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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63,903 | oplexx keto 2022 – Another Scam or Good Diet Pills? | Shark Tank, Side effects, Results | 3 | dx.doi.org/10.17504/protocols.io.14egn7j5yv5d/v1 | https://www.protocols.io/view/oplexx-keto-2022-another-scam-or-good-diet-pills-s-cam7sc9n | Pure Keto, Anonymous For Review | TITLE: oplexx keto 2022 – Another Scam or Good Diet Pills? | Shark Tank, Side effects, Results
AUTHORS: Pure Keto, Anonymous For Review
[DESCRIPTION]
oplexx keto
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.fbcbiiw | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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48,364 | Expression and purification protocol of Homo sapiens E2-like enzyme ATG3 | 4 | dx.doi.org/10.17504/protocols.io.btgknjuw | https://www.protocols.io/view/expression-and-purification-protocol-of-homo-sapie-btgknjuw | Eleonora Turco, Dorotea Fracchiolla | TITLE: Expression and purification protocol of Homo sapiens E2-like enzyme ATG3
AUTHORS: Eleonora Turco, Dorotea Fracchiolla
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes expression and purification procedures for obtaining human recombinant autophagy E2-like enzyme ATG3 (A... | ["[Protein Purification]\nCells are lised via freeze/thaw cycles and sonication: thaw pellet corresponding to culture by freeze/thawing in water bath. All following steps are to be executed at or on ice.\n1 L\n0 Room temperature\n4 °C", "[Protein Purification]\nLyse cells by sonicating them using an immersion tip So... |
60,084 | NEBNext® Immune Sequencing Kit (Mouse) (NEB #E6330S/L) | 4 | dx.doi.org/10.17504/protocols.io.yxmvmn9e5g3p/v1 | https://www.protocols.io/view/nebnext-immune-sequencing-kit-mouse-neb-e6330s-l-b6wurfew | New England Biolabs, jbonnevie | TITLE: NEBNext® Immune Sequencing Kit (Mouse) (NEB #E6330S/L)
AUTHORS: New England Biolabs, jbonnevie
[DESCRIPTION]
The NEBNext Immune Sequencing Kit (Mouse) contains enzymes and buffers that are ideal to convert a small amount of RNA input into indexed libraries for next-generation sequencing on the Illumina MiSeq ... | ["[NEBNext Immune Sequencing Reverse Transcription and cDNA Synthesis] Mix the following components in a sterile nuclease-free tube:", "[NEBNext Immune Sequencing Reverse Transcription and cDNA Synthesis] Set a 100 µl or 20 µl pipette to 15 µl and then pipette the entire volume up and down at least 10 times to mix thor... |
71,481 | Organotypic Hippocampal Slice Culture PROTOCOL | 4 | dx.doi.org/10.17504/protocols.io.81wgby6pnvpk/v1 | https://www.protocols.io/view/organotypic-hippocampal-slice-culture-protocol-ch2zt8f6 | Machlusil Husna, Kusworini Handono, Hidayat Sujuti, Aulanni'am, Ettie Rukmigarsari | TITLE: Organotypic Hippocampal Slice Culture PROTOCOL
AUTHORS: Machlusil Husna, Kusworini Handono, Hidayat Sujuti, Aulanni'am, Ettie Rukmigarsari
[DESCRIPTION]
Neurodegeneration due to neurotoxicity is one of the phenomena in temporal lobe epilepsy. Experimentally, hippocampal excitotoxicity process can occur due to k... | ["[Preparation of Materials] Prepare your Equipment and Reagents", "[Sterilization of Tools and Materials] The tools and materials that need to be sterilized inside the autoclave are as follows:\n•Millicell cell culture inserts that have been cut into 3, then put in a petri dish\n•Surgical tools\n•Blue tip and yellow t... |
48,067 | Ultra-Rapid Sequencing (PCR) | 4 | null | https://www.protocols.io/view/ultra-rapid-sequencing-pcr-bs7bnhin | Jack Wadden | TITLE: Ultra-Rapid Sequencing (PCR)
AUTHORS: Jack Wadden
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol accompanies the paper "Ultra-Rapid Somatic Variant Detection via Real-Time Threshold Sequencing." This protocol was followed to initiate a sequencing run that resulted in a somatic ... | ["[DNA Extraction]\nWhen acquired, place tumor tissue into DNA extraction tube\n20 µg\n2 mL", "[Target Amplification]\nAdd extracted DNA to PCR reaction tube\n1 µl", "[Library Preparation]\nAdd PCR product to tagmentation mix tube, flick to mix, and spin down\n7.5 µl", "[Preparation]\nPrepare the PCR reaction tube ... |
43,125 | Cultivating Melanized Fungi from Biological Soil Crust and Rock Surfaces | 1 | dx.doi.org/10.17504/protocols.io.4r3l25z2ql1y/v2 | https://www.protocols.io/view/cultivating-melanized-fungi-from-biological-soil-c-bncvmaw6 | Tania Kurbessoian, Jason E. Stajich, Renata Haro | TITLE: Cultivating Melanized Fungi from Biological Soil Crust and Rock Surfaces
AUTHORS: Tania Kurbessoian, Jason E. Stajich, Renata Haro
[DESCRIPTION]
As the interest to understand melanized fungi becomes more of a focus due to pathological diseases, there needs to be a clearer method to isolate and identify the fung... | ["[Prepare Media] Prepare Nutrient Poor Media Glucose Asparagine Agar (GAA) - Krainsky's Media/1 L\n0.500 g \n0.500 g\n10.00 g \n15.00 g \n\nAutoclave\n\nPrepare filtered antibiotics for 1 L agar solution. Either Gentamycin, Tetracycline, Kanamycin, Streptomycin or Chloramphenicol will work.", "[Prepare Media]", "[Pre... |
null | null | null | dx.doi.org/10.17504/protocols.io.iscceaw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Purification of nucleocapsid of tospoviruses from <em>Chenopodium quinoa</em> leaves</p>
[STEPS]
?.
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90,937 | Renal Multicompartment Segmentation Object Boundaries | 1 | dx.doi.org/10.17504/protocols.io.dm6gp35p8vzp/v1 | https://www.protocols.io/view/renal-multicompartment-segmentation-object-boundar-c42zyyf6 | Nicholas Lucarelli | TITLE: Renal Multicompartment Segmentation Object Boundaries
AUTHORS: Nicholas Lucarelli
[DESCRIPTION]
Boundary descriptions for segmentations produced by the CMILab multicompartment segmentation pipeline for PAS-stained renal whole slide images.
[STEPS]
SECTION: segmentations.ome.tiff channels
1. Cortical Interstit... | ["[segmentations.ome.tiff channels] Cortical Interstitium: Defined as the spaces in the renal cortex situated between basement membranes of glomeruli, tubules, and vessels. Does not include perivascular stroma.", "[segmentations.ome.tiff channels] Medulla Interstitium: Defined as the spaces in the renal medulla situate... |
null | null | null | dx.doi.org/10.17504/protocols.io.jfacjie | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This study examined the effects of the ActiGraph’s (AG) low-frequency extension (LFE) filter on steps and physical activity classification in the free-living environment. Thirty-four African-American women (age, 24.5±5.2 years; BMI, 24.9±4.5 kg/m<sup>2</sup>) had daily activ... | [] |
57,783 | CRISPResso analysis | 4 | dx.doi.org/10.17504/protocols.io.b4nxqvfn | https://www.protocols.io/view/crispresso-analysis-b4nxqvfn | Hanqin Li, Yogendra Verma, Dirk Hockemeyer, Frank Soldner | TITLE: CRISPResso analysis
AUTHORS: Hanqin Li, Yogendra Verma, Dirk Hockemeyer, Frank Soldner
[DESCRIPTION]
This protocol describes the process of using CRISPResso to analyze Next Generation Sequencing (NGS) data from CRISPR-targeted, genome-edited samples.
