|
| Status |
Public on Dec 27, 2018 |
| Title |
mammary gland WT_r1 (RNA-seq) |
| Sample type |
SRA |
| |
|
| Source name |
mammary gland
|
| Organism |
Mus musculus |
| Characteristics |
tissue: mammary gland
age: 8-wk-old transplants
genotype: WTfl/flmTmGfl/fl cre+
cell type: GFP+ basal cells (CD24+CD49fhigh) sorted from mammary epithelial cell (MECs)
|
| Treatment protocol |
In all cases MECs were isolated from WT and miR205fl/fl cre+ outgrowth according to our lab protocol and FACS-purified into basal and luminal subpopulations using cell surface markers.
|
| Growth protocol |
Mice were maintained in standard conditions
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the Arcturus® PicoPure® RNA Isolation Kit (Applied Biosystems)
NuGEN RNA-Seq and Illumina DNA Seq library preparation protocol were used to prepare the library
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
mammary gland transplants 8-wk
|
| Data processing |
TopHat 2.02 is used to align reads to reference genome.
Htseq-count is used to count the reads in each gene for each sample against the Ensembl NCBIM37.67 gtf file
Genome_build: mm9
Supplementary_files_format_and_content: read counts for each gene extracted by Htseq-count from the bam files aligned by TopHat
|
| |
|
| Submission date |
Dec 26, 2018 |
| Last update date |
Dec 27, 2018 |
| Contact name |
Zheng Xia |
| E-mail(s) |
xiaz@ohsu.edu
|
| Organization name |
Oregon Health & Science University
|
| Department |
Department of Biomedical Engineering
|
| Lab |
Xia Lab
|
| Street address |
3181 SW Sam Jackson Park Rd
|
| City |
Portland |
| State/province |
Oregon |
| ZIP/Postal code |
97239 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE124364 |
miR205 Regulates Mammary Gland Development and Stem Cell Self-renewal through YAP and Wnt signaling |
|
| Relations |
| BioSample |
SAMN10644220 |
| SRA |
SRX5180035 |
