Bonn 2012, Analisys of H3 modifications in mesoderm


This experiment describes several histone signatures in mesodermal cells of D. malanogaster. The BAM files of this dataset have been downloaded from EBI and converted into SGA files.


Files downloaded from EBI via URL:
Input file format: BAM


From Fruit Fly Apr. 2006 (R5/dm3) Assembly

Filename Description Feature GEO-ID
1 ERR031126.sga Mesoderm input Rep1 input -
2 ERR031127.sga Mesoderm input Rep2 input -
3 ERR031128.sga Mesoderm H3 Rep1 H3 -
4 ERR031129.sga Mesoderm H3 Rep2 H3 -
5 ERR031130.sga Mesoderm H3K27ac Rep1 H3K27ac -
6 ERR031131.sga Mesoderm H3K27ac Rep2 H3K27ac -
7 ERR031132.sga Mesoderm H3K4me1 Rep1 H3K4me1 -
8 ERR031133.sga Mesoderm H3K4me1 Rep2 H3K4me1 -
9 ERR031134.sga Mesoderm H3K4me3 Rep1 H3K4me3 -
10 ERR031135.sga Mesoderm H3K4me3 Rep2 H3K4me3 -
11 ERR031136.sga Mesoderm H3K36me3 Rep1 H3K36me3 -
12 ERR031137.sga Mesoderm H3K36me3 Rep2 H3K36me3 -
13 ERR031138.sga Mesoderm H3K79me3 Rep1 H3K79me3 -
14 ERR031139.sga Mesoderm H3K79me3 Rep2 H3K79me3 -
15 ERR031140.sga Mesoderm H3K27me3 Rep1 H3K27me3 -
16 ERR031141.sga Mesoderm H3K27me3 Rep2 H3K27me3 -
17 ERR031142.sga Mesoderm PolII Rep1 PolII -
18 ERR031143.sga Mesoderm PolII Rep2 PolII -
19 ERR031144.sga Mesoderm BiTS_Mef2 BiTS_Mef2 -
20 ERR031145.sga Mesoderm Mef2 Rep1 Mef2 -
21 ERR031146.sga Mesoderm Mef2 Rep2 Mef2 -

Technical Notes

BAM files of the ERP000560 serie were downloaded from EBI and processed using the following bash commands:

  1. Download information file:
  2. Download BAM files:
    awk 'BEGIN{FS="\t"} $17 ~ "ERR" {print "wget", $17}' ERP000560 | bash
  3. Make BED file:
    bamToBed -i SAMPLE.bam > SAMPLE.bed
  4. Clean chromosome name in the BED file:
    sed -i 's/^/chr/' SAMPLE.bed
  5. Make SGA file: -s dm3 -f FEATURE < SAMPLE.bed | sort -s -k1,1 -k3,3n -k4,4 -T . | compactsga > SAMPLE.sga


  1. Bonn S, Zinzen RP, Girardot C, Gustafson EH, Perez-Gonzalez A, Delhomme N, Ghavi-Helm Y, Wilczyski B, Riddell A, Furlong EE.
    Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development. Nat Genet. 2012 Jan 8;44(2):148-56. PMID: 22231485