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).

• Raw data was downloaded from: GSE89299
• Input file format: FASTQ
• Download date: 04-09-2021

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

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.

• Batut PJ, Gingeras TR.
  Conserved noncoding transcription and core promoter regulatory code in early Drosophila development. Elife. 2017 Dec 20;6:e29005. doi: 10.7554/eLife.29005. 29260710
• GEO series GSE89299: Drosophila species embryonic development RAMPAGE time series (Biological replicate #2)