Batut 2017, RAMPAGE data for embryonic developmental time course.


This series contains single-base resolution TSS mapping data from an embryonic developmental time course of Drophila melanogaster. The same time course epxeriment has been carried out in four other Drosophila species: simulans, ananassae, pseudoobscura and erecta. All data were presented in the same paper (reference given see below).



From D. melanogaster (Aug 2014 BDGP Rel6 + ISO1 MT/dm6).

Transcription Profiling data:

Filename Description Feature GEO-ID
1 GSM2365625_Dmel2_01.sga Embryo stage 0-1 hour RAMPAGE GSM2365625
2 GSM2365626_Dmel2_02.sga Embryo stage 1-2 hours RAMPAGE GSM2365626
3 GSM2365627_Dmel2_03.sga Embryo stage 2-3 hours RAMPAGE GSM2365627
4 GSM2365628_Dmel2_04.sga Embryo stage 3-4 hours RAMPAGE GSM2365628
5 GSM2365629_Dmel2_05.sga Embryo stage 4-5 hours RAMPAGE GSM2365629
6 GSM2365630_Dmel2_06.sga Embryo stage 5-6 hours RAMPAGE GSM2365630
7 GSM2365631_Dmel2_07.sga Embryo stage 6-7 hours RAMPAGE GSM2365631
8 GSM2365632_Dmel2_08.sga Embryo stage 7-8 hours RAMPAGE GSM2365632
9 GSM2365633_Dmel2_09.sga Embryo stage 8-9 hours RAMPAGE GSM2365633
10 GSM2365634_Dmel2_10.sga Embryo stage 9-10 hours RAMPAGE GSM2365634
11 GSM2365635_Dmel2_11.sga Embryo stage 10-11 hours RAMPAGE GSM2365635
12 GSM2365636_Dmel2_12.sga Embryo stage 11-12 hours RAMPAGE GSM2365636
13 GSM2365637_Dmel2_13.sga Embryo stage 12-13 hours RAMPAGE GSM2365637
14 GSM2365638_Dmel2_14.sga Embryo stage 13-14 hours RAMPAGE GSM2365638
15 GSM2365639_Dmel2_15.sga Embryo stage 14-15 hours RAMPAGE GSM2365639
16 GSM2365640_Dmel2_16.sga Embryo stage 15-16 hours RAMPAGE GSM2365640
17 GSM2365641_Dmel2_17.sga Embryo stage 16-17 hours RAMPAGE GSM2365641
18 GSM2365642_Dmel2_18.sga Embryo stage 17-18 hours RAMPAGE GSM2365642
19 GSM2365643_Dmel2_19.sga Embryo stage 18-19 hours RAMPAGE GSM2365643
20 GSM2365644_Dmel2_20.sga Embryo stage 19-20 hours RAMPAGE GSM2365644
21 GSM2365645_Dmel2_21.sga Embryo stage 20-21 hours RAMPAGE GSM2365645
22 GSM2365646_Dmel2_22.sga Embryo stage 21-22 hours RAMPAGE GSM2365646
23 GSM2365647_Dmel2_23.sga Embryo stage 22-23 hours RAMPAGE GSM2365647
24 GSE89299_all_merged.sga Embryo 1-23 hours merged RAMPAGE GSE89299
Merged samples:

Technical Notes

FASTQ were downladed from SRA using fastq-dump v1.10.8 from SRA toolkit and mapped to the genome using Bowtie v1.2.2 in single end mode, using only the first sequence of a mate pair. Note that 10 bp of invariant primer sequences were chopped of from the 5' end of each read.

SAM files were then converted to BAM using samtools v1.9 and to BED using bamToBed v2.27.0 from bedtools Finally, BED to SGA conversion was carried out using bed2sga from ChIP-Seq v1.5.5.


Last update: 18 Sep 2021, page made by Philipp Bucher.:2