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| Status |
Public on Sep 08, 2015 |
| Title |
STARRSeq_Input |
| Sample type |
SRA |
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| Source name |
Cell line
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| Organism |
Homo sapiens |
| Characteristics |
cell line: K-562
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| Extracted molecule |
genomic DNA |
| 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.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
whole genome library (in STARR-seq vector); plasmid DNA (containing genomic DNA fragments); PCR amplified cDNA (STARR-seq transcript)
Sample 109
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| 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
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| Submission date |
Apr 08, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Philipp Rathert |
| E-mail(s) |
philipp.rathert@ibtb.uni-stuttgart.de
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| Organization name |
University Stuttgart
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| Department |
Biochemistry
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| Street address |
Allmandring 31
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| City |
Stuttgart |
| State/province |
Germany |
| ZIP/Postal code |
70569 |
| Country |
Germany |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE63782 |
Transcriptional plasticity promotes primary and acquired resistance to BET bromodomain inhibition |
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| Relations |
| BioSample |
SAMN03465327 |
| SRA |
SRX982501 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1652930_STARRseq_input.bw |
1.2 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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