The Genboree Commons: Latest projectshttp://genboree.org/theCommons/2023-08-03T11:19:21-05:00The Genboree Commons
Redmine MIBlood-EV (ISEV) - Project: MIBlood-EV (ISEV)http://genboree.org/theCommons/projects/5512023-08-03T11:19:21-05:00
<p><strong>MIBlood-EV: Minimal Information to Enhance the Quality and Reproducibility of Blood Extracellular Vesicle Research</strong></p>
<p>Blood is the most commonly used body fluid for extracellular vesicle (EV) research. The composition of a blood sample and its derivatives (i.e., plasma and serum) are not only donor-dependent but also influenced by collection and preparation protocols. Since there are hundreds of pre-analytical protocols and over forty variables, the development of standard operating procedures for EV research is very challenging. To improve the reproducibility of blood EV research, the International Society for Extracellular Vesicles (ISEV) Blood EV Task Force proposes standardized reporting of (i) the applied blood collection and preparation protocol and (ii) the composition of the prepared plasma and serum samples. Gathering detailed information provides insight into the performance of the protocols and in the presence of confounders in the prepared plasma and serum samples. To collect this information, the ISEV Blood EV Task Force created the Minimal Information for Blood EV research (MIBlood-EV), a tool to record and report information about pre-analytical protocols used for plasma and serum preparation as well as assays used to assess the quality of these preparations. This tool can be easily implemented in existing databases allowing for future meta-analysis and followed by evidence-based optimization of pre-analytical protocols. Taken together, insight into the quality of prepared plasma and serum samples will (i) improve the quality of biobanks for EV research, (ii) allow the exchange of plasma and serum samples between biobanks and laboratories, (iii) facilitate comparative EV studies, (iv) improve the peer review process, and, finally (v) does not require modifications of local pre-analytical protocols.</p>
<p>The MIBlood-EV v1.0 includes 27 items the following components: i) General study information (items 1.0 – 1.9), ii) Blood collection and processing (items 2.0 – 2.23), and iii) Plasma/serum quality control (QC; items 3.0 – 3.27).<br />The MIBlood-EV will be accessible on the ISEV website under Rigor & Standardization Subcommittee/Position Papers & Guidelines alongside the MIFlowCyt-EV [[<a class="external" href="https://www.isev.org/rigor-standardization">https://www.isev.org/rigor-standardization</a>]]<br />The original version (v1.0) is an editable pdf document that can be attached as Supplementary Material in manuscripts and referred to in sections of the Materials and Methods that describe blood specimens and characteristics. In addition, researchers are invited to upload the MIBlood-EV in the dedicated figshare data repository (Link). The file name should be as follows: First Author Last Name_First Author First Name_Year of Publication.</p> Allelic_Epigenome - Project: Allelic_Epigenomehttp://genboree.org/theCommons/projects/4972018-07-13T14:26:45-05:00
<p>Project contains annotation file required for processing files as described on the GitHub page</p> All Dataset Submissions - Project: All Dataset Submissionshttp://genboree.org/theCommons/projects/4712017-09-06T13:40:38-05:00
<p>This subproject keeps track of the different <a href="http://genboree.org/theCommons/projects/exrna-subs/wiki" class="external">submissions</a> that have been deposited into the Atlas as well as those submissions that are currently awaiting processing.</p> Other Documents - Project: Other Documentshttp://genboree.org/theCommons/projects/4592016-12-02T11:21:41-06:00Relevant Literature (Michael) - Project: Relevant Literature (Michael)http://genboree.org/theCommons/projects/4582016-12-02T11:12:37-06:00Relevant Literature (Eugene) - Project: Relevant Literature (Eugene)http://genboree.org/theCommons/projects/4572016-12-02T11:10:40-06:00Epigenomic Deconvolution - Project: Epigenomic Deconvolutionhttp://genboree.org/theCommons/projects/4452016-07-06T16:43:42-05:00
<p>This page contains all the material associated with the publication named: "Epigenomic Deconvolution reveals association between stromal composition and metabolic phonotype of breast tumors".<br />You will find scripts and datasets associated with that publication in the Documents tab.<br />Any inquiries regarding that publication, or any of the files associated with it should be directed to Vitor Onuchic (<a href="mailto:onuchic@bcm.edu" class="email">onuchic@bcm.edu</a>).</p> Amin V et al Nat Comm 2015 - Project: Amin V et al Nat Comm 2015http://genboree.org/theCommons/projects/3972015-01-22T16:36:10-06:00exRNA Data Coordination Center - Project: exRNA Data Coordination Centerhttp://genboree.org/theCommons/projects/3822014-09-19T13:29:03-05:00
<p>This project contains information about the Data Coordination Center (DCC) of the exRNA Communication Consortium.</p>
<p>This <a href="http://genboree.org/theCommons/attachments/7251/exRNA_DMRR_Infrastructure.png" class="external">figure</a> gives an overview of the DMRR infrastructure.</p>
