilization of ISE</div></div>
[STEPS]
?. [Sterilization]
Standard cleaning is best done with DI water.If sterilization is needed, use ethyl alcohol (typically >90%) or isopropyl alcohol (typically... | ["[Sterilization]\nStandard cleaning is best done with DI water.If sterilization is needed, use ethyl alcohol (typically >90%) or isopropyl alcohol (typically 60-70%) and swirl in the solution for ~10 seconds.", "[Sterilization]\nThen rinse vigorously with DI or tap water and recondition in the applicable analyte Stand... |
75,182 | FLASH-seq protocol | 4 | dx.doi.org/10.17504/protocols.io.kxygxzkrwv8j/v4 | https://www.protocols.io/view/flash-seq-protocol-cmnnu5de | Simone Picelli, Vincent Hahaut | TITLE: FLASH-seq protocol
AUTHORS: Simone Picelli, Vincent Hahaut
[DESCRIPTION]
The single-cell RNA-sequencing (scRNA-seq) field has evolved tremendously since the first paper was published back in 2009. While the first methods analysed just a handful of cells, the throughput and performance rapidly increased over a... | ["[Prepare lysis mix] Prepare the following lysis mix:\n ReagentReaction concentrationVolume (µl)384-well plateTriton-X100 (10% v/v)0.2%0.0208.448dNTP mix (25 mM each)6 mM0.240101.376SMART dT30VN (100 µM)1.8 mM0.0187.603RNAse inhibitor (40 U/µL)1.2 U/µL0.03012.672DTT (100 mM)1.2 mM0.0125.069FS TSO (100 µM)9.2 µM0.09... |
43,815 | TMA-TNP Design | 1 | dx.doi.org/10.17504/protocols.io.bn2fmgbn | https://www.protocols.io/view/tma-tnp-design-bn2fmgbn | Heidi Feiler, Koei Chin | TITLE: TMA-TNP Design
AUTHORS: Heidi Feiler, Koei Chin
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Human Tumor Atlas Tissue MicroArrary TNP (TMA-TNP)</div><br/><div class = "text-block">The Tissue MicroArray (TMA) TNP will extend the SARDANA-TNP characterization and analytics methodologies fo... | ["[TMA Map of Participant IDs]\nA custom breast TMA design generated by Dr. Koei Chin (OHSU) was sent to Pantomics for TMA FFPE block generation and sectioning. The randomized array design, outlined below, was used to generate 2 identical TMAs, TMA1 and TMA2. Cores from tumor samples with Pantomics Ref. No. were arr... |
55,908 | Processing human frontal cortex brain tissue for population-scale Oxford Nanopore long-read DNA sequencing SOP | 4 | dx.doi.org/10.17504/protocols.io.b2ucqesw | https://www.protocols.io/view/processing-human-frontal-cortex-brain-tissue-for-p-b2ucqesw | Kimberley J Billingsley, Ramita Dewan, Laksh Malik, Pilar Alvarez Jerez, Stith Kiley, Cornelis Blauwendraat, on behalf of the CARD Long-read Team | TITLE: Processing human frontal cortex brain tissue for population-scale Oxford Nanopore long-read DNA sequencing SOP
AUTHORS: Kimberley J Billingsley, Ramita Dewan, Laksh Malik, Pilar Alvarez Jerez, Stith Kiley, Cornelis Blauwendraat, on behalf of the CARD Long-read Team
[DESCRIPTION]
Processing human frontal cortex ... | ["Part 1: Brain Tissue Cutting (~2.5 hours for 16 samples)", "[Part 2: TissueRuptor Brain Tissue Disruption (~3 hours)]", "Part 3: KingFisher Apex Nanobind Tissue Big DNA protocol (~2 hours)", "Part 4: DNA Shearing (8 hours per 48 samples)", "Part 5: DNA Quantification", "Part 6: Library Prep (~6 hours, not including f... |
19,389 | Instructions for recreating elPrep 4.0.0 WES benchmarks | null | dx.doi.org/10.17504/protocols.io.w65fhg6 | null | Charlotte Herzeel | TITLE: Instructions for recreating elPrep 4.0.0 WES benchmarks
AUTHORS: Charlotte Herzeel
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Instructions for recreating the elPrep4.0.0 WES benchmarks used in the following paper:</div><div class = "text-block">Herzeel C, Costanza P, Decap D, Fostier J, ... | ["Configuration1.1 Hardware1.2 Software\nThese instructions have been tested with elPrep v.4.0.0. The following assumes that everything is performed from a working directory WORKDIR.\n* 2x18-core Intel Xeon processor E5-2699v3 Haswell @ 2.3GHz* 256 GB RAM* 2x400 GB SSD\n* Ubuntu 14.04.5 LTS* elPrep 4.0.1", "Installatio... |
68,655 | PCR (Instructor Protocol) | 4 | null | https://www.protocols.io/view/pcr-instructor-protocol-cfaptidn | Brian Teague | TITLE: PCR (Instructor Protocol)
AUTHORS: Brian Teague
[DESCRIPTION]
This is the instructor protocol for the CURE's two PCRs,
and
The URA3 PCR is preparative, to make the URA3 cassette for the gene knockout. The knockout PCR is diagnostic, to see whether the knockout succeeded.
