|
| Status |
Public on Jul 08, 2020 |
| Title |
vector_IM_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
ATCC
|
| Organism |
Homo sapiens |
| Characteristics |
origin: Human-derived blast crisis CML cell line
cell line: K562
|
| Treatment protocol |
Transduced cells were treated for 48 h with 0.5uM imatinib
|
| Growth protocol |
K562 cells were obtained commercially from ATCC and maintained in RPMI supplemented with 10% FBS and 1% pen-strep. Cells were transduced with virus packaging either the SRSF1 gene or an empty vector control
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Suspension cells were harvested by centrifugation. RNA was extracted with the Qiagen RNeasy mRNA kits following manufacturer's instructions
Only RNA with RIN>7 was used. Library prep was performed using the illumina Truseq Stranded Total RNA kit with Ribozero Gold. Each experimental condition for RNA-seq was performed in triplicate, each at a sequencing depth of 50M reads.
RNA 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 |
RNA-seq aligned to hg19 genome and UCSC refrence transcript with STAR(version 2.4.0).
Bigwig files are converted by bedGraphToBigWig from bedGraph generted by bedtools.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig
|
| |
|
| Submission date |
Nov 13, 2019 |
| Last update date |
Jul 08, 2020 |
| Contact name |
Jia Li |
| Organization name |
Duke-NUS
|
| Street address |
8 College Road
|
| City |
Singapore |
| ZIP/Postal code |
169857 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE140322 |
Transcriptomic analysis of SRSF1 overexpression and imatinib treatment in K562 CML cell lines |
|
| Relations |
| BioSample |
SAMN13279753 |
| SRA |
SRX7135352 |
