|
| 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 |
|
| Relations |
| BioSample |
SAMN04219110 |
| SRA |
SRX1389792 |
