|
| Status |
Public on Mar 22, 2013 |
| Title |
CX137 input DNA 1 |
| Sample type |
SRA |
| |
|
| Source name |
HT1080 human fibrosarcoma cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue origin: derived from biopsy of fibrosarcoma of Human male
treatment: curaxin
antibody: none, input
|
| Treatment protocol |
HT1080 cells were treated with 3 uM CX 137 for 1 hour
|
| Growth protocol |
HT1080 cells were maintaned in DMEM with 10% FBS, 1% pen-strep, used at a confluency 80%
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with SSRP1 antibody.
ChIP isolated DNA was treated using the standard ChIP-seq protocol from Illumina with the following modification. After adaptor ligation the library was separated on a 2% agarose gel and the 150 to 500 bp region was excised and purified. This larger excision region allows successfully sequencing libraries from low quality (< 10 ng) ChIP samples.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.8.2
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie v0.12.7 with parameters -n 1 -m 1 -e 70 -l 28 -k 1 -t -p 8 -q -S —best
Control bam files were merged using bamtools merge, version 1.0.2 using default parameters
Peaks were called using PeakRanger, version 1.16, with parameters ccat --format bam -l 300
Genome_build: hg19
Supplementary_files_format_and_content: The *summit.bed files are tab delimited text files containing coordinates of peak summits of androgen receptor binding sites in the absence/presence of curaxin
Supplementary_files_format_and_content: The *region.bed files are tab delimited text files containing coordinates of peak regions of androgen receptor binding sites in the absence/presence of curaxin
|
| |
|
| Submission date |
Mar 21, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Robert William Leach |
| E-mail(s) |
rwleach@ccr.buffalo.edu
|
| URL |
http://ccr.buffalo.edu/people/staff/leach.html
|
| Organization name |
Center of Excellence in Bioinformatics
|
| Department |
Center for Computational Research
|
| Street address |
701 Ellicott Street
|
| City |
Buffalo |
| State/province |
NY |
| ZIP/Postal code |
14203 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE45393 |
Facilitates chromatin transcription complex is a marker and target of aggressive cancers with lower survival rates |
|
| Relations |
| SRA |
SRX253236 |
| BioSample |
SAMN01985583 |
