|
| Status |
Public on Jun 23, 2015 |
| Title |
SOX9_ChIP-seq |
| Sample type |
SRA |
| |
|
| Source name |
RCS cells
|
| Organism |
Rattus norvegicus |
| Characteristics |
cell type: Rat chondrosarcoma cell
chip-seq antibody: SOX9 (AB5535, Millipore)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
RCS cell lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibodies.
ChIP-seq DNA libraries wereprepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to rn5 whole genome using Strand NGS software version 1.6 with default parpemters.
Duplicated reads were filted. Peaks for SOX6, SOX9 and histone modifications were identified using MACS software (version 1.4.5) with default settings
Genome_build: rn5
|
| |
|
| Submission date |
Jun 22, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Chia-Feng Liu |
| E-mail(s) |
[email protected]
|
| Organization name |
Cleveland Clinic Lerner Research Institute
|
| Department |
Cardiovascular & Metabolic Sciences
|
| Lab |
NE3-216
|
| Street address |
9500 Euclid Avenue,
|
| City |
Cleveland |
| State/province |
OH |
| ZIP/Postal code |
44195 |
| Country |
USA |
| |
|
| Platform ID |
GPL18694 |
| Series (2) |
| GSE70143 |
The transcription factors SOX9 and SOX5/SOX6 cooperate genome-wide through super-enhancers to drive chondrogenesis (ChIP-Seq) |
| GSE70144 |
The transcription factors SOX9 and SOX5/SOX6 cooperate genome-wide through super-enhancers to drive chondrogenesis |
|
| Relations |
| BioSample |
SAMN03785381 |
| SRA |
SRX1068225 |
