Transcript data for Desulfovibrio alaskensis G20

Transcript data from "Functional genomics with a comprehensive library of transposon mutants for the sulfate-reducing bacterium Desulfovibrio alaskensis G20"

This page includes downloads for viewing transcript data from D. alaskensis G20, a table of potential transcript starts (TSS), and R source code for inferring high-confidence TSS.

Viewing Transcript Data in Artemis

You can download a zip file here (37 MB). You should start by opening the genbank file and then use Graph / Add User Plot to add the art files, which including tiling data for rich and minimal media (richnorm3, minnorm3) and the 5' RNASeq data.

Tips:

Artemis is available here. You may need to change its settings so that it can use 6 GB of memory.
Smooth the tiling data to 10-15 nt and do not smooth the 5' RNASeq at all (window=1). Smoothing is controlled by the slider at the right of each track.
Do not log-transform the tiling data.
The scale of the 5' RNASeq data varies widely, so you might want to log-transform it, or else use the scaling option (right click on the track).
In each track, the plus strand will be in red, and the minus strand will be in green.
Use Go / Navigate to go to a gene of interest based on its locus tag (i.e., Dde_3365).

Potential Transcript Starts

See TSS_candidates.tab (tab-delimited file, 14,706 data rows).

Every local peak in the 5' RNASeq data with at least 50 reads and in a non-redundant part of the genome is included. The fields are:

start, strand -- the location in the genome of the putative TSS
nReads -- the number of 5' RNASeq reads
bits.rpoD, bits.rpoN -- the bit score of the best hit to the respective motif, within 1 nt of the TSS
loN, loBits, loTiling -- log odds for this to be a genuine TSS, given the number of reads, the motif bit scores, or the tiling data
lo -- the log odds for this to be a genuine TSS. lo > 4 was considered high confidence.

R source code and image

paper1.R -- source code in R for computing high-confidence TSS. (The table above corresponds to rpeaksG, although some column names were changed for clarity.)
R image (80 MB)

Links to GEO

Tiling data: GSE39471
5' RNASeq data: GSE49484
Gene expression data: GSE49527, GSE49528, GSE49529

Page by Morgan Price, April 2014