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| Name | Authors | DOI | Group |
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Oil Red O Staining Drosophila Larval and Prepupal Tissues Resource Report Resource Website |
Sonia Hall | DOI:10.17504/protocols.io.euhbet6 | University of Massachusetts Medical School | 1 | 2016 | Sonia Hall 2016. Oil Red O Staining Drosophila Larval and Prepupal Tissues. protocols.io https://dx.doi.org/10.17504/protocols.io.euhbet6 | 2021-04-15 09:15:50 | |||||
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Acidified Distilled Water Resource Report Resource Website |
Sonia Hall | DOI:10.17504/protocols.io.dh338m | Combine2mls glacial acetic acid1L distilled water | University of Massachusetts Medical School | 1 | 2015 | Sonia Hall 2015. Acidified Distilled Water. protocols.io https://dx.doi.org/10.17504/protocols.io.dh338m | 2021-04-15 09:15:31 | ||||
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Phenol/chloroform extraction Resource Report Resource Website |
Openwetware | DOI:10.17504/protocols.io.cdts6m | 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] | OpenWetWare | http://openwetware.org/wiki/Phenol/chloroform_extraction | 1 | 2015 | Openwetware 2015. Phenol/chloroform extraction. protocols.io https://dx.doi.org/10.17504/protocols.io.cdts6m | 2021-04-15 09:15:32 | |||
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Modified Oxford Maneuver - anesthesiologist protocol Resource Report Resource Website |
Gabriel Magalhães Nunes Guimarães | DOI:10.17504/protocols.io.rctd2wn | Universidade de Brasília | 1 | 2018 | Gabriel Magalhães Nunes Guimarães 2018. Modified Oxford Maneuver - anesthesiologist protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.rctd2wn | 2021-04-15 09:15:32 | |||||
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CGAP Human Spleen Dissociation Resource Report Resource Website |
Adam Hunter | DOI:10.17504/protocols.io.qz3dx8n | Human Cell Atlas Method Development Community | Mechanical dissociation of human spleen tissue to single cells for use in 10X chromium scRNA-Seq preparation. | CGAP | 1 | 2018 | Adam Hunter 2018. CGAP Human Spleen Dissociation. protocols.io https://dx.doi.org/10.17504/protocols.io.qz3dx8n | 2021-04-15 09:15:32 | |||
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Preparation of Single-Cell RNA-Seq Libraries for Next Generation Sequencing Resource Report Resource Website |
John J. Trombetta, David Gennert, Diana Lu, Rahul Satija, Alex K. Shalek, Aviv Regev | DOI:10.17504/protocols.io.n6gdhbw | Human Cell Atlas Method Development Community | 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. | Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA, Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA, Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA, Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA, Department of Chemistry and Chemical Biology and Department of Physics, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA, Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02140, USA | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4338574/ | 1 | 2018 | 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 | 2021-04-15 09:15:32 | ||
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GHRU (Genomic Surveillance of Antimicrobial Resistance) Retrospective 1 Bioinformatics Methods Resource Report Resource Website |
Anthony Underwood | Centre for Genomic Pathogen Surveillance | 4 | 2020 | Anthony Underwood 2020. GHRU (Genomic Surveillance of Antimicrobial Resistance) Retrospective 1 Bioinformatics Methods. protocols.io https:// | 2021-04-15 09:15:52 | ||||||
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Efficacy of Underwater EMR for non-pedunculated colorectal lesions: a systematic review and meta-analysis protocol Resource Report Resource Website |
