|
| Status |
Public on Dec 06, 2023 |
| Title |
Mammary epithelium luminal progenitors, MMTVcre/Brca2/Trp53 knockdown, bio rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
Mammary epithelium
|
| Organism |
Mus musculus |
| Characteristics |
strain: MMTVcre Brca2(fl/fl) Trp53(fl/+)
tissue: Mammary epithelium
cell type: Luminal progenitors (LP)
genotype: Brca2KO
|
| Extracted molecule |
total RNA |
| Extraction protocol |
miRNeasy micro kit (Qiagen Cat#217084) following manufacturer's protocol.
Illumina TruSeq RNA v2 protocol (Illumina #RS-122-2001, RS-122-2002).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
1574-P7-KO_S8
|
| Data processing |
Sequencing was undertaken on an Illumina NextSeq 500 to produce 81bp pair-end reads.
Read alignment was performed with the align function of the Rsubread package version 2.6.1.
Genewise read counts were obtained with the featureCounts function of the Rsubread package and Rsubread's inbuilt mm10 annotation.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files with columns for Entrez Gene ID, gene length (number of bases in union of all exons), and the number of reads. The supplementary file GenewiseCounts.txt.gz gives read counts for all samples in one file.
|
| |
|
| Submission date |
May 16, 2023 |
| Last update date |
Dec 06, 2023 |
| Contact name |
Gordon K Smyth |
| E-mail(s) |
smyth@wehi.edu.au
|
| Phone |
(+61 3) 9345 2326
|
| Fax |
(+61 3) 9347 0852
|
| URL |
http://www.wehi.edu.au
|
| Organization name |
Walter and Eliza Hall Institute of Medical Research
|
| Department |
Bioinformatics
|
| Lab |
Smyth
|
| Street address |
1G Royal Pde
|
| City |
Parkville |
| State/province |
Vic |
| ZIP/Postal code |
3052 |
| Country |
Australia |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE232631 |
RNA-seq profiling of mammary epithelial cell populations from Brca2 knockout and wildtype mice |
|
| Relations |
| BioSample |
SAMN35107081 |
| SRA |
SRX20366675 |
