Note! This page contains a snapshot of the exRNA Atlas for the "ExRNA Atlas Analysis Reveals Distinct Extracellular RNA Cargo Types and Their Carriers Present Across Human Biofluids" paper published in Cell (Murillo et al., 2019). The latest release of the Atlas can always be found at https://exrna-atlas.org.
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- Added citation for exceRpt paper (https://www.cell.com/cell-systems/fulltext/S2405-4712(19)30074-2) and adjusted URL associated with exceRpt on front page of Atlas.
- Fixed bug with "Contact Us" mailer.
- Announced release of exRNA Atlas paper (https://www.cell.com/cell/fulltext/S0092-8674(19)30167-9) in News.
- Updated public analysis results for deconvolution tool.
- Updated description of deconvolution tool output on Public Analysis Results page.
- Removed restriction on using DESeq2 from biofluid vs assay type / condition grids.
- Added dbGaP accessions for "Profiles of Extracellular RNA in Cerebrospinal Fluid and Plasma from Subarachnoid Hemorrhage Patients" and "Identifying novel small RNA biomarkers unique to patients with gastric cancer" studies.
- Added / updated BioGPS links for Atlas studies.
- Added publication for "TLDA miRNA Screen for Candidate AD Biomarkers in CSF from Living Donors" study.
- Added numerous GEO/dbGaP accessions for Atlas studies.
- Updated bar charts on front page with new content (removed Transcriptome Mapped Reads / Biofluid chart, added Submitted Samples / RNA Isolation Kit chart, updated Read Mappings / RNA Type chart).
- Updated RNA profile histogram for individual samples in Atlas grids.
- Rearranged facets in RNA Isolation Kit donut.
- Changed title of table on front page to be "Overview of Studies" instead of "Dataset Submissions".
- Added new deconvolution results to Public Analysis Results page for 21 deconvolution datasets (used in our "ExRNA Atlas resource reveals a diversity of extracellular RNA cargo in human body fluids" paper (in preparation).
- Updated warning for faceted chart search so that large sample searches (>2000) receive warning message BEFORE grid loads (as opposed to while grid is loading). This gives users a chance to cancel their search.
- Made URLs cleaner for individual analysis links in Dataset Submissions table on front page of Atlas.
- Further improved instructions for downloading list of URLs from bulk download text files.
- Improved instructions for downloading list of URLs from bulk download text files.
- Fixed date associated with two earlier releases (and added note about DESeq2 fix to one of those earlier releases).
- Standardized first layer of nodes in linear tree so that node layout is visually clear (no node overlap, for example).
- Added support for viewing user-driven analysis results on the Atlas website (as opposed to users having to go to the Genboree Workbench).
- Added a number of additional public (precomputed) analysis results.
- Clicking a given dataset accession ID in the Dataset Submissions table will now highlight the particular card of interest on the Datasets page.
- Updated Atlas statistics tables to be clearer.
- Added exceRpt FASTQ identifier and dataset accession ID to results grids (clicking dataset accession ID will take you to appropriate (highlighted) card on Datasets page).
- Added option to download metadata files and qPCR target data files in bulk via grids.
- Various bug fixes to grids.
- Census ncRNA files are now hosted in GenboreeKB as opposed to on local disk.
- Slightly revised content of "Cite Us".
- Multiple datasets under same study are now condensed better in Dataset Submissions table.
- Changed name of post-processing tool to be "Generate Summary Report".
- Updated "Cite Us" in header to give better, more complete information about how to cite Atlas data.
- Fixed bug with DESeq2 where all-zero rows weren't being discarded (thus incorrectly altering adjusted p-value).
- Removed ERCC9 conference notice from front page.
- Grids should now load more quickly on average, especially for larger grids.
- Added warning if user searches for over 2000 samples (grid will be slow).
- Various bug fixes.
- Added 302 new RNA-seq profiles (from 3 datasets: EXR-SADAS1EXER1-AN, EXR-SADAS1UJ0CzW-AN, EXR-MTEWA1cHYLo6-AN) to the exRNA Atlas.
- Re-added 80 RNA-seq profiles that were incorrectly processed previously (EXR-MBITZ12SHVIr-AN).
- Added 2940 new qPCR profiles (from 1 dataset: EXR-JFREE1UH2qPCR-AN) to the exRNA Atlas.
- Corrected condition for healthy control samples in EXR-JSAUG1UH2001-AN dataset (samples previously had incorrect condition of Alzheimer's Disease).
- Updated Precomputed Results page to include new RNA-seq data for Dimensionality Reduction Plotting Tool.
- Updated ncRNA Search bar to include new RNA-seq data, and added support for snoRNAs and snRNAs.
- Updated header navigation menu to emphasize precomputed results (as opposed to analysis features that are coming soon).
- Fixed small bug with Atlas statistics being calculated incorrectly in certain edge cases.
- Fixed grid downloads for raw FASTQ files hosted on Genboree (not public FTP area).
- Updated tables on Atlas so that "Return to Default" button appears once there is ANY difference from default table (including different sorting).
- Made some small fixes to FTP data submission pipeline.
- Fixed bug where downloads on Datasets page weren't working properly for consortium-only datasets
- Removed unnecessary column(s) from biofluid vs assay type grid.
- Made some small styling updates.
- Made some small bug fixes for FTP data processing pipeline.
- Edited some help text for the various results grids.
- Temporarily removed Markus Bitzer's 'Identifying urinary RNA as non-invasive biomarkers for progression of chronic kidney disease' dataset for reprocessing (incorrect 3' adapter sequence was used in previous version).
