|
| Status |
Public on Oct 20, 2016 |
| Title |
Hypoxia_6days (precursor miRNA)_11 |
| Sample type |
SRA |
| |
|
| Source name |
A2780 cancer cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue of origin: Ovarian cancer
cell line: epithelial ovarian cancer cell line A2780
stress: Hypoxia
time: 6days
|
| Treatment protocol |
Cells incubated in an oxygen-controlled hypoxia chamber at 1% O2 for 6hr, 48hr, 6days.
|
| Growth protocol |
Cells were maintained in 5% CO2 at 37°C in RPMI 1640 supplemented with 10-15% fetal bovine serum (FBS) and 0.1% gentamicin sulfate. For Hypoxia treatments, cells were incubated in an oxygen-controlled hypoxia chamber at 1% O2 for respective treatment intervals.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using miRVANA RNA isolation kit (Lifetechnologies). RNA qulaity was meassured using Agilent Bioanalyzer, with atleast RIN<8.
Starting with 3ug of total RNA for each sample, Ribosomal RNA was depleted using Ribominus (Invitrogen/Life Technologies, Carlsbad, CA) following manufacturer's recommendations. Sequencing libraries were then prepared and barcoded individually using the SOLiD™ Total RNA-Seq Kit for Whole Transcriptome Libraries (Life Technologies, Inc., Carlsbad, CA) following manufacturer's recommendations. Prepared samples were then pooled and sequenced using the Life Technology 5500xl sequencer using 75 base forward read only.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
AB 5500xl Genetic Analyzer |
| |
|
| Description |
Library_11
precursor miRNA
|
| Data processing |
XSQ files containing the read sequences and quality values were loaded onto a compute cluster and the reads mapped in colorspace using the Life Technologies LifeScope 2.5.1 software using default parameters. Reads were mapped to the human genome (hg19) downloaded from the UCSC Genome Bioinformatics Site (http://genome.ucsc.edu). The hg19 genome was slightly modified by deleting the Y chromosome in order to make a female genome. An hg19 exon reference file provided by Life Technologies was required by LifeScope in order to create the exon junction libraries needed to map reads that cross exon boundaries. This file was derived from the refGene database from UCSC. Also, a human filter reference file was required (provided by Life Technologies) that contains the sequences of ribosomal and repetitive regions of the genome in order to filter reads that mapped to those regions. Mapped reads were outputted in the standard BAM (Binary Alignment/Map) format. BAM files were imported into Partek Genomics Suite 6.6 (Partek Incorporated, St. Louis, MO) for gene expression analysis. Mapped reads contained in the BAM files were cross-referenced against the RefSeq database (downloaded from UCSC Genome Browser) and a smallRNA database (UCSC Genome Browser) to generate RPKM (Reads Per Kilobase of exon per Million mapped reads) values for each gene. Low expressing genes were excluded. Differential expression using the derived RPKM values was performed using ANOVA. Genes with a False Discovery Rate (FDR) < 5% were considered significant.
Genome_build: hg19
Supplementary_files_format_and_content: Two tab-delimited text file include RPKM values for mRNAs (Sood_Ovarian_RefSeq_RPKM_Values.txt) and Precursor miRNAs (Sood_Ovarian_Precursor_microRNAs_RPKM_Values.txt) for each Sample
|
| |
|
| Submission date |
Nov 25, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
anil k sood |
| E-mail(s) |
asood@mdanderson.org
|
| Phone |
7137455266
|
| Organization name |
UT MD Anderson Cancer Center
|
| Department |
Gyn Oncology and Rep Medicine
|
| Street address |
7777 knight road, unit 173
|
| City |
HOUSTON |
| State/province |
TEXAS |
| ZIP/Postal code |
77054 |
| Country |
USA |
| |
|
| Platform ID |
GPL16288 |
| Series (2) |
| GSE52695 |
RNA-seq analysis of Hypoxia and Normoxia cultured cancer cells |
| GSE52744 |
Hypoxia Mediated Downregulation of miRNA Biogenesis Leads to Increased Tumor Progression |
|
| Relations |
| BioSample |
SAMN02420291 |
| SRA |
SRX382927 |
