|
Status |
Public on Apr 03, 2024 |
Title |
A15 |
Sample type |
SRA |
|
|
Source name |
Liver
|
Organism |
Mus musculus |
Characteristics |
tissue: Liver strain: C57BL/6J Sex: male genotype: Wild-type treatment: ADV
|
Treatment protocol |
After DD condition, mice were returned to normal light condition (8:00 to 20:00) and then divided into two groups of light-schedule conditions: LD-condition (light–dark condition with an 8:00–20:00 light period, n=19) and ADV-condition (8-h phase advance once every 4 days, n=23). Tissue sampling was done from 9:30 to 18:00 in 47 weeks after chronic jet lag condition when ADV mice were in the same light-dark cycle as LD mice with an 8:00–20:00 light period.
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Growth protocol |
Male C57BL/6J (10 weeks old) were purchased from SLC (Hamamatsu, Japan). Mice was housed separately in individual cages (170 × 350 × 145 mm) with a 120-mm diameter running wheel (SANKO, Osaka, Japan) in light-shield mouse housing boxes (1800 × 360 × 520 mm) at the room temperature of 25.0 ± 1.5 ºC with food and water available ad libitum. The light intensity was set at approximately 200 lx within the cages. The mice were entrained to a 12:12-h light-dark cycle with an 8:00–20:00 light period for 2 weeks and then housed in the constant darkness (DD) for 2 weeks.
|
Extracted molecule |
polyA RNA |
Extraction protocol |
Mouse livers were homogenized in TRIzol reagent (Thermo Fischer Scientific). Total RNA was extracted using RNeasy column (QIAGEN) according to the manufacturer’s instructions. Poly(A)-enriched stranded RNA sequencing was carried out using TruSeq stranded mRNA kit 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 NovaSeq 6000 |
|
|
Data processing |
Illumina bcl2fastq was used for conversion into Fastq files. Trimmotatic (version 0.39) was used to remove adaptor sequences (Bolger et al. 2014). Sequence reads were mapped to mouse genome mm10 with STAR (2.7.2) (Dobin et al. 2013). To obtain reliable alignments, the reads with mapping quality less than 10 were removed by SAM tools (1.7) (Li et al. 2009). 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. Raw reads and Fragments Per Kilobase per Million mapped reads (RPKM) were calculated using HOMER (v4.11) (Heinz et al. 2010) Assembly: mm10 Supplementary files format and content: bigWig and tab-delimited text files include raw read counts and FPKM values for each Sample.
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|
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Submission date |
Oct 16, 2023 |
Last update date |
Apr 03, 2024 |
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 |
GPL24247 |
Series (1) |
GSE245519 |
Inter-individual variations in circadian misalignment-induced NAFLD pathophysiology in mice |
|
Relations |
BioSample |
SAMN37849815 |
SRA |
SRX22106929 |