|
| Status |
Public on Sep 08, 2015 |
| Title |
STARRSeq_JQ1 |
| Sample type |
SRA |
| |
|
| Source name |
Cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: K-562
treatment: JQ1, 24h
diagnosis: Leukemia
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
BAC DNA was fragmented using a Covaris sonicator. Following the instructions of NEBNext® DNA Library Prep Reagent Set for Illumina® (NEB; cat. no. E6000L), Illumina Multiplexing Adapters (Illumina Inc; cat. no. PE-400-1001) were ligated and homology arms for In-Fusion® recombination were added by PCR, followed by recombination into the STARR-seq vector. The In-Fusion® reactions were transformed (MegaX DH10B; Invitrogen), grown in liquid culture and plasmids were isolated.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
polyA+ RNA; PCR amplified cDNA (STARR-seq transcript)
Sample 108
|
| Data processing |
Library strategy: STARR-Seq
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 |
GPL11154 |
| Series (1) |
| GSE63782 |
Transcriptional plasticity promotes primary and acquired resistance to BET bromodomain inhibition |
|
| Relations |
| BioSample |
SAMN03465326 |
| SRA |
SRX982500 |
