|
| Status |
Public on Oct 16, 2020 |
| Title |
Pten+/+ luminal_4 [19_4392WT_L_S7] |
| Sample type |
SRA |
| |
|
| Source name |
Pten+/+ luminal
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6
genotype/variation: Pten+/+
Sex: female
age: 12-14 weeks old
cell type: mammary epithelial cells
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA were isolated from FACS sorted cells using TRI Reagent and Direct-zol RNA Microprep kit (Zymo Research)
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
19_4392WT_L_S7
|
| Data processing |
RNA-seq data was converted to a per-gene read-count matrix using RNAsik pipeline v1.5.3 as implemented in Laxy.
Reads were mapped to the mouse genome (GRCm38) using STAR
duplicates were marked using Picard Markduplicates
reads were assigned to gene models (exonic only) from the GRCm38 annotation using featureCounts
Genome_build: GRCm38
Supplementary_files_format_and_content: counts tsv format
|
| |
|
| Submission date |
Nov 12, 2019 |
| Last update date |
Oct 06, 2020 |
| Contact name |
David Richard Powell |
| E-mail(s) |
david.powell@monash.edu
|
| Organization name |
Monash University
|
| Department |
Bioinformatics Platform
|
| Street address |
Wellington Road
|
| City |
Clayton |
| State/province |
VIC |
| ZIP/Postal code |
3800 |
| Country |
Australia |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE140289 |
RNA seq of mammary epithelial cells with loss-of-function Pten mutations |
|
| Relations |
| BioSample |
SAMN13266650 |
| SRA |
SRX7131151 |
