|
| Status |
Public on Jul 27, 2022 |
| Title |
Gluca3 |
| Sample type |
SRA |
| |
|
| Source name |
Primary hepatocyte
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/14
genotype: wild type
treatment: Glucagon-treated
|
| Treatment protocol |
described in growth protocol
|
| Growth protocol |
Primary hepatocyte were isolated with two step-digestion method (Charni-Natan, M. et al, STAR Protocol 2020). Primary hepatocytes were incubated with or without 10 ng/mL recombinant IL-13 (rIL-13) for 2 h at 37°C and then stimulated with 100 µM cAMP or 100 nM glucagon, with or without 10 ng/ml rIL-13 for 3 h at 37°C. Then, RNA were extracted.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from 10^6 primary hepatocytes were extracted using the RNeasy Plus Micro Kit (Qiagen).
Libraries were prepared using a TruSeq RNA Sample Prep Kit (Illumina, 20020594)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
Gluca3
|
| Data processing |
Sequencing was performed on the Illumina HiSeq 1500 platform using the TruSeq Rapid SBS Kit (Illumina, FC-402-4002) in the 50-base single-end mode.
The TopHat program (version 1.3.2 with default parameters) was used to align reads to a mouse reference genome (mm10).
Then, gene expression values were calculated as reads per kilobase of exon unit per million mapped reads using the Cufflinks program (version 2.0.2).
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph.gz
Supplementary_files_format_and_content: FPKMCuffDiff.xlsx
Supplementary_files_format_and_content: TagCountCuffDiff.xlsx
|
| |
|
| Submission date |
Nov 21, 2021 |
| Last update date |
Jul 27, 2022 |
| Contact name |
Masanori Fujimoto |
| E-mail(s) |
fujimoto212@gmail.com
|
| Organization name |
Chiba University
|
| Department |
Graduate School of Medicine
|
| Lab |
1. Department of Molecular Diagnosis, 2. Department of Endocrinology, Hematology and Gerontology
|
| Street address |
Inohana 1-8-1
|
| City |
Chiba-city |
| State/province |
Chiba-prefecture |
| ZIP/Postal code |
260-8677 |
| Country |
Japan |
| |
|
| Platform ID |
GPL18480 |
| Series (2) |
| GSE189282 |
Liver ILC2s suppress gluconeogenesis and limit blood glucose elevation through IL-13 signaling [bulkRNA-seq_Hepatocyte] |
| GSE189287 |
Liver ILC2s suppress gluconeogenesis and limit blood glucose elevation through IL-13 signaling |
|
| Relations |
| BioSample |
SAMN23375717 |
| SRA |
SRX13185564 |
