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Sample GSM2719940 Query DataSets for GSM2719940
Status Public on Jul 28, 2017
Title HGSC_JB4912
Sample type RNA
Source name primary ovarian tumor tissue
Organism Homo sapiens
Characteristics stic: No
age: 55
path.stage: IIIC
surgical.outcome: Optimal
diagnosis.of.record: Ovarian Ca Ovarian Ca
platinumfreeinterval.mos..: 37
platinumstatus: Sensitive
recurrence: N
pfs.mos..: 43.2
os.mos..: 43.2
vitalstatus: Alive
race: ASIAN
tcga_subtype_dif: -0.187
tcga_subtype_imr: 0.048
tcga_subtype_mes: -0.252
tcga_subtype_pro: 0.422
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.
Label NA
Label protocol Not applicable
Hybridization protocol Total RNA (100 ng) was obtained from 95 of 96 samples, and hybridized to the nCounter Human miRNA sample probes (Seattle, WA).
Scan protocol Each sample was scanned for 600 FOV on the nCounter Digital Analyzer
Description JB4912
Data processing The nanoStringNorm procedure as implemented in the nanoStringNorm Bioconductor package was used to pre-process the miRNA data, followed by differential expression analysis with Empirical Bayes methods via the limma Bioconductor package.
Submission date Jul 27, 2017
Last update date Jul 28, 2017
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 GPL17904
Series (2)
GSE101976 Molecular analysis of high-grade serous ovarian carcinoma with and without associated serous tubal intra-epithelial carcinoma [miRNA expression]
GSE102094 Molecular analysis of high-grade serous ovarian carcinoma with and without associated serous tubal intra-epithelial carcinoma

Data table header descriptions
VALUE normalized counts

Data table
hsa-let-7a-5p 13.96620863
hsa-let-7b-5p 13.09563314
hsa-let-7c 9.949754386
hsa-let-7d-5p 9.857398301
hsa-let-7e-5p 9.103378371
hsa-let-7f-5p 9.06437093
hsa-let-7g-5p 12.76832734
hsa-let-7i-5p 10.03912324
hsa-miR-1 5.600053739
hsa-miR-100-5p 9.811299817
hsa-miR-101-3p 5.47418155
hsa-miR-103a-3p 5.151969873
hsa-miR-105-5p 5.275281566
hsa-miR-106a-5p+hsa-miR-17-5p 8.726142495
hsa-miR-106b-5p 10.07966611
hsa-miR-107 8.764048854
hsa-miR-10a-5p 9.902591863
hsa-miR-10b-5p 8.687225379
hsa-miR-1178 5.564301144
hsa-miR-1179 4.493209098

Total number of rows: 822

Table truncated, full table size 20 Kbytes.

Supplementary data files not provided
Processed data included within Sample table
Processed data are available on Series record

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