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Sample GSM2800628 Query DataSets for GSM2800628
Status Public on Sep 30, 2017
Title Wt2-L2
Sample type SRA
 
Source name epithelial cells
Organism Mus musculus
Characteristics strain: FVB/NJ
tissue: mammary gland at lactation day 2
age: postnatal week 11
Extracted molecule total RNA
Extraction protocol RNA was isolated form the mouse mammary tissue slides using the RecoverAllâ„¢ Total Nucleic Acid Isolation Kit (ThermoFisher).
RNA libraries were prepared for sequencing using standard Illumina protocols.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Description lactation day 2
Data processing Tophat2 (2.0.7) [1] was applied to align sequencing reads to the reference mouse genome (GRCm38/mm10).
The relative gene expression RPKM and read counts were estimated using SAMMate (2.7.4) and Ensembl database (Mus Musculus.GRCm38.82).
Protein coding genes with at least 2 RPKM on average in either condition were used to perform the differential gene expression analysis (MMTV-FOXC1 transgenic vs. wildtype mice) using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...
 
Submission date Sep 29, 2017
Last update date May 15, 2019
Contact name Xiaojiang Cui
E-mail(s) bowen.gao@cshs.org
Phone 3104237437
Organization name Cedars Sinai Medical Center
Department Surgery Dept
Lab Breast Cancer Research Lab
Street address 3884 Fredonia Dr#F
City Los Angeles
State/province CA
ZIP/Postal code 90068
Country USA
 
Platform ID GPL21493
Series (1)
GSE104443 Regulation of gene expression by FOXC1 in mouse mammary epithelial cells.
Relations
BioSample SAMN07722436
SRA SRX3234398

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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