NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM7360221 Query DataSets for GSM7360221
Status Public on Dec 06, 2023
Title Mammary epithelium mature luminal cells, wildtype, bio rep 2
Sample type SRA
 
Source name Mammary epithelium
Organism Mus musculus
Characteristics strain: MMTVcre Brca2(fl/fl) Trp53(fl/+)
tissue: Mammary epithelium
cell type: Mature luminal (ML)
genotype: WT
Extracted molecule total RNA
Extraction protocol miRNeasy micro kit (Qiagen Cat#217084) following manufacturer's protocol.
Illumina TruSeq RNA v2 protocol (Illumina #RS-122-2001, RS-122-2002).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description 1577-P8-WT_S12
Data processing Sequencing was undertaken on an Illumina NextSeq 500 to produce 81bp pair-end reads.
Read alignment was performed with the align function of the Rsubread package version 2.6.1.
Genewise read counts were obtained with the featureCounts function of the Rsubread package and Rsubread's inbuilt mm10 annotation.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files with columns for Entrez Gene ID, gene length (number of bases in union of all exons), and the number of reads. The supplementary file GenewiseCounts.txt.gz gives read counts for all samples in one file.
 
Submission date May 16, 2023
Last update date Dec 06, 2023
Contact name Gordon K Smyth
E-mail(s) smyth@wehi.edu.au
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 (1)
GSE232631 RNA-seq profiling of mammary epithelial cell populations from Brca2 knockout and wildtype mice
Relations
BioSample SAMN35107077
SRA SRX20366679

Supplementary file Size Download File type/resource
GSM7360221_featureCounts_1577-P8-WT_S12.txt.gz 170.4 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap