|
| Status |
Public on Feb 08, 2023 |
| Title |
snATAC-seq_NC_3mo_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
whole liver
|
| Organism |
Mus musculus |
| Characteristics |
tissue: whole liver
strain: C57BL/6J
treatment: Normal chow for 3 months
|
| Treatment protocol |
C57BL/6J were fed normal chow or modified ALIOS diet for 3 months or 9 months
C57BL/6J were injected with AAV8-TBG-GFP or AAV-TBG-Ephb2 and fed normal chow for a week
|
| Growth protocol |
C57BL/6J mice were housed in the animal facility with 12h dark/light cycle (7:00am to 7:00pm) and ad libitum access to food and water
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For snRNA-seq and snATAC-seq, liver nuclei were isolated and loaded to 10X Genomics Chromium controller
For liver RNA-seq, RNA were extracted from whole liver using Trizol and Qiagen RNeasey Mini kit.
For Stellate Cell RNA-seq, RNA were extracted from stellate cells isolated from livers injected with AAV-TBG-GFP and AAV-TBG-Ephb2.
snRNAseq libraries were prepared according to manufacturer’s instructions of Chromium Next GEM Single Cell 3′ Kit
snATACseq libraries were prepared according to manufacturer’s instructions of Chromium Next GEM Single Cell ATAC kit
liver RNA-seq were submitted to Novogene for library preparation
Stellate Cell RNA-seq were prepared according to manufacturer’s instructions of KAPA RNA HyperPrep with RiboErase
snRNA-seq, snATAC-seq, bulk RNA-seq
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
snATACseq_3mo9mo_metadata.csv
|
| Data processing |
The raw fastq files of snRNA-seq were mapped to Mus musculus assembly GRCm38 (mm10) using CellRanger (3.0.2). Unique molecular identifiers (UMI) count matrices were imported into Seurat (3.2.0) (Stuart et al., 2019) to generate Seurat object to each experiment.
The raw fastq files of mouse livers and human livers were mapped to Mus musculus genome assembly GRCm38 (mm10) and Homo sapiens genome assembly GRCh38 (hg38) respectively using Cellranger-atac (1.2.0). The fragment count matrix was imported into ArchR
The raw fastq files of RNA-seq were mapped to Mus musculus assembly GRCm38 (mm10) using STAR (2.5.4) with --quantMode GeneCounts to generate gene count matrix. The matrix was imported into R package DEseq2 to quantify gene expression
Genome_build: mm10 and hg38
Supplementary_files_format_and_content: raw counts files and metadata of cell identity with assigned cluster identity for snRNA-seq; fragment counts files and metadata with assigned cluster identity for snATAC-seq; raw counts files and Deseq2 output for RNA-seq
|
| |
|
| Submission date |
Nov 26, 2021 |
| Last update date |
Feb 09, 2023 |
| Contact name |
Yang Xiao |
| E-mail(s) |
[email protected]
|
| Phone |
8323604597
|
| Organization name |
UNIVERSITY OF PENNSYLVANIA
|
| Street address |
12-193 Smilow Translational Research Center, 3400 Civic Center Boulevard
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE189600 |
Hepatocytes demarcated by EphB2 contribute to the progression of non-alcoholic steatohepatitis |
|
| Relations |
| BioSample |
SAMN23454406 |
| SRA |
SRX13234443 |