Takeshi Yamashina, Noboru Hanaoka, Takeshi Setoyama, Masahiro Banno, Jun Watanabe, Hiroyuki Marusawa | DOI:10.17504/protocols.io.bj5rkq56 | Department of Gastroenterology and Hepatology, Osaka Red Cross Hospital, Department of Gastroenterology and Hepatology, Osaka Red Cross Hospital, Department of Gastroenterology and Hepatology, Osaka Red Cross Hospital, Department of Psychiatry, Seichiryo Hospital, Division of Community and Family Medicine, Jichi Medical University, Department of Gastroenterology and Hepatology, Osaka Red Cross Hospital | 1 | 2020 | 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 | 2021-04-15 09:15:37 | |||||
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LAMP Master Mix + Reaction Protocol Resource Report Resource Website |
Caterina Villari | DOI:10.17504/protocols.io.bm27k8hn | Protocols Bark Beetle Mycobiome | 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. | University of Georgia | 1 | 2020 | Caterina Villari 2020. LAMP Master Mix + Reaction Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.bm27k8hn | 2021-04-15 09:15:37 | |||
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cecal bacteria DNA extraction Resource Report Resource Website |
Shiu-Ming Kuo | DOI:10.17504/protocols.io.tfeejje | Zheng W, Wang K, Sun Y, Kuo S (2018) Dietary or supplemental fermentable fiber intake reduces the presence of Clostridium XI in mouse intestinal microbiota: The importance of higher fecal bacterial load and density. PLoS ONE 13(10): e0205055. doi: 10.1371/journal.pone.0205055 | University at Buffalo | https://doi.org/10.1371/journal.pone.0205055 | 1 | 2018 | Shiu-Ming Kuo 2018. cecal bacteria DNA extraction. protocols.io https://dx.doi.org/10.17504/protocols.io.tfeejje | 2021-04-15 09:15:37 | |||
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Hornwort sporophyte induction -OXF Resource Report Resource Website |
Eftychis Frangedakis | DOI:10.17504/protocols.io.4x4gxqw | University of Cambridge | 1 | 2019 | Eftychis Frangedakis 2019. Hornwort sporophyte induction -OXF. protocols.io https://dx.doi.org/10.17504/protocols.io.4x4gxqw | 2021-04-15 09:15:37 | |||||
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Protocol for Albuwell M kit: Murine Microalbuminuria ELISA By Exocell Inc Resource Report Resource Website |
Kathi Burke, Peter Reifsnyder | DOI:10.17504/protocols.io.34mgqu6 | Diabetic Complications Consortium | 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: | University of Arizona, Frank Brosius Lab, The Jackson Laboratory, Ed Leiter Lab | https://www.diacomp.org/shared/document.aspx?id=22&docType=Protocol | 1 | 2019 | 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 | 2021-04-15 09:15:37 | ||
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Secagem química de pequenos artrópodes (PT-BR) Resource Report Resource Website |
Ana Dal Molin | DOI:10.17504/protocols.io.s9aeh2e | 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. | Universidade Federal do Espírito Santo | 1 | 2018 | Ana Dal Molin 2018. Secagem química de pequenos artrópodes (PT-BR). protocols.io https://dx.doi.org/10.17504/protocols.io.s9aeh2e | 2021-04-15 09:15:37 | ||||
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Mikro SARS-CoV-2 Multiplex Protocol Resource Report Resource Website |
Toby | DOI:10.17504/protocols.io.bk8dkzs6 | XPRIZE Rapid Covid Testing | Mikro | 1 | 2020 | Toby 2020. Mikro SARS-CoV-2 Multiplex Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.bk8dkzs6 | 2021-04-15 09:15:37 | ||||
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New Identification Equations Based on Erythrocyte and Reticulocyte Characteristics for Screening Thalassaemia Trait in Pregnancy Resource Report Resource Website |
