|
| Status |
Public on Sep 30, 2017 |
| Title |
Wt3-L2 |
| Sample type |
SRA |
| |
|
| Source name |
epithelial cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: FVB/NJ
tissue: mammary gland at lactation day 2
age: postnatal week 11
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated form the mouse mammary tissue slides using the RecoverAll™ Total Nucleic Acid Isolation Kit (ThermoFisher).
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
lactation day 2
|
| Data processing |
Tophat2 (2.0.7) [1] was applied to align sequencing reads to the reference mouse genome (GRCm38/mm10).
The relative gene expression RPKM and read counts were estimated using SAMMate (2.7.4) and Ensembl database (Mus Musculus.GRCm38.82).
Protein coding genes with at least 2 RPKM on average in either condition were used to perform the differential gene expression analysis (MMTV-FOXC1 transgenic vs. wildtype mice) using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...
|
| |
|
| Submission date |
Sep 29, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Xiaojiang Cui |
| E-mail(s) |
bowen.gao@cshs.org
|
| Phone |
3104237437
|
| Organization name |
Cedars Sinai Medical Center
|
| Department |
Surgery Dept
|
| Lab |
Breast Cancer Research Lab
|
| Street address |
3884 Fredonia Dr#F
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90068 |
| Country |
USA |
| |
|
| Platform ID |
GPL21493 |
| Series (1) |
| GSE104443 |
Regulation of gene expression by FOXC1 in mouse mammary epithelial cells. |
|
| Relations |
| BioSample |
SAMN07722435 |
| SRA |
SRX3234399 |
