|
| Status |
Public on May 27, 2017 |
| Title |
U87DOX whole genome bisulfite p4 |
| Sample type |
SRA |
| |
|
| Source name |
Human glioblastoma cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Brain
cell type: Human glioblastoma cells
passage: in vitro for a long time
|
| Treatment protocol |
for +Dox samples, cells were treated with doxycycline at 1 ug/ml for 48h
|
| Growth protocol |
U87 cells grown in MEM +10% FCS medium
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
RNA was extracted for RNA-seq, genomic DNA was extracted for ChIP-seq and WGBS
Library was constructed by microarray facility at Johns Hopkins University using commercially available kits (illumina)
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Tophat2 was used to map all RNA-seq reads to human genome (hg19) then Cufflink was employed to summarize the gene/transcript expression based on mapped reads.
KLF4 ChIP-Seq data were mapped by Bowtie2, followed by MACS 1.4 being used to call peaks with cutoff of p < 1E-5
The peaks of H3K27ac was recognized by MACS2 as broad peaks based on their ChIP-Seq data mapped by Bowtie2. The cutoff of broad peak call was q < 0.1.
An R package, DEGseq, was taken on RNA-seq data to identify differentially expressed genes (DEGs) for p < 0.001 between 0 hr and 48 hr in KLF4 WT and R458A cells, respectively.
WGBS were aligned using Bismark, context-dependent methylation were extracted using bismark_methylation_extractor from merged bam files and format with coverage2cytosine.
Genome_build: hg19
|
| |
|
| Submission date |
Apr 11, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Shuli Xia |
| E-mail(s) |
xia@kennedykriger.org
|
| Phone |
443-923-9498
|
| Organization name |
Kennedy Krieger Institute
|
| Street address |
707 N Broadway
|
| City |
Baltimore |
| State/province |
Maryland |
| ZIP/Postal code |
21205 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE97632 |
Methylation DNA mediated KLF4 binding activity in glioblastoma cells |
|
| Relations |
| BioSample |
SAMN06706925 |
| SRA |
SRX2732476 |
