|
Status |
Public on Nov 21, 2017 |
Title |
WT_rep2 |
Sample type |
SRA |
|
|
Source name |
wildtype
|
Organism |
Mus musculus |
Characteristics |
strain: C57BL/6N genotype: wildtype tissue: heart
|
Growth protocol |
Mice were housed in standard cages (45 cm × 29 cm × 12 cm) under a 12-hr light/dark schedule (lights on 7 a.m. to 7 p.m.) in controlled environmental conditions of 22 ± 2°C and 50 + 10% relative humidity and fed a normal chow diet (Rat & Mouse Chow, Specialty Foods) and water were provided ad libitum.
|
Extracted molecule |
total RNA |
Extraction protocol |
RNA was isolated from total hearts using the miRNeasy Mini kit (QIAGEN) incorporating an on-column RNase-free DNase digestion to remove all DNA. RNA sequencing was performed on total RNA from four control and four Lrpprc knockout mice using the Illumina HiSeq platform, according to the Illumina Tru-Seq protocol.
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
|
|
Data processing |
A transcriptome assembly was performed with RSEM v1.2.31 (--bowtie2 --strandedness reverse --paired-end) against the GENCODE vM13 transcript set combined with custom mitochondrial rRNA/mRNA sequences with an additional 50 adenine residues added to the 3′ ends to allow mapping of polyA tails. RSEM generated gene counts were imported and analysed for differential expression with tximport v1.4.0 and DESeq2 v1.16.1. Coverage profiles for each mitochondrial transcript were generated with bedtools v2.26.0. Genome_build: mm10 Supplementary_files_format_and_content: Tab-delimited txt files containing RSEM abundances are available on the samples record. DESeq normalized values and results are available on the series record.
|
|
|
Submission date |
Jul 03, 2017 |
Last update date |
May 15, 2019 |
Contact name |
Stefan J Siira |
Organization name |
The Kids Research Institute Australia
|
Department |
Precision Health
|
Lab |
Mitochondrial Medicine and Biology
|
Street address |
15 Hospital Ave, Nedlands
|
City |
Perth |
State/province |
Western Australia |
ZIP/Postal code |
6009 |
Country |
Australia |
|
|
Platform ID |
GPL13112 |
Series (2) |
GSE100732 |
LRPPRC-mediated folding of the mitochondrial transcriptome [RNA-seq] |
GSE100733 |
LRPPRC-mediated folding of the mitochondrial transcriptome |
|
Relations |
BioSample |
SAMN07311862 |
SRA |
SRX2978729 |