Gan 2010, histone modifications in S2 and testis cells

Description:

Profiling chromatin modifications using antibodies against 3 histone modifications and RNA Pol II in S2 and bam testis cells.

Source

Files downloaded from GEO series: GSE19325
Input file format: BED

Samples

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

Filename Description Feature GEO-ID
1 GSM480156_dm3-S2-H3K4me3.sga S2 cell, H3K4me3 H3K4me3 GSM480156
2 GSM480157_dm3-S2-H3K27me3.sga S2 cell, H3K27me3 H3K27me3 GSM480157
3 GSM480158_dm3-S2-H3K36me3.sga S2 cell, H3K36me3 H3K36me3 GSM480158
4 GSM480159_dm3-S2-PolII.sga S2 cell, PolII PolII GSM480159
5 GSM480446_dm3-bam-H3K4me3.sga Testis cell, H3K4me3 H3K4me3 GSM480446
6 GSM480447_dm3-bam-H3K27me3.sga Testis cell, H3K27me3 H3K27me3 GSM480447
7 GSM480448_dm3-bam-H3K36me3.sga Testis cell, H3K36me3 H3K36me3 GSM480448
8 GSM480449_dm3-bam-PolII.sga Testis cell, PolII PolII GSM480449

Technical Notes

BED files of the serie were downloaded from GEO and processed using the following bash commands:

  1. Download data file:
    wget ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/series/GSE19325/GSE19325_RAW.tar
    
  2. Make SGA file:
    bed2sga.pl -s dm3 -f FEATURE < SAMPLE.bed | sort -s -k1,1 -k3,3n -k4,4 -T . | compactsga > SAMPLE.sga
    

References

  1. Gan Q, Schones DE, Ho Eun S, Wei G et al.
    Monovalent and unpoised status of most genes in undifferentiated cell-enriched Drosophila testis. Genome Biol 2010;11(4):R42. PMID:20398323

  2. GEO series GSE19325 Monovalent and unpoised status of most genes in undifferentiated cell-enriched Drosophila testis.