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Authors: Mitchell Arnold
Proper citation: Mitchell Arnold 2020. ORCHARDS Household Substudy Protocol 2017. protocols.io dx.doi.org/10.17504/protocols.io.bhssj6ee Copy
Authors: Jeyanthi Suppiah
Summary: 1) The primers and probes utilized were obtained from published research article as referenced in the text.2) First, Dengue virus RNA was extracted from patient serum by using Qiagen
Proper citation: Jeyanthi Suppiah 2018. Dengue serotyping by Real-Time Taqman PCR. protocols.io dx.doi.org/10.17504/protocols.io.rabd2an Copy
Authors: Courtney Comrie
Summary: This protocol will provide instruction on where to access the HPC lab account, and where our data is stored.Only for internal use.
Proper citation: Courtney Comrie 2019. HPC Account Set up and Access. protocols.io dx.doi.org/10.17504/protocols.io.7ezhjf6 Copy
Authors: Tatiana Karakasheva, Kathryn Hamilton
Group: CHOP Gastrointestinal Epithelium Modeling Program
Summary: This protocol describes dissociation of a human intestinal biopsy tissue into single cells, followed by depletion of dead cells via annexin V MACS beads. The outcome is a single-cell suspension with viability ≥ 90% that is used for single-cell sequencing or establishemt of enteroid/colonoid culture.
Proper citation: Tatiana Karakasheva, Kathryn Hamilton 2021. Isolation of live single cells from intestinal biopsy. protocols.io dx.doi.org/10.17504/protocols.io.bst7nern Copy
Authors: Ivan Sanchez Fernandez et al
Summary: Code and results for the article "Deep learning in rare disease. Detection of tubers in tuberous sclerosis complex".
Proper citation: Ivan Sanchez Fernandez et al 2020. Deep learning in rare disease. Detection of tubers in tuberous sclerosis complex. protocols.io dx.doi.org/10.17504/protocols.io.bdt3i6qn Copy
Authors: Anindita Basu, Inbal Avraham-Davidi, Naomi Habib, Aviv Regev, Feng Zhang, Karthik Shekhar, Matan Hofree, David Weitz, Orit Rozenblatt-Rosen, Tyler Burks, Sourav Choudhury, François Aguet, Ellen Gelfand, Kristin Ardlie
Group: Human Cell Atlas Method Development Community
Summary: Currently, most single cell protocols require the preparation of a single cell suspension from fresh tissue, a major roadblock to clinical deployment, to archived materials and to certain tissues such as adult brain. In the adult brain the harsh enzymatic dissociation harms the integrity of the cells and their RNA, and biases toward easily dissociated cell types, and is restricted to young animals.We developed DroNc-seq, a droplet microfluidic and DNA barcoding technique for analysis of RNA profiles of single nuclei from fresh, frozen or lightly fixed tissues at high throughput and low cost. The utility of DroNc-Seq lies in working with hard-to-dissociate, frozen and/or archived tissues. To demonstrate the utility of this technique, we sequenced over 39 thousand nuclei from mouse and human archived brain samples, including post-mortem human brain tissue from GTEx project.
Proper citation: Anindita Basu, Inbal Avraham-Davidi, Naomi Habib, Aviv Regev, Feng Zhang, Karthik Shekhar, Matan Hofree, David Weitz, Orit Rozenblatt-Rosen, Tyler Burks, Sourav Choudhury, François Aguet, Ellen Gelfand, Kristin Ardlie 2018. DroNc-seq step-by-step. protocols.io dx.doi.org/10.17504/protocols.io.md2c28e Copy
Authors: Kelley Knizner, Christopher Simmons
Group: Human BioMolecular Atlas Program (HuBMAP) Method Development Community, GE Research
Summary: This method details formalin fixation and paraffin embedding of the HuBMAP tissue specimens.Protocol adopted from Marda Jorgensen, Jerelyn Nick (02/24/2020). HuBMAP: Paraffin Embedding Tissue Samples . https://dx.doi.org/10.17504/protocols.io.bam9ic96
Proper citation: Kelley Knizner, Christopher Simmons 2020. HuBMAP | Formalin Fixation and Paraffin Embedding of Tissue Samples . protocols.io dx.doi.org/10.17504/protocols.io.bqp6mvre Copy
Authors: H.K. Jeevan Dhanarisi, Indika B. Gawarammana, Fahim Mohamed, Michael Eddleston
Proper citation: H.K. Jeevan Dhanarisi, Indika B. Gawarammana, Fahim Mohamed, Michael Eddleston 2019. Test-mate (Model 400) erythrocyte acetylcholinesterase (AChE) test. protocols.io dx.doi.org/10.17504/protocols.io.wpyfdpw Copy
Authors: Laura Ruiz Remolina
Proper citation: Laura Ruiz Remolina 2017. Carrageenan air pouch (mice). protocols.io dx.doi.org/10.17504/protocols.io.j8dcrs6 Copy
Authors: Haven Himmighoefer, Rachel Ancar
Summary: Often used in Western Blots. Kept on the bottom shelf of the fridge.