[STEPS]
1. Install CRISPResso2
2. In linux, use the fol... | ["Install CRISPResso2", "In linux, use the following command:\n\nCRISPResso --fastq_r1 R1_reads.fastq.gz –fastq_r2 R2_reads.fastq.gz --amplicon_seq amplicon_seqeunce_here -g sgRNA_sequence_here", "Use CRISPRessoBatch command if having many samples", "For more details, https://github.com/pinellolab/CRISPResso2"] |
33,294 | Assembling Cooled LED Illuminator | null | dx.doi.org/10.17504/protocols.io.bcrniv5e | null | Jakub Nedbal | TITLE: Assembling Cooled LED Illuminator
AUTHORS: Jakub Nedbal
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The cooled LED illuminator is a large heatsink with self-adhesive LED strips, four axial fans, and the LED controller attached to it.</div><div class = "text-block"><span style = "font-wei... | ["Prepare two meters of the LED strip.Cut the LED strip into ten 200 mm (8\") long segments using scissors. Cut along the designated lines going through the solder pads.Prepare the heatsink. The recommended heatsink features a 200 mm × 150 mm flat surface area, 40 mm height, and 0.5 °C/K thermal resistance. Other heats... |
47,319 | Growing overnight bacterial culture in 96WP (Cabreiro Lab) | 1 | null | https://www.protocols.io/view/growing-overnight-bacterial-culture-in-96wp-cabrei-bsfxnbpn | Saul Moore | TITLE: Growing overnight bacterial culture in 96WP (Cabreiro Lab)
AUTHORS: Saul Moore
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Luria broth (LB) is a nutrient-rich media commonly used to culture bacteria in the lab. LB agar plates are frequently used to isolate individual (clonal) colonies of ... | ["Obtain LB Broth from the Media kitchen LB Broth contents: 4gNaCl4 g Tryptone2 g Yeast Extract Add dH2O to 400 mL", "Wipe the work area with 70% ethanol and create a sterile environment on the laboratory bench by using a bunsen or gas burner. Work under the hood if you have a large number of plates. Book the hood in a... |
null | null | null | dx.doi.org/10.17504/protocols.io.dky4xv | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
<table width="149">
<tbody>
<tr>
<td width="83">Tris-HCl pH7.4</td>
<td width="66">50 mM</td>
</tr>
<tr>
<td>NaCl</td>
<td>150 mM</td>
</tr>
<tr>
<td>Sodium Deoxycholate</td>
<td>1 %</td>
</tr>
<tr>
<td>SDS</td>
<td>0.10 %</td>
</tr>
<tr>
<td>Triton-X100</td>
<td>1 %</td>
</tr>
<... | [] |
12,929 | Assessment of trachoma in suspected endemic areas within 14 provinces in mainland China | null | dx.doi.org/10.17504/protocols.io.qu9dwz6 | null | Jialiang Zhao, Silvio Paolo Mariotti, Serge Resnikoff, Yuqin Wang, Shicheng Yu, Mingguang He, Yingchuan Fan, Haidong Zou, Wenfang Zhang, Yading Jia, Lihua Wang, Huaijin Guan, Xiao Xu, Leilei Zhan, Lei An, Quanfu Ye, Ningli Wang | TITLE: Assessment of trachoma in suspected endemic areas within 14 provinces in mainland China
AUTHORS: Jialiang Zhao, Silvio Paolo Mariotti, Serge Resnikoff, Yuqin Wang, Shicheng Yu, Mingguang He, Yingchuan Fan, Haidong Zou, Wenfang Zhang, Yading Jia, Lihua Wang, Huaijin Guan, Xiao Xu, Leilei Zhan, Lei An, Quanfu Ye, ... | ["[Background and rationale]\nChina used to be among the countries with a high prevalence of trachoma. Since the new China was founded in 1949, the government has actively supported trachoma control activities. In 1960s, the Chinese government adopted a policy to strengthen healthcare provision in rural areas, which in... |
70,244 | Staphylococcus Aureus Sampling | 4 | dx.doi.org/10.17504/protocols.io.81wgb6pk1lpk/v10 | https://www.protocols.io/view/staphylococcus-aureus-sampling-cguctwsw | Mar Roca Cugat, Olga Sánchez | TITLE: Staphylococcus Aureus Sampling
AUTHORS: Mar Roca Cugat, Olga Sánchez
[DESCRIPTION]
This protocol is intended to study the affectation of Staphylococcus Aureus, including the MRSA, VISA and VRSA variants, even if it makes the test more difficult to perform. It outlines the basic protocol for a multi-subject stud... | ["[Preparation] Wash your hands with soap. Put on your lab coat, your mask, and your goggles or face shield. Make sure your mask is airtight and air cannot escape through the sides.", "[Preparation] Prepare the area where you are going to work. Disinfect the surfaces with the bleach solution.\nThe subjects should not b... |
86,499 | Sonication of α-synuclein Fibrils for injection into the mouse brain | 1 | null | https://www.protocols.io/view/sonication-of-synuclein-fibrils-for-injection-int-cyqbxvsn | Vijay Singh, Marta Castellana-Cruz, Nunilo Cremades, Laura Volpicelli-Daley | TITLE: Sonication of α-synuclein Fibrils for injection into the mouse brain
AUTHORS: Vijay Singh, Marta Castellana-Cruz, Nunilo Cremades, Laura Volpicelli-Daley
[DESCRIPTION]
Animal models that accurately recapitulate the accumulation of alpha-synuclein (α-syn) inclusions, progressive neurodegeneration of the nigrost... | ["[Sonicating Fibrils] Thaw and pipet 25-22 µL in 1.5 mL polystyrene sonication tube.", "[Sonicating Fibrils] Fill Qsonica water reservoir with about 900 mL.", "[Sonicating Fibrils] Attach cooling system to Qsonica and set the temperature at 10 °C.", "[Sonicating Fibrils] Place 1.5 mL , therefore,sonication tube with f... |
51,967 | nPOP | 1 | null | https://www.protocols.io/view/npop-bwy7pfzn | Andrew Leduc, Nikolai Slavov, Richard Huffman | TITLE: nPOP
AUTHORS: Andrew Leduc, Nikolai Slavov, Richard Huffman
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol for preparing single cells for mass-spec analysis by nPOP using the CellenONE system liquid handling and cell sorting system as described by Leduc et al. DOI. This protocol as... | ["[Carrier and Reference preperation]\nPrepare cell pellets of all relevant cell types of at least 500,000 cells. Add 100% DMSO to cells to a cellular concentration of 6000 cells/ul. Incubate cells in DMSO for 20 minutes to lyse cells. Add mass spectrometry grade water to bring solution to 2000 cells/ul.", "[Carrier an... |
92,341 | RSVAB WGS and GF protocols | 1 | dx.doi.org/10.17504/protocols.io.kqdg3xbzqg25/v3 | https://www.protocols.io/view/rsvab-wgs-and-gf-protocols-c6evzbe6 | miglesias | TITLE: RSVAB WGS and GF protocols
AUTHORS: miglesias
[DESCRIPTION]
This SOP describes the procedure for generating cDNA from RSV viral nucleic acid extracts and subsequently producing amplicons tiling the viral genome using. We propose two systems for genomic characterization of RSV. First, a novel RSV amplicon-based ... | ["[dsCDNA generation:] During this step three master mixes will be prepared: MMI, MMII and MMIII.\nMaterials: Kit Superscript III First Strand (Invitrogen)\n 100% DMSO\n RNAseH (Invitrogen)\n Klenow fragment 3' ->5' exo (New England Biolab... |
null | null | null | dx.doi.org/10.17504/protocols.io.et3beqn | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
This protocol assumes that salt extracts lysin from the virion rather than from cell walls. Yield seems to confirm this assumption.<br /><br />Quality control: lysin assay shows that all chlorophyll has been released and no cell wall material pellets at low speed (wall has been s... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.c26yhd | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Version 1b<br />17 October 2012<br /><br />This protocol decribes the extraction of DNA from viral particles using Wizard Prep Resin and Columns from Promega.
[GUIDELINES]
This protocol is part of a larger collection of Cesium-Chloride related protocols. This is number (3) of (... | [] |
71,698 | Macrofauna Occidental Farms | 4 | dx.doi.org/10.17504/protocols.io.rm7vzby75vx1/v1 | https://www.protocols.io/view/macrofauna-occidental-farms-ch9st96e | Carlos Alberto Zuniga Gonzalez, Conrado Ronaldo Quiroz Medina, Alvaro Jose Caballero Hernandez | TITLE: Macrofauna Occidental Farms
AUTHORS: Carlos Alberto Zuniga Gonzalez, Conrado Ronaldo Quiroz Medina, Alvaro Jose Caballero Hernandez
[DESCRIPTION]
The protocol was divided into two phases, the first was the collection of the sample, and the second was the classification, coding, and storage of the extracted macr... | ["Phase 1: Field: It includes steps 1, 2, 3, 4, 5: Following the methodology modified by Rousseaua in the cocoa plantations in Costa Rica and by Laurente in the Quenzalgual systems in agroforestry systems. (Rousseaua, Deheuvelsb, Rodriguez-Arias, & Somarriba, 2012; Rousseaua, Fonte, Téllez, van der Hoekc, & Lavelle, 20... |
91,745 | Preparation and culture of mouse intestinal organoids | 4 | dx.doi.org/10.17504/protocols.io.ewov1qmqkgr2/v1 | https://www.protocols.io/view/preparation-and-culture-of-mouse-intestinal-organo-c5t9y6r6 | arpine.sokratian, Ian Williamson, Ramos Chavez Katherine, Liddle Roger | TITLE: Preparation and culture of mouse intestinal organoids
AUTHORS: arpine.sokratian, Ian Williamson, Ramos Chavez Katherine, Liddle Roger
[DESCRIPTION]
This protocol details an approach for the dissociation of colon epithelial cells from the murine samples. The key goal is to yield intact crypt samples suitable for... | ["[Dissect Mouse Intestine]", "[Dissect Mouse Intestine] Euthanize mouse in chemical hood with isoflurane followed by cervical dislocation in accordance with IACUC-approved protocol.", "[Murine Small Intestine Epithelial Dissociation]", "[Dissect Mouse Intestine] Dissect intestine", "[Dissect Mouse Intestine] Collect t... |
102,990 | Bioinformatic pipeline for analysing variations in long-reads reconstructed human genomes | 0 | dx.doi.org/10.17504/protocols.io.36wgqnoz3gk5/v1 | https://www.protocols.io/view/bioinformatic-pipeline-for-analysing-variations-in-dgtn3wme | Angelo Sante Varvara, Ilenia Urso, Sharon Natasha Cox, Graziano Pesole | TITLE: Bioinformatic pipeline for analysing variations in long-reads reconstructed human genomes
AUTHORS: Angelo Sante Varvara, Ilenia Urso, Sharon Natasha Cox, Graziano Pesole
[DESCRIPTION]
Recent advances in sequencing technologies have paved the way for personalized medicine and clinical genomics, providing unprece... | ["[Basecalling and alignment] Basecalling raw data in pod5 format with Dorado basecalling.\n\nDorado is a high-performance open-source basecaller for Oxford Nanopore reads.\nFirst, let's download the latest models for our needs with Dorado download.\n \nThen, we can run Dorado basecaller on our raw data in pod5. \nIf y... |
49,463 | Cryopreservation of microalgal cultures | 4 | null | https://www.protocols.io/view/cryopreservation-of-microalgal-cultures-buixnufn | Victoria Jackson | TITLE: Cryopreservation of microalgal cultures
AUTHORS: Victoria Jackson
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol for long-term .cryopreservation of microalgal cell cultures.</div></div>
[STEPS]
?. [Preparing the cryoprotectant]
Make a solution of DMSO in the appropriate culture me... | ["[Preparing the cryoprotectant]\nMake a solution of DMSO in the appropriate culture medium for the strains being preserved.Eg. medium and to make cryoprotectant.\n[culture medium]\n[DMSO]\n50 mL\nWork in the fume hood when using DMSO.", "[Preparing the cultures]\nPrepare the cryotubes with a 1:1 ratio of cryoprot... |
96,651 | Prospective Human Liver, Adipose and Blood Collection v.2 -- University of Minnesota TMC | 0 | dx.doi.org/10.17504/protocols.io.j8nlko7j5v5r/v2 | https://www.protocols.io/view/prospective-human-liver-adipose-and-blood-collecti-damj2c4n | Laura J Niedernhofer, David A Bernlohr | TITLE: Prospective Human Liver, Adipose and Blood Collection v.2 -- University of Minnesota TMC
AUTHORS: Laura J Niedernhofer, David A Bernlohr
[DESCRIPTION]
Collection protocol obtained from the attached BioNet Specimen Procurement Agreement provided by the UMN CTSI Biorepository and Laboratory Services (BLS). *Updat... | [] |
44,746 | SOLUTION- 02 - Phosphate Buffered Saline (PBS) | 3 | dx.doi.org/10.17504/protocols.io.bpximpke | https://www.protocols.io/view/solution-02-phosphate-buffered-saline-pbs-bpximpke | Marco Cosentino, Elisa Storelli, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Marco Ferrari, Franca Marino | TITLE: SOLUTION- 02 - Phosphate Buffered Saline (PBS)
AUTHORS: Marco Cosentino, Elisa Storelli, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Marco Ferrari, Franca Marino
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This recepe is used in the following protocols:</div><div class = "tex... | [] |
94,696 | Elevated body swing test in rats | 1 | dx.doi.org/10.17504/protocols.io.bp2l6x58zlqe/v1 | https://www.protocols.io/view/elevated-body-swing-test-in-rats-c8qgzvtw | eduard.bentea, María Sanchiz Calvo, Veerle Baekelandt | TITLE: Elevated body swing test in rats
AUTHORS: eduard.bentea, María Sanchiz Calvo, Veerle Baekelandt
[DESCRIPTION]
Protocol for performing the elevated body swing test in rats. The elevated body swing evaluates motor asymmetry in body swings when the rat is briefly hanged by the tail, and can be used in animal model... | ["[Test] Bring cages to the behavioral room for at least 60 min prior to the test for habituation", "[Test] Place rat individually in a new cage", "[Test] Wait until attains neutral position with all four limbs touching the bottom of the cage", "[Test] Lift vertically by the base of the tail", "[Test] Record the first ... |
null | null | null | dx.doi.org/10.17504/protocols.io.gvabw2e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div class="page" title="Page 2">
<div class="layoutArea">
<div class="column">
<p>IRDye 800CW Maleimide is a functional derivative of infrared dye IRDye 800CW that is reactive toward free–SH (thiol, sulfhydryl) groups. Most molecules that contain free–SH groups can be labeled w... | ["[Labeling of Affibody® Molecules with IRDye 800CW Maleimide] Prepare a fresh 500 mM solution of TCEP in water (47.5 mg/331 μl).", "[Labeling of Affibody® Molecules with IRDye 800CW Maleimide] {\"blocks\":[{\"key\":\"bh4g3\",\"text\":\" Add 1 \\u03bcl of 500 mM TCEP to 99 \\u03bcl Affibody molecule in PBS (1 mg\\/ml)... |
93,618 | Querying for Bacterial Pathogen Genomic Data at NCBI | 1 | dx.doi.org/10.17504/protocols.io.36wgq3kbklk5/v1 | https://www.protocols.io/view/querying-for-bacterial-pathogen-genomic-data-at-nc-c7nszmee | Maria Balkey, Ruth Timme, Tina Lusk Pfefer, Candace Hope Bias | TITLE: Querying for Bacterial Pathogen Genomic Data at NCBI
AUTHORS: Maria Balkey, Ruth Timme, Tina Lusk Pfefer, Candace Hope Bias
[DESCRIPTION]
PURPOSE: This document provides detailed instructions on how to find bacterial pathogen genomic data and associated contextual information at NCBI, specifically at the BioSam... | ["[NCBI SRA (Sequence Read Archive) Run Sector] WGS submissions of pathogen genomes will become public and searchable almost immediately in SRA Run Selector. \n\nNCBI's SRA Run Selector serves as a platform for querying contextual data, or metadta, from both BioSample and SRA. This is a good first place to check for a ... |
22,674 | Convergence model for effectual prevention and control of zoonotic diseases: a health system study on ‘One Health’ approach in Ahmedabad, India | null | dx.doi.org/10.17504/protocols.io.2dsga6e | null | Sandul Yasobant, Walter Bruchhausen, Deepak Saxena, Timo Falkenberg | TITLE: Convergence model for effectual prevention and control of zoonotic diseases: a health system study on ‘One Health’ approach in Ahmedabad, India
AUTHORS: Sandul Yasobant, Walter Bruchhausen, Deepak Saxena, Timo Falkenberg
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The complexity and incre... | [] |
44,713 | Toxicity Assay | 4 | null | https://www.protocols.io/view/toxicity-assay-bpwhmpb6 | Elizabeth Fozo | TITLE: Toxicity Assay
AUTHORS: Elizabeth Fozo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Toxicity Assay (based on growth curves protocol)</div></div>
[STEPS]
?. [Rules of thumb]
Never remove > 1/3 of a culture for a growth curve
?. [Rules of thumb]
Read OD600 (optical density at 600 nm) of 200... | ["[Rules of thumb]\nNever remove > 1/3 of a culture for a growth curve", "[Rules of thumb]\nRead OD600 (optical density at 600 nm) of 200 microliters of culture added to 800 microliters of fresh media -> 1,000 microliters of fluid in cuvette; = 1:5 dilution\nRemember to set the factor equal to 5 when reading from the s... |
65,025 | Ward lab alkaline bleaching protocol | 4 | dx.doi.org/10.17504/protocols.io.j8nlkkyxdl5r/v1 | https://www.protocols.io/view/ward-lab-alkaline-bleaching-protocol-cbq9smz6 | Jordan Ward | TITLE: Ward lab alkaline bleaching protocol
AUTHORS: Jordan Ward
[DESCRIPTION]
Current protocol for how Ward lab synchronizes C. elegans by alkaline bleaching.
[STEPS]
1. Add M9+0.05% gelatin to nematode plates containing gravid adults, swirl the plate, recover the liquid with the worms and transfer to centrifuge tub... | ["Add M9+0.05% gelatin to nematode plates containing gravid adults, swirl the plate, recover the liquid with the worms and transfer to centrifuge tubes. For 10 cm plates, pour enough M9+0.05% gelatin to cover the surface of the plate and transfer to a sterile 15 ml conical tube.", "Let the worms sink to the bottom of t... |
88,003 | Co-extraction of RNA and DNA from soil and sediment samples | 1 | dx.doi.org/10.17504/protocols.io.rm7vzb6m4vx1/v2 | https://www.protocols.io/view/co-extraction-of-rna-and-dna-from-soil-and-sedimen-cz7bx9in | Dominik Buchner, Lisa Wolany | TITLE: Co-extraction of RNA and DNA from soil and sediment samples
AUTHORS: Dominik Buchner, Lisa Wolany
[DESCRIPTION]
This protocol describes extracting RNA and DNA from soil and sediment samples. 2 g of soil or up to 5 g of sediment can be processed in one extraction. The protocol is based on the RNeasy PowerSoil To... | ["[Cell lysis] Prepare one 15 mL conical centrifuge tube per sample by adding 0.5 g of a) 0.1 mm glass beads, b) 0.5 mm glass beads, c) 1 mm zirconia/silica beads d) 2 mm zirconia beads.", "[Cell lysis] Add up to 2 g of soil or up to 5 g of the sediment sample.", "[Cell lysis] Add 2.5 mL , 0.25 mL , 0.8 mL and 3.5 mL ... |
22,023 | What does the latest generation CAR-T look like? | null | dx.doi.org/10.17504/protocols.io.zrff53n | null | Alex Brown | TITLE: What does the latest generation CAR-T look like?
AUTHORS: Alex Brown
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">In the past decade, new advances in tumor treatment have been made. Immunotherapy works by activating the patient's own immune system to target cancer cells. CAR-T cell therapy... | [] |
21,747 | Standard Interview of Evidence Use (SIEU) | null | dx.doi.org/10.17504/protocols.io.zgtf3wn | null | Drew Gitomer | TITLE: Standard Interview of Evidence Use (SIEU)
AUTHORS: Drew Gitomer
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"> This is a modification of Palinkas' SIEU - we removed items 16-20 because they were not appropriate for an educational setting</div><div class = "text-block">We also changed langua... | [] |
79,922 | Glucocerebrosidase is imported into mitochondria and preserves complex I integrity and energy metabolism - ASAP protocol collection | 2 | dx.doi.org/10.17504/protocols.io.x54v9d44mg3e/v1 | https://www.protocols.io/view/glucocerebrosidase-is-imported-into-mitochondria-a-csaswaee | michela.deleidi, Pascale Baden, María José Pérez J., Hariam Raji, Federico Bertoli | TITLE: Glucocerebrosidase is imported into mitochondria and preserves complex I integrity and energy metabolism - ASAP protocol collection
AUTHORS: michela.deleidi, Pascale Baden, María José Pérez J., Hariam Raji, Federico Bertoli
[DESCRIPTION]
Collection of protocols of Deleidi Lab used in the publication: "Glucoce... | [] |
54,794 | Spatial Transcriptomics Protocol | 4 | dx.doi.org/10.17504/protocols.io.bzrip54e | https://www.protocols.io/view/spatial-transcriptomics-protocol-bzrip54e | Michael Eadon, Ricardo Melo Ferreira, Ying-Hua Cheng, Tarek Ashkar | TITLE: Spatial Transcriptomics Protocol
AUTHORS: Michael Eadon, Ricardo Melo Ferreira, Ying-Hua Cheng, Tarek Ashkar
[DESCRIPTION]
The tissue in OCT undergoes cryosectioning, affixment to the cDNA capture slide, H+E staining, 20x Keyence imaging, tissue permeabilization, RNA capture, and cDNA synthesis. Data is anal... | ["[Cryosectioning Procedure] Specimens should be handled wearing clean gloves treated with RNAse Away or with a clean RNAse Away treated forceps.", "[Cryosectioning Procedure] Cool Cryostat to -22 °C. Clean the work surfaces with RNAse away and install a new cutting blade.", "[Cryosectioning Procedure] Place a clean sm... |
41,147 | ENNOLIFE SARS-CoV-2 Antigen Test Kit Protocol | 4 | dx.doi.org/10.17504/protocols.io.bke3ktgn | https://www.protocols.io/view/ennolife-sars-cov-2-antigen-test-kit-protocol-bke3ktgn | Hsiao-Chung Tsai | TITLE: ENNOLIFE SARS-CoV-2 Antigen Test Kit Protocol
AUTHORS: Hsiao-Chung Tsai
[STEPS]
?. [Setup ENNOLIFE Clinical Chemistry Analyzer]
Keyin Patient IDs then press “START” to check the connection of Analyzer and Notebook.
