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Sample GSM894310 Query DataSets for GSM894310
Status Public on May 24, 2019
Title Mouse placenta RNAseq PA E17
Sample type SRA
Source name mouse embryonic day 17.5 placental tissue
Organism Mus musculus
Characteristics genetic background: PWD/PhJ mother x AKR/J father
developmental stage: E17.5
tissue: placenta
Sex: Female
Extracted molecule total RNA
Extraction protocol mRNA-seq libraries were made for F1 female placenta total RNA from AKRxPWD E17.5, PWDxAKR E17.5, B6xCAST E17.5, CASTxB6 E17.5, B6xCAST E13.5 and CASTxB6 E13.5 (mother comes first) crosses, using Illumina TruSeq RNA Sample Prep Kit (Illumina Inc., CA) with 4 µg of total mRNA input . The six mRNA-seq libraries were pooled and sequenced for three 51bp lanes on Illumina HiSeq2000 machine (Illumina Inc., CA). Image analysis and base calling were performed by the Illumina instrument software (Illumina pipeline CASAVA v1.7).
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
Description Illumina mRNA-seq
Data processing Illumina short reads were mapped to the mouse reference genome (UCSC mm9) using TopHat program with a maximum of 3 mismatches. Only uniquely mapped reads were used for allele-specific expression quantification. On average, 84% of the reads were uniquely mapped to the mouse genome. AKR-PWD and B6-CAST SNP information is obtained from Sanger mouse SNP database.
Genome Build:
mouse66_PA_E17_SNP_counts.txt: UCSC mm9
Submission date Mar 13, 2012
Last update date May 24, 2019
Contact name Andrew Clark
Organization name Cornell University
Street address 227 Biotech Building
City Ithaca
ZIP/Postal code 14853
Country USA
Platform ID GPL13112
Series (1)
GSE36463 Profiling of differential allelic expression in mouse placental tissues from two reciprocal crosses at embryonic day 13.5 and 17.5.
SRA SRX129169
BioSample SAMN00811153

Supplementary file Size Download File type/resource
GSM894310_mouse66_PA_E17_SNP_counts.txt.gz 1.2 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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