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Sample GSM2722961 Query DataSets for GSM2722961
Status Public on Aug 01, 2017
Title HGSC_JB4900
Sample type SRA
Source name primary ovarian tumor tissue
Organism Homo sapiens
Characteristics stic: Yes
age: 53
path.stage: IIIC
surgical.outcome: Optimal
diagnosis.of.record: Ovarian Ca Fallopian Tube Ca
platinumfreeinterval.mos..: 38.8
platinumstatus: Sensitive
recurrence: Y
pfs.mos..: 43.7
os.mos..: 46.8
vitalstatus: Alive
race: WHITE
tcga_subtype_dif: -0.156
tcga_subtype_imr: 0.358
tcga_subtype_mes: -0.433
tcga_subtype_pro: 0.289
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 (
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
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
BioSample SAMN07427901
SRA SRX3050157

Supplementary file Size Download File type/resource
GSM2722961_Sample_JB4900_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

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