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Sample GSM1585275 Query DataSets for GSM1585275
Status Public on Apr 08, 2015
Title cjes001 P91
Sample type SRA
 
Source name Embryonic stem cells
Organism Callithrix jacchus
Characteristics age: P91
cell type: Embryonic stem cells
Extracted molecule total RNA
Extraction protocol RNA was isolated using Trizol Reagent according to instructions
Library preparation for RNA-Seq was performed using the TruSeq RNA Sample Preparation Kit (Illumina, Cat. N°RS-122-2002) starting from 500 ng of total RNA according to Illumina's instructions. Accurate quantitation of cDNA libraries was performed by using the QuantiFluor™ dsDNA System (Promega). The size range of final cDNA libraries was determined applying the DNA 1000 chip on the Bioanalyzer 2100 from Agilent (280 bp). The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq2000 following the manufacturer's protocols.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description ESCcjes001P91
Data processing Illumina Casava 1.8.2 software used for basecalling. Quality check was done via fastqc (v. 0.10.0, Babraham Bioinformatics)
The Alignment was performed using Bowtie2 v2.1.0 to mm10. Data were conversed and sorted by samtools 0.1.19 and reads per gene were counted via htseq version 0.5.4.p3. Data analysis was performed using R/Bioconductor (3.0.2/2.12) loading DESeq, gplots and goseq packages.
Candidate genes were filtered to a minimum of 2x fold change and FDR-corrected pvalue<0.05. For functional analysis gene ontology enrichment was tested accounting for gene length via R-package goseq.
Supplementary_files_format_and_content: Excel file containing read counts after normalization by DESeq2
 
Submission date Jan 14, 2015
Last update date May 15, 2019
Contact name Gabriela Salinas
E-mail(s) Gabriela.Salinas-Riester@medizin.uni-goettingen.de
Organization name Universitaetsmedizin Goettingen
Department Department of Pathology
Lab NGS Integrative Genomics
Street address Kreuzbergring 57
City Goettingen
State/province Lower-Saxony
ZIP/Postal code 37075
Country Germany
 
Platform ID GPL17712
Series (1)
GSE64966 Non-viral generation of marmoset monkey iPS cells by a six-factor-in-one-vector approach
Relations
BioSample SAMN03284351
SRA SRX842698

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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