|
| Status |
Public on Jun 13, 2017 |
| Title |
Bptf_KO-Bsecs-Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
BptfKO Mice
|
| Organism |
Mus musculus |
| Characteristics |
gender: Female
tissue: Mammary Gland
cell type: Mammary Epithelial Cells: Bsecs
|
| Treatment protocol |
Tamoxifen was given to mice (total 15mg/kg body) prioir to cell isolation
|
| Growth protocol |
none
|
| Extracted molecule |
total RNA |
| Extraction protocol |
FACS-sorted, mammary epithelial cells were collected and homogenized in TRIzol for RNA extraction.
Purified RNA was utilized for double strand cDNA synthesis utilizing the Ovation RNA-seq system (V2). RNA-seq libraries were prepared and barcoded utilizing the Ovation ultralow DR multiplex system (Nugen), then pooled for sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
STAR was used for mapping reads to the transcriptome, retaining only uniquely mapped reads.
Deseq was used to asses changes in expression levels simultaneously across multiple conditions and in multi-factor experimental designs, incorporating information from multiple replicates (2 biological replicates per cell type).
Gene Set Enrichment Analysis (GSEA) for global analysis of differentially expressed genes.
Additionally, the top 100 differentially expressed genes were loaded into the Enrichr for gene ontology enrichment analysis.
Genome_build: mm9
|
| |
|
| Submission date |
Apr 20, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Wesley D. Frey |
| E-mail(s) |
[email protected]
|
| Organization name |
Cold Spring Harbor Laboratory
|
| Street address |
One Bungtown Road
|
| City |
Cold Spring Harbor |
| State/province |
New York |
| ZIP/Postal code |
11724 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE98003 |
Bptf maintains chromatin accessibility and the self-renewal capacity of mammary gland stem cells [RNA-Seq] |
| GSE98004 |
Bptf maintains chromatin accessibility and the self-renewal capacity of mammary gland stem cells |
|
| Relations |
| BioSample |
SAMN06768556 |
| SRA |
SRX2748818 |