[STEPS]
SECTION: Setup
1. Ali... | ["[Setup] Aliquot into 100 µL aliquots, 1 per 4 students.", "[Setup] If not done already, aliquot into 1 mL aliquots, 1 per 4 students.", "[Setup] For the URA3 PCR: grow and miniprep the E. coli hosting YTK74, using or similar. Dilute to 1 ng/ul in elution buffer and make 20 µL aliquots, 1 tube for every 4 stud... |
99,368 | 0.1xBWT+SDS buffer | 3 | dx.doi.org/10.17504/protocols.io.kqdg32p7qv25/v1 | https://www.protocols.io/view/0-1xbwt-sds-buffer-ddag22bw | Anna Schmidt, Sarah Nagel, Matthias Meyer, Elena Essel | TITLE: 0.1xBWT+SDS buffer
AUTHORS: Anna Schmidt, Sarah Nagel, Matthias Meyer, Elena Essel
[DESCRIPTION]
Protocol for the preparation of 0.1x BWT+SDS buffer (Bind and wash buffer I) for automated single-stranded DNA library preparation using the ssDNA2.0 method (Gansauge et al. 2020).
References
Gansauge, M.-T., Aximu... | [] |
64,241 | Luminex Magnetic Bead Assay for Assessment of the Immune Response to Vibrio cholerae | 1 | dx.doi.org/10.17504/protocols.io.3byl4b1x8vo5/v1 | https://www.protocols.io/view/luminex-magnetic-bead-assay-for-assessment-of-the-cayrsfv6 | dmslater, Jason Harris | TITLE: Luminex Magnetic Bead Assay for Assessment of the Immune Response to Vibrio cholerae
AUTHORS: dmslater, Jason Harris
[DESCRIPTION]
This protocol provides instructions for assessing antibody responses to Vibrio cholerae in human blood plasma samples using a multiplex bead assay (MBA).
Magnetic microspheres (be... | ["[Definitions/Abbreviations] Beads: Luminex® MagPlex® microspheres\nBSA: bovine serum albumin\nMFI: mean fluorescent intensity\nPBS: phosphate buffered saline\nPPE: personal protective equipment \nrpm: revolutions per minute\nO1 Standard: A high-titer pooled plasma sample prepared from convalescent plasma of patients ... |
64,949 | Standard Operating Procedure for performing Human Landing Catch (HLC) | 1 | dx.doi.org/10.17504/protocols.io.j8nlkkypwl5r/v1 | https://www.protocols.io/view/standard-operating-procedure-for-performing-human-cbnvsme6 | Tanya L L Russell, Kyran Staunton, Thomas R Burkot | TITLE: Standard Operating Procedure for performing Human Landing Catch (HLC)
AUTHORS: Tanya L L Russell, Kyran Staunton, Thomas R Burkot
[DESCRIPTION]
The purpose of this SOP is to outline the materials and processes required to perform a human landing catch (HLC) of adult mosquitoes.
