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Authors: Sam Li
Group: BioLegend

Proper citation: Sam Li 2019. Whole Mouse Brain Processing for Microglia Isolation, Cell Separation, and Flow Cytometry. protocols.io https://dx.doi.org/10.17504/protocols.io.97dh9i6 Copy   

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Authors: Marijn Ceelen
Group: iGEM Wageningen 2019
Summary: This protocol explains how to use the Abor BiosciencesSigma 70 TXTL mix to produce bacteriophages. This protocol works for bacteriophage T7. It has been tested on phage lambda. However, it seems that the current protocol does not work for phage lambda. 

Proper citation: Marijn Ceelen 2019. TXTL phage production. protocols.io https://dx.doi.org/10.17504/protocols.io.77thrnn Copy   

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Authors: Tomasz Suchan

Proper citation: Tomasz Suchan 2020. Bead-based normalization for NGS. protocols.io https:// Copy   

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Authors: Rita Graze
Group: Graze Lab
Summary: A protocol for the making of 1M Propionic Acid for the use in Drosophila food. 

Proper citation: Rita Graze 2018. Propionic Acid Preparation. protocols.io https://dx.doi.org/10.17504/protocols.io.qjjdukn Copy   

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Authors: Jianmin Liu, Jing Liu, Guang’an Wang, Guangya Liu, Huanjiao Zhou, Yun Fan, Fengxia Liang, Hua Wang
Summary: A protocol of Electroacupuncture (EA) treatment on sub-acutely aging rats.

Proper citation: Jianmin Liu, Jing Liu, Guang’an Wang, Guangya Liu, Huanjiao Zhou, Yun Fan, Fengxia Liang, Hua Wang 2018. A protocol of Electroacupuncture (EA) treatment on sub-acutely aging rats. protocols.io https://dx.doi.org/10.17504/protocols.io.ky8cxzw Copy   

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Authors: Andrea Argouarch
Group: Neurodegeneration Method Development Community
Summary: Protocols included in this collection describe cell isolation from human dura mater, culturing, and banking.

Proper citation: Andrea Argouarch 2020. Dural Cell Isolation and Culturing - Collection. protocols.io https://dx.doi.org/10.17504/protocols.io.8m2hu8e Copy   

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Authors: Ruth-Anne Sandaa, Steven M. Short, and Declan C. Schroeder
Group: VERVE Net
Summary: The viral concentrate used for PFGE analysis must be molded into plugs, followed by lysis of the virus particles to release their DNA. It is possible to run solution-based preparation of viral DNA for PFGE (Steward 2001); however, large DNA molecules (>100 kb) are extremely sensitive to mechanical shearing in aqueous solution (Bouchez and Camilleri 1997). The consensus is that lysis inside viral plugs prevents mechanical shearing of the DNA, resulting in more discrete PFGE bands. Intact viral genomes are then separated by size by PFGE. After separation, the banding pattern is visualized by staining with a fluorescent DNA stain. This banding pattern provides a visual record of the genome size distribution that can be used for qualitative and quantitative comparisons between samples.

Proper citation: Ruth-Anne Sandaa, Steven M. Short, and Declan C. Schroeder 2016. Fingerprinting aquatic virus communities using pulsed field gel electrophoresis (PFGE). protocols.io https://dx.doi.org/10.17504/protocols.io.dy27yd Copy   

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Authors: Linlin Yin, Lisette A. Maddison, Mingyu Li, Nergis Kara, Matthew C. LaFave, Gaurav K. Varshney, Shawn M. Burgess, James G. Patton, and Wenbiao Chen
Group: Genetics
Summary: This protocols is from:Linlin Yin, et al. (2015) Multiplex Conditional Mutagenesis Using Transgenic Expression of Cas9 and sgRNAs. Genetics 200:431-441; doi:10.1534/genetics.115.176917Please see the full manuscript for additional details.

Proper citation: Linlin Yin, Lisette A. Maddison, Mingyu Li, Nergis Kara, Matthew C. LaFave, Gaurav K. Varshney, Shawn M. Burgess, James G. Patton, and Wenbiao Chen 2015. Construction of pGGDestTol2LC-sgRNA vectors. protocols.io https://dx.doi.org/10.17504/protocols.io.drv565 Copy   

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Authors: Ken Youens-Clark
Group: MetaFunc Course

Proper citation: Ken Youens-Clark 2016. Setting $PATH on UA HPC. protocols.io https://dx.doi.org/10.17504/protocols.io.fsybnfw Copy   

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Authors: Joao Vitor Molino

Proper citation: Joao Vitor Molino 2020. Algae strain maintenance (Chlamydomonas reinhardtii). protocols.io https:// Copy   

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Authors: Heather Robeson, Jing Jin, Mohammed S. Orloff
Summary: The protocol is based on Qiagen-AllPrep DNA/RNA/Protein Mini kit for tissue

Proper citation: Heather Robeson, Jing Jin, Mohammed S. Orloff 2020. Qiagen- AllPrep DNA/RNA/protein Mini Kit for tissue. protocols.io https://dx.doi.org/10.17504/protocols.io.bn9kmh4w Copy   

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Authors: David Eccles
Group: High molecular weight DNA extraction from all kingdoms
Summary: This protocol is for a semi-manual method for read demultiplexing, as used after my presentation Sequencing DNA with Linux Cores and Nanopores to work out the number of reads captured by different barcodes.Input: reads as a FASTQ file, barcode sequences as a FASTA fileOutput: reads split into single FASTQ files per target [barcode]Note: barcode / adapter sequences are not trimmed by this protocol

Proper citation: David Eccles 2019. Demultiplexing Nanopore reads with LAST. protocols.io https://dx.doi.org/10.17504/protocols.io.xj3fkqn Copy   

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Authors: Christopher Bartley
Summary: Basic Protocol for culturing Neuro2a cells.

