|
| Status |
Public on May 31, 2021 |
| Title |
Sample4: MDMXC462A NPC scRNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
liver
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype: Cre(+); Mdmx C642A(+/-)
cell type: Neural progenitor cells
scrna-seq: scRNA-Seq (10X Genomics)
treatment: acetaminophen treatment
|
| Treatment protocol |
Carbon tetrachloride (CCl4) (Sigma Aldrich) was delivered at 1 mg/kg (1:3 in corn oil) (Sigma-Aldrich) by a single intraperitoneal injection.
|
| Growth protocol |
C57BL/6J wild-type (WT) (The Jackson Laboratory, Stock No: 000664) and hepatocyte-specific MdmxC462A-knockin (Mdmx-KI) mice were used in the present study. Mdmx-KI mice were obtained by crossing MdmxC462A-floxed mice (the 11th exon of the Mdmx gene was floxed by two loxP sites) (Kuser-Abali et al., 2018) with albumin-Cre mice (The Jackson Laboratory, Stock No: 003574) on a C57BL/6J background. PCR-based genotyping was performed using the primer pairs listed in Supplementary Table 1. All mice were housed under a specific pathogen-free condition with a 12-h light/dark cycle. 7–10-week-old male mice were used for the experiments. All animal procedures were conducted in accordance with the Guidelines for the Care and Use of Laboratory Animals and were approved by the Harvard Medical Area Animal Care and Use Committee.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Liver nuclei were isolated for single cell analysis using the Nuclei PURE Prep kit (Sigma Aldrich) following manufacturer’s instructions. Isolated nuclei were stored at -80oC in nuclei PURE storage buffer (provided within the kit) until library preparation.
Libraries were prepared using NextSeq 500/550 kit following Illumina’s recommended protocol. The diluted denatured libraries were loaded onto a sequencing cartridge and then sequenced on the Illumina NextSeq 500.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Sample4
|
| Data processing |
10X Genomics' CellRanger pipeline
R Bioconductor package Seurat standard differential analysis
Genome_build: mm10 (pre-mRNA)
Supplementary_files_format_and_content: Final data format for the processed datais attached as an R data file (corrected for batch effects).
Supplementary_files_format_and_content: FASTQ files are uploaded for samples 1-6, which were run in duplicate (names are identical, but appended to avoid conflict in file name).
|
| |
|
| Submission date |
Aug 04, 2020 |
| Last update date |
May 31, 2021 |
| Contact name |
Zhi-Min Yuan |
| Organization name |
Harvard University
|
| Department |
Environmental Sciences
|
| Street address |
677 Huntington Ave.
|
| City |
Boston |
| State/province |
Massachusetts |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE155695 |
scRNA-Seq of MDMX C462A and wildtype mice treated with acetaminophen |
| GSE155696 |
Hepatic p53 protein level governs liver s sensitivity to drug-induced liver injury |
|
| Relations |
| BioSample |
SAMN15731015 |
| SRA |
SRX8886359 |