Description: HLC consists of c... | ["Ensure collectors have mouth aspirators to sample mosquitoes.", "Ensure collectors have collection cups to store collected mosquitoes in during sampling. At the start of the night, set up sufficient paper cups for the work. Ensure that the cups are used in the correct order for time.", "Collector position: \n\nCommon... |
81,643 | Efficacy of Electrical Stimulation (ES) on Upper Limb Neurological and Functional recovery in Patients with Spinal Cord Injury: Protocol for a Randomised Controlled Trial | 1 | dx.doi.org/10.17504/protocols.io.4r3l27wzjg1y/v1 | https://www.protocols.io/view/efficacy-of-electrical-stimulation-es-on-upper-lim-ctyjwpun | Md Obaidul Haque, Hassan M. Al- Emran | TITLE: Efficacy of Electrical Stimulation (ES) on Upper Limb Neurological and Functional recovery in Patients with Spinal Cord Injury: Protocol for a Randomised Controlled Trial
AUTHORS: Md Obaidul Haque, Hassan M. Al- Emran
[DESCRIPTION]
Background: Spinal cord injury (SCI) causes physical disability including a dete... | [] |
28,914 | Bacteria Staining | null | dx.doi.org/10.17504/protocols.io.8gshtwe | null | Guillermo Fernández Rodríguez | TITLE: Bacteria Staining
AUTHORS: Guillermo Fernández Rodríguez
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">A bacteria staining protocol has been automated by OT-2. It allows to check the amount of target we had coated on the 96 well plate. </div><div class = "text-block">(We used 5 replicates p... | ["[Staining bacteria ]\nInoculate a single colony of E.Coli DH5α from LB agar plate in of LB. Use a sterile pipette tip, selecting a single colony from LB agar plate. The liquid culture is incubated overnight .\n10 ml\n37 °C", "[Staining bacteria ]\nSpin at for . Discard the supernatant, collect pellet and re-susp... |
97,101 | USDA LTAR Common Experiment measurement: Cereal crop mycotoxin concentration | 1 | dx.doi.org/10.17504/protocols.io.j8nlk8b6xl5r/v1 | https://www.protocols.io/view/usda-ltar-common-experiment-measurement-cereal-cro-da3m2gk6 | Brook J. Wilke, Martin I. Chilvers | TITLE: USDA LTAR Common Experiment measurement: Cereal crop mycotoxin concentration
AUTHORS: Brook J. Wilke, Martin I. Chilvers
[DESCRIPTION]
Crop pests and diseases can reduce crop yields, but they can also worsen crop quality via reduced grain density or accumulation of toxins produced by fungal diseases. Several my... | ["[Sample collection, processing, and analysis] Collect a representative subsample of grain from each experimental unit in the study that contains grains produced by grass species possibly infected with DON, including plots and fields.", "[Sample collection, processing, and analysis] If using the whole plot/field harve... |
33,266 | Isolating human intestinal crypts from biopsies for organoid generation | null | dx.doi.org/10.17504/protocols.io.bcqsivwe | null | Ran Zhou, Candace Cham, Jason Koval | TITLE: Isolating human intestinal crypts from biopsies for organoid generation
AUTHORS: Ran Zhou, Candace Cham, Jason Koval
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol provides details on crypt isolation from human terminal ileum and colon to robustly generate organoids.</div></div... | ["Collect biopsies in PBS or culture media in 1.5 ml Eppendorf tubes.", "Incubate all the tissues from each biopsy in 25mL of 8 mM EDTA/PBS in a 50 ml conical tube for 30 min, rocking (not shaking) at 4C.\n4 °C", "Place one 100 um cell strainer on each well of a 6-well plate. Pre-wet the cell strainer with 1mL culture ... |
102,545 | Yale Murine TMC - H&E staining following Phenocycler-Fusion Imaging | 0 | dx.doi.org/10.17504/protocols.io.ewov19zjklr2/v1 | https://www.protocols.io/view/yale-murine-tmc-h-amp-e-staining-following-phenocy-dgdr3s56 | Jungmin Nam, Yale Pathology Tissue Services, Rong Fan, Archibald Enninful | TITLE: Yale Murine TMC - H&E staining following Phenocycler-Fusion Imaging
AUTHORS: Jungmin Nam, Yale Pathology Tissue Services, Rong Fan, Archibald Enninful
[DESCRIPTION]
Flow cell removal after Phenocycler-Fusion imaging and following H&E staining steps from Yale Pathology Tissue Services (YPTS).
