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Sample GSM4223691 Query DataSets for GSM4223691
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.
 
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.
 
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

Supplementary file Size Download File type/resource
GSM4223691_L104.neg.bw 42.0 Mb (ftp)(http) BW
GSM4223691_L104.pos.bw 42.6 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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