|
Status |
Public on Sep 08, 2015 |
Title |
STARRSeq_DMSO |
Sample type |
SRA |
|
|
Source name |
Cell line
|
Organism |
Homo sapiens |
Characteristics |
cell line: K-562 treatment: DMSO, 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 107
|
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 |
SAMN03465325 |
SRA |
SRX982499 |