[STEPS]
SECTI... | ["[Hematoxylin and eosin staining] Stain with hematoxylin for 5 min.", "[Hematoxylin and eosin staining] Bluing for 1 min.", "[Hematoxylin and eosin staining] Rinse with water.", "[Hematoxylin and eosin staining] Clarifier for 30 seconds.", "[Hematoxylin and eosin staining] Rinse with water.", "[Hematoxylin and eosin s... |
22,569 | Increased sensitivity of Euplotes crassus to selective agents using 0.3 M glucose-based culture conditions. | null | dx.doi.org/10.17504/protocols.io.2ahgab6 | null | Lawrence A. Klobutcher, Larry Klobutcher | TITLE: Increased sensitivity of Euplotes crassus to selective agents using 0.3 M glucose-based culture conditions.
AUTHORS: Lawrence A. Klobutcher, Larry Klobutcher
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Numerous unpublished studies indicate that </span><span style = "font-style:itali... | ["Distribute a dense culture of Dunaliella salina to two 50 ml screw-cap centrifuge tubes, and pellet the algae by centrifugation at 1,000 RPM (~200 x g) for 2 min. in a clinical centrifuge.", "Remove all but the last 2.5 ml of supernatant from each tube, resuspend the algae pellets, and combine.", "To the above tube, ... |
63,303 | 10X Genomics Single-Nucleus Multiome (RNA + ATAC) Assay for Profiling Adult Human Tissues | 1 | dx.doi.org/10.17504/protocols.io.5qpvoby69l4o/v2 | https://www.protocols.io/view/10x-genomics-single-nucleus-multiome-rna-atac-assa-b93fr8jn | Kimberly Conklin, Bo Zhang, Amanda Knoten, Dinh Diep, Blue Lake, Sanjay Jain, Kun Zhang | TITLE: 10X Genomics Single-Nucleus Multiome (RNA + ATAC) Assay for Profiling Adult Human Tissues
AUTHORS: Kimberly Conklin, Bo Zhang, Amanda Knoten, Dinh Diep, Blue Lake, Sanjay Jain, Kun Zhang
[DESCRIPTION]
10X Genomics Single Cell 3' (v3) RNA sequencing is a microdroplet-based method that permits the effective cap... | ["[Isolate Nuclei] Prepare nuclei according to the protocol \"Isolation of single nuclei from solid tissues\" steps 1-14, with the following modifications:\nTissue sections are cut and stored on dry ice until processed for nuclei isolation (locally or shipped/stored overnight). Sections cannot be stored in RNAlater or ... |
104,289 | Wheat spike meristem micro-dissection | 0 | dx.doi.org/10.17504/protocols.io.3byl49r2zgo5/v1 | https://www.protocols.io/view/wheat-spike-meristem-micro-dissection-dh3938r6 | Isabel Faci, Anna Elisabeth Backhaus, Cristobal Uauy | TITLE: Wheat spike meristem micro-dissection
AUTHORS: Isabel Faci, Anna Elisabeth Backhaus, Cristobal Uauy
[DESCRIPTION]
The aim of this protocol is to micro-dissect young wheat plants to access developing meristems which are found enveloped within growing leaves. This protocol can be used to dissect spikes during ear... | ["[Materials needed - Setup] Gather the following materials: \n\nDissection knives: GeeEdge ophtalmic slit knife model CJY-01-2.2. Another recommended knife is the GeeEdge MVR CJY-04-20g(Z), up to personal preference. \nThese are one-use knives, however we clean and re-use them until the blade is worn off (they last fo... |
77,324 | nanochromosome arrays combinatory assembly | 1 | dx.doi.org/10.17504/protocols.io.bp2l69p95lqe/v1 | https://www.protocols.click/view/nanochromosome-arrays-combinatory-assembly-cprkvm4w | Dariusz Abramczyk, Dariusz Abramczyk | TITLE: nanochromosome arrays combinatory assembly
AUTHORS: Dariusz Abramczyk, Dariusz Abramczyk
[DESCRIPTION]
