Streptomyces venezuelae transcription start sites

Download zip file of genome and track files for genome browsers

The raw data has been deposited in ArrayExpress under accession number E-MTAB-10690.

RNA was prepared from 4 time points—10hr, 14hr, 18hr and 24hr to represent the transition throughout development (Vegetative, pre-sporulation, onset of sporulation and mid/late sporulation). For details of how the cDNA libraries were constructed and sequenced by Vertis please see the accompanying PDF.

Each time-point has the following files associated with it:

1xh_control_for.wigNormalised coverage by control reads on the forward strand
2xh_control_rev.wigNormalised coverage by control reads on the reverse strand
3xh_TSS_for.wigNormalised coverage by TSS reads on the forward strand
4xh_TSS_rev.wigNormalised coverage by TSS reads on the reverse strand
5xh_for_diff.wigResult of subtracting 1. from 3.
6xh_rev_diff.wigResult of subtracting 2. from 4.
7xh_for_lfc.wigResult of subtracting log(2) of 1. from log(2) of 3.
8xh_rev_lfc.wigResult of subtracting log(2) of 2. from log(2) of 4.

If you want to quickly look at the TSS of your favourite gene, the best place to start is with the xh_for_diff.wig and xh_rev_diff.wig files (#5 and #6). This gives you the reads that are only from 5' triphosphate ends i.e. with the reads from monophosphate ends subtracted from the overall normalised coverage. However if you want to look at the data in more detail—select the xh_control_for/rev.wig (#1 and #2) and xh_TSS_for/rev.wig (#3 and #4) files. This will allow you to view the contribution of RNA ends with monophosphates (resulting from mRNA degradation and RNAs that are not transcribed) versus those with triphosphates (genuine TSSs). The xh_for/rev_lfc.wig files (#7 and #8) are equivalent to the xh_for/rev_diff files but have been transformed by log(2). This can allow you to more easily view transcripts of varying abundance across the genome. However, you can still do this by changing the scale in IGB using the xh_for/rev_diff.wig files (see below).

Instructions/tips for viewing the data

Matt Bush
June 2021