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Authors: Sonia Hall

Proper citation: Sonia Hall 2016. Oil Red O Staining Drosophila Larval and Prepupal Tissues. protocols.io https://dx.doi.org/10.17504/protocols.io.euhbet6 Copy   

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Authors: Sonia Hall
Summary: Combine2mls glacial acetic acid1L distilled water

Proper citation: Sonia Hall 2015. Acidified Distilled Water. protocols.io https://dx.doi.org/10.17504/protocols.io.dh338m Copy   

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Authors: Openwetware
Summary: Phenol/chloroform extraction is an easy way to remove proteins from your nucleic acid samples and can be carried out in a manner that is very close to quantitative. Nucleic acids remain in the aqueous phase and proteins separate into the organic phase or lie at the phase interface. Please see the OpenWetWare website for more details.Citation: OpenWetWare contributors, 'Phenol/chloroform extraction', OpenWetWare, , 13 September 2010, 13:37 UTC, http://openwetware.org/index.php?title=Phenol/chloroform_extraction&oldid=453981> [accessed 21 January 2015]

Proper citation: Openwetware 2015. Phenol/chloroform extraction. protocols.io https://dx.doi.org/10.17504/protocols.io.cdts6m Copy   

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Authors: Gabriel Magalhães Nunes Guimarães

Proper citation: Gabriel Magalhães Nunes Guimarães 2018. Modified Oxford Maneuver - anesthesiologist protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.rctd2wn Copy   

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Authors: Adam Hunter
Group: Human Cell Atlas Method Development Community
Summary: Mechanical dissociation of human spleen tissue to single cells for use in 10X chromium scRNA-Seq preparation. 

Proper citation: Adam Hunter 2018. CGAP Human Spleen Dissociation. protocols.io https://dx.doi.org/10.17504/protocols.io.qz3dx8n Copy   

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Authors: John J. Trombetta, David Gennert, Diana Lu, Rahul Satija, Alex K. Shalek, Aviv Regev
Group: Human Cell Atlas Method Development Community
Summary: For the past several decades, due to technical limitations, the field of transcriptomics has focused on population‐level measurements that can mask significant differences between individual cells. With the advent of single‐cell RNA‐Seq, it is now possible to profile the responses of individual cells at unprecedented depth and thereby uncover, transcriptome‐wide, the heterogeneity that exists within these populations. This unit describes a method that merges several important technologies to produce, in high‐throughput, single‐cell RNA‐Seq libraries. Complementary DNA (cDNA) is made from full‐length mRNA transcripts using a reverse transcriptase that has terminal transferase activity. This, when combined with a second “template‐switch” primer, allows for cDNAs to be constructed that have two universal priming sequences. Following preamplification from these common sequences, Nextera XT is used to prepare a pool of 96 uniquely indexed samples ready for Illumina sequencing. Curr. Protoc. Mol. Biol. 107:4.22.1‐4.22.17. © 2014 by John Wiley & Sons, Inc.

Proper citation: John J. Trombetta, David Gennert, Diana Lu, Rahul Satija, Alex K. Shalek, Aviv Regev 2018. Preparation of Single-Cell RNA-Seq Libraries for Next Generation Sequencing. protocols.io https://dx.doi.org/10.17504/protocols.io.n6gdhbw Copy   

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Authors: Anthony Underwood

Proper citation: Anthony Underwood 2020. GHRU (Genomic Surveillance of Antimicrobial Resistance) Retrospective 1 Bioinformatics Methods. protocols.io https:// Copy   

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Authors: Takeshi Yamashina, Noboru Hanaoka, Takeshi Setoyama, Masahiro Banno, Jun Watanabe, Hiroyuki Marusawa

Proper citation: Takeshi Yamashina, Noboru Hanaoka, Takeshi Setoyama, Masahiro Banno, Jun Watanabe, Hiroyuki Marusawa 2020. Efficacy of Underwater EMR for non-pedunculated colorectal lesions: a systematic review and meta-analysis protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.bj5rkq56 Copy   

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Authors: Caterina Villari
Group: Protocols Bark Beetle Mycobiome
Summary: This protocol describes the LAMP (Loop-mediated isothermal amplification) master mix and reaction.This protocol is part of the Bark Beetle Mycobiome (BBM) Research Coordination Network. For more information on the BBM international network: Hulcr J, Barnes I, De Beer ZW, Duong TA, Gazis R, Johnson AJ, Jusino MA, Kasson MT, Li Y, Lynch S, Mayers C, Musvuugwa T, Roets F, Seltmann KC, Six D, Vanderpool D, & Villari C. 2020. Bark beetle mycobiome: collaboratively defined research priorities on a widespread insect-fungus symbiosis. Symbiosis 81: 101–113 https://doi.org/10.1007/s13199-020-00686-9.

Proper citation: Caterina Villari 2020. LAMP Master Mix + Reaction Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.bm27k8hn Copy   

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Authors: Shiu-Ming Kuo

Proper citation: Shiu-Ming Kuo 2018. cecal bacteria DNA extraction. protocols.io https://dx.doi.org/10.17504/protocols.io.tfeejje Copy   

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Authors: Eftychis Frangedakis

Proper citation: Eftychis Frangedakis 2019. Hornwort sporophyte induction -OXF. protocols.io https://dx.doi.org/10.17504/protocols.io.4x4gxqw Copy   

