|
Status |
Public on Oct 01, 2013 |
Title |
HelaS_WT |
Sample type |
SRA |
|
|
Source name |
Cervical Cancer Cells
|
Organism |
Homo sapiens |
Characteristics |
cell line: ATCC-HeLa shRNA expression: Scrambled Control culture condition: Normoxia
|
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 |
cDNA |
Instrument model |
AB SOLiD 4 System |
|
|
Data processing |
SOLiD fragment colorspace transcriptome reads (50nt) were mapped to the human genome (hg19) and assigned to Ensembl transcripts using default settings in Bioscope 1.3.1 (Life Technologies). RPKM values were determined using the Bioscope 1.3.1 CountTags tool using default parameters. Primary alignments with a minimum mapping quality of 10 and minimum alignment score of 10 were counted. Genome_build: Hg19 Supplementary_files_format_and_content: Tab delimited file text file with RPKM measurements for each transcript feature
|
|
|
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) |
GSE44801 |
Next-Generation Sequencing for Whole Transcriptome Analysis 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 |
SRX248413 |
BioSample |
SAMN01974711 |