- Added a couple of fixes to FTP submission pipeline.
- Made some fixes to ncRNA search bar.
- Added help button (question mark) with example queries built in to the ncRNA search bar.
- Made some bug fixes to mature miRNAs for ncRNA search bar.
- Made some bug fixes to FTP data processing pipeline.
- Made bug fix to "Return to Default" button on stand-alone Datasets page.
- Added "hamburger menu" for ncRNA search bar at Atlas Census Results error page.
- Changed default RPM threshold for census results from 15 to 10.
- Updated certain study titles to better reflect contents of studies.
- Fixed ncRNA search bar so it is present (under a hamburger menu) at lower window widths, and changed placeholder text to specify mature miRNAs (as opposed to just miRNAs).
- Added some additional mature miRNAs to Atlas census, and removed all precursor miRNAs from Atlas census.
- Now automatically handle (and fix) situation where users put lowercase 'r' in miRNA / piRNA identifiers for ncRNA search bar.
- Added new ncRNA search bar to front page of Atlas (including link in header). Select a ncRNA library (miRNAs, tRNAs, or piRNAs) and a database (Atlas Census), type your ncRNAs of interest, and then click the magnifying glass (or hit enter) to search for those ncRNAs in the selected database.
- Added Atlas Census page to Atlas. Page displays presence of selected ncRNAs in each biofluid in the public Atlas according to various dynamic parameters. User can also perform downstream analysis (Pathway Finder) with selected miRNAs.
- Added new DESeq2 results page. Instead of linking directly to Pathway Finder, page now allows you to see DESeq2 output, select miRNAs of interest, and perform downstream analysis (Pathway Finder) with those selected miRNAs.
- Added My Analyses link to "Browse exRNA Profiles - Alternative Options" panel on front page.
- Added "Return to Default" button for datasets table and stand-alone datasets page.
- Increased font size of dates for news and version history pages.
- Fixed a couple of bugs in FTP data submission pipeline.
- Updated header bar with more obvious link to exRNA Portal.
- Added note to front page about ERCC9 conference.
- Changed symbols associated with each news item.
- Updated faceted charts and bar charts on front page to be slightly larger, and fixed overlapping text issues for certain labels.
- Updated styling for My Analysis Results / Public Analysis Results pages.
- Added Dataset Submissions table to front page.
- Re-arranged header navigation bar and added some new options (like Select Profiles).
- Updated tooltips throughout Atlas to be more accurate and informative.
- Fixed bug related to ERCC Data Policy popup being hidden behind biofluid / assay grid.
- Updated Datasets page and Public Analysis Results page with new features like: better reporting of embargo status (on Datasets page), ascending/descending sorting, load more / load all buttons, and dynamic reporting of number of results currently being displayed.
- Fixed bug related to sorting on datasets page upon page load.
- Updated location of "Sort by" navbar on datasets page, and added checkmark to selected sort method.
- Updated display of atlas statistics on front page to include new samples, datasets, reads, and conditions across different time frames.
- Fixed bug related to user-specific requests.
- Added sorting to Datasets page (via "Sort by" navbar). Page also sorts datasets by sample count (descending) upon page load.
- "Download Dataset Files" popover for each dataset on Datasets page now provides explanatory text alongside each icon. Width is also fixed for this popover so that explanatory text for each icon is formatted properly.
- Fixed borders for all popovers on Datasets page.
- Updated "My Analyses" and "Public Analysis Results" pages by displaying number of analyses per tool, and provided additional description to differentiate "My Analyses" page from "Public Analysis Results" page.
- Added initial support for downloading single qPCR target files via grids (use first icon in "Download Data" column) and updated help text accordingly.
- Fixed a couple of bugs related to loading the Datasets page.
- Fixed a couple of visual bugs related to borders on some of the sample grids.
- Did visual overhaul of all Atlas pages.
- Added usage info at bottom of Datasets page and Analyses page.
- Fixed bug on Linear Tree page by removing animation for floating menubar (still need to fix bug where floating menubar disappears if window is made too narrow).
- Fixed Dimensionality Reduction plots for TPATE1_HEALTHYVSCANCER_ALL, LLAUR1_PLACDYS_ALL, MBITZ1_KIDNEY_ALL, and miRNeasy (biofluids for points were mislabeled).
- Retroactively added an update for version 4.6.5 (2017-05-25) below and on news page (including short news section on front page).
- Added links to version history page from short news section.
- Edited text for short news section to make language more concise (v4.6.5 and v4.6.0 updates).
- Significant overhaul of FTP data submission pipeline to make metadata submission easier (one file per metadata type).
- Improved error reporting for metadata errors (error report more concise and should now usually report all errors in a given file at the same time).
- Added local copies of indices to many computing nodes to ensure faster processing times (and reduce competition between exceRpt jobs).
- User can now give different adapter sequences on a per-sample basis when submitting files to the Atlas.
- Removed animation effect for floating menubar on Atlas homepage, based on user feedback.
- Fixed date for version 4.6.0 update on News page.
- Fixed date for version 4.6.0 update below.
- New RNA-seq dataset added to Atlas: "small RNA Sequencing of Biofluids from Healthy Controls" (PI: Kendall Jensen). Dataset contains 428 profiles and consists of plasma, saliva, and urine samples from healthy college athletes.
- New RNA-seq dataset added to Atlas: "small RNA Sequencing of CSF Samples from Patients with IVH" (PI: Kendall Jensen). Dataset contains 70 profiles.
- Version History page added (available via News page and header's "More" menu).
- Link to News page added to header's "More" menu.