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Sample GSM3057418 Query DataSets for GSM3057418
Status Public on Aug 28, 2018
Title smchd1MD1.rep2
Sample type SRA
Source name E13.5 MEF
Organism Mus musculus
Characteristics developmental stage: E13.5
cell type: mouse embryonic fibroblasts
genotype: Smchd1 MD1/MD1; 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
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
BioSample SAMN08743485
SRA SRX3824814

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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