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Sample GSM1274255 Query DataSets for GSM1274255
Status Public on Oct 20, 2016
Title Hypoxia_6hr (total RNA)_3
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: 6hr
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 cDNA
Instrument model AB 5500xl Genetic Analyzer
 
Description Library_3
RNA
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 SAMN02420271
SRA SRX382907

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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