Haynes:ChIPDataMining1

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Preliminary Analysis (UCSC Browser and ENCODE)

Use the Genome Browser to visualize chromatin mapping data within the human genome sequence.

1. Go to the UCSC Genome Browser at http://genome.ucsc.edu/cgi-bin/hgGateway.
2. Enter a gene or region under search term. For instance, try “chr21:34398216-34401503” (these are the coordinates for the RefSeq annotation of the Polycomb-silenced OLIG2 gene). Click “submit.”
3. A human genome browser window that shows the selected region should appear. Click the “hide all” button to hide all of the information.
4. Under Genes and Gene Prediction Tracks, set RefSeq Genes to “full” and click the “refresh” button. The annotation of genes in the region you selected should appear in the browser window. Repeat this step for other features, if desired.
5. To find ChIP-seq data from a publicly shared ChIP-seq experiment,
   1. Click the “track search” button. You will navigate away from the browser, but your coordinates will remain the same. In the next window, click the Advanced search tab. For the first and, set the menu to “Antibody or target protein,” and for is among, set the menu to the chromatin marks of interest. For instance, try H3K27me3 (07-449).
   2. For the second and, set the menu to “Cell, tissue, or DNA sample,” and for is among, set the menu to the chromatin marks of interest. For instance, try H1-hESC.
   3. Click the “search” button. In the list of results select one or more tracks and set each to “full.” Tracks designated as “Peaks” or “Hotspots” will show the mapping data as low-resolution, horizontal bars. Tracks designated as “Signal” will show signal intensities as high-resolution, vertical bars
6. Click the “View in Browser” button.
7. If you are viewing any Signal tracks and high values are cut-off by a red bar, right-click on the track in the genome browser and select configure. Select “auto-scale to data view” on the drop down list for “Data view scaling.”

Use the Table Browser to retrieve chromatin mapping data values for a preliminary subset of genomic regions (500 bp surrounding transcription start sites of twenty control genes).

Go to the UCSC Table Browser at http://genome.ucsc.edu/cgi-bin/hgTables?hgsid=356574357. Set clade to mammal, genome to human, and assembly to Feb. 2009 (GRCh37/hg19). To add a track that contains the chromatin mapping data of interest, set group to Regulation, and track to a type of interest. For instance, try Broad Histone or UW Histone to analyze a histone mark. On the region line, click the “define regions” button. In the text window, paste in the text below (tab-delimited), then click the “submit” button. chr7 5569982 5570482 ACTB chr3 52231849 52232349 ALAS1 chr15 45003435 45003935 B2M chrX 153774983 153775483 G6PD chr12 6643335 6643835 GAPDH chr7 65447051 65447551 GUSB chrX 133593925 133594425 HPRT1 chrX 77359416 77359916 PGK1 chr7 44835991 44836491 PPIA chr6 170863171 170863671 TBP chr1 212738426 212738926 ATF3 chr12 4382652 4383152 CCND2 chr9 21974882 21975382 CDKN2A chr2 38303073 38303573 CYP1B1 chr4 107957203 107957703 DKK2 chr7 27224585 27225085 HOXA11 chr16 56701727 56702227 MT1G chr20 62795577 62796077 MYT1 chr21 34397966 34398466 OLIG2 chr3 25469584 25470084 RARB

Set output format as “selected fields from primary and related tables.” Click the “get output” button. On the proceeding “Select Fields” page, select chrom, chromStart, chromEnd, name, and signalValue. Click the “get output” button. The output will be the coordinates of signalValues (from the track, from step 3) that fall within the regions of interest (from step 4). Note: coordinates for which the chromatin-mapping signalValue is zero will be absent from the output list.