|
| Status |
Public on Nov 28, 2017 |
| Title |
RNAseq.patski.Inv-Dxz4.rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Patski cells
|
| Organism |
Mus musculus x Mus spretus |
| Characteristics |
cell line: Patski
cell type: Fibroblasts derived from hybrid embryonic kidney
strain/background: BL6/spretus
genotype/variation: Inv-Dxz4
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA were extracted from Patski cells by the Qiagen RNeasy kit with on-column DNaseI digestion.
RNA-seq indexed libraries were prepared using Illumina TruSeq RNA sample preparation kit with standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
RNA-seq experiment in CRISPR/cas9-modified Patski cells (Inv-Dxz4, clone a).
RNAseq.patski.Inv-Dxz4.rep1.HMGHYBGX2.CAGATC
Processed data file: RNAseq.geneCounts.tsv.gz
|
| Data processing |
RNA-seq single-end reads were mapped to the UCSC mm10 (NCBI build v38) refSeq transcriptome as downloaded and packaged in the iGenomes reference sequences and annotation files on July 17, 2015 (https://support.illumina.com/sequencing/sequencing_software/igenome.html). Tophat2 (v 2.0.12) (calling bowtie2 (v2.2.3)) was used to perform single-end mapping allowing 6 mismatches but otherwise default parameters.
To determine biallelic expression levels, mapped reads were assigned to refSeq genes using HT-seq and counts were converted into TPMs using custom R scripts.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: RNAseq.geneCounts.tsv: Tab-delimited text file includes gene expression measured by read counts per gene.
|
| |
|
| Submission date |
Nov 22, 2017 |
| 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 |
GPL20213 |
| Series (2) |
| GSE59779 |
Studies of regulation of mouse X inactivation and genes escaping XCI |
| GSE107291 |
An evaluation of the effects of CRISPR/cas9-mediated editing of the Dxz4 locus on regulation of the mouse inactive X chromosome in Patski cells [RNA-seq] |
|
| Relations |
| BioSample |
SAMN08092898 |
| SRA |
SRX3418194 |
