|
| Status |
Public on Sep 16, 2020 |
| Title |
NASH liver-whole |
| Sample type |
SRA |
| |
|
| Source name |
Hepatic non-parenchymal cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Hepatic non-parenchymal cells
strain: C57BL/6 p16-CREERT2 ROS26-CMV-lsl-tdTomato
treatment: Fed with CDHFD for 6 months, 7m mouse
disease state: NASH
|
| Treatment protocol |
All the mice were sacrificed two weeks after the daily i.p. injection with 80 mg/kgBW tamoxifen for 5 days at designated age. For NASH induction, the mice were maintained on rodent diet with 45% kcal% fat without added choline (CDHFD) for 6 months.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The sorted cells were suspended in PBS, and then the single cell cDNA libraries were generated through following the protocol of Chromium Single Cell 3’GEM, Library & Gel Bead Kit v3.
scRNA libraries were prepared for sequencing using standard 10X Genomic protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
scRNA-derived cDNA library
Sacrificed two weeks after daily i.p. injection with TAM for 5 days
NASH 7m liver.h5ad
Merge for Kup and LSEC.h5ad
|
| Data processing |
CellRanger v3.0.2 software used for base-calling, UMI recognization, and sequence alignment to mm10 reference.
Low quality single cell transcriptomes were filtered out with low gene content (genes<200), low UMI counts (UMI<800), doublet (genes>7000), and high mitochondial gene content (<10% for liver, <40% for kidney) through scanpy 1.4.5.post1
The UMI counts were normalized and log transformed by scanpy
After UMAP visualization and leiden clustering (n_neighbors=10), the cluster-dependent ranking genes were calculated by log-regression method, which were used in the marker gene defined cell type identification.
Genome_build: mm10
Supplementary_files_format_and_content: h5ad file for anndata structure
|
| |
|
| Submission date |
Jul 27, 2020 |
| Last update date |
Sep 16, 2020 |
| Contact name |
Satotaka Omori |
| E-mail(s) |
satotaka.omori.r@gmail.com
|
| Phone |
0354495449
|
| Organization name |
the university of Tokyo
|
| Street address |
shirokanedai, 4-6-1
|
| City |
Minato ku |
| State/province |
tokyo |
| ZIP/Postal code |
108-0071 |
| Country |
Japan |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE155182 |
Single cell RNA seq of hepatic and renal p16 positive cells |
|
| Relations |
| BioSample |
SAMN15650974 |
| SRA |
SRX8831608 |
