|
| Status |
Public on Feb 13, 2018 |
| Title |
Tumor Kidney (Dox ON)_whole transcriptome_RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
Tumor Kidney (Dox ON)
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6 x DBA/2 F1
genotype/variation: Tet-OSKM/mPer2-luc
dox treatment: yes
tissue: Kidney
|
| Treatment protocol |
Doxycycline (Dox) treatment was performed as previously described (Ohnishi et al. 2014).
|
| Growth protocol |
Chimeric embryos were generated from Rosa26-M2rtTA TetO-OSKM mPer2-luc ESCs by injection into C57BL/6 x DBA/2 F1 hybrid blastocysts.
|
| 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.
Total RNA (0.25 μg) was depleted of ribosomal RNAs using Ribo-Zero Gold (Illumina). Sequencing libraries were constructed using a TruSeq Stranded Total RNA LT Sample Prep Kit according to the manufacturer’s instruction (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Dox+/ exons (Total: 33169818.0) RPKM
|
| Data processing |
Illumina bcl2fastq Conversion Software v2.17.1.14 was used for conversion into FASTQ files.
Trimmotatic was used to remove adaptor sequences (Bolger et al. 2014). Sequence reads were mapped to mouse genome mm10 with STAR (2.5.0c) (Dobin et al. 2013). To obtain reliable alignments, the reads with mapping quality less than 10 were removed by SAM tools (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 Reads Per Kilobase per Million mapped reads (RPKM) were calculated using HOMER (Heinz et al. 2010)
Genome_build: mm10
Supplementary_files_format_and_content: bigWig and tab-delimited text files include raw reads and RPKM values for each Sample.
|
| |
|
| Submission date |
Nov 22, 2017 |
| Last update date |
May 15, 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 |
GPL19057 |
| Series (1) |
| GSE107261 |
Disruption of circadian clockwork in in vivo reprogramming-induced mouse kidney tumors |
|
| Relations |
| BioSample |
SAMN08057451 |
| SRA |
SRX3415674 |
