|
| Status |
Public on Jul 27, 2022 |
| Title |
HepatocyteIL33 |
| Sample type |
SRA |
| |
|
| Source name |
primary hepatocyte
|
| Organism |
Mus musculus |
| Characteristics |
strain: BALB/c
genotype: wild type
celltype: primary hepatocyte from IL-33-treated mice
|
| Treatment protocol |
described in growth protocol
|
| Growth protocol |
Mice received daily i.p. injections of PBS or rIL-33 (0.5 µg) for 5 days. Primary hepatocyte were isolated with two step-digestion method and approximately 14000-16000 hepatocyte were loaded on ChIP G.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The cells were encapsulated into single droplets using Chromium Controller (10x Genomics) according to manufacturer's protocol.
Libraries were prepared using Chromium Single Cell 3' Reagent Kits v3.1 according to the manufacturer's protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
HepatocyteIL33
|
| Data processing |
Sequencing was performed using the Illumina Novaseq6000 on a paired-end read flow cell, and sequenced on R1 (10× barcode and the UMIs), followed by eight cycles of the I7 index (sample index) and 89 based on R2 (transcript).
The 10× Genomics Cell Ranger Single Cell Software was used for sample demultiplexing, alignment to the mouse reference genome (mm10), filtering, UMI counting, single-cell 3ʹ-end gene counting, and quality control, according to the manufacturer’s parameters.
Genome_build: mm10
Supplementary_files_format_and_content: barcodes.tsv.gz
Supplementary_files_format_and_content: features.tsv.gz
Supplementary_files_format_and_content: matrix.mtx.gz
|
| |
|
| 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 |
GPL24247 |
| Series (2) |
| GSE189286 |
Liver ILC2s suppress gluconeogenesis and limit blood glucose elevation through IL-13 signaling [scRNA-seq_Hepatocyte] |
| GSE189287 |
Liver ILC2s suppress gluconeogenesis and limit blood glucose elevation through IL-13 signaling |
|
| Relations |
| BioSample |
SAMN23375725 |
| SRA |
SRX13185584 |
