|
Status |
Public on Nov 28, 2017 |
Title |
RNAseq.patski.WT.4u5aza.rep2 |
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: wild-type
|
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 wild-type Patski cells with 4uM 5-aza treatment. RNAseq.patski.WT.4u5aza.rep2.HF5TFBGXY.GTGAAA 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 |
SAMN08092890 |
SRA |
SRX3418185 |