Yu-wei Yang1, Bi Peng2, Xiao-hong Chen1, Jun Ying3, and Tao Yang3 | DOI:10.17504/protocols.io.irmcd46 | Department of Laboratory Medicine, Mianyang Central Hospital, Sichuan China; 2. Department of Laboratory Medicine, The Third Hospital of Mianyang, Sichuan China; 3. Department of Laboratory Medicine, Santai Peoples Hospital, Sichuan China, Department of Laboratory Medicine, Mianyang Central Hospital, Sichuan China; 2. Department of Laboratory Medicine, The Third Hospital of Mianyang, Sichuan China; 3. Department of Laboratory Medicine, Santai Peoples Hospital, Sichuan China, Department of Laboratory Medicine, Mianyang Central Hospital, Sichuan China; 2. Department of Laboratory Medicine, The Third Hospital of Mianyang, Sichuan China; 3. Department of Laboratory Medicine, Santai Peoples Hospital, Sichuan China, Department of Laboratory Medicine, Mianyang Central Hospital, Sichuan China; 2. Department of Laboratory Medicine, The Third Hospital of Mianyang, Sichuan China; 3. Department of Laboratory Medicine, Santai Peoples Hospital, Sichuan China, Department of Laboratory Medicine, Mianyang Central Hospital, Sichuan China; 2. Department of Laboratory Medicine, The Third Hospital of Mianyang, Sichuan China; 3. Department of Laboratory Medicine, Santai Peoples Hospital, Sichuan China | 2 | 2017 | 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 | 2021-04-15 09:15:37 | |||||
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Vibrio Natriegens - Glycerol stock Resource Report Resource Website |
Nili O | DOI:10.17504/protocols.io.hakb2cw | vnat | 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. | 1 | 2017 | Nili O 2017. Vibrio Natriegens - Glycerol stock. protocols.io https://dx.doi.org/10.17504/protocols.io.hakb2cw | 2021-04-15 09:15:52 | ||||
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QIIME:Moving Pictures of the human microbiome Resource Report Resource Website |
Bonnie Hurwitz | DOI:10.17504/protocols.io.d5288d | VERVE Net, Hurwitz Lab, ABE487_HMP, ABE487_EMP | 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. | Kindler L, Stoliartchouk A, Teytelman L, Hurwitz BL, Method-centered digital communities on protocols.io for fast-paced scientific innovation. F1000Research doi: 10.12688/f1000research.9453.2 | University of Arizona | http://nbviewer.ipython.org/github/biocore/qiime/blob/1.9.1/examples/ipynb/illumina_overview_tutorial.ipynb | 1 | 2015 | Bonnie Hurwitz 2015. QIIME:Moving Pictures of the human microbiome. protocols.io https://dx.doi.org/10.17504/protocols.io.d5288d | 2021-04-15 09:15:52 | |
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Preparing water samples for analysis using ultrahigh resolution mass spectrometry Resource Report Resource Website |
Krista Longnecker | DOI:10.17504/protocols.io.y36fyre | Kujawinski Lab, Metabolomics Protocols & Workflows | 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 | Woods Hole Oceanographic Institution | 1 | 2019 | Krista Longnecker 2019. Preparing water samples for analysis using ultrahigh resolution mass spectrometry. protocols.io https://dx.doi.org/10.17504/protocols.io.y36fyre | 2021-04-15 09:15:52 | |||
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Purification of Nosema bombycis spores Resource Report Resource Website |
Zhu Feng | DOI:10.17504/protocols.io.if3cbqn | 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. | Chen G, Wang W, Chen H, Dai W, Peng X, Li X, Tang X, Xu L, Shen Z (2017) Functional characterization of an aquaporin from a microsporidium, Nosema bombycis. PLoS ONE 12(7): e0181703. doi: 10.1371/journal.pone.0181703 | Jiangsu University of Science and Technology | https://doi.org/10.1371/journal.pone.0181703 | 1 | 2017 | Zhu Feng 2017. Purification of Nosema bombycis spores. protocols.io https://dx.doi.org/10.17504/protocols.io.if3cbqn | 2021-04-15 09:15:37 | ||
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Isolation of peripheral blood mononuclear cells Resource Report Resource Website |
Devi Oktafiani | DOI:10.17504/protocols.io.7j5hkq6 | 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. | Universitas Airlangga | 1 | 2019 | Devi Oktafiani 2019. Isolation of peripheral blood mononuclear cells. protocols.io https://dx.doi.org/10.17504/protocols.io.7j5hkq6 | 2021-04-15 09:15:52 |
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