|
| Status |
Public on Jul 17, 2017 |
| Title |
deltaA_TB_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
E7.5 trophoblast
|
| Organism |
Mus musculus |
| Characteristics |
developmental stage: E7.5
tissue: trophoblast
genotype: Xist +/deltaA
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 |
SAMN06192117 |
| SRA |
SRX2452553 |
