|
| Status |
Public on Jan 11, 2022 |
| Title |
81-rmec-10_GTTTCG |
| Sample type |
SRA |
| |
|
| Source name |
Mammary epithelial cells
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Wistar-Furth
tissue: Mammary epithelial cells
|
| Treatment protocol |
Mammary epithelial cell isolation began with fresh abdominal and inguinal mammary glands with lymph nodes removed that were finely minced and digested for 2 hours at 37°C in 10 mL of GIBCO Dulbecco’s modified Eagle’s medium/F12 (DMEM/F12; Life Technologies) containing 0.01 g/mL of type III collagenase (Worthington).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cell pellets were collected by centrifugation and resuspended in 5 mL DMEM/F12. The suspension was loaded onto a 40μm nylon filter to eliminate stromal cells and collect mammary ductal fragments, consisting of an enriched mammary epithelial cell population. To isolate RNA, cells were homogenized in TRI Reagent (Ambion), followed by RNA extraction using the MagMAX-96 for Microarrays Total RNA kit (Ambion). RNA was extracted using the RNeasy Mini Kit (Qiagen).
The fastq files were processed by the UW Biotech center.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Merge/Aggregate data from 2 independent runs on the same samples
TPM computed with RSEM v1.2.22
edgeR, EBSeq and DESeq2 were used for differential expression analysis
Genome_build: rn5
|
| |
|
| Submission date |
Sep 16, 2021 |
| Last update date |
Jan 11, 2022 |
| Contact name |
Sushmita Roy |
| E-mail(s) |
sroy@biostat.wisc.edu
|
| Organization name |
University of Wisconsin-Madison
|
| Department |
Wisconsin Institute For Discovery
|
| Street address |
330 N Orchard St
|
| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53715 |
| Country |
USA |
| |
|
| Platform ID |
GPL18694 |
| Series (2) |
| GSE184284 |
Deciphering the role of 3D genome organization in breast cancer susceptibility (RNA-Seq) |
| GSE184285 |
Deciphering the role of 3D genome organization in breast cancer susceptibility |
|
| Relations |
| BioSample |
SAMN21461227 |
| SRA |
SRX12204298 |
