|
| Status |
Public on Aug 31, 2012 |
| Title |
A549 shRNA Con |
| Sample type |
SRA |
| |
|
| Source name |
A549 cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: lung adenocarcinoma cell line
cell line: A549
knockdown: H1TetO-shRNA-Con
|
| Treatment protocol |
The A549-H1tetO-shRNA-SOX2 and its control cell A549-H1tetO-shRNA-Con were collected after 4 day's incubation with Doxycycline to induce the expression of shRNA.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
4 ug total RNA from each sample was extracted by TRIzol reagent.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Base calling files was generated by RTA1.12 and converted to quality and sequence files using BclConverter.
Low quality reads were trimmed and adapter sequences were clipped with the aid of a dynamic programming algorithm. Clean tags were mapped to human reference genome (hg19) using SOAPaligner.
The number of unambiguous clean tags for each gene was calculated and then normalized to TPM (number of transcripts per million clean tags).
Genome_build: hg19
Supplementary_files_format_and_content: excel file includes TPM values for each Sample
|
| |
|
| Submission date |
Mar 19, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
NA LI |
| E-mail(s) |
ligroup@hotmail.com
|
| Organization name |
NANKAI University
|
| Street address |
94 Weijin Road
|
| City |
Tianjin |
| ZIP/Postal code |
300071 |
| Country |
China |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE36597 |
SOX2 gene regulates the transcriptional network of oncogenes and affects tumorigenesis of human lung cancer cells |
|
| Relations |
| SRA |
SRX130218 |
| BioSample |
SAMN00829005 |
