Open Chromatin Regions
Open Chromatin Regions
Chromatin accessibility by ATACseq displayed on a window powered by the UCSC genome browser.
1 Select the subset of ImmGen cell-types you wish to survey
then choose to search OCRs:
A by genomic region
B around a specific gene
A By genomic region
2 Select the chromosome.
3 Set the width of the region to display.
4 Choose a display layout mode (per UCSC standards Full , Dense, or Pack). Group scaling will be used.
5 Explore the data. Once in the browser, you can zoom in or out, move along the chromosome.
6 For more details, open a new window to visualize directly on the USCS portal. Once there, use all the functionalities of the UCSC browser to change the representation parameters (scale, relative position), or to put the data in relation to the wealth of additional information is available there. For more details on the UCSC browser: genome.ucsc.edu/goldenPath/help/hgTracksHelp.html
7 Download a table of the associations between signal intensity at the different OCRs and the presence of transcription factors motifs (per Yoshida et al, 2019).
B OCRs around a gene
1 Enter Gene Symbol (official NCBI nomenclature).
2 Select up to 2 cell types to compare.
3 Set the width of the region to display around the selected gene (10Kb default).
4 Choose a display layout mode (per UCSC standards Full , Dense, or Pack). Group scaling will be used.
5 Explore the data. Once in the browser, you can zoom in or out, move along the chromosome.
6 For more details, open a new window to visualize directly on the USCS portal. Once there, use all the functionalities of the UCSC browser to change the representation parameters (scale, relative position), or to put the data in relation to the wealth of additional information is available there. For more details on the UCSC browser: genome.ucsc.edu/goldenPath/help/hgTracksHelp.html
7 Download a table of the associations between signal intensity at the different OCRs and the presence of transcription factors motifs (per Yoshida et al, 2019).