|
| Status |
Public on Jun 23, 2015 |
| Title |
RCS_2_RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
RCS cells
|
| Organism |
Rattus norvegicus |
| Characteristics |
cell type: Rat chondrosarcoma cell
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA-Seq libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| 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 and reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using DESeq.
Genome_build: rn5
|
| |
|
| Submission date |
Jun 22, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Chia-Feng Liu |
| E-mail(s) |
liuc2@ccf.org
|
| 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) |
| GSE70142 |
The transcription factors SOX9 and SOX5/SOX6 cooperate genome-wide through super-enhancers to drive chondrogenesis (RNA-Seq) |
| GSE70144 |
The transcription factors SOX9 and SOX5/SOX6 cooperate genome-wide through super-enhancers to drive chondrogenesis |
|
| Relations |
| BioSample |
SAMN03785374 |
| SRA |
SRX1068190 |
