|
| Status |
Public on Jul 29, 2019 |
| Title |
WT_24h |
| Sample type |
SRA |
| |
|
| Source name |
differentiated mES cells (control)
|
| Organism |
Mus musculus |
| Characteristics |
cell type: differentiated ES cells
genotype: Per2::Luciferase knock-in
hours after dexamethasone stimulation: 24
|
| Treatment protocol |
Cells were treated with 100 nM dexamethasone and frozen at the indicated time points.
|
| Growth protocol |
Mouse ES cells were seeded in low-attachment 96-well plates and cultured for 2 days for embryoid body EB formation. EBs were then plated onto gelatin-coated 24-well plates and cultured for 26 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA samples were prepared using RNeasy Mini Kit (Qiagen) with RNase-Free DNase Set (Qiagen). Total RNA from differentiated cells from three embryoid bodies were pooled and used for the analysis.
PolyA RNA selection, library construction using TruSeq RNA Sample Prep Kit v2, and sequencing were performed by Macrogen Japan (Kyoto) using Illumina NovaSeq6000 with 101-bp paired-end reads according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| 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.
After adaptor sequence trimming using Trimmomatic (version 0.36), the sequence reads were mapped to the mouse genome (GRCm38/mm10) using STAR (2.5.4b). To obtain reliable alignments, the reads with a mapping quality of less than 10 were removed by SAMtools. 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.
Genome_build: mm10
Supplementary_files_format_and_content: The bigWig files were normalized to display uniquely mapped reads per 10 million uniquely mapped reads with duplicates. Tab-delimited text files include RPKM values for each Sample.
|
| |
|
| Submission date |
Jan 25, 2019 |
| Last update date |
Jul 29, 2019 |
| 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) |
| GSE125696 |
REV-ERBa and REV-ERBb function as key factors regulating Mammalian Circadian Output |
|
| Relations |
| BioSample |
SAMN10822071 |
| SRA |
SRX5294358 |
