|
| Status |
Public on Sep 08, 2015 |
| Title |
H3K27ac_LT |
| Sample type |
SRA |
| |
|
| Source name |
Cell line
|
| Organism |
Mus musculus |
| Characteristics |
cell line: RN2
shRNA: Suz12.1842
treatment: Longterm JQ1
diagnosis: Leukemia
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
H3K27ac antibody (Abcam, 4729)
Sample 103
|
| Data processing |
Adaptors of the single-read fragments were removed using cutadapt v1.4.25 and reads with a length of less than 18bp in any read of the pair were discarded.
The remaining reads were aligned to the genome (mouse: mm10, human: hg19) using Bowtie v1.0.0
Reads with same start and end position on the same strand were removed from the alignment
Remaining reads were normalized to total mapped reads.
Genome_build: hg19/mm10
Supplementary_files_format_and_content: ChIP-Seq bigWig-files for each individual IP
Read processing was performed as described in Arnold et al., Science 2013, PMID: 23328393
Genome_build: hg19
Supplementary_files_format_and_content: STARR-Seq bigWig-files were generated for each STARR-Seq sample
|
| |
|
| Submission date |
Apr 08, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Philipp Rathert |
| E-mail(s) |
philipp.rathert@ibtb.uni-stuttgart.de
|
| Organization name |
University Stuttgart
|
| Department |
Biochemistry
|
| Street address |
Allmandring 31
|
| City |
Stuttgart |
| State/province |
Germany |
| ZIP/Postal code |
70569 |
| Country |
Germany |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE63782 |
Transcriptional plasticity promotes primary and acquired resistance to BET bromodomain inhibition |
|
| Relations |
| BioSample |
SAMN03465321 |
| SRA |
SRX982495 |
