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Sample GSM2692150 Query DataSets for GSM2692150
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

Supplementary file Size Download File type/resource
GSM2692150_55227.genes.results.txt.gz 1.1 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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