NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM3142972 Query DataSets for GSM3142972
Status Public on May 15, 2018
Title PerPool_2
Sample type SRA
 
Source name normal peritoneal tissue pool
Organism Homo sapiens
Characteristics tissue: normal peritoneal brushings
stic: No
age: NA
path.stage: NA
surgical.outcome: NA
diagnosis.of.record: NA
diagnosis.after.path.re.review: NA
platinumfreeinterval.mos..: NA
platinumstatus: NA
recurrence: NA
pfs.mos..: NA
os.mos..: NA
vitalstatus: NA
race: NA
tcga_subtype_dif: NA
tcga_subtype_imr: NA
tcga_subtype_mes: NA
tcga_subtype_pro: NA
Treatment protocol NA
Growth protocol NA
Extracted molecule total RNA
Extraction protocol RNA was isolated from fresh brushings, utilizing Ambion’s ToTALLY RNA™ RNA Isolation Kit (Part Number AM1910, ©Ambion, Inc.). RNA quality was assessed 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
 
Description s_PerPool_2
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, Gene Name and counts
 
Submission date May 15, 2018
Last update date May 16, 2018
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)
GSE102094 Molecular analysis of high-grade serous ovarian carcinoma with and without associated serous tubal intra-epithelial carcinoma
GSE114493 Molecular analysis of high-grade serous ovarian carcinoma with and without associated serous tubal intra-epithelial carcinoma [RNA-Seq; normal samples]
Relations
BioSample SAMN09211147
SRA SRX4085690

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

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