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| Status |
Public on Oct 02, 2012 |
| Title |
Chromatin modification by SUMO-1 stimulates the promoters of translation machinery genes |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
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| Summary |
We determined the occupancy of SUMO-1 on chromatin in HeLa cells by use of chromatin affinity purification coupled with next generation sequencing
RNA-Seq: The goal is to compare differential gene expression in SUMO-1 depleted cells and control cells (GL2 depleted) to verify the observation in the paper, and to cross-check with RT-PCR results.
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| Overall design |
18 samples examined in syncrhonized HeLa cells: Cells in G1, early S (S0)/mid (S3)/ late S phase (S6), and mitosis (M), triplicates for each sample. 1 ChIP-SUMO1 sample in S0, and 1 ChIP-IgG control
RNA-Seq: Six cDNA samples containing three pairs of biological replicates (three SUMO-1 depleted samples and three GL2 control samples) were barcoded, pooled together in equal concentration and subjected to sequencing in one lane of Illumina GAII
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| |
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| Contributor(s) |
Liu H, Zhang J, Parvin J |
| Citation(s) |
22941651 |
| |
| Submission date |
Oct 01, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Jeffrey Parvin |
| URL |
http://parvinlab.bmi.ohio-state.edu/index.php?title=Main_Page
|
| Organization name |
the Ohio State University
|
| Department |
Biomedical Informatics
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| Street address |
904 Biomedical Research Tower
|
| City |
Columbus |
| State/province |
OH |
| ZIP/Postal code |
43202 |
| Country |
USA |
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| Platforms (1) |
| GPL9115 |
Illumina Genome Analyzer II (Homo sapiens) |
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| Samples (24)
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| Relations |
| BioProject |
PRJNA176421 |
| SRA |
SRP015955 |
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