<ul>
<li><a href="http://genboree.org/theCommons/projects/exrna-mads/wiki" class="external">General Overview of the DCC and Available Tools</a></li>
<li><a href="http://genboree.org/theCommons/projects/exrna-mads/wiki/exRNA%20Metadata%20Standards" class="external">exRNA Data and Metadata Standards</a></li>
<li><a href="http://genboree.org/theCommons/projects/exrna-mads/wiki/ExRNA_Atlas" class="external">exRNA Atlas</a></li>
</ul>
<h2 id="Data-Submission-xx-Analysis-Tutorials">Data Submission & Analysis Tutorials<a href="#Data-Submission-xx-Analysis-Tutorials" class="wiki-anchor">¶</a></h2>
<ul>
<li><a href="http://genboree.org/theCommons/projects/exrna-mads/wiki/Data%20Submission%20to%20DCC%20using%20FTP" class="external">Data & Metadata Processing Guide</a></li>
</ul>
<ul>
<li><a href="http://genboree.org/theCommons/projects/exrna-tools-may2014/wiki" class="external">exRNA Data Analysis Tools</a></li>
</ul> exRNA Tools - Project: exRNA Toolshttp://genboree.org/theCommons/projects/3462014-05-13T16:01:28-05:00
<p>This project contains tutorial materials for the extracellular RNA data analysis tools available on Genboree.</p>
<ul>
<li><a href="http://genboree.org/theCommons/projects/exrna-tools-may2014/wiki" class="external">Introduction to Processing Your exRNA Samples Using the Genboree Workbench</a></li>
<li><a href="http://genboree.org/theCommons/projects/exrna-tools-may2014/wiki/Small%20RNA-seq%20Pipeline" class="external">Small RNA-Seq Data Analysis for exRNA Profiling Using the exceRpt Small RNA-seq Pipeline</a>
<ul>
<li><a href="http://genboree.org/theCommons/projects/exrna-tools-may2014/wiki/Version_Updates" class="external">Version Updates for exceRpt</a></li>
<li><a href="http://genboree.org/theCommons/projects/exrna-tools-may2014/wiki/exRNA%20Data%20Analysis" class="external">Performing Data Analysis on Your Results from exceRpt</a></li>
</ul>
</li>
<li><a href="http://genboree.org/theCommons/projects/exrna-tools-may2014/wiki/Long%20RNA-seq%20Pipeline" class="external">Long RNA-Seq Data Analysis Using RSEQtools</a></li>
<li><a href="http://genboree.org/theCommons/projects/exrna-tools-may2014/wiki/KNIFE%20%28Known%20and%20Novel%20IsoForm%20Explorer%29" class="external">Detecting Circular and Linear Isoforms from RNA-seq Data Using KNIFE</a></li>
<li><a href="http://genboree.org/theCommons/projects/exrna-tools-may2014/wiki/Pathway%20and%20Interaction%20Analysis" class="external">Performing Pathway and Interaction Analysis Using the Genboree Workbench</a></li>
<li><a href="http://genboree.org/theCommons/projects/exrna-tools-may2014/wiki/DESeq2" class="external">Performing Differential Expression Analysis (Fold Change Calculation) with DESeq2</a></li>
<li><a href="http://genboree.org/theCommons/projects/exrna-tools-may2014/wiki/Deconvolution" class="external">Performing Deconvolution Analysis for exRNA Data Using the Genboree Workbench</a></li>
<li><a href="http://genboree.org/theCommons/ezfaq/index/exrna-tools-may2014" class="external">General FAQ for Transcriptome Toolset</a></li>
</ul>
<p>Please contact the exRNA Team (<a href="mailto:brl-exrna@bcm.edu" class="email">brl-exrna@bcm.edu</a>) for more information on these exRNA Data Analysis Tools.</p> Transcriptome Toolset - Project: Transcriptome Toolsethttp://genboree.org/theCommons/projects/3452014-05-13T15:59:49-05:00
<p>This project contains tutorials, use cases, workshop materials for Transcriptome toolset in the Genboree workbench</p> ASHG Workshop - Oct 2013 - Project: ASHG Workshop - Oct 2013http://genboree.org/theCommons/projects/2612013-10-08T08:19:31-05:00
<p>This project contains information and documents related to the American Society of Human Genetics (ASHG) Workshop held in Boston in October 2013. The workshop was organized by the Bioinformatics Research Laboratory (BRL) at the Baylor College of Medicine. The workshop, titled "Human Epigenome Atlas and Epigenomic Profile Analysis Using the Genboree Workbench" focused on analysis using various tools within the Genboree Workbench. The BRL wishes to acknowledge the NIH Epigenomics Roadmap Project for its generous support of this workshop.</p> 6th Workshop - March 2013 - Project: 6th Workshop - March 2013http://genboree.org/theCommons/projects/1982013-03-01T14:34:33-06:00
<p>This project contains information and documents related to the 6th Epigenome Informatics Workshop held in Houston in March 2013, and organized by the Bioinformatics Research Laboratory (BRL) at the Baylor College of Medicine. The workshop focused on using tools within the Genboree Workbench. The BRL wishes to acknowledge the NIH Epigenomics Roadmap Project for its generous support of this workshop.</p> Epigenome_Informatics_Workshop - Project: Epigenome_Informatics_Workshophttp://genboree.org/theCommons/projects/1522012-02-28T09:21:12-06:00
<p>This project contains sub-projects for each Epigenome Informatics Workshop starting in 2012.</p> Public - Project: Publichttp://genboree.org/theCommons/projects/882010-10-13T16:16:11-05:00
<p>This Public Genboree Commons Project contains information pertaining to the Genboree Commons and Genboree Workbench (getting started, Workbench icons, FAQs, etc.).</p>