|
| Status |
Public on Aug 01, 2019 |
| Title |
culture-Cont LC |
| Sample type |
SRA |
| |
|
| Source name |
cultured luminal cells in condition of DMSO
|
| Organism |
Mus |
| Characteristics |
tissue: mammary gland
cell type: luminal cell
developmental stage: adult virgin
age: 8 weeks
|
| Treatment protocol |
Cells were freshly sorted from mouse mammary gland.Cultured luminal cells were treated with either vehicle [DMSO] or [E2Pg, 1 mM E2, 2.5 mM Pg]
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from freshly isolated Lin-, CD24+, CD29lo, Sca1+and Sca1- cells were extracted with Trizol. Total RNA from cultured luminal cell extracted with Trizol.
RNA-seq libraries were prepared according to the manufacturer’s instructions (Illumina) and then applied to sequencing on Illumina HiSeq 2000 in BGI-tech, Beijing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
culture-Cont LC
|
| Data processing |
Quality control using Illumina 1.5+
Basecalling usingHCS1.5.15.1+RTA1.13.48+OLB-1.9.4
Reads were aligned against the mm10 mouse reference genome with the UCSC Genes annotation (mm10 knownGene.txt) using TopHat2 (Kim et al., 2013) 2.0.9 (parameters: -g 1 -no-coverage-search -microexon-search -m 2). 80% of mapping rate.
Differential gene expression analysis using FDR≤0.001 AND |log2Ratio|≥1
Genome_build: mm10
Supplementary_files_format_and_content: Quantification of gene expression using RPKM algorithm and screening of differentially expressed genes using Poisson distribution model.
|
| |
|
| Submission date |
Jun 29, 2017 |
| Last update date |
Aug 01, 2019 |
| Contact name |
Ajun Geng |
| E-mail(s) |
gengajun2014@sibcb.ac.cn
|
| Organization name |
Chinese Academy of Sciences
|
| Department |
Shanghai Institute of Biochemistry and Cell Biology
|
| Lab |
Yi Arial Zeng
|
| Street address |
320 Yue-Yang Road
|
| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
200031 |
| Country |
China |
| |
|
| Platform ID |
GPL23575 |
| Series (1) |
| GSE100664 |
Amphiregulin Mediates the Hormonal Regulation on R-spondin1 Expression in the Mammary Gland |
|
| Relations |
| BioSample |
SAMN07299359 |
| SRA |
SRX2971179 |
