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Status |
Public on Oct 02, 2023 |
Title |
liver mitochondrial RNA, C57BL-ob |
Sample type |
SRA |
|
|
Source name |
liver mitochondria
|
Organism |
Mus musculus |
Characteristics |
strain: C57BL/6J tissue: liver age: post natal week 7 genotype: B6.Cg-Lepob/J
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was extracted using QIAGEN miRNeasy Mini Kit (Qiagen) with manufacturer's instructions. Total RNA obtained from each sample was subjected to a sequencing library construction using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs, MA) with NEBNext rRNA Depletion Kit (Human/Mouse/Rat) according to the manufacturer’s protocols.
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|
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
|
|
Data processing |
Basecalls performed using bcl2fastq v2.20. Sequencing adaptors, low quality reads, and bases were trimmed with Trimmomatic-0.32 tool. The sequence reads were aligned to the Mouse reference genome (mm10) using Tophat2-2.1.1 (Bowtie2-2.3.2). The read counts allocated for each gene and transcript (Ensembl Genes 2013.4.3) were quantified using a Trimmed Mean of M-value (TMM) method using StrandNGS 3.1 software (Agilent Technologies, Santa Clara, CA). Genome_build: mm10 Supplementary_files_format_and_content: An excel format file (XLSX) includes TMM quantification values and Ensembl gene annotations of all samples.
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|
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Submission date |
Oct 02, 2020 |
Last update date |
Oct 02, 2023 |
Contact name |
Yoshimi Homma |
E-mail(s) |
yoshihom@fmu.ac.jp
|
Organization name |
Fukushima Medical University School of Medicine
|
Department |
Biomolecular Research
|
Street address |
1 Hikariga-oka
|
City |
Fukushima |
ZIP/Postal code |
9601295 |
Country |
Japan |
|
|
Platform ID |
GPL19057 |
Series (1) |
GSE158914 |
Comparative analysis of liver mitochondrial ncRNA in metabolic disease model mice. |
|
Relations |
BioSample |
SAMN16351300 |
SRA |
SRX9234596 |