|
| Status |
Public on Oct 01, 2013 |
| Title |
HelaHS_smRNA |
| Sample type |
SRA |
| |
|
| Source name |
Cervical Cancer Cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: ATCC-HeLa
shRNA expression: Scrambled Control
culture condition: Hypoxia
|
| Treatment protocol |
Same density of HeLa cells expressing scrambled control (S) or EGFR shRNA-E1 (A1) were seed and allowed for 6-8h attachment. After that, half of the experimental groups (HS and HA1) were moved into hypoxia chamber (1% O2) while the other groups (S and A1) were continuingly cultured under normoxia for another 24h.
|
| Growth protocol |
Cells were cultured in DMEM/F12 medium with 10%FBS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from HeLa stable clones expressing scrambled control or EGFR shRNA-E1 that were seeded at same density and cultured under normoxia or hypoxia (1% O2) for 24h using miRNeasy Mini Kit (Qiagen). All RNA samples passed quality test with RIN-values greater than 8 as measured by Agilent Technologies Bioanalyzer, were subjected to RNA deep sequencing.
RNA libraries were prepared according to the standard procedures instructed by Applied Biosystems for Deep Sequencing
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
AB SOLiD 4 System |
| |
|
| Data processing |
50 nt colorspace reads were trimmed to 35nt. Resulting 35nt reads were trimmed of adaptor sequence and mapped against human pre-miR sequences (miRBase version 16.0).
Reads per million mapped reads (RPM) values were based on mapped reads with no more than 2 mismatches total. A read was considered to come from a mature miRNA if it mapped to pre-miRNA sequences with no more than three upstream or downstream bases, and missing no more than two upstream or downstream bases from predicted mature or mature* sequences as defined in miRBase version 16.0. All the other pre-miRNA mapped reads were assigned as pre-miRNA signal.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each miR
|
| |
|
| Submission date |
Mar 01, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Mien-Chie Hung |
| E-mail(s) |
mhung@mdanderson.org
|
| Organization name |
MD Anderson Cancer Center
|
| Street address |
1515 Holcombe Boulevard
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL13393 |
| Series (2) |
| GSE44802 |
Next-Generation Sequencing for Small RNA Application in Scrambled Control and EGFR Knockdown Cells Cultured under Normoxia and Hypoxia |
| GSE44804 |
Scrambled Control and EGFR Knockdown Cells Cultured under Normoxia and Hypoxia |
|
| Relations |
| SRA |
SRX248419 |
| BioSample |
SAMN01974717 |