?. [Running a nasal swab sample]
For specimen collection of nasal swabs, follow the CDC Swab Coll... | ["[Setup ENNOLIFE Clinical Chemistry Analyzer]\nKeyin Patient IDs then press “START” to check the connection of Analyzer and Notebook.", "[Running a nasal swab sample]\nFor specimen collection of nasal swabs, follow the CDC Swab Collection Guidelines and swab manufacturers' recmommandations. Use a flocked tapered swab... |
52,677 | Assaying starvation-induced autophagy in HeLa cells | 1 | dx.doi.org/10.17504/protocols.io.bxpdpmi6 | https://www.protocols.io/view/assaying-starvation-induced-autophagy-in-hela-cell-bxpdpmi6 | Julia F Riley, holzbaur | TITLE: Assaying starvation-induced autophagy in HeLa cells
AUTHORS: Julia F Riley, holzbaur
[DESCRIPTION]
A method for assaying starvation-induced autophagy in HeLa cells that have been transfected with Halo-tagged constructs. This protocol was specifically used to investigate the impact of various mutations in the ... | ["[Cell Treatment] Culture cells in DMEM (plus 10% FBS, 1% Penicillin/Streptomycin, 1% GlutaMAX) on glass-bottom imaging dishes. Grow until 40-50% confluent.", "[Cell Treatment] Transfect cells 24 hours prior to starvation treatment with 0.75 μg of the appropriate Halo-tagged WIPI2 plasmid using FuGENE transfection rea... |
24,110 | Thiobarbituric acid reactive substances (TBARS) Assay | null | dx.doi.org/10.17504/protocols.io.3sngnde | null | Eva Feldman | TITLE: Thiobarbituric acid reactive substances (TBARS) Assay
AUTHORS: Eva Feldman
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span></div><div class = "text-block">Plasma concentrations of thiobarbituric acid reactive substances (TBARS) are an index of ... | ["[Sample Preparation: ]\nPlasma:• Place 100µL plasma into a labeled 1.5mL micro-centrifuge tube. Tissue:• Label 1 sets of 1.5mL micro-centrifuge tubes, 1 set screw top tubes and 1 set of 0.5mL tubes. • Weighed out ~20mg and sonicate in 200µL RIPA buffer + inhibitors. • Sonicate. • Centrifuged @ 3000 for 10 min @ 4º . ... |
null | null | null | dx.doi.org/10.17504/protocols.io.qyedxte | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>In the past, identifying a gene of interest for a mutant phenotype in maize has proven to be a laborious process. Now, with the aid of next generation sequencing technology, the researcher can quickly identify the region containing a mutant gene and in some cases identify the... | [] |
23,613 | Mouse dissection and preparation of heart (aortic sinus) and brachiocephalic artery for lesion quantitation by sectioning | null | dx.doi.org/10.17504/protocols.io.3a5gig6 | null | Jan Breslow, Daniel Teupser | TITLE: Mouse dissection and preparation of heart (aortic sinus) and brachiocephalic artery for lesion quantitation by sectioning
AUTHORS: Jan Breslow, Daniel Teupser
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Diabetic complication:</span></div><div style = "tex... | ["Prepare a 1 ml syringe by filling with 15µl 0.5 M EDTA ph 8.0 and then capping with a 23g needle. The syringe will be used for drawing blood from the heart.", "Prepare a 10 ml syringe with 50-100 µl of heparin (1000 units per ml), then fill the syringe to 10 ml with PBS. Remove all the air from the syringe. Cap with ... |
104,903 | Immunoblotting using precast gels | 0 | dx.doi.org/10.17504/protocols.io.14egn6j8pl5d/v1 | https://www.protocols.io/view/immunoblotting-using-precast-gels-dipf4djn | Francisco Bustos | TITLE: Immunoblotting using precast gels
AUTHORS: Francisco Bustos
[DESCRIPTION]
Immunoblotting is a key technique to visualize changes in protein levels upon treatments. This technique can be challenging and established procedures are required to ensure reproducibility. Here we present our optimized protocol for immu... | ["[SDS-PAGE Electrophoresis] Prepare 500 mL 1X MES-SDS Buffer (50 millimolar (mM) MES, 50 millimolar (mM) Tris Base, 0.1 Mass / % volume SDS, 1 Mass / % volume EDTA, pH 7.3) by diluting stock 1:20 in Milli-Q water.", "[SDS-PAGE Electrophoresis] Unpack a and remove protective tape and comb.", "[SDS-PAGE Electrophor... |
24,081 | CTAB DNA Extraction for genotyping | null | dx.doi.org/10.17504/protocols.io.3rrgm56 | null | Yaowu Yuan | TITLE: CTAB DNA Extraction for genotyping
AUTHORS: Yaowu Yuan
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. Grind fresh plant tissue with liquid nitrogen or silica-gel dried tissue in a 1.5 ml Eppie tube.
A little silica gel grains in the tube actually helps the grinding.
?. Add .
[CTAB DNA Extraction bu... | ["Grind fresh plant tissue with liquid nitrogen or silica-gel dried tissue in a 1.5 ml Eppie tube.\nA little silica gel grains in the tube actually helps the grinding.", "Add .\n[CTAB DNA Extraction buffer]", "Incubate the CTAB/plant extract mixture for at in the heat block and invert to mix throughout the 15 minutes... |
null | null | null | dx.doi.org/10.17504/protocols.io.eajbacn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
A protocol to separate chloroplasts from diatom cells using ammonium fluoride to permeate the silica frustrule and a percoll gradient to separate the plastid from other cellular components.
[STEPS]
?. | [] |
33,035 | SPARC Segmentation Conversion: Binary mask tracings to MBF XML | null | dx.doi.org/10.17504/protocols.io.bchjit4n | null | Maci Heal, Susan Tappan | TITLE: SPARC Segmentation Conversion: Binary mask tracings to MBF XML
AUTHORS: Maci Heal, Susan Tappan
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Convert binary mask tracings from Nikon's NIS Elements software into MBF XML format.</div></div>
[STEPS]
?. [Conversion]
Launch Neurolucida 360.
?. ... | ["[Conversion]\nLaunch Neurolucida 360.", "[Conversion]\nOpen binary mask tracings (.tif) into program window.", "[Conversion]\nSelect the Outline Objects icon from the Trace ribbon.", "[Conversion]\nClick on a black or white pixel on the binary mask tracings to automatically contour the representative object. Repeat u... |
106,591 | Collection and shipment of specimen for Bulk RNA-sequencing (Bulk RNA-seq) | 0 | dx.doi.org/10.17504/protocols.io.4r3l2qz5ql1y/v1 | https://www.protocols.io/view/collection-and-shipment-of-specimen-for-bulk-rna-s-dkb74srn | Laura Robinson, Susan Sheehan, Gaven Garland, Ron Korstanje | TITLE: Collection and shipment of specimen for Bulk RNA-sequencing (Bulk RNA-seq)
AUTHORS: Laura Robinson, Susan Sheehan, Gaven Garland, Ron Korstanje
[DESCRIPTION]
These samples are part of the JAX-Sen project in the SenNet Consortium. Here we provide details on specimen collection and shipment to the Robson laborato... | ["[Reagents and Materials:] 2mL Eppendorf tubes or 5 ml Eppendorf tubes\nRNA Later solution\nWet Ice\nTweezers (clean, sterile)", "[Quality Key Points:] The tissue specimen should be always kept at 4 degrees Celsius and RNase-free. \nIt is crucial to not store the tissue specimen at RT to avoid any cell death, and tiss... |
42,686 | Tissue delipidation | 1 | dx.doi.org/10.17504/protocols.io.bmw6k7he | https://www.protocols.io/view/tissue-delipidation-bmw6k7he | yang1832 , Julia Laskin | TITLE: Tissue delipidation
AUTHORS: yang1832 , Julia Laskin
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This step is to wash lipids off the tissue to prevent their interferences for imaging of proteins.</div></div>
[STEPS]
?. Immerse the tissue section in 70%, 90%, 100% ethanol, 20s each.
?. Im... | ["Immerse the tissue section in 70%, 90%, 100% ethanol, 20s each.", "Immerse in 99.8% chloroform for 25s.", "Dry in desiccator for 10min."] |
36,284 | SILICONE INDUCED GRANULOMA OF BREAST IMPLANT CAPSULE | 1 | dx.doi.org/10.17504/protocols.io.bfn4jmgw | https://www.protocols.io/view/silicone-induced-granuloma-of-breast-implant-capsu-bfn4jmgw | Eduardo Fleury | TITLE: SILICONE INDUCED GRANULOMA OF BREAST IMPLANT CAPSULE
AUTHORS: Eduardo Fleury
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Objective: To evaluate the ability of BMRI to detect silicone gel bleeding in a prospective observational study including consecutive patients referred for a BMRI scan.... | ["OBSERVATIONBeginning of 2017: we had our first case of Breast Implant-Associated Anaplastic Large Cell Lymphoma (BIA-ALCL) in IBCC- Instituto Brasileiro de Controle do Câncer (IBCC)Middle of 2017: we had a suspected case of BIA-ALCL. The case was confirmed as Silicone Induced Granuloma of Breast Implant Capsule. Imag... |
76,654 | Dispensing C. elegans to 96 well tracking plate using Integra VIAFILL | 4 | null | https://www.protocols.io/view/dispensing-c-elegans-to-96-well-tracking-plate-usi-cn4nvgve | e.warren | TITLE: Dispensing C. elegans to 96 well tracking plate using Integra VIAFILL
AUTHORS: e.warren
[DESCRIPTION]
Protocol for dispensing C. elegans into 96 well plates using the Interga VIAFILL dispenser. Bleach synchronized C. elegans should be prepared in advance. The X,Y,Z positions for dispensing can be adjusted accor... | ["[Configure the Integra VIAFILL] Insert a small cassette into the machine.", "[Configure the Integra VIAFILL] Configure X, Y, and Z settings for the multiwell plate by clicking on tool symbol -> stage alignment.", "[Configure the Integra VIAFILL] Put the plate into the stage and then press 'Move' so that the plate mov... |
64,296 | Copying Archived LTEE Samples | 1 | dx.doi.org/10.17504/protocols.io.bp2l61yykvqe/v1 | https://www.protocols.click/view/copying-archived-ltee-samples-ca2gsgbw | Zachary D Blount, Jeffrey E Barrick | TITLE: Copying Archived LTEE Samples
AUTHORS: Zachary D Blount, Jeffrey E Barrick
[DESCRIPTION]
This protocol describes how to replenish the frozen "fossil" record of the E. coli Long-Term Evolution Experiment (LTEE) by making copies of freezer stocks. Different methods are used to copy population samples versus clo... | ["[Copying Archived Population Samples] Prepare an autoclaved 50-mL Erlenmeyer flask capped with a 20-mL beaker for each sample that will be revived, plus a blank. Fill each flask with 9.9 mL of DM1000.", "[Copying Archived Population Samples] Vortex each freezer vial and pipette 120 µL of the thawed stock into one of ... |
86,041 | Automated Immunohistochemistry Staining | 1 | dx.doi.org/10.17504/protocols.io.3byl4qjz2vo5/v1 | https://www.protocols.io/view/automated-immunohistochemistry-staining-cx9zxr76 | Toby J Curless, Hemanth Ramesh Nelvagal, Zane Jaunmuktane | TITLE: Automated Immunohistochemistry Staining
AUTHORS: Toby J Curless, Hemanth Ramesh Nelvagal, Zane Jaunmuktane
[DESCRIPTION]
The protocols describes the steps for automated immunohistochemistry staining using the Ventana Discovery® XT
Immunostainer.
