|
| Status |
Public on Sep 08, 2023 |
| Title |
Basal cells, biol rep 3 |
| Sample type |
SRA |
| |
|
| Source name |
Mammary epithelial cells
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Mammary epithelial cells
cell type: myoepithelial
strain: FVB/N mice
developmental stage: adult (9-10 weeks of age)
Sex: female
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Qiagen's miRNeasy kit and DNase treated.
100ng of total RNA was used to construct libraries following Illumina's recommended protocol for TruSeq RNA Library Prep Kit v2.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Ba3
|
| Data processing |
Libraries were sequenced on an Illumina NextSeq 500, generating 80 bp paired-end reads.
Reads were aligned to the mouse genome mm10 by the subjunc function of the Rsubread software tool version 1.34.4.
Read counts were summarized by Entrez Gene ID using the Rsubread featureCounts function and Rsubread's inbuilt RefSeq annotation.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files; columns represent Entrez Gene ID, gene length (total base count of all exons) and the number of reads mapped to that gene.
|
| |
|
| Submission date |
Mar 20, 2023 |
| Last update date |
Sep 08, 2023 |
| Contact name |
Yunshun Chen |
| E-mail(s) |
yuchen@wehi.edu.au
|
| Organization name |
Walter and Eliza Hall Institute of Medical Research
|
| Department |
ACRF Cancer Biology and Stem Cells
|
| Lab |
Chen
|
| Street address |
1G Royal Parade
|
| City |
Parkville |
| State/province |
VIC |
| ZIP/Postal code |
3052 |
| Country |
Australia |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE227748 |
3D genome organization coordinates key regulators of lineage specification in mammary epithelial cells [RNASeq_MEC] |
| GSE227750 |
3D genome organization coordinates key regulators of lineage specification in mammary epithelial cells |
|
| Relations |
| BioSample |
SAMN33830217 |
| SRA |
SRX19731159 |
