Links for viewing platelet RNA-seq data sets in the UCSC Genome Browser
| Site . | Reference . | Description: Web link > access instructions . |
|---|---|---|
| 1 | 1 | Coverage track: https://hci-bio-app.hci.utah.edu/gnomex/gnomexFlex.jsp?dataTrackNumber=DT1837 > select “UCSC Browser”* |
| 2 | 1 | Bam (individual reads and sequences) track: https://hci-bio-app.hci.utah.edu/gnomex/gnomexFlex.jsp?dataTrackNumber=DT11785 > select “UCSC Browser”* |
| 3 | 20 | Coverage tracks and individual reads tracks: https://cm.jefferson.edu/data-tools-downloads/platelets-2012/ > select “A” to enter UCSC Browser* |
| 4 | 21 | Coverage tracks and individual reads tracks: https://cm.jefferson.edu/data-tools-downloads/platelets-2014/ > select “A” to enter UCSC Browser* |
| Site . | Reference . | Description: Web link > access instructions . |
|---|---|---|
| 1 | 1 | Coverage track: https://hci-bio-app.hci.utah.edu/gnomex/gnomexFlex.jsp?dataTrackNumber=DT1837 > select “UCSC Browser”* |
| 2 | 1 | Bam (individual reads and sequences) track: https://hci-bio-app.hci.utah.edu/gnomex/gnomexFlex.jsp?dataTrackNumber=DT11785 > select “UCSC Browser”* |
| 3 | 20 | Coverage tracks and individual reads tracks: https://cm.jefferson.edu/data-tools-downloads/platelets-2012/ > select “A” to enter UCSC Browser* |
| 4 | 21 | Coverage tracks and individual reads tracks: https://cm.jefferson.edu/data-tools-downloads/platelets-2014/ > select “A” to enter UCSC Browser* |
UCSC, University of California, Santa Cruz.
Tips for the UCSC Genome Browser: After entering UCSC’s Web site, select “Genome Browser.” Search for a gene (“GP9”), location (“chr3:128 779 645-128 781 253”), or term of interest (“rs6065”). Scroll down to see the available tracks. The platelet tracks can be found under the header “Custom Tracks” for sites 1 and 2 or under the header “Mapping and Sequencing Tracks” for sites 3 and 4. Using the toggle boxes, set the visibility settings to “Full” for the platelet data track(s) of interest (ie, “B2_Pltlts_...”). Set visibility to “Full” for one of the Gene Predictions tracks (ie, RefSeq). “Hide” other tracks and “zoom” to view the data as presented in the figures. Select “Refresh” after making any changes to update the viewer. Other data sets, including mouse data sets, are accessible from within Gnomex by searching for “platelet” in the search box at the top. Alternatively, the .Bam and .Bai index files can be downloaded from Gnomex and opened in a genome browser such as the Integrated Genome Viewer.22 If the links don’t work initially, try a different browser. For more information on using the UCSC Genome Browser, see: https://genome.ucsc.edu/training.html.