NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2722913 Query DataSets for GSM2722913
Status Public on Aug 01, 2017
Title HGSC_GL4226
Sample type SRA
 
Source name primary ovarian tumor tissue
Organism Homo sapiens
Characteristics stic: No
age: 66
path.stage: IIIC
surgical.outcome: Optimal
diagnosis.of.record: Ovarian Ca
diagnosis.after.path.re.review: Ovarian Ca
platinumfreeinterval.mos..: 54.1
platinumstatus: Sensitive
recurrence: Y
pfs.mos..: 59.3
os.mos..: 63.2
vitalstatus: Alive
race: WHITE
tcga_subtype_dif: -0.536
tcga_subtype_imr: 0.009
tcga_subtype_mes: 0.619
tcga_subtype_pro: -0.23
tissue: primary tumor tissue from high grade serous ovarian tumors
Extracted molecule total RNA
Extraction protocol DNA and RNA were co-isolated from frozen tissue tumor blocks, and RNA was isolated from normal tissues utilizing Ambion’s ToTALLY RNA™ RNA Isolation Kit (Part Number AM1910, ©Ambion, Inc.). DNA concentration was confirmed using a PicoGreen protocol. RNA quality was confirmed by utilizing an Agilent Bioanalyzer and assigning an RNA Integrity Number (RIN) to each sample.
RNA sequencing libraries were prepared using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit. Briefly, 500ng of total RNA was purified by Ribo-Zero to remove rRNA and fragmented by divalent cations under elevated temperature. The fragmented RNA underwent first strand synthesis using reverse transcriptase and random primers. Second strand synthesis created the cDNA fragments using DNA polymerase I and RNaseH. The cDNA fragments then went through end repair, adenylation of the 3’ ends, and ligation of adapters. The cDNA library was enriched using 10 cycles of PCR and purified.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing RNA sequences were aligned to the NCBI human genome build 37 using STAR aligner (v2.3.1z).
Quantification of genes annotated in Gencode (version 18) was performed using featureCounts (v1.4.3).
DESeq2 (doi:10.1101/002832) was used to normalize feature counts.
Picard and RSeQC 50 was used to collect QC metrics (http://broadinstitute.github.io/picard/)
Genome_build: NCBI human genome build 37
Supplementary_files_format_and_content: Tab delimited text file containing Gene ID, Chr, Start, End, Strand, Length and counts
 
Submission date Jul 31, 2017
Last update date May 15, 2019
Contact name leslie cope
E-mail(s) cope@jhu.edu
Organization name leslie cope
Street address 550 N. Broadway
City Baltimore
State/province MD
ZIP/Postal code 21209
Country USA
 
Platform ID GPL16791
Series (2)
GSE102073 Molecular analysis of high-grade serous ovarian carcinoma with and without associated serous tubal intra-epithelial carcinoma [RNA-Seq]
GSE102094 Molecular analysis of high-grade serous ovarian carcinoma with and without associated serous tubal intra-epithelial carcinoma
Relations
BioSample SAMN07427923
SRA SRX3050134

Supplementary file Size Download File type/resource
GSM2722913_Sample_GL4226_counts.txt.gz 3.0 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap