|
| 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 |
| 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 |
SAMN08743485 |
| SRA |
SRX3824814 |