Proper citation: Haven Himmighoefer, Rachel Ancar 2017. 5x SDS (10 mL). protocols.io dx.doi.org/10.17504/protocols.io.kuycwxw Copy
Authors: Dr. Steven Wilhelm
Group: The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs)
Summary: Please contact Dr. Steven Wilhelm ([email protected]) for additional information regarding this protocol.Modified from J Mol Biol 13,269 (1965)
Proper citation: Dr. Steven Wilhelm 2017. Propidium Iodide (PI) Staining Method. protocols.io dx.doi.org/10.17504/protocols.io.ibxcapn Copy
Authors: Adriana Lopes Dos Santos, Claude Lemieux, Monique Turmel
Summary: Method used to eliminate bacterial contamination of a marine micro-algal culture. Note, this method is not guaranteed to be 100% successful either due to the fact that the antibiotic combination is not lethal to the bacteria present or it is possible that the strain may not be capable of prolonged growth without the presence of bacteria. This method is based on that of Droop, adapted according to Andersen but using a modern antibiotic mix suggested by S. Slocombe (SAMS - Scottish Association for Marine Science). The method described here have been successfully used by Christian Jeanthon (ECOMAP) to produce axenic cultures of diatoms and E. huxleyi.1. Droop, M. R. A procedure for routine purification of algal cultures with antibiotics. Br. Phycol. Bull. 3, 295–297 (1967).2. Andersen, R. Algal Cultering Techniques. (Academic Press, 2005).
Proper citation: Adriana Lopes Dos Santos, Claude Lemieux, Monique Turmel 2020. Basic protocol for elimination of bacteria from microalgal culture using antibiotics. protocols.io dx.doi.org/10.17504/protocols.io.be9wjh7e Copy
Authors: Izabela Rezende, Lívia Sacchetto
Group: MRCA
Summary: For isolate the desired product or reoptimize the PCR to obtain a single product.
Proper citation: Izabela Rezende, Lívia Sacchetto 2018. Gel PCR Product Purification. protocols.io dx.doi.org/10.17504/protocols.io.pxbdpin Copy
Authors: Angel Justiz-Vaillant
Group: Carbon
Summary: This ELISA was used to study the interactions between protein-LAG (PLAG) and streptococcal protein-G (SpG) with different immunoglobulin preparations of mammalian and avian species.
Proper citation: Angel Justiz-Vaillant 2021. Chimeric Protein-LAG and Streptococcal protein G sandwich ELISA. protocols.io dx.doi.org/10.17504/protocols.io.btbcniiw Copy
Authors: David Lowry
Group: Mimulus
Proper citation: David Lowry 2019. Tissue collection and extractions for RNA-seq. protocols.io dx.doi.org/10.17504/protocols.io.basiiece Copy
Authors: Matthew Sullivan Lab
Group: VERVE Net, Sullivan Lab
Summary: Supplement to seawater for growth of cyanobacteria.
Proper citation: Matthew Sullivan Lab 2015. 0.5M NH4Cl. protocols.io dx.doi.org/10.17504/protocols.io.c77zrm Copy
Authors: Lukas Snoek, Tinka Beemsterboer
Group: Spinoza Centre, REC-L
Summary: This protocol lists all the steps necessary to run your MRI experiment/data acquisition safely and in a way that yields high-quality data. Moreover, if you use the centre's QC/preprocessing service, it lists the steps necessary to make sure we can convert the data into BIDS and run them through the QC/preprocessing pipelines.
Proper citation: Lukas Snoek, Tinka Beemsterboer 2019. During data acquisition. protocols.io dx.doi.org/10.17504/protocols.io.w8ffhtn Copy
Authors: Bonnie Hurwitz
Group: Hurwitz Lab, MetaFunc Course
Summary: Create a script to add functional information about the samples into Anvi'o.
Proper citation: Bonnie Hurwitz 2016. C_HW10: Sample read count to functional categories for Anvi'o bar chart. protocols.io dx.doi.org/10.17504/protocols.io.gkibuue Copy
Authors: Alan Cone
Group: Ju Lab
Summary: Quick and easy method to transform a free plasmid into either budding or fission yeast.
Proper citation: Alan Cone 2015. One-Step Transformation of Yeast. protocols.io dx.doi.org/10.17504/protocols.io.ddv265 Copy
Authors: Janet Keast, Peregrine Osborne, Nicole Wiedmann
Group: SPARC
Summary: This protocol is used for analysing expression pattens of immediate early gene products (e.g., c-Fos) in immunostained transverse sections of spinal cord.
Proper citation: Janet Keast, Peregrine Osborne, Nicole Wiedmann 2020. Image analysis of immediate early gene expression in spinal cord sections. protocols.io dx.doi.org/10.17504/protocols.io.bakmicu6 Copy
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