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Sample GSM7844349 Query DataSets for GSM7844349
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.
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.
 
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.
 
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

Supplementary file Size Download File type/resource
GSM7844349_A15.neg.bw 29.5 Mb (ftp)(http) BW
GSM7844349_A15.pos.bw 29.8 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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