|
| Status |
Public on Nov 20, 2017 |
| Title |
Pregnancy basal cell 58 |
| Sample type |
SRA |
| |
|
| Source name |
Mammary gland
|
| Organism |
Mus musculus |
| Characteristics |
strain: FVB/NJ
age: Pregnancy
cell source: Basal
|
| Treatment protocol |
none
|
| Growth protocol |
none
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Freshly sorted cells were submitted to a Fluidigm C1 System machine for single cell capture and cDNA synthesis.
Libraries were prepared using the Nextera XT kit and sequencing was carried out on an Illumina Nextseq 500 using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Reads were aligned to the mouse genome by Subread version 1.5.0
Read counts were summarized by Entrez Gene ID using the Rsubread featureCounts function and Rusbread's in-built NCBI annotation.
Genome_build: 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 |
Feb 27, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Gordon K Smyth |
| E-mail(s) |
[email protected]
|
| 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 (2) |
| GSE95448 |
Single cell RNA-seq of 312 basal epithelial cells from the mammary glands of pregnant and adult mice |
| GSE98131 |
Single cell RNA-seq of basal, luminal and total epithelial cells from the mammary glands of female mice |
|
| Relations |
| SRA |
SRX2597055 |
| BioSample |
SAMN06466569 |
