Brian Oliver’s group has provided FlyBase with updated RNA-Seq coverage data for D. pseudoobscura. This data has been re-aligned to the new HGSC D. pseudoobscura release 3 genome assembly. In addition to the previous data for adult heads, this update also includes data for new tissue samples: whole fly, reproductive tissues and carcass for male and female.
This data can be accessed through GBrowse 1 here. Make sure to select ‘D. pseudoobscura’ as the ‘Data Source’ from the pull down menu at the top left.
Briefly, polyadenylated mRNA was sequenced by Illumina high throughput sequencing. Reads were trimmed to 75 nt and realigned to the new HGSC D. pseudoobscura release 3 genome assembly using TopHat (v2.0.8b). For most samples, the alignment parameters were
-g 1 -r 150 --solexa1.3-quals. For adult head data, the parameters were
-g 1 -r 150. Please see the GEO (GSE) accessions below for more experimental details.
- Female (whole fly) – 130 million reads (GSE28078).
- Male (whole fly) – 109 million reads (GSE28078).
- Female_Head – 12 million reads (GSE19989).
- Male_Head – 17 million reads (GSE19989).
- Female_Ovary – 358 million reads (GSE31302).
- Male_Testis – 351 million reads (GSE31302).
- Female_Carcass – 251 million reads (GSE31302).
- Male_Carcass – 283 million reads (GSE31302).
FlyBase would like to thank Brian Oliver, Zhen-Xia Chen and David Sturgill for making this newly aligned RNA-Seq coverage data available to the community!