[STEPS]
SECTION: Preparation
2. Generate tissue sections using... | ["[Preparation] Generate tissue sections using standard microtome sectioning protocols.", "[Preparation] Heat tissue dry tissue sections for 60 min at 60 °C", "[Preparation] Prepare primary and secondary antibody solutions as per manufacturer's protocol - see below for example for AT8.", "[Preparation] Primary AT8 anti... |
null | null | null | dx.doi.org/10.17504/protocols.io.rj4d4qw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>A collection of protocols released as part of the IOS EDGE: Functional-genomics tools for Cnidarian-dinoflagellate symbiosis NSF grant (#1645164).</p>
<p> </p>
<p><strong>Lead PIs: </strong></p>
<p>Virginia Weis, Oregon State University</p>
<p>Mauricio Rodriguez-Lanetty, Flor... | [] |
105,383 | Sample fixation and RNA extraction of brackish and marine samples with high sediment loads for metatranscriptomics sequencing | 0 | dx.doi.org/10.17504/protocols.io.n92ld8j4ov5b/v1 | https://www.protocols.io/view/sample-fixation-and-rna-extraction-of-brackish-and-di6f4hbn | Apoorva Prabhu, Chris Rinke | TITLE: Sample fixation and RNA extraction of brackish and marine samples with high sediment loads for metatranscriptomics sequencing
AUTHORS: Apoorva Prabhu, Chris Rinke
[DESCRIPTION]
Water samples from estuaries are brackish to marine and in cases of many subtropical rivers, such as the Brisbane River in Queensland, ... | ["[Sample processing in the laboratory] Use equipment such as filters, filtration towers and lines in the fume hood, for RNA purposes only. Wipe down all surfaces with 70% Ethanol, and use Alfoil (Aluminium foil) to cover working area (taped down). Use RNaseZap‱ RNase Decontamination Solution to wipe down all surfaces.... |
20,952 | UC Davis - Inflammation pathway | null | dx.doi.org/10.17504/protocols.io.ypyfvpw | null | Fawaz G. Haj | TITLE: UC Davis - Inflammation pathway
AUTHORS: Fawaz G. Haj
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span></div><div class = "text-block">
This test is designated to determine if rodents exhibit inflammatory disorders, through evaluation of the act... | ["Unless otherwise requested by the PI or stated in the protocol, mice will be euthanized using cervical dislocation.", "Collect maximum blood from portal vein and isolate plasma according to standard protocols or as desired by the P.I.", "Quickly collect tissues designated by the P.I. Each tissue should be divided int... |
null | null | null | dx.doi.org/10.17504/protocols.io.i5bcg2n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Cycloplegic agents are used routinely during the examination in pediatric patients to investigate the correct refraction without accommodation.</p>
<p>Cycloplegia was performed using the following regimen. Cyclopentolate hydrochloride 1% (Cyplegin 1% ophthalmic solution, Sant... | [] |
35,821 | sci-ATAC-seq3 | 1 | dx.doi.org/10.17504/protocols.io.be8mjhu6 | https://www.protocols.io/view/sci-atac-seq3-be8mjhu6 | Silvia Domcke, Andrew J. Hill, Riza M. Daza, Cole Trapnell, Darren A. Cusanovich, Jay Shendure | TITLE: sci-ATAC-seq3
AUTHORS: Silvia Domcke, Andrew J. Hill, Riza M. Daza, Cole Trapnell, Darren A. Cusanovich, Jay Shendure
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:left">We developed an improved assay for single cell profiling of chromatin accessib... | ["[Reagent preparation (30-45 mins)]\nATAC-RSB buffer (Corces et al. Nature Methods 2017 PMCID: PMC5623106)In a 50 ml falcon tube, combine 500 ul 1M Tris-HCl pH 7.4 (10 mM Tris-HCl final), 100 ul 5M NaCl (10 mM NaCl final), 300 ul 0.5M MgCl2 (3 mM MgCl2 final) and 49.1 ml nuclease free water. Filter sterilize by using... |
null | null | null | dx.doi.org/10.17504/protocols.io.pyvdpw6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Environmental and housing conditions experienced by laboratory animals exert profound effects on their biology, physiology, and behavior. These parameters are important and often overlooked sources of potential variation in experiments, and should be reported in peer-reviewe... | [] |
40,755 | Bacterial Transformation - Mix & Go Competent Cells - CHEM 584 | 4 | dx.doi.org/10.17504/protocols.io.bj2tkqen | https://www.protocols.io/view/bacterial-transformation-mix-amp-go-competent-cell-bj2tkqen | Ken Christensen | TITLE: Bacterial Transformation - Mix & Go Competent Cells - CHEM 584
AUTHORS: Ken Christensen
[STEPS]
?. Add to plasmid DNA to a aliqanuot of thawed competent cells (Mix & Go) on ice, mix gently for a few seconds (try to keep the added volume of DNA less than 5% of the total). Place tube on ice for minutes.
1 µ... | ["Add to plasmid DNA to a aliqanuot of thawed competent cells (Mix & Go) on ice, mix gently for a few seconds (try to keep the added volume of DNA less than 5% of the total). Place tube on ice for minutes.\n1 µl\n5 µl\n50 µl\nWhen selecting with Kanamycin, Tetracycline, etc., an outgrowth performed in SOC medium i... |
null | null | null | dx.doi.org/10.17504/protocols.io.rhkd34w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Script R to estimate Bacterial OTU richness using a rarefaction curve. Script used in the POIr</p>
[STEPS] | [] |
98,596 | MERS-CoV Mpro large scale purification protocol | 1 | dx.doi.org/10.17504/protocols.io.bp2l62b11gqe/v1 | https://www.protocols.io/view/mers-cov-mpro-large-scale-purification-protocol-dcic2uaw | Korvus Wang, michael fairhead, Eleanor Williams | TITLE: MERS-CoV Mpro large scale purification protocol
AUTHORS: Korvus Wang, michael fairhead, Eleanor Williams
[DESCRIPTION]
This protocol details the expression and purification of MERS Mpro construct bearing a N-terminal His-SUMO tag at large scale (>6L).
[GUIDELINES]
Construct / plasmid resource-name: MERS-Mpro ... | ["[Plasmid Transformation] MERS Mpro N-terminal His-SUMO tagged construct was inoculated from its BL21(DE3)-RR glycerol stock.", "[Protein Purifcation] Perform IMAC to extract target protein from the lysed cell mixture", "[Protein Purifcation] Wash the column with 10 CV of wash buffer twice. Allow wash buffer to pass t... |
68,682 | Human Knee Meniscus Collection Protocol for scRNA-seq | 4 | dx.doi.org/10.17504/protocols.io.6qpvr614zvmk/v1 | https://www.protocols.io/view/human-knee-meniscus-collection-protocol-for-scrna-cfbitike | molmer, Martin Lotz | TITLE: Human Knee Meniscus Collection Protocol for scRNA-seq
AUTHORS: molmer, Martin Lotz
[DESCRIPTION]
Meniscus is taken from the medial knee compartment is collected for scRNA-seq processing. The attached image indicates where the meniscal tissue is collected from.
[BEFORE_START]
Knee blocks are shipped on wet ice ... | ["Prepare harvesting area with sterile drapes, tools and gauze. All harvesting is completed within an aseptic environment.", "Wipe down the knee blocks with 95% ethanol prior to opening the joint capsule.", "Once the joint capsule is opened, the femur and tibia are disarticulated and menisci are resected.", "A full-thi... |
97,621 | Processing of pediatric whole blood samples for single cell analysis | 0 | dx.doi.org/10.17504/protocols.io.ewov19y37lr2/v1 | https://www.protocols.io/view/processing-of-pediatric-whole-blood-samples-for-si-dbjv2kn6 | Liam Gubbels, Shivanthan Shanthikumar, Melanie R Neeland | TITLE: Processing of pediatric whole blood samples for single cell analysis
AUTHORS: Liam Gubbels, Shivanthan Shanthikumar, Melanie R Neeland
[DESCRIPTION]
This protocol describes the collection, processing, and cryopreservation of whole blood samples for downstream single-cell analysis.