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Authors: Kathi Burke, Peter Reifsnyder
Group: Diabetic Complications Consortium
Summary: Albuwell M is an indirect competitive ELISA designed to monitor kidney function in the mouse by measurement of urinary albumin. To complete the assay, sample and rabbit anti-murine albumin antibody are added to albumin coated wells. The antibody interacts and binds with the albumin immobilized to the stationary phase or with albumin in the fluid phase, hence the notion of competitive binding. A subsequent reaction with anti-rabbit -HRP conjugate labels the probe with enzyme. After washing, only the antibody-conjugate bound to the stationary phase remains in the well, and this is detected using a chromogenic reaction. Color intensity is inversely proportional to the logarithm of albumin in the fluid phase. The assay may be completed in less than 2.5 hoursDiabetic Complication:

Proper citation: Kathi Burke, Peter Reifsnyder 2019. Protocol for Albuwell M kit: Murine Microalbuminuria ELISA By Exocell Inc. protocols.io https://dx.doi.org/10.17504/protocols.io.34mgqu6 Copy   

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Authors: Ana Dal Molin
Summary: Protocolo para preparação de pequenos artrópodes de cutícula pouco esclerotizada quando não há disponibilidade de secador de ponto crítico. Adaptado de:Brown, B.V. 1993. A further chemical alternative to critical- point-drying for preparing small (or large) flies. Fly Times 11: 10. Heraty, J. & D. Hawks. 1998. Hexamethyldisilazane - a chemical alternative for drying insects. Entomological News 109(5): 369-374.Rumph, J. A. & W. J. Turner. 1998. Alternative to Critical Point Drying for Soft-Bodied Insect Larvae. Annals of the Entomological Society of America 91(5): 693–699.

Proper citation: Ana Dal Molin 2018. Secagem química de pequenos artrópodes (PT-BR). protocols.io https://dx.doi.org/10.17504/protocols.io.s9aeh2e Copy   

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Authors: Toby
Group: XPRIZE Rapid Covid Testing

Proper citation: Toby 2020. Mikro SARS-CoV-2 Multiplex Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.bk8dkzs6 Copy   

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Authors: Yu-wei Yang1, Bi Peng2, Xiao-hong Chen1, Jun Ying3, and Tao Yang3

Proper citation: Yu-wei Yang1, Bi Peng2, Xiao-hong Chen1, Jun Ying3, and Tao Yang3 2017. New Identification Equations Based on Erythrocyte and Reticulocyte Characteristics for Screening Thalassaemia Trait in Pregnancy. protocols.io https://dx.doi.org/10.17504/protocols.io.irmcd46 Copy   

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Authors: Nili O
Group: vnat
Summary: Preparation of Vibrio natriegens cell stocks for long-term storage at -80C. Principle is to remove any accumulated metabolic waste from overnight culture and resuspend in 20% glycerol final.

Proper citation: Nili O 2017. Vibrio Natriegens - Glycerol stock. protocols.io https://dx.doi.org/10.17504/protocols.io.hakb2cw Copy   

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Authors: Bonnie Hurwitz
Group: VERVE Net, Hurwitz Lab, ABE487_HMP, ABE487_EMP
Summary: This tutorial covers a full QIIME workflow using Illumina sequencing data and was adapted from a tutorial on the QIIME website.. This tutorial is intended to be quick to run, and as such, uses only a subset of a full Illumina Genome Analyzer II (GAIIx) run. We'll make use of the Greengenes reference OTUs, which is the default reference database used by QIIME. You can determine which version of Greengenes is being used by running print_qiime_config.py. This will be Greengenes, unless you've configured QIIME to use a different reference database by default.The data used in this tutorial are derived from the Moving Pictures of the Human Microbiome study, where two human subjects collected daily samples from four body sites: the tongue, the palm of the left hand, the palm of the right hand, and the gut (via fecal samples obtained by swapping used toilet paper). These data were sequenced using the barcoded amplicon sequencing protocol described in Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. A more recent version of this protocol that can be used with the Illumina HiSeq 2000 and MiSeq can be found here.

Proper citation: Bonnie Hurwitz 2015. QIIME:Moving Pictures of the human microbiome. protocols.io https://dx.doi.org/10.17504/protocols.io.d5288d Copy   

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Authors: Krista Longnecker
Group: Kujawinski Lab, Metabolomics Protocols & Workflows
Summary: Solid phase extraction using PPL modified from Dittmar et al. (2008): Dittmar, T.; Koch, B.; Hertkorn, N.; Kattner, G., A simple and efficient method for the solid-phase extraction of dissolved organic matter (SPE-DOM) from seawater. Limnology and Oceanography Methods 2008, 6, 230-235

Proper citation: Krista Longnecker 2019. Preparing water samples for analysis using ultrahigh resolution mass spectrometry. protocols.io https://dx.doi.org/10.17504/protocols.io.y36fyre Copy   

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Authors: Zhu Feng
Summary: Infected beetles were collected and homogenized in sterile water. The homogenates were filtered through four layers of cheesecloth and centrifuged at 3000g for 15 min. The pellets were resuspended in sterile water, and the spores were purified by Percoll gradient centrifugation using 90% Percoll at 15,000g for 40 min. The spore band was collected and washed several times with sterile water. The purified spores (n = 50) were measured under a light microscope (IL/Leica Microsystems, Inc., Deerfield) with an ocular micrometer and photographed with the Microscope USB Camera.

Proper citation: Zhu Feng 2017. Purification of Nosema bombycis spores. protocols.io https://dx.doi.org/10.17504/protocols.io.if3cbqn Copy   

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Authors: Devi Oktafiani
Summary: Peripheral blood mononuclear cells (PBMCs) are chiefly lymphocytes and monocytes. PBMCs are separated from the whole blood by a density gradient centrifugation method using Ficoll-Paque.

Proper citation: Devi Oktafiani 2019. Isolation of peripheral blood mononuclear cells. protocols.io https://dx.doi.org/10.17504/protocols.io.7j5hkq6 Copy   

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