Proper citation: Christopher Bartley 2015. Neuro-2a cell culture (Neuro 2a, N2a). protocols.io https://dx.doi.org/10.17504/protocols.io.cpvvn5 Copy   

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Authors: Peter Szabo, Steven Wells, Peter A. Sims, Donna Farber
Group: Human Cell Atlas Method Development Community, Coronavirus Method Development Community
Summary: This protocol describes the isolation of lymphocytes and pan-mononuclear cells from airway samples.

Proper citation: Peter Szabo, Steven Wells, Peter A. Sims, Donna Farber 2020. COVID Airway Processing for scRNAseq. protocols.io https://dx.doi.org/10.17504/protocols.io.bjj8kkrw Copy   

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Authors: Chris Englert, Dennis Koroma, Alex Bertrams, Corinna Martarelli
Summary: The attention control video has been frequently applied to test the ego depletion effect. However, its validity has never been tested, a shortcoming we address in this preregistered study. In the first task, self-control strength was temporarily depleted in the depletion condition (n = 56) but remained intact in the control condition (n = 56). The attention control video served as the secondary task, and we assumed that the depletion condition would perform significantly worse compared to the control condition. Attention regulation was measured with an eye-tracking device. The results revealed that the gaze behavior in the two conditions differed statistically significantly; however, the actual difference was small, indicating that the attention control video may not be an optimal measure of self-control.

Proper citation: Chris Englert, Dennis Koroma, Alex Bertrams, Corinna Martarelli 2019. S1File_FullQuestionnaire. protocols.io https://dx.doi.org/10.17504/protocols.io.uj3euqn Copy   

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Authors: Bonnie Hurwitz, Ken Youens-Clark
Group: VERVE Net, Hurwitz Lab
Summary: Long-standing questions in marine viral ecology are centered on understanding how viral assemblages change along gradients in space and time. However, investigating these fundamental ecological questions has been challenging due to incomplete representation of naturally occurring viral diversity in single gene- or morphology-based studies and an inability to identify up to 90% of reads in viral metagenomes (viromes).  In this protocol, I describe how to use an annotation- and assembly-free strategy for comparative metagenomics that combines shared k-mer and social network analyses (regression modeling). This robust statistical framework enables visualization of complex sample networks and determination of ecological factors driving community structure.  This tutorial describes a protocol to reproduce work from the Pacific Ocean virome comprised of 32 viromes from diverse sites in the Pacific Ocean. "Modeling ecological drivers in marine viral communities using comparative metagenomics and network analyses" (July 7, 2014, doi: 10.1073/pnas.1319778111, PNAS July 22, 2014 vol. 111 no. 29 10714-10719)Code is freely available at Github.

Proper citation: Bonnie Hurwitz, Ken Youens-Clark 2016. Modeling ecological drivers in marine viral communities using comparative metagenomics and network analyses. protocols.io https://dx.doi.org/10.17504/protocols.io.efgbbjw Copy   

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Authors: Hongbo Zhang
Summary: A protocol for isolation single cells from human skeletal muscle. The isolated single cells can be used for scRANseq.

Proper citation: Hongbo Zhang 2018. Single cell isolation from human skeletal muscle. protocols.io https://dx.doi.org/10.17504/protocols.io.q5wdy7e Copy   

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Authors: Dennis Dienst, Oliver Mantovani, Pia Lindberg
Group: CyanoWorld, Metabolomics Protocols & Workflows, Chemistry Method Development Community
Summary: This is a quick guide for the preparation of (-)-α-bisabolol samples and external standards in dodecane for GC analysis. This protocol has been established in the Lindberg lab at Ångström laboratory (Uppsala University) for direct analysis of dodecane-based ex-situ extracts from cyanobacterial strains producing (-)-α-bisabolol. The protocol includes the preparation of stock solutions for the internal standard β-caryophyllene (BCP) and the external standard. The preparation of a fresh external standard series is suggested for each sample analysis. The calibration curve is required for quantification of (-)-α-bisabolol in the samples of interest. This protocol is used in combination with the following GC protocol:dx.doi.org/10.17504/protocols.io.kj2cuqe

Proper citation: Dennis Dienst, Oliver Mantovani, Pia Lindberg 2019. (-)-α-Bisabolol GC sample preparation. protocols.io https://dx.doi.org/10.17504/protocols.io.xiufkew Copy   

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Authors: California Digital Library
Group: Data Management Plans

Proper citation: California Digital Library 2018. National Science Foundation Generic Template. protocols.io https://dx.doi.org/10.17504/protocols.io.sx2efqe Copy   

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Authors: Andrew Potter
Group: Human Cell Atlas Method Development Community
Summary: This protocol was developed to dissociate adult (8-10 wk) mouse skin "on ice". It utilizes two layers of digestion with a Bacillus licheniformis protease cocktail, combined with mechanical disruption from a dounce homogenizer. The cell yield is 3000 cells/mg.

Proper citation: Andrew Potter 2018. Adult mouse skin dissociation protocol (on ice). protocols.io https://dx.doi.org/10.17504/protocols.io.tupenvn Copy   

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