|
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.
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|
|
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
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|
|
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 |