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Status |
Public on Feb 27, 2020 |
Title |
L104_Liver_mRNA-seq |
Sample type |
SRA |
|
|
Source name |
Liver
|
Organism |
Mus musculus |
Characteristics |
tissue: Liver strain: C57BL/6J Sex: male chronic jet lag (cjl) conditions: LD period of cjl: 85 w
|
Growth protocol |
Male C57BL/6J mice exposed to the three light conditions for 65 weeks (aged 77 weeks) or 85 weeks (aged 97 weeks): LD-condition (light–dark condition with an 8:00–20:00 light period) and ADV-condition (8-h phase advance once every 4 days)
|
Extracted molecule |
total RNA |
Extraction protocol |
Tissue samples were homogenized in Invitrogen TRIzol reagent. RNA was extracted by using QIAGEN RNeasy columns as per manufacturer’s protocol. Poly(A)-enriched stranded RNA sequencing was carried out by Takara Bio, Japan, on Illumina HiSeq 2500 with 100-bp paired-end reads and by Macrogen Japan on Illumina NovaSeq 6000 with 101-bp paired-end reads.
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|
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
|
|
Data processing |
The Illumina sequencer generates raw images utilizing sequencing control software for system control and base calling through an integrated primary analysis software called RTA (Real Time Analysis). The BCL (base calls) binary is converted into FASTQ utilizing illumina package bcl2fastq. Trimmotatic (Version 0.38) was used to remove adaptor sequences (Bolger et al. 2014). Sequence reads were mapped to mouse genome mm10 with STAR (2.5.4b) (Dobin et al. 2013). To obtain reliable alignments, the reads with mapping quality less than 10 were removed by SAM tools (1.9) (Li et al. 2009). The University of California, Santa Cruz (UCSC) known canonical gene set (32,989 genes) was used for annotation, and the reads mapped to the exons were quantified using Homer (Heinz et al. 2010). The bigWig files were normalized to display uniquely mapped reads per 10 million uniquely mapped reads with duplicates. There are separate bigWig files for + and - genomic strands. Fragments Per Kilobase per Million mapped reads (FPKM) were calculated using HOMER Genome_build: mm10 Supplementary_files_format_and_content: bigWig and tab-delimited text files include and FPKM values for each Sample.
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|
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Submission date |
Dec 18, 2019 |
Last update date |
Feb 27, 2020 |
Contact name |
Kazuhiro Yagita |
E-mail(s) |
kyagita@koto.kpu-m.ac.jp
|
Organization name |
Kyoto Prefectural University of Medicine
|
Street address |
Kawaramachi-Hirokoji, Kamigyo-ku
|
City |
Kyoto |
ZIP/Postal code |
602-8566 |
Country |
Japan |
|
|
Platform ID |
GPL17021 |
Series (1) |
GSE142248 |
Chronic circadian misalignment accelerates immune senescence and abbreviates lifespan in mice |
|
Relations |
BioSample |
SAMN13620591 |
SRA |
SRX7405738 |