|
| Status |
Public on Jul 13, 2016 |
| Title |
BL/6J:NZB Liver mix3 |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
mitochondria: NZB
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 |
NC_mix3_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 |
SAMN02730168 |
| SRA |
SRX522676 |
