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Sample GSM2254467 Query DataSets for GSM2254467
Status Public on Jul 29, 2016
Title mESC_stranded_RNASeq
Sample type SRA
 
Source name Embryonic stem cells
Organism Mus musculus
Characteristics cell type: Embryonic stem cells
genotype: wild type
library type: Illumina Truseq stranded library
Growth protocol mES cells were cultured in regular media containing 15% FBS, 1% PEN/STREP, 1% glutamine, 1% NEAA, and LIF. For mES cell maintenance, dishes were coated with 0.2% gelatin and irradiated CF1 mouse embryonic fibroblasts were plated as a confluent layer of feeder cells. mES cells were seeded at a density of 50,000 cells/6-well plate and were split every 2-3 days.
Extracted molecule total RNA
Extraction protocol RNA from mES cells was extracted using an RNeasy kit (Qiagen, USA). Polyadenylated RNA was isolated using Oligo dT beads (Invitrogen, USA).
Illumina Truseq stranded and unstranded mRNA library prep kits (Illuminca, USA) were used for deep sequencing library preparation from 6ug of total RNA according to the manufacturer's protocol.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing Illumina Casava1.8 sotfware used for basecalling.
To check RNA-seq data quality, RNA-seq reads were mapped to the mm9 genome assembly using Bowtie (version 1.0.0) with default parameters.
We calculate mismatch rates across the mapped read positions.
If the raw read end(s) had a mismatch rate higher than 10%, they were trimmed off using Seqtk (version 1.0-r31).
The tirmmed reads with Phred base qulaity ≦ 20 were filtered using Sickle (version 1.200).
The remaining reads were mapped to the mm9 genome assembly using Tophat (veriosn 2.0.6) with paramters "-i 52 -I 240764 --min-segment-intron 52 --max-segment-intron 240764 -g 5".
Base transcriptome assemblies were performed using Cufflinks (version 2.1.1) with defeault parameters for mapped reads.
Genome_build: mm9
Supplementary_files_format_and_content: gtf files were generated using Cufflinks (version 2.1.1).
 
Submission date Jul 28, 2016
Last update date May 15, 2019
Contact name Jin-Wu Nam
E-mail(s) jwnam@hanyang.ac.kr
Phone +82 2-2220-2428
Organization name Hanyang University
Department Department of Life Science
Street address Seongdong-Gu Hangdang-dong
City Seoul
ZIP/Postal code 133-791
Country South Korea
 
Platform ID GPL13112
Series (2)
GSE84946 Co-assembly of stranded and unstranded RNA-seq data improves coding and noncoding transcriptome maps
GSE97212 The Project for High-Confidence Coding and Noncoding Transcriptome Maps
Relations
Reanalyzed by GSE97211
BioSample SAMN05452818
SRA SRX1984829

Supplementary file Size Download File type/resource
GSM2254467_mESC_stranded_assembled.gtf.gz 4.6 Mb (ftp)(http) GTF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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