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Sample GSM1371860 Query DataSets for GSM1371860
Status Public on Jul 13, 2016
Title NZB:C57 Liver rep1
Sample type SRA
 
Source name Liver
Organism Mus musculus
Characteristics strain: NZB
mitochondria: C57
tissue: liver
gender: male
age: 10 weeks old
Growth protocol Conplastic strains were obtained after 10 generations of backcrossing to create a new line harboring the nuclear genome of one strain and the mtDNA of another (C57BL/6 and NZB were purchased from Harlan Laboratories).
Extracted molecule polyA RNA
Extraction protocol Twelve 10-week-old males per genotype were killed by cervical decapitation and liver (median lobe) and heart (left ventricle) tissues were dissected and immediately frozen in liquid nitrogen. Total RNA was extracted with QIAzol Lysis Reagent and then purified on RNeasy spin columns (Qiagen). RNA integrity (RNA Integrity Score ≥ 7.9) and quantity were determined on the Agilent 2100 Bioanalyzer. RNA samples from different animals were mixed in equal proportion at four samples per pool, and three pools per genotype were analyzed in the Illumina Genome Analyzer IIx.
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer IIx
 
Description CN_1_Liver
Data processing Illumina RTA software v 1.13.48.0
Illumina2bam v:0.03
SamToFastq.jar v1.86
Reads were pre-processed with Cutadapt 1.2.1, To remove TruSeq adaptor.
Resulting reads were mapped on the mouse transcriptome (Ensembl gene-build GRCm38.v70) And genome, Using RSEM v1.2.3 and Bowtie2 v2.0.6.
Data were normalized using TMM with the Bioconductor package EdgeR
Data were batch corrected with Bioconductor package ComBat.R
Differential expression were tested using GLM with the Bioconductor package EdgeR
Genome_build: GRCm38.v70
Supplementary_files_format_and_content: matrix_table.txt file contains ENSEMBL gene Ids, TMM-Normalized counts per million for each sample.
 
Submission date Apr 21, 2014
Last update date May 15, 2019
Contact name Fatima Sanchez-Cabo
E-mail(s) fscabo@cnic.es
Phone +34 91 4531200
Organization name CNIC
Street address Melchor Fernandez Almagro
City Madrid
ZIP/Postal code 28029
Country Spain
 
Platform ID GPL11002
Series (1)
GSE56933 Mismatch between mtDNA and nuclear DNA determines metabolism and healthy aging
Relations
BioSample SAMN02730172
SRA SRX522686

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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