|
| Status |
Public on Nov 13, 2019 |
| Title |
WP_AdCre_MMECs_DMSO_repl1 |
| Sample type |
SRA |
| |
|
| Source name |
Primary mouse mammary epithelial cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: FVB
cell type: Primary MMECs
genotype: WcrH;P53F/F
treatment: AdCre transduction followed by 72hrs hormone deprivation; 6hrs DMSO
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the AllPrep DNA/RNA universal kit (Qiagen) according to the manufacturer’s instruction with Qiagen’s QIAcube robot. Samples with a RIN>8 were considered for library preparation.
Libraries were generated with the Illumina TruSeq RNA Library Preparation kit (RS-122-2001/2, Illumina Inc.).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
log2_norm_counts_MMECs.txt
|
| Data processing |
Libraries were generated with the Illumina TruSeq RNA Library Preparation kit (RS-122-2001/2, Illumina Inc.) and sequenced on a HiSeq 2500 (using 65bp reads)
Sequencing data was aligned to GRCh38 (MCF7) or GRCm38 (MMECs) using TopHat and number of reads per gene were measured with HTSeq count.
Read counts were corrected for differences in sequencing depth by using DESeqs median-of-ratios and the normalized counts were log2-transformed.
Genome_build: GRCh38 (MCF7), GRCm38 (MMECs)
Supplementary_files_format_and_content: Expression table of samples (columns) by transcript (rows) reporting normalized counts.
|
| |
|
| Submission date |
Mar 05, 2019 |
| Last update date |
Nov 13, 2019 |
| Contact name |
Lisette Cornelissen |
| E-mail(s) |
l.cornelissen@nki.nl
|
| Organization name |
The Netherlands Cancer Institute
|
| Street address |
Plesmanlaan 121
|
| City |
Amsterdam |
| ZIP/Postal code |
1066 CX |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE127862 |
ERα over-expression does not accelerate development of p53-deficient mammary tumors in mice [RNA-Seq] |
| GSE127863 |
ERα over-expression does not accelerate development of p53-deficient mammary tumors in mice |
|
| Relations |
| BioSample |
SAMN11055558 |
| SRA |
SRX5465802 |
