|
| Status |
Public on Jul 23, 2023 |
| Title |
WL1D3 |
| Sample type |
SRA |
| |
|
| Source name |
AB17
|
