|
| Status |
Public on Jul 13, 2021 |
| Title |
ctrl2 |
| Sample type |
SRA |
| |
|
| Source name |
Mouse HCC tissue
|
| Organism |
Mus musculus |
| Characteristics |
tissue: HCC tissue
strain: C57BL/6
age: 5 months
genotype: Miz1F/F
|
| Treatment protocol |
For different groups of mice (Miz1F/F, Miz1ΔHep), HCC was induced by the combination of DEN (25 mg/kg i.p.) given at Week 2 postpartum followed by weekly injections of CCl4 (0.5 ml/kg i.p., dissolved in corn oil). Mice were sacrificed at the age of 5 months
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Liver was digested and the cell suspension (300-600 living cells per microliter, determined by Count Star) was loaded onto the Chromium single cell controller (10xGenomics) to generate single-cell gel beads in the emulsion according to the manufacturer’s protocol
Single-cell RNA-seq libraries were constructed using 10xGenomics Single Cell 3’ Library Gel Bead Kit V2. Sequencing was performed on the Illumina HiSeq XTEN platform
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.8
Cellranger was utilized to calculate the raw counts and cell whitelist by default parameter
1. We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria: MT% < 20%; Cell Gene Number < Median Gene Number * 2; Cell Gene Number > 200. PCA and tSNE analysis was used for the single cell to cell relation description. Graphcluster and K-mean was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Genome_build: mm10
Supplementary_files_format_and_content: TXT file contain counts for each sample
|
| |
|
| Submission date |
Jan 02, 2020 |
| Last update date |
Jul 13, 2021 |
| Contact name |
Guangyan Zhangyuan |
| E-mail(s) |
[email protected]
|
| Phone |
8615895822018
|
| Organization name |
Ruijin Hospital, Shanghai Jiao Tong University School of Medicine
|
| Department |
Department of General Surgery, Pancreatic Disease Center
|
| Street address |
197 Ruijin Er Road
|
| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
200025 |
| Country |
China |
| |
|
| Platform ID |
GPL21273 |
| Series (1) |
| GSE142868 |
Miz1 Limits Tumor-promoting Function of Hepatocyte NF-κB independently of Its Transcriptional Activity in Chemical Hepatocarcinogenesis |
|
| Relations |
| BioSample |
SAMN13714325 |
| SRA |
SRX7494176 |
