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Sample GSM4815737 Query DataSets for GSM4815737
Status Public on Oct 02, 2023
Title liver mitochondrial RNA, C57BL-NASH
Sample type SRA
 
Source name liver mitochondria
Organism Mus musculus
Characteristics strain: C57BL/6J
tissue: liver
age: post natal week 7
genotype: wild type-NASH
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.
 
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.
 
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 SAMN16351299
SRA SRX9234597

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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