|
| Status |
Public on Sep 08, 2016 |
| Title |
H3K27me3 DAC + EPZ6438 IMR5-75 |
| Sample type |
SRA |
| |
|
| Source name |
IMR5-75
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: neuroblastoma cell line
chip antibody: ab6002 (Abcam, Cambridge, UK)
|
| Treatment protocol |
The neuroblastoma cell lines Be(2)-C and IMR5-75 were treated with a combination of DAC (1µM, 72h) and EPZ-6438 (1µM 96h) . Controls were treated with solvent (DMSO).
|
| Growth protocol |
Cells were grown in RPMI medium (10%FCS) under standard conditions.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibodies. Antibodies against H3K27ac (ab4729), H3K4me3 (ab8580, Abcam) and H3K27me3 (ab6002, Abcam) were used for precipitation.
Library preparation was performed using the NEBNext Ultra DNA Library Prep Kit for Illumina (New England BioLabs, Ipswich, MA, US) according to the manufacturer’s protocol. Libraries were sequenced (50 bases single-end) on the Illumina sequencing platform (German Cancer Research Center Core facility).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
ChIP-seq single-end reads were aligned to the hg19 genome using Bowtie and only uniquely aligned reads were kept.
BAM-Files of aligned reads were further processed using the deepTools suite2. Input files were subtracted from the treatment files using the bamCompare tool, applying the SES method for normalization of signal to noise.
Resulting signals were normalized to an average 1X coverage to produce signal (bigWig) files.
Genome_build: hg19
|
| |
|
| Submission date |
Apr 19, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Chunxuan Shao |
| E-mail(s) |
c.shao@Dkfz-Heidelberg.de
|
| Organization name |
German Cancer Research Center
|
| Street address |
Im Neuenheimer Feld 280
|
| City |
Heidelberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE80445 |
ChIP-seq-based analysis of differential K27me3 coverage in neuroblastoma cell lines treated with epigenetic drugs |
|
| Relations |
| BioSample |
SAMN04870076 |
| SRA |
SRX1713592 |
