|
| Status |
Public on Apr 01, 2020 |
| Title |
NIC_Carm1_2 |
| Sample type |
SRA |
| |
|
| Source name |
mammary epithelial cells (MEC)
|
| Organism |
Mus musculus |
| Characteristics |
strain: FVB
tissue: Mammary gland
cell type: mammary epithelial cells (MEC)
genotype: NIC-Carm1
|
| Growth protocol |
each mammary epithelial cells (MEC) sample was isolated from the number #3 and #4 mammary glands through enzymatic digestion and pulse centrifugation. Cells were prepared using the DMEM/F12 medium. Purified cells were kept in Trizol reagent and stored at -80oC freeezer.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol method followed by the Dnase I digestion to remove the potential genomic DNA. poly A selection
TruSeq RNA Library Prep Kit v2 (illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
DESeq_counts.txt
|
| Data processing |
Basecalling was done by Illumina HiSeq Control Software (version 3.3.76).
The reads were mapped to mouse genome (mm10) by TopHat (version 2.0.10).
The number of fragments in each known gene from RefSeq database (downloaded from UCSC Genome Browser on July 17, 2015) was enumerated using htseq-count from HTSeq package (version 0.6.0).
Genes with less than 10 fragments in all the samples were removed, and then the normalized fragment count for each gene was calculated by R/Bioconductor package DESeq (version 1.18.0).
Genome_build: mm10
Supplementary_files_format_and_content: The first column is gene symbol. The other columns are normalized expression values (estimated by DESeq) for all the samples.
|
| |
|
| Submission date |
Mar 09, 2018 |
| Last update date |
Apr 01, 2020 |
| Contact name |
Jianqiang Bao |
| E-mail(s) |
jbao2@mdanderson.org
|
| Phone |
5122376613
|
| Organization name |
University of Texas MD Anderson Cancer Center
|
| Department |
Epigenetics and Molecular Carcinogenesis
|
| Lab |
Bedford's Laboratory
|
| Street address |
1808 Park Road 1C (P.O. Box 389), Smithville TX 78957
|
| City |
Smithville |
| State/province |
Texas |
| ZIP/Postal code |
78957 |
| Country |
USA |
| |
|
| Platform ID |
GPL21493 |
| Series (1) |
| GSE111624 |
Distinct oncogenic roles of protein arginine methyltransferases (PRMTs) in mammary gland tumorigenesis using transgenic overexpression mouse models |
|
| Relations |
| BioSample |
SAMN08668406 |
| SRA |
SRX3777951 |
