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| Status |
Public on Apr 16, 2010 |
| Title |
Monovalent and unpoised status of most genes in undifferentiated cell-enriched Drosophila testis |
| Organism |
Drosophila melanogaster |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
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| Summary |
We use male gonads isolated from a Drosophila strain that allows us to obtain enough cells at their primitive status as the starting material to study the endogenous chromatin structure of undifferentiated cells using ChIP-seq. We integrate the ChIP-seq data with RNA-seq data that measures the transcriptome in a digital manner. Our genome-wide analyses indicate that the majority of differentiation genes in undifferentiated cells lack an active chromatin mark and paused Pol II; instead, they are associated with either the repressive H3K27me3 mark or no detectable mark. In order to address the possibility that distinct techniques are responsible for such a difference, we also use the Drosophila S2 cells to perform ChIP-seq and RNA-seq and compare the results directly with published work using ChIP-chip and microarray on S2 cells.
For the S2 cell ChIP-chip data, we used data from the following paper:
Muse GW, Gilchrist DA, Nechaev S, Shah R, Parker JS, Grissom SF, Zeitlinger J, Adelman K: RNA polymerase is poised for activation across the genome. /Nat Genet /2007, 39(12):1507-1511. The accession number for this data is: GSE6714.
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| Overall design |
ChIP-seq: Profiling chromatin modifications using antibodies against 3 histone modifications and RNA Pol II in S2 cells
Profiling chromatin structure in bam testis using antibodies against 3 histone modifications and RNA Pol II
RNA-seq: Profiling transcriptome of S2 cells using RNA-seq
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| Contributor(s) |
Gan Q, Schones D, Eun S, Wei G, Cui K, Zhao K, Chen X |
| Citation(s) |
20398323 |
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| Submission date |
Dec 04, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
Dustin E Schones |
| E-mail(s) |
[email protected]
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| Organization name |
City of Hope
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| Street address |
1500 E Duarte Rd.
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| City |
Duarte |
| State/province |
CA |
| ZIP/Postal code |
91010 |
| Country |
USA |
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| Platforms (1) |
| GPL9061 |
Illumina Genome Analyzer II (Drosophila melanogaster) |
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| Samples (9)
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| Relations |
| SRA |
SRP002124 |
| BioProject |
PRJNA120421 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE19325_RAW.tar |
255.0 Mb |
(http)(custom) |
TAR (of BED, BEDGRAPH, XLS) |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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