[GUIDELINES]
This is an exper... | ["[COLLECTION OF WHOLE BLOOD] Label an EDTA blood collection tube with study/patient ID.", "[COLLECTION OF WHOLE BLOOD] Whole blood samples must remain at Room temperature and be processed in the laboratory within 30 min to 60 min of the procedure.", "[COLLECTION OF WHOLE BLOOD] After obtaining informed consent from fa... |
67,396 | Growth Matrix Male Enhancement Reviews Get More Blood Flow, Longer Endurance, Larger Erection, Libedo(REAL OR HOAX) | 3 | dx.doi.org/10.17504/protocols.io.bp2l61qk1vqe/v1 | https://www.protocols.io/view/growth-matrix-male-enhancement-reviews-get-more-bl-cd3cs8iw | Growth Matrix Male Enhancement | TITLE: Growth Matrix Male Enhancement Reviews Get More Blood Flow, Longer Endurance, Larger Erection, Libedo(REAL OR HOAX)
AUTHORS: Growth Matrix Male Enhancement
[DESCRIPTION]
[SALE IS LIVE] Get Growth Matrix Male Enhancement Online Program “Now Available in World Wide” Hurry Limited Time Offer Only For 1st User!!
... | [] |
89,442 | Immunofluorescence on paraffin sections | 4 | dx.doi.org/10.17504/protocols.io.36wgq3m3klk5/v1 | https://www.protocols.io/view/immunofluorescence-on-paraffin-sections-c3kaykse | Núria Peñuelas | TITLE: Immunofluorescence on paraffin sections
AUTHORS: Núria Peñuelas
[DESCRIPTION]
Immunofluorescence protocol on paraffin-embedded rodent brain sections
[STEPS]
SECTION: 1. Deparaffinization and hydratation :
1. Put the slides 30 min in the incubator at 60ºC
SECTION: 1. Deparaffinization and hydratation :
2. Wash... | ["[1. Deparaffinization and hydratation :] Put the slides 30 min in the incubator at 60ºC", "[1. Deparaffinization and hydratation :] Wash 3x3 min in xylene", "[1. Deparaffinization and hydratation :] Wash 1x10 min in ethanol 100%", "[1. Deparaffinization and hydratation :] Wash 1x10 min in ethanol 95%", "[1. Deparaffi... |
35,876 | Unique insights from ClinicalTrials.gov by mining protein mutations and RSids in addition to applying the Human Phenotype Ontology | null | dx.doi.org/10.17504/protocols.io.bfacjiaw | https://www.protocols.io/view/unique-insights-from-clinicaltrials-gov-by-mining-bfacjiaw | Shray Alag | TITLE: Unique insights from ClinicalTrials.gov by mining protein mutations and RSids in addition to applying the Human Phenotype Ontology
AUTHORS: Shray Alag
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Researchers and clinicians face a significant challenge in keeping up-to-date with the r... | ["Two publicly-available datasets were used in this study: ClinicalTrials.gov and HPO.", "Clinical Trial DataThe complete repository of clinical trials displayed at ClinicalTrials.gov is available in XML format with a well-defined schema.Download: https://clinicaltrials.gov/ct2/resources/downloadDownload all clinical t... |
null | null | null | dx.doi.org/10.17504/protocols.io.mumc6u6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>We describe a chemical-genetic approach for inducible silencing of <em>Caenorhabditis elegans </em>neurons in intact animals, using the histamine-gated chloride channel HisCl1 from <em>Drosophila</em> and exogenous histamine. Administering histamine to freely moving <em>C. el... | [] |
98,627 | Protocol to use for direct RNA sequencing of plants with Oxford Nanopore Technologies | 0 | null | https://www.protocols.io/view/protocol-to-use-for-direct-rna-sequencing-of-plant-dcjb2uin | Nivedha Nataraj | TITLE: Protocol to use for direct RNA sequencing of plants with Oxford Nanopore Technologies
AUTHORS: Nivedha Nataraj
[DESCRIPTION]
Transcriptomic analysis is a key component of understanding gene expression and regulatory mechanisms. Oxford Nanopore’s direct RNA sequencing kit is optimized to sequence native RNA with... | ["[RNA Extraction - ThermoScientific GeneJET Plant RNA Purification Mini Kit] Add 10 μL of 2M DTT for each 500 μL of Plant RNA Lysis Solution.", "[RNA Extraction - ThermoScientific GeneJET Plant RNA Purification Mini Kit] Add 500 μL of the Lysis+DTT Solution is added to a 1.5 mL Eppendorf Microcentrifuge tube.", "[RNA ... |
75,476 | RNA and gDNA Isolation from stabilized Whole Blood (Tempus Blood RNA Tube) using semi-automated Promega Chemistry | 4 | dx.doi.org/10.17504/protocols.io.5jyl8j1r7g2w/v1 | https://www.protocols.io/view/rna-and-gdna-isolation-from-stabilized-whole-blood-cmxuu7nw | Merz MP, Treue D, Hummel M, Stege A, ZeBanC - Zentrale Biobank Charité | TITLE: RNA and gDNA Isolation from stabilized Whole Blood (Tempus Blood RNA Tube) using semi-automated Promega Chemistry
AUTHORS: Merz MP, Treue D, Hummel M, Stege A, ZeBanC - Zentrale Biobank Charité
[DESCRIPTION]
Here we describe a semi-automated way to isolate RNA and gDNA from (the same) TEMPUS Tube. This allows t... | ["[Blood draw, tube handling and storage] Draw up to 3 mL of blood directly into a Tempus™ Blood RNA Tube according to your laboratory's or hospital standard. See manufacurers SOP for more information.", "[Blood draw, tube handling and storage] Immediately after filling the tube, shake the tube vigorously or vortex the... |
32,036 | Yeast growth and fluorescence 96-well plate reader experiment, set up from a 96 deep well plate | 1 | dx.doi.org/10.17504/protocols.io.bbicikaw | https://www.protocols.io/view/yeast-growth-and-fluorescence-96-well-plate-reader-bbicikaw | Jamie Auxillos, Clémence Alibert, Edward Wallace | TITLE: Yeast growth and fluorescence 96-well plate reader experiment, set up from a 96 deep well plate
AUTHORS: Jamie Auxillos, Clémence Alibert, Edward Wallace
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol is used to measure a time-series of growth and fluorescence output in y... | ["[Growth of cells in a 96 deep well plate]\nPlan the plate set up for the experiment, both the 1) pre-culture plate and 2) the final 96-well black microtiter plate. Tips for plate design:For the pre-culture plate, fill the plate, skipping every other row to allow a checkered pattern of loadingPlan the final plate set ... |
40,849 | Efficacy of Underwater EMR for non-pedunculated colorectal lesions: a systematic review and meta-analysis protocol | 4 | dx.doi.org/10.17504/protocols.io.bj5rkq56 | https://www.protocols.io/view/efficacy-of-underwater-emr-for-non-pedunculated-co-bj5rkq56 | Takeshi Yamashina, Noboru Hanaoka, Takeshi Setoyama, Masahiro Banno, Jun Watanabe, Hiroyuki Marusawa | TITLE: Efficacy of Underwater EMR for non-pedunculated colorectal lesions: a systematic review and meta-analysis protocol
AUTHORS: Takeshi Yamashina, Noboru Hanaoka, Takeshi Setoyama, Masahiro Banno, Jun Watanabe, Hiroyuki Marusawa
[STEPS] | [] |
79,822 | Schistosoma mansoni cercariae transformation (with needle) | 4 | null | https://www.protocols.io/view/schistosoma-mansoni-cercariae-transformation-with-cr7nv9me | Sarah K Buddenborg | TITLE: Schistosoma mansoni cercariae transformation (with needle)
AUTHORS: Sarah K Buddenborg
[DESCRIPTION]
Free-living aquatic S. mansoni cercariae transform into the first intramammalian stage,called schistosomula or somules, by burrowing in the host skin. Upon contact, cercariae begin to enter the skin and lose the... | ["[Cercariae collection] Shed cercariae from snails in a 6-well plate (see protocol \"Schistosoma mansoni cercariae shedding\"). The snails can be shed for up to 2 hrs by collecting cercariae and replacing with fresh water every 30 min", "[Cercariae collection] Using a sterile transfer pipette, dispense cercariae into ... |
58,618 | Colony PCR for screening transgenic yeast | 4 | dx.doi.org/10.17504/protocols.io.b5g2q3ye | https://www.protocols.io/view/colony-pcr-for-screening-transgenic-yeast-b5g2q3ye | Anbarasu Karthikaichamy | TITLE: Colony PCR for screening transgenic yeast
AUTHORS: Anbarasu Karthikaichamy
[DESCRIPTION]
Colony PCR protocol for screening transgenic yeast
[BEFORE_START]
Prepare 10 millimolar (mM) sodium hydroxide (NaOH)
[STEPS]
1. Pick single yeast colony from the transformation plate and re-streak to a fresh plate with... | ["Pick single yeast colony from the transformation plate and re-streak to a fresh plate with appropriate selection marker.", "Incubate the plate in a 30 °C incubator for 2 days.", "After 2 days, pick around 8 colonies from the re-streaked plate using the smallest micropipette tip or sterile wooden toothpick.", "Re-susp... |
null | null | null | dx.doi.org/10.17504/protocols.io.ciiucd | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol is for PCR with Q5® High-Fidelity 2X Master Mix (M0492)
[GUIDELINES]
<strong>Please note that protocols with Q5 High-Fidelity DNA Polymerase may differ from protocols with other polymerases. Conditions recommended below should be used for optimal per... | [] |
78,495 | Economic and easy bacterial and yeast colony PCR with 2x premix Gotaq-Green (Promega) or DreamTaq-Green (Thermo Fisher) | 4 | null | https://www.protocols.io/view/economic-and-easy-bacterial-and-yeast-colony-pcr-w-cqv7vw9n | Darek Abramczyk | TITLE: Economic and easy bacterial and yeast colony PCR with 2x premix Gotaq-Green (Promega) or DreamTaq-Green (Thermo Fisher)
AUTHORS: Darek Abramczyk
[DESCRIPTION]
Slightly modified method Gotaq Promega or DreamTaq (Thermo), economical, quick and ready-to-load. Perfect for yeast genotyping and screening
[STEPS]
1... | ["Bacterial colony PCR \n \n PCR reactions using ProFlex PCR system, Applied Biosystems. Thermal Cycler", "Yeast colony PCR (S.cerevisiae, Pichia, Candida)", "Reagent NameInitial Conc.Volume (μL)gotaq green 2x2X6.25oligo 1oligo 210 uM 10 uM 0.75 0.75cell suspension in water1ddH2ON/A3.75TOTAL Volume:12.5 uL\n \n Stage... |
53,884 | Nucleic acid & protein electrophoresis | 4 | dx.doi.org/10.17504/protocols.io.byu4pwyw | https://www.protocols.io/view/nucleic-acid-amp-protein-electrophoresis-byu4pwyw | Shuning Guo | TITLE: Nucleic acid & protein electrophoresis
AUTHORS: Shuning Guo
[DESCRIPTION]
This protocol concludes two types of the electrophoresis used to detect target DNA or protein.
