|
Status |
Public on Sep 30, 2017 |
Title |
Tg3-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 RecoverAllâ„¢ 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 |
SAMN07722432 |
SRA |
SRX3234402 |