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Sample GSM2442810 Query DataSets for GSM2442810
Status Public on Jul 17, 2017
Title CAG_TB_rep1
Sample type SRA
 
Source name E7.5 trophoblast
Organism Mus musculus
Characteristics developmental stage: E7.5
tissue: trophoblast
genotype: Xist +/CAG
strain: JF1 x C57BL6/J
Sex: female
Extracted molecule total RNA
Extraction protocol Trophoblasts were isolated from E7.5 embryos. RNA was prepared using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#15027078) was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
 
Data processing RNA-seq reads were mapped to a concatenated custom reference, including strain-specific genomes and sequences spanning splice junctions based on RefSeq genes, using BWA. The coordinates of mapped reads were converted to mm9 genomic coordinates using custom scripts.
The numbers of maternal and paternal allele-specific reads for each gene were counted using custom scripts.
Gene expression was quantified in a non-allelic manner using Cufflinks v2.2.1 cuffdiff with option '--library-type ff-firststrand --library-norm-method classic-fpkm --multi-read-correct'.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file include average of % paternal reads (avePat) and average of FPKM values (aveFPKM) for each genotype; FDR adjusted p-value (qVal) for comparison with wild-type; % paternal reads (Pat), the total number of allele-specific reads, both maternal and paternal (ASreads), and FPKM value (FPKM) for each sample.
 
Submission date Dec 30, 2016
Last update date May 15, 2019
Contact name Koji Nagao
E-mail(s) nagao@bio.sci.osaka-u.ac.jp
Organization name Osaka University
Department Graduate School of Science
Lab Obuse Lab.
Street address 1-1 Machikaneyama
City Toyonaka
State/province Osaka
ZIP/Postal code 560 0043
Country Japan
 
Platform ID GPL18480
Series (1)
GSE93031 Defects in dosage compensation impact global gene regulation in the mouse trophoblast
Relations
BioSample SAMN06192114
SRA SRX2452556

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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