[BEFORE_START]
Prepare 50 x TAE, 1.5 mol/L Tris-Gly (pH 8.8), 1.0 mol/L Tris-Gly (pH 6.8), 5× Tris-Gly electrophoresis solution, coomas... | ["Choose suitable electrophoresis method depends on the type of the sample.", "Weigh appropriate agarose depends on the concentration of the gel (1% agarose gel for detection and 1% or 2% for gel extraction).", "Add 1X TAE to a conical flask. Need to prepare 1X TAE with 50X TAE.", "Heat up by microwave until the soluti... |
87,114 | Plaque Assay for Microcystis aeruginosa NIES-298 and phage Ma-LMM01 | 4 | dx.doi.org/10.17504/protocols.io.e6nvwd1j7lmk/v1 | https://www.protocols.io/view/plaque-assay-for-microcystis-aeruginosa-nies-298-a-czbix2ke | Laura E Smith, Steven W Wilhelm | TITLE: Plaque Assay for Microcystis aeruginosa NIES-298 and phage Ma-LMM01
AUTHORS: Laura E Smith, Steven W Wilhelm
[DESCRIPTION]
This protocol describes a plaque assay for the enumeration of phage infecting Microcystis aeruginosa NIES-298. It is a single agarose layer assay and reproducibly quantifies infection by t... | ["[Prepare CT Agarose] Make 0.56% agarose in CT medium base by adding 0.56 g low melting point agarose / 100 mL CT medium prior to autoclaving. You will need 12 mL of CT agarose per plate. Note: the final agarose concentration in plates will be ~ 0.45% once culture and lysate are added (see below). CT medium is modifie... |
null | null | null | dx.doi.org/10.17504/protocols.io.n5ydg7w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><span style="font-weight: 400;">Nanopore sequencing (Oxford Nanopore Technologies MinION instrument) requires high quality, high molecular weight DNA (HMW) to produce long sequence reads. Extracting high purity, HMW DNA is a difficult challenge, especially for a biotrophic r... | [] |
99,609 | Differentiation of Mesenchymal Stromal Cells to Endothelial-like cells in Spheroidal Culture | 0 | dx.doi.org/10.17504/protocols.io.5jyl82m17l2w/v2 | https://www.protocols.io/view/differentiation-of-mesenchymal-stromal-cells-to-en-ddhz2376 | Simeng Li, Isabel Arias Quiros, Guenther Eissner | TITLE: Differentiation of Mesenchymal Stromal Cells to Endothelial-like cells in Spheroidal Culture
AUTHORS: Simeng Li, Isabel Arias Quiros, Guenther Eissner
[DESCRIPTION]
In this protocol, an easy and cost-friendly method to form mesenchymal stromal cell (MSC) spheroids was specified. The MSC spheroids would form in ... | ["[Mesenchymal stromal cell spheroids formation] Split and resuspend MSC in fully-supplemented MesenCult-ACF plus medium.", "[Mesenchymal stromal cell spheroids formation] Count cells with Trypan blue and dilute cell to 3x10e5/ml or 12x10e5/ml. Cells need to be over 95% viable in order to form spheroids.", "[Mesenchyma... |
78,443 | Preparation of parts HygR-LHRZ and ZeoR-LHRZ | 1 | dx.doi.org/10.17504/protocols.io.4r3l271o3g1y/v1 | https://www.protocols.click/view/preparation-of-parts-hygr-lhrz-and-zeor-lhrz-cqujvwun | Dariusz Abramczyk | TITLE: Preparation of parts HygR-LHRZ and ZeoR-LHRZ
AUTHORS: Dariusz Abramczyk
[DESCRIPTION]
This cloning protocol is for preparation tandem pair HygR-LHRZ and ZeoR-LHRZ as a part of combinatory assembly system for preparation of integration/insertion arrays.
https://www.protocols.io/edit/nanochromosome-arrays-combina... | ["[PreparationZeoR-LHRZ - cloning steps]", "[Cloning and preparation of HygR-LHRZ and ZeoR-LHRZ, integrative/insertion array lasting 3'-part] Preparation of LHRZ - the first part of sequential cloning into pUC19", "[Cloning and preparation of HygR-LHRZ and ZeoR-LHRZ, integrative/insertion array lasting 3'-par... |
70,812 | Radiolabeled polyamine uptake in cells | 4 | dx.doi.org/10.17504/protocols.io.yxmvm2x85g3p/v1 | https://www.protocols.io/view/radiolabeled-polyamine-uptake-in-cells-chd4t28w | Marine Houdou, Nathalie Jacobs, Peter Vangheluwe | TITLE: Radiolabeled polyamine uptake in cells
AUTHORS: Marine Houdou, Nathalie Jacobs, Peter Vangheluwe
[DESCRIPTION]
This protocol provides a technique to determine the radiolabeled polyamine uptake capacity in cells, via the acquisition of disintegrations per minute (DPM) using a Liquid Scintillation Counter.
[GUI... | ["Cells are seeded in 12-well plates, such that 70-80% confluency is reached on the day of the assay. Seed out 2 'treatment' wells, 1 'quick wash' well and 1 'untreated' well per cell line and treatment dose.", "Remove the culturing medium in 'treatment wells' and add 500 µL of medium, containing the desired concentrat... |
62,102 | Lean Belly Juice Is 100% Natural And Effective{Buy Now} | 3 | dx.doi.org/10.17504/protocols.io.rm7vzy7d2lx1/v1 | https://www.protocols.io/view/lean-belly-juice-is-100-natural-and-effective-buy-b8vwrw7e | DinaWhalty | TITLE: Lean Belly Juice Is 100% Natural And Effective{Buy Now}
AUTHORS: DinaWhalty
[DESCRIPTION]
Lean Belly Juice is natural and effective and healthy for the body to burn extra fat it is available on official website Buy now
[STEPS] | [] |
59,006 | Culturing Primary Cortical Neurons | 4 | dx.doi.org/10.17504/protocols.io.b5u6q6ze | https://www.protocols.io/view/culturing-primary-cortical-neurons-b5u6q6ze | Haley Geertsma | TITLE: Culturing Primary Cortical Neurons
AUTHORS: Haley Geertsma
[DESCRIPTION]
This protocol is used to isolate and culture primary cortical neurons from mouse embryos at E14.5-E15.5.
[STEPS]
SECTION: Day 1
1. Coat culture dishes with 0.05mg/mL Poly-D-lysine overnight at 37oC.
SECTION: Day 2
2. Wash culture dishes... | ["[Day 1] Coat culture dishes with 0.05mg/mL Poly-D-lysine overnight at 37oC.", "[Day 2] Wash culture dishes with sterile water x2 then leave to dry.", "[Day 2] Isolate uterus with embryos and place in a tube of 1X PBS.", "[Day 2] In a laminal flow hood, dissect the brains of E14.5-15.5 embryos in Hank's Balanced Salt ... |
53,848 | Planktoscope protocol for plankton imaging | 1 | null | https://www.protocols.io/view/planktoscope-protocol-for-plankton-imaging-bytypwpw | Lombard Fabien | TITLE: Planktoscope protocol for plankton imaging
AUTHORS: Lombard Fabien
[DESCRIPTION]
this protocol is for using planktoscope and collect usable result for quantitative imaging of plankton
see also https://www.planktoscope.org/
[BEFORE_START]
-Test the protocol before acquisition of your first sample
-Calibrate yo... | ["[Get your sample] Use a net to collect plankton", "[Get your sample] Get the content of the collector.", "[Get your sample] Pass the volume through a 200µm sieve", "[Get your sample] Rinse the sieve using seawater and a squeezing bottle (helps to pass small objects)", "[Get your sample] Recover the fluid / measure it... |
75,842 | Protocol 2: MD simulation with Gromacs | 3 | dx.doi.org/10.17504/protocols.io.36wgqjmp5vk5/v1 | https://www.protocols.io/view/protocol-2-md-simulation-with-gromacs-cnbavaie | Phaniendra Alugoju, Vishwambhar Vishnu Bhandare, Vishal S Patil, Krishna Swamy V K D, Prem Kumar Borugadda, Tewin Tencomnao | TITLE: Protocol 2: MD simulation with Gromacs
AUTHORS: Phaniendra Alugoju, Vishwambhar Vishnu Bhandare, Vishal S Patil, Krishna Swamy V K D, Prem Kumar Borugadda, Tewin Tencomnao
[DESCRIPTION]
Structural stability of the docked complexes was monitored using MD simulation with Gromacs 2020.5 (RRID:SCR_014565). The pro... | [] |
91,134 | Cell specificity | 5 | dx.doi.org/10.17504/protocols.io.6qpvr3243vmk/v1 | https://www.protocols.io/view/cell-specificity-c486yzze | Xianjun Dong | TITLE: Cell specificity
AUTHORS: Xianjun Dong
[DESCRIPTION]
This protocol describes the method to perform cell specificity analysis.