The yeast Pichia pastoris is used widely to biomanufacture high-value recombinant proteins. Its cells can secrete copious quantities of post-translationally modified proteins. Currently, however, heterologous ... | ["[Preparation of triple-LHR integration array LHRA-PAOXPDI-LHRE-HygR-LHRZ] DNA parts preparation by PCR reactions\nList of DNA parts \n \n* see 1.1 for prepartion (below)\n**link https://www.protocols.io/view/preparation-of-parts-hygr-lhrz-and-zeor-lhrz-cqujvwun", "[Preparation of triple-LHR integration array LHRA-PAO... |
null | null | null | dx.doi.org/10.17504/protocols.io.imncc5e | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
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64,402 | Exipure Reviews 2022: Does Exipure Weight Loss Pills Works? Know This Before Buying | 3 | dx.doi.org/10.17504/protocols.io.rm7vzyqd5lx1/v1 | https://www.protocols.io/view/exipure-reviews-2022-does-exipure-weight-loss-pill-ca5ssg6e | exipure | TITLE: Exipure Reviews 2022: Does Exipure Weight Loss Pills Works? Know This Before Buying
AUTHORS: exipure
[DESCRIPTION]
(LOWEST PRICE ONLINE) Click Here to Buy Exipure For The Lowest Price Guaranteed
[STEPS] | [] |
14,561 | Molecular screening for intestinal parasites | null | dx.doi.org/10.17504/protocols.io.sf9ebr6 | null | Chiara Piubelli, Fabio Formenti, Francesca Perandin | TITLE: Molecular screening for intestinal parasites
AUTHORS: Chiara Piubelli, Fabio Formenti, Francesca Perandin
[STEPS] | [] |
102,774 | JAX-Sen: Mouse heart dissociation for single-cell RNA sequencing | 0 | dx.doi.org/10.17504/protocols.io.rm7vzj55xlx1/v1 | https://www.protocols.io/view/jax-sen-mouse-heart-dissociation-for-single-cell-r-dgkw3uxe | Ramalakshmi Ramasamy, Juliana Alcoforado Diniz, Patrick Fleming, Jessica Garofalo, Paul Robson | TITLE: JAX-Sen: Mouse heart dissociation for single-cell RNA sequencing
AUTHORS: Ramalakshmi Ramasamy, Juliana Alcoforado Diniz, Patrick Fleming, Jessica Garofalo, Paul Robson
[DESCRIPTION]
These samples are part of the JAX-Sen project in the SenNet Consortium. We aim to study and characterize senescence in the C57Bl/... | ["[Reagents and Materials] 5 ml Protein lobind tubes\n1.5 or 2 ml Protein lobind tubes\nMicro scissors/ scalpel\nIce-cold PBS\nWide-bore pipette tips\n0.25% Trypsin/EDTA (Gibco, 25200056). - 2 ml/sample\n20 mg/mL collagenase A and B (Sigma, 10103578001, 11088807001) – 2 ml/sample\nDMEM + 10% FBS\n100 µm cell strainer ... |
27,417 | Ex vivo stimulation of peripheral blood mononuclear cells (PBMC) | null | dx.doi.org/10.17504/protocols.io.6zzhf76 | null | John Davis Coakley | TITLE: Ex vivo stimulation of peripheral blood mononuclear cells (PBMC)
AUTHORS: John Davis Coakley
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Stimulation of PBMCs to study TH1 and TH17 Lymphocytes.</div><div class = "text-block">PBMCs were incubated in medium alone, or stimulated for 5 hours w... | ["Label a 96 well flat bottomed microtiter plate:A = Medium (no stimulation)B = P/IC = LPSD= CD3/CD28 coated wells ABCD1MediumP/ILPSNo CD3/CD282MediumP/INo LPSCD3/CD28 bound3MediumP/INo LPSCD3/CD28 bound4MediumP/INo LPSCD3/CD28 bound5MediumP/INo LPSCD3/CD28 bound6MediumP/INo LPSCD3/CD28 bound7MediumP/INo LPSCD3/CD28 b... |
27,737 | U Michigan - Illumina 16S rRNA gene sequencing using DNA | null | dx.doi.org/10.17504/protocols.io.7bzhip6 | null | Vincent Young | TITLE: U Michigan - Illumina 16S rRNA gene sequencing using DNA
AUTHORS: Vincent Young
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span></div><div class = "text-block">
