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Sample GSM2863769 Query DataSets for GSM2863769
Status Public on Nov 28, 2017
Title RNAseq.patski.WT.4u5aza.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: 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.rep1.HF5TFBGXY.CTTGTA
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 SAMN08092891
SRA SRX3418184

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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