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Series GSE60106 Query DataSets for GSE60106
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)
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
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
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
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (11)
GSM1465024 HCT116 whole genome bisulfite sequence
GSM1465025 DKO1 whole genome bisulfite sequence
GSM1465026 DKO1 RNA-seq replicate 1
BioProject PRJNA257496
SRA SRP045269

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Supplementary file Size Download File type/resource
GSE60106_RAW.tar 529.4 Mb (http)(custom) TAR (of BED, BW, GFF)
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Raw data are available in SRA
Processed data provided as supplementary file

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