This protocol is for the submission of DNA to generate libraries for 16S rRNA seque... | ["In a clean hood, add at least 20 uL of DNA to each well of the twin.tec plates. Reserve at least two wells in the full-skirted PCR plate for controls. Maximum number of samples per plate is 94. Seal with sterile foil seal. Clearly label plates with PI, Reference ID, and date.IMPORTANT: Seal plates very well to reduce... |
null | null | null | dx.doi.org/10.17504/protocols.io.fw3bpgn | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?. | [] |
35,933 | Kit-free automated RNA extraction for SARS-CoV-2 testing | null | dx.doi.org/10.17504/protocols.io.bfb5jiq6 | https://www.protocols.io/view/kit-free-automated-rna-extraction-for-sars-cov-2-t-bfb5jiq6 | Efthymios Fidanis, Maria Greco, Amelia Edwards, Margaret Crawford, Laura Cubitt, Sophia Ward, Robert Goldstone, Nnenna Kanu, James MacRae, Michael Hubank, Jerome Nicod | TITLE: Kit-free automated RNA extraction for SARS-CoV-2 testing
AUTHORS: Efthymios Fidanis, Maria Greco, Amelia Edwards, Margaret Crawford, Laura Cubitt, Sophia Ward, Robert Goldstone, Nnenna Kanu, James MacRae, Michael Hubank, Jerome Nicod
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style... | ["[Biomek FX Setup]\nOpen the Biomek software, and select the program “RNA Extraction vFINAL” which is located in the “Covid-19” project:\nRNA extraction automated on Biomek FX using IN HOUSE protocol.This protocol descibes the processing of one 96-well plate (93 samples and 3 controls).[Note: At the Crick we have two ... |
107,522 | Manual Basescope Duplex Assay | 0 | dx.doi.org/10.17504/protocols.io.x54v9245ml3e/v1 | https://www.protocols.io/view/manual-basescope-duplex-assay-dk9a4z2e | Hector Martell Martinez | TITLE: Manual Basescope Duplex Assay
AUTHORS: Hector Martell Martinez
[DESCRIPTION]
This protocol details the manual basescope duplex assay.
[STEPS]
SECTION: Day 1
1. Bake slides @ 60 °C for 60 min.
SECTION: Day 2
9. Turn on oven to 40 °C. Spray everything with RNase Away.
Wash slides in 1X Wash buffer for 2 min 2X... | ["[Day 1] Bake slides @ 60 °C for 60 min.", "[Day 2] Turn on oven to 40 °C. Spray everything with RNase Away.\n\nWash slides in 1X Wash buffer for 2 min 2X.\n\nWash slides in 1X Wash buffer for 2 min (1/2).\nWash slides in 1X Wash buffer for 2 min (2/2).", "[Day 1] Deparaffinize", "[Day 1] Target Retrieval", "[Day 1] H... |
93,357 | Virus injections and lens placement (Mendonça et al 2024) | 1 | dx.doi.org/10.17504/protocols.io.81wgbx813lpk/v1 | https://www.protocols.io/view/virus-injections-and-lens-placement-mendon-a-et-al-c7emzjc6 | Marcelo D Mendonça | TITLE: Virus injections and lens placement (Mendonça et al 2024)
AUTHORS: Marcelo D Mendonça
[DESCRIPTION]
Protocol for viral injections and GRIN lens placement used in Mendonça et al 2024.
[BEFORE_START]
Mice were kept in deep anesthesia using 1-3% isoflurane and oxygen (at 1L/min flow rate).
[GUIDELINES]
All pro... | ["[Stereotaxic Surgery] Place the anesthetized mouse in the stereotaxic apparatus then stabilize the head.", "[Stereotaxic Surgery] Make a skin incision to expose the skull.", "[Stereotaxic Surgery] Carefully remove any connective and muscle tissue from the exposed area.", "[Stereotaxic Surgery] Level the skull surface... |
47,417 | Salivary DNA Extraction | 4 | dx.doi.org/10.17504/protocols.io.3byl4k598vo5/v1 | https://www.protocols.io/view/salivary-dna-extraction-bsizncf6 | Clemens Scherzer, Bradley Hyman, Charles Jennings | TITLE: Salivary DNA Extraction
AUTHORS: Clemens Scherzer, Bradley Hyman, Charles Jennings
[DESCRIPTION]
This protocol explains the Standard Operating Protocol for extracting salivary DNA.
