|
| Status |
Public on Feb 20, 2015 |
| Title |
Brain_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Mouse adult hybrid brain
|
| Organism |
Mus musculus x Mus spretus |
| Characteristics |
tissue: Adult whole brain
strain: BL6/spretus
genotype: Xist+/-
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mouse tissues were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent and then was subject to DNaseI digestion and purification using Qiagen RNAeasy Kit . Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 4 ug of total RNA 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 Genome Analyzer IIx |
| |
|
| Description |
One brain was collected from female F1 hybrid (BL6/spretus) carring an Xist mutation (B6.Cg-Xist<tm5Sado>) and thus having complete skewing of inactivation of the spretus X chromosome.
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
A pseudo-spretus genome was assembled by replacing available SNPs between C57BL/6J and M. spretus (Sanger Center) into the BL6 reference genome. 36bp reads were aligned to the C57BL/6J reference sequence (mm9, UCSC) and to the pseudo-spretus genome separately using TopHat/v2.0.0 with default parameters. The RefSeq mouse gene annotation was used.
RPKM values were obtained using Cufflinks/v2.0.2 with default parameters.
Only high-quality uniquely-mapped reads were used for assignment to each haploid genome based on available SNPs.
The SNP-associated read counts were used to assess allelic expression.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include 5 columns: gene_id, locus, regular RPKM values, BL6-exon-SNP-read counts, spretus-exon-SNP-read count.
|
| |
|
| Submission date |
Jul 25, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Xinxian Deng |
| E-mail(s) |
dengx2@u.washington.edu
|
| Organization name |
University of Washington
|
| Department |
Laboratory Medicine and Pathology
|
| Lab |
HSB C526
|
| Street address |
1959 NE Pacific St.
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98195 |
| Country |
USA |
| |
|
| Platform ID |
GPL16617 |
| Series (2) |
| GSE59777 |
Escape from X inactivation in mouse tissues (RNA-Seq) |
| GSE59779 |
Studies of regulation of mouse X inactivation and genes escaping XCI |
|
| Relations |
| BioSample |
SAMN02941040 |
| SRA |
SRX661580 |
