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Sample GSM1920179 Query DataSets for GSM1920179
Status Public on Jan 31, 2017
Title 1013140_1
Sample type SRA
Source name normal breast epithelial cells
Organism Homo sapiens
Characteristics tissue: adjacent normal tissue from patient with lobular carcinoma in situ
Sex: female
age: 69 year old
Treatment protocol none
Growth protocol Normal breast epithelial cells were grown in 1:1 DMEM/F12 medium with 2.4 g/L sodium bicarbonate, 5% chelated horse serum, 20 ng/ml EGF (BD Biosciences), 100 ng/ml cholera toxin (Sigma-Aldrich), 10 mg/L insulin (Sigma-Aldrich), 0.5 mg/L hydrocortisone (Sigma-Aldrich), and 0.04 mM calcium chloride (Sigma-Aldrich)
Extracted molecule total RNA
Extraction protocol RNA was isolated using Rneasy Mini Kit (Qiagen)
Strand-specific RNA libraries were generated from 1μg of RNA using TruSeq stranded total RNA with Ribo-Zero Gold (Illumina)
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
Description Adjacent normal breast tissue was isolated from breast cancer patients, then epithelial cells were isolated and grown in culture for a few passages before DNA isolation
Data processing Illumina HiSeq2500 single end sequencing
tophat2 --sensitive alignment of the reads in two fastq files from each sample to hg19, generating one BAM file per sample
ht-seq-count with default settings to generate counts of each gene
edgeR to generate RPKM values for each sample
Genome_build: hg19
Supplementary_files_format_and_content: The processed files are in excel format that contain RPKMs all genes
Submission date Oct 27, 2015
Last update date May 15, 2019
Contact name Takahiro Sato
Organization name Temple University
Department Fels Institute for Cancer Research and Molecular Biology
Street address 3307 North Broad Street
City Philadelphia
State/province PA
ZIP/Postal code 19140
Country USA
Platform ID GPL16791
Series (1)
GSE74417 RNA-seq of normal breast epithelial cells
BioSample SAMN04219110
SRA SRX1389792

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

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