[BEFORE_START]
DNA Q/C GOALS
1. Cary Concentration Assay
a. 260/280 = 1.8-2.0
b. Manual Puragene Extraction: ... | ["[Salivary DNA Extraction] Mix sample in the DNA Genotek kit by inversion and gentle shaking.", "[Salivary DNA Extraction] Weigh sample in original tube and subtract 6.81g to estimate saliva volume provided – amount of saliva collected is directly proportional to the amount of DNA recovered.", "[Salivary DNA Extractio... |
84,263 | Phenocycler Fusion BIDMC-TMC | 4 | null | https://www.protocols.click/view/phenocycler-fusion-bidmc-tmc-cwifxcbn | aploumak, tvthrasher, nkalavro | TITLE: Phenocycler Fusion BIDMC-TMC
AUTHORS: aploumak, tvthrasher, nkalavro
[DESCRIPTION]
The PhenoCycler Fusion protocol used by the Spatial Technologies Unit at the BIDMC for the profiling of lymphatic vessels in the BIDMC - Lymphatic Vessels TMC.
The Phenocycler Fusion (PCF, AKOYA Biosciences) consists of a liqu... | ["[Sample Collection] Isolate and collect lymphatic vessels following consent as part of surgical procedures according to criteria and procedures outlined in dx.doi.org/10.17504/protocols.io.e6nvwjeb7lmk/v1.", "[Sample Treatment] Following sectioning, the slides are placed sample side up on drierite beads for 5 min, fo... |
92,479 | DNA Barcoding Protocol for Arthropods | 4 | null | https://www.protocols.io/view/dna-barcoding-protocol-for-arthropods-c6i7zchn | Valerie Warhol | TITLE: DNA Barcoding Protocol for Arthropods
AUTHORS: Valerie Warhol
[DESCRIPTION]
This is a basic protocol for doing extraction and amplification of DNA barcodes (COI) for arthropods (typically small insects or spiders).
[STEPS]
SECTION: Prepare sample and equipment
1. Make sure all instruments, such as forceps and ... | ["[Prepare sample and equipment] Make sure all instruments, such as forceps and pestle, are clean and sterile.", "[Lyse cells] Put sample in tube. Grind sample with pestle until broken up into tiny pieces.", "[Prepare sample and equipment] Prepare water bath at 65 °C.", "[Prepare sample and equipment] Dissect sample fr... |
58,849 | Preparing 10x TBE Electrophoresis buffer | 4 | dx.doi.org/10.17504/protocols.io.j8nlkkok5l5r/v1 | https://www.protocols.io/view/preparing-10x-tbe-electrophoresis-buffer-b5p9q5r6 | Nadine Mowoh, Jenny Molloy | TITLE: Preparing 10x TBE Electrophoresis buffer
AUTHORS: Nadine Mowoh, Jenny Molloy
[DESCRIPTION]
TBE and TAE buffers are often used in procedures involving nucleic acids, the most common being electrophoresis. Tris-acid solutions are effective buffers for slightly basic conditions, which keep DNA deprotonated and... | ["[Preparing 10x TBE buffer solution (1 liter)] Use an electronic balance to weigh out 108 g Tris base (CAS# 77-86-1, free base) into a 1000 mL ml or higher volume beaker ( depending on what volume of beaker is available and should be big enough to contain the powders to be dissolved).", "[Preparing 10x TBE buffer solu... |
41,824 | 1DROP SARS-CoV-2 antigen test | 4 | dx.doi.org/10.17504/protocols.io.bk38kyrw | https://www.protocols.io/view/1drop-sars-cov-2-antigen-test-bk38kyrw | Mahe Raccaud, Manon Garzuel, Joerg Ziegler, Luc Gervais | TITLE: 1DROP SARS-CoV-2 antigen test
AUTHORS: Mahe Raccaud, Manon Garzuel, Joerg Ziegler, Luc Gervais
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Our capillary-driven microfluidic chips automatically detect multiple SARS-CoV-2 antigens after the addition of a few drops of saliva, triggering a ca... | ["[Sample collection]\nCollect patient saliva in the Collection Tube. Saliva must be collected until the amount reaches above the line.\n1 mL", "[Device preparation]\nSwitch on the 1DROP Analyzer with the side switch.", "[Device preparation]\nScan the Chip on the scanner of the 1DROP Analyzer.", "[Device preparation]\... |
null | null | null | dx.doi.org/10.17504/protocols.io.himb4c6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol was developed for isolating high quality genomic DNA from Heterosigma akashiwo for the purpose of Next generation sequencing technologies. We successfully repeated this protocol to obtain genomic DNA. </p>
[STEPS]
?.
