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Sample GSM3057416 Query DataSets for GSM3057416
Status Public on Aug 28, 2018
Title smchd1WT.rep2
Sample type SRA
 
Source name E13.5 MEF
Organism Mus musculus
Characteristics developmental stage: E13.5
cell type: mouse embryonic fibroblasts
genotype: Smchd1 +/+; Xist deltaA/+
strain: C57BL6/J x (JF1 x C57BL6/J F1)
Sex: female
Extracted molecule total RNA
Extraction protocol Total RNAs were extracted from MEFs using ALLPrep DNA/RNA mini kit (QIAGEN).
Total RNA (1 µg) was subjected to enrichment for polyadenylated RNA, and libraries were prepared using TruSeq stranded mRNA LT sample prep kit-set (Illumina) according to the manufacturer’s instructions.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
 
Description allelic_expression.txt.gz
Data processing Allele-specific RNA-seq analysis was performed as described by Sakata et al., (2017) with minor modifications: (i) paired-end reads were used as single-end reads; (ii) the number of allele-specific reads in two replicates were summed; (iii) genes with the number of allele-specific reads ≥20 in both X^ΔA/X^JF1 and [X^ΔA/X^JF1; Smchd1^MD1/MD1] were considered as informative genes to assess the expression of JF1 alleles.
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 --multi-read-correct'.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file include average of JF1 probability (aveJF1prob), sum of the number of allele-specific reads (sumASreads), and average of FPKM values (aveFPKM) for each genotype; JF1 probability (JF1prob) and the number of allele-specific reads (ASreads) for each sample.
 
Submission date Mar 20, 2018
Last update date Aug 28, 2018
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 (2)
GSE112095 Role of SmcHD1 in the establishment of the epigenetic states required for the maintenance of X chromosome inactivation [RNA-seq]
GSE112097 Role of SmcHD1 in the establishment of the epigenetic states required for the maintenance of X chromosome inactivation
Relations
BioSample SAMN08743488
SRA SRX3824812

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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