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| Status |
Public on Aug 01, 2017 |
| Title |
HGSC_40201 |
| Sample type |
SRA |
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| Source name |
primary ovarian tumor tissue
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| Organism |
Homo sapiens |
| Characteristics |
stic: No
age: 55
path.stage: IIIC
surgical.outcome: Optimal
diagnosis.of.record: Not available
diagnosis.after.path.re.review: Not available
platinumfreeinterval.mos..: Not available
platinumstatus: Not available
recurrence: Y
pfs.mos..: 22
os.mos..: Not available
vitalstatus: Not available
race: Not available
tcga_subtype_dif: 0.259
tcga_subtype_imr: 0.335
tcga_subtype_mes: -0.392
tcga_subtype_pro: -0.126
tissue: primary tumor tissue from high grade serous ovarian tumors
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| 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
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| Submission date |
Jul 31, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
leslie cope |
| E-mail(s) |
cope@jhu.edu
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| Organization name |
leslie cope
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| Street address |
550 N. Broadway
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| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21209 |
| Country |
USA |
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| 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 |
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| Relations |
| BioSample |
SAMN07427933 |
| SRA |
SRX3050125 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2722894_40201_counts.txt.gz |
3.0 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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