?.
?.
?.
?.
?.
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?.
?.
?.
?.... | [] |
46,672 | MinION DNA Library Prep (SQK-LSK109) | 4 | null | https://www.protocols.io/view/minion-dna-library-prep-sqk-lsk109-brtqm6mw | Victoria Jackson, Michelle Michelsen | TITLE: MinION DNA Library Prep (SQK-LSK109)
AUTHORS: Victoria Jackson, Michelle Michelsen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol for ligation sequencing DNA library prep for MinION slightly modified from the ONT protocol.</div></div>
[STEPS]
?. [Bead clean-up 1]
Make up of DNA sa... | ["[Bead clean-up 1]\nMake up of DNA sample in nuclease-free water to a volume of in an Eppendorf DNA LoBind tube.Make of fresh 70% ethanol. Place an 1.5 mL tube of nuclease-free water on a heat block set to .\n1 µg\n49 µl\n150 µl\n55 °C", "[Bead clean-up 1]\nResuspend the by vortexing.Add to the DNA and gently flic... |
103,094 | Purification of NIX-GFP | 0 | dx.doi.org/10.17504/protocols.io.x54v9219zl3e/v1 | https://www.protocols.io/view/purification-of-nix-gfp-dgww3xfe | Elias Adriaenssens | TITLE: Purification of NIX-GFP
AUTHORS: Elias Adriaenssens
[DESCRIPTION]
This protocol details the purification of NIX-GFP.
[STEPS]
SECTION: Purification - NIX-GFP
1. To purify GFP-tagged
NIX-GFP (available from Addgene) or NIX(W36A/L39A)-GFP (ΔLIR)(available from Addgene),
fuse the cytosol-exposed domain of NIX ... | ["[Purification - NIX-GFP] To purify GFP-tagged \n\nNIX-GFP (available from Addgene) or NIX(W36A/L39A)-GFP (ΔLIR)(available from Addgene), \n\nfuse the cytosol-exposed domain of NIX (1-182aa) to a C-terminal GFP-tag through cloning into a pET-DUET1 vector (available from Addgene).", "[Purification - NIX-GFP] Introduce ... |
17,397 | Isolate prokaryotes from sponge tissue (SAP) | null | dx.doi.org/10.17504/protocols.io.u8vezw6 | null | Martin Thomas Jahn | TITLE: Isolate prokaryotes from sponge tissue (SAP)
AUTHORS: Martin Thomas Jahn
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Protocoll to create a fixed suspension of sponge associated prokaryotes</span><span> (SAP) from sponge tissue.This can serve as the basis ... | ["[Dissect and homogenise tissue]\nMince sponge tissue in ice cold CMASW using a razor blade within a petry dish on ice\nTissue can be either fresh or thawed from -20°C samplesProcess about the tissue volume that would fit in a 1.5 ml eppendorf tube", "[Dissect and homogenise tissue]\nSqueeze remaining pieces using 15 ... |
25,422 | Sequence Analysis of a Plasmid | null | dx.doi.org/10.17504/protocols.io.43ngyme | null | Addgene The Nonprofit Plasmid Repository | TITLE: Sequence Analysis of a Plasmid
AUTHORS: Addgene The Nonprofit Plasmid Repository
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol is for sequence analysis of a plasmid. To see the full abstract and additional resources, please visit </span><a href="https://www.addgene.org/p... | [] |
49,603 | Sampling of Human Islets for Quality Control Purposes | 1 | dx.doi.org/10.17504/protocols.io.bupbnvin | https://www.protocols.io/view/sampling-of-human-islets-for-quality-control-purpo-bupbnvin | James Lyon, Aliya Spigelman, Jocelyn E Manning Fox, Patrick Macdonald | TITLE: Sampling of Human Islets for Quality Control Purposes
AUTHORS: James Lyon, Aliya Spigelman, Jocelyn E Manning Fox, Patrick Macdonald
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol described the sampling of human islets for quality control purposes, as performed by the Alb... | ["[Solution Preparation]\nTo of Milli-Q water add the following reagents and allow to mix into solution. The citric acid will not completely go into solution until the pH is set to 7.4 Sodium Citrate Dihydrate Sodium Chloride Disodium EDTA Bring to volume with Milli-Q water and set the pH to... |
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