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| Status |
Public on Sep 10, 2014 |
| Title |
Global loss of DNA methylation uncovers intronic enhancers in genes |
| Organism |
Homo sapiens |
| Experiment type |
Methylation profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
We used HCT116 colorectal cancer cells with and without mutations in DNA methyltransferases (resulting in a 95% reduction in global DNA methylation levels) to study the relationship between DNA methylation, histone modifications, and gene expression. (The double knockout cell line is called DKO1)
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| Overall design |
Examination of DNA methylation, two histone modifications, RNA polymerase II ChIP-seq and RNA expression in two cell line (HCT116 and DKO1).
One of relipates of HCT116 RNA P II ChIP-seq is from GSM970210. Histone modification data(H3K27ac, H3K4me3) of HCT116 are from GSM945304, GSE31755. Two replicates of RNA-seq data in HCT116 are from GSM1266733 and GSM1266734
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| Contributor(s) |
Blattler A, Witt H, Guo Y, Nicolet C, Farnham P, Lay F, Jones P |
| Citation(s) |
25239471 |
| |
| Submission date |
Aug 05, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Peggy J Farnham |
| E-mail(s) |
Peggy.Farnham@med.usc.edu
|
| Organization name |
University of Southern California Graduate Student
|
| Department |
GMCB
|
| Street address |
1450 Biggy Street NRT 6503
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90033 |
| Country |
USA |
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| Platforms (1) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
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| Samples (11)
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| Relations |
| BioProject |
PRJNA257496 |
| SRA |
SRP045269 |
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