|
| Status |
Public on Sep 26, 2019 |
| Title |
HFD-PC |
| Sample type |
SRA |
| |
|
| Source name |
parietal cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: stomach
cell type: parietal
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared from sorted cells by using an AllPrep DNA/RNA Micro Kit (Qiagen), and then treated with DNase I. Ribosomal RNA (rRNA) was removed from total RNA using Low Input RiboMinus Eukaryote System v2 (Life Technologies).
RNA-seq libraries were prepared for sequencing using Ion Total RNA-Seq Kit v2 and multiplexed by using Ion Xpress™ RNA-seq Barcoding 01-16 Kit according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
| |
|
| Data processing |
Sequenced reads were mapped to mm10 whole genome using Torrent Suite Software version 4.0.2.
Fragments Per Kilobase of exon per Megabase of library size (RPKM) were calculated using Strand NGS v2.8 Software.
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph files were generated using bedtools version 2.25.0; tab-delimited text files include RPKM values for each gene;
|
| |
|
| Submission date |
Oct 04, 2016 |
| Last update date |
Sep 26, 2019 |
| Contact name |
noriko nishi |
| Organization name |
Axiohelix Co. Ltd.
|
| Street address |
5-11 hakozaki 5F Yunibasaru Bldg
|
| City |
tyuo-ku |
| State/province |
Tokyo |
| ZIP/Postal code |
103-0015 |
| Country |
Japan |
| |
|
| Platform ID |
GPL18635 |
| Series (1) |
| GSE87594 |
Transcriptome Analysis of parietal cells isolated from high fat diet (HFD)-fed mice by using Next Generation Sequencing |
|
| Relations |
| BioSample |
SAMN05860835 |
| SRA |
SRX2209227 |