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.qbxdspn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Sterilization cycle perfomance are proven adequate during validation and it should be done in accordance to current international standards to guarantee that all critical parameters were met. Low temperature sterilization using vaporized hydrogen peroxide do not have a specif... | [] |
93,152 | Illumina DNA Prep (M) Tagmentation Library Preparation for use on an Illumina MiSeq Sequencer | 1 | dx.doi.org/10.17504/protocols.io.x54v9m7ezg3e/v3 | https://www.protocols.io/view/illumina-dna-prep-m-tagmentation-library-preparati-c678zhrw | Julie Haendiges, Narjol Gonzalez-Escalona, Ruth Timme, Maria Balkey | TITLE: Illumina DNA Prep (M) Tagmentation Library Preparation for use on an Illumina MiSeq Sequencer
AUTHORS: Julie Haendiges, Narjol Gonzalez-Escalona, Ruth Timme, Maria Balkey
[DESCRIPTION]
This procedure outlines the protocol for whole genome sequencing of bacterial organisms using the Illumina DNA Prep library pre... | ["[Dilute and Tagment Input DNA] Bring BLT (stored in refrigerator) and TB1 (stored in freezer) to room temperature. \n\nEnsure that BLT is stored upright at all times, so that the beads remain submerged in the\nbuffer", "[Dilute and Tagment Input DNA] Label a 96-well PCR plate with the Run ID.", "[Dilute and Tagment ... |
99,475 | Thawing frozen hematopoietic stem cells (HPCs) | 4 | null | https://www.protocols.io/view/thawing-frozen-hematopoietic-stem-cells-hpcs-dddt226n | Jessie Buth | TITLE: Thawing frozen hematopoietic stem cells (HPCs)
AUTHORS: Jessie Buth
[DESCRIPTION]
Protocol to thaw frozen hematopoietic stem cells made with the StemDiff Hematopoietic Kit for subsequent differentiation into microglia.
[BEFORE_START]
Make sure you have:
Enough GFR matrigel + DMEM/F12 to coat the plates
Microg... | ["[Prep Matrigel Plates] Coat tissue culture treated plates with 1 mg/mL GFR Matrigel (Growth factor reduced).", "[Prep Matrigel Plates] Get a frozen aliquot of GFR Matrigel from the hallway -30. The aliquots are typically labeled \"6.5\" or \"12.5\", this is the number of mL DMEM/F12 you will add. \n \nYou need:\n ... |
16,495 | Qiime 2 Workflow - Longitudinal study | null | dx.doi.org/10.17504/protocols.io.ucpesvn | null | Carlotta Catozzi, Anna Cusco | TITLE: Qiime 2 Workflow - Longitudinal study
AUTHORS: Carlotta Catozzi, Anna Cusco
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This workflow was performed using QIIME2 for a longitudinal study. The aim was to investigate the changes in mcirobiota after antibiotic and </span><span style = "... | [] |
63,820 | Qiagen All-Prep DNA/RNA Mini Kit | 1 | null | https://www.protocols.io/view/qiagen-all-prep-dna-rna-mini-kit-cajksckw | George Testo | TITLE: Qiagen All-Prep DNA/RNA Mini Kit
AUTHORS: George Testo
[DESCRIPTION]
The AllPrep DNA/RNA Mini Kit is designed to purify genomic DNA and total RNA simultaneously from a single biological sample. Lysate is first passed through an AllPrep DNA spin column to selectively isolate DNA and then through an RNeasy spin ... | ["[Homogenization] Add 600 µL of to Lysing Matrix E tubes.", "[Homogenization] Place the entire tissue or a portion into Lysing Matrix E tubes for homogenization.", "[Homogenization] For Swab(s): pick up with tweezers and cut with surgical scissors sterilized in a Germinator 500. Place the cut end of a single swab in... |
62,834 | Behavioral Testing - Open Field and Dyskinesia Scoring | 1 | dx.doi.org/10.17504/protocols.io.6qpvr67oovmk/v1 | https://www.protocols.io/view/behavioral-testing-open-field-and-dyskinesia-scori-b9ksr4we | Alexandra Nelson | TITLE: Behavioral Testing - Open Field and Dyskinesia Scoring
AUTHORS: Alexandra Nelson
[DESCRIPTION]
This protocol describes behavioral testing to assess motor deficits in mice. It includes open field locomotor testing and scoring of levodopa-induced dyskinesia.
[STEPS]
SECTION: Open Field Locomotor Testing
2. HABIT... | ["[Open Field Locomotor Testing] HABITUATION - Day 1\nPlace mouse in the open field chamber for 30 minutes; clean chambers with ethanol between mice30 min", "[Open Field Locomotor Testing] HABITUATION - Day 2\nPlace mice in the open field chamber for 30 minutes; clean chambers with ethanol between mice30 min", "[Open F... |
67,087 | Quality control analysis for 10X snRNA-seq | 5 | dx.doi.org/10.17504/protocols.io.261genbqjg47/v2 | https://www.protocols.io/view/quality-control-analysis-for-10x-snrna-seq-cdrps55n | Daniel Jacobsen, Dinh H Diep | TITLE: Quality control analysis for 10X snRNA-seq
AUTHORS: Daniel Jacobsen, Dinh H Diep
[DESCRIPTION]
Here we describe a computational protocol for performing quality control analysis on shallow sequencing data obtained from 10X snRNA-seq experiments. The workflow starts with raw MiSeq run folders and uses cellrange... | ["Install cellranger using instructions from https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/installation", "Download the tar.gz file from this protocol.", "Extract the tar.gz file from this protocol.\n<FILENAME> is the name of the downloaded tar.gz file.", "Install anaconda or min... |
null | null | null | dx.doi.org/10.17504/protocols.io.p8fdrtn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol describes a generalizable, long-read, low-input metagenomic sequencing approach ('VirION') for the survey of viral communities. A significant obstacle in adopting long-read technology for viral metagenomics lies in obtaining the amount of DNA required; e.g. vira... | [] |
94,426 | Chronic optrode recordings from the Locus coeruleus (Optrode construction, implantation, and recording) | 1 | dx.doi.org/10.17504/protocols.io.rm7vzxd45gx1/v1 | https://www.protocols.io/view/chronic-optrode-recordings-from-the-locus-coeruleu-c8f2ztqe | Ernesto Durán, Cristian González-Cabrera, Matthias Prigge | TITLE: Chronic optrode recordings from the Locus coeruleus (Optrode construction, implantation, and recording)
AUTHORS: Ernesto Durán, Cristian González-Cabrera, Matthias Prigge
[DESCRIPTION]
This protocol covers chronic optrode construction, implantation, and recording in the Locus coeruleus (LC). It begins with buil... | ["[Building Optrode] Body parts the optrode\n\n\n \n\nFigure 1. Overview of the driver. From top to bottom. Drive screw, thumbnut, and plastic housing (black part) with the interference dowel pins (two white pieces).\n\n\nScrew the vented screw into the thumbnut halfway, so that the bottom half is protruding from the t... |
null | null | null | dx.doi.org/10.17504/protocols.io.evjbe4n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol describes how to make a 5 nmol L<sup>-1</sup> cobalt standard for measuring dissolved cobalt by cathodic stripping voltammetry.
[STEPS]
?.
?.
?. | [] |
34,206 | Single-gene long-term CRISPRi knockdown viability assay | 1 | null | https://www.protocols.io/view/single-gene-long-term-crispri-knockdown-viability-bdm6i49e | Nolan Bick, Benjamin Gaeta, Tsukasa Shibue, Francisca Vazquez | TITLE: Single-gene long-term CRISPRi knockdown viability assay
AUTHORS: Nolan Bick, Benjamin Gaeta, Tsukasa Shibue, Francisca Vazquez
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>As an alternative to '</span><span style = "font-weight:bold;">Single-gene short-term CRISPR ko viability assay<... | ["[Virus Titration]\nViral Titration", "[Virus Titration]\nMix following in a 12-well plate, AB1cells500,000 cells2virus(see below; with differing amount of virus)38 mg/mL polybrene1 uL410% FBS, RPMIup to 2 mLPlate map (volume of virus) ABCD10 uL (0 uL)0 uL (0 uL)225 uL (200 uL)50 uL (400 uL)3100 uL (800 uL)200 uL (1... |
40,204 | Human Nasopharyngeal Swab Processing for Viable Single-Cell Suspension | 4 | dx.doi.org/10.17504/protocols.io.bjhkkj4w | https://www.protocols.io/view/human-nasopharyngeal-swab-processing-for-viable-si-bjhkkj4w | Ying Tang, Carly G.K. Ziegler, Vincent N. Miao, Andrew W. Navia, Joshua D. Bromley, Kenneth J. Wilson, Yilianys Pride, Mohammad Hasan, Taylor Christian, Hannah Laird, Anna Owings, Meredith Sloan, Haley B. Williams, Tanya O. Robinson, George E. Abraham III, Michal Senitko, Sarah C. Glover, Bruce Horwitz, Alex K. Shalek,... | TITLE: Human Nasopharyngeal Swab Processing for Viable Single-Cell Suspension
AUTHORS: Ying Tang, Carly G.K. Ziegler, Vincent N. Miao, Andrew W. Navia, Joshua D. Bromley, Kenneth J. Wilson, Yilianys Pride, Mohammad Hasan, Taylor Christian, Hannah Laird, Anna Owings, Meredith Sloan, Haley B. Williams, Tanya O. Robinson,... | ["[Tube A]\nRapidly thaw cryovial (Tube A) in hands or thermal block set to .\n37 °C\nCarefully perform in accordance with your institute's safety guidelines. If handling potentially infectious material, inspect for cracks or leaks during warming", "[Tube A]\nRemove swab from Tube A using clean forceps, trim swab handl... |
99,563 | Amplicon Sequencing for Genotyping S. Typhi | 4 | dx.doi.org/10.17504/protocols.io.36wgq31dylk5/v2 | https://www.protocols.io/view/amplicon-sequencing-for-genotyping-s-typhi-ddgj23un | Jaspreet Mahindroo, Anton Spadar, Catherine Troman, Zoe Dyson, Kathryn Holt, Nick Grassly | TITLE: Amplicon Sequencing for Genotyping S. Typhi
AUTHORS: Jaspreet Mahindroo, Anton Spadar, Catherine Troman, Zoe Dyson, Kathryn Holt, Nick Grassly
[DESCRIPTION]
The following protocol is for amplifying and sequencing amplicons targeting Salmonella Typhi. It is primarily for use with samples that are already suspect... | ["[Preparation for sequencing using ONT Native barcodes] From the ONT kit (SQK-NBD114.24 or .96) thaw AMPure XP beads (AXP), mix by vortexing, then keep at room temperature.\n\nThaw the NEBnext Ultra II End Repair reagents on ice, flick or invert the tubes to mix, then spin down.", "[Preparation for sequencing using ON... |
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