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Sample GSM1386589 Query DataSets for GSM1386589
Status Public on Nov 01, 2014
Title Msx1-2 (d-d) KO - LCM RNA-Seq - Luminal Epithelium
Sample type SRA
Source name uterus (luminal epithelial cells)
Organism Mus musculus
Characteristics strain: Msx1^d/d/Msx2^d/d
genotype: Knockout (d/d)
tissue: uterus
cell type: Luminal Epithelium
Treatment protocol Extracted on day 4 of pregnancy after mating with vasectomized male
Extracted molecule total RNA
Extraction protocol Laser capture microdissection of indicated cell type onto CapSure HS LCM caps, extracted with Arcturus PicoPure kit following manufacturers instructions
TruSeq Stranded Total RNA Sample Prep kit with Ribo-Zero Deplete treatment
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
Description Laser capture microdissected
Data processing Illumina Casava v1.8.2 software was used for basecalling.
Sequenced reads were mapped to the UCSC mouse mm9 genome using tophat v2.0.5.
Transcript abundances was estimated in Reads Per Kilobase of exon per Million mapped reads (RPKM) by using Cufflinks v2.0.2 package, following a protocol from "Trapnell C. et al., Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks, Nature Protocol, 2012 Mar 1;7(3):562-78.".
Genome_build: mm9
Supplementary_files_format_and_content: text files with RPKM with statistics for identifying differentially expressed genes
Submission date May 14, 2014
Last update date May 15, 2019
Contact name SK Dey
Phone 513-803-1158
Organization name Cincinnati Children's Hospital
Department Reproductive Sciences
Street address 3333 Burnet Ave
City Cincinnti
ZIP/Postal code 45229
Country USA
Platform ID GPL18480
Series (1)
GSE57680 RNA-sequencing of luminal epithelium and stroma cells isolated by LCM from pseudopregnant day 4 Msx1/Msx2 knockout and control uteri
BioSample SAMN02777844
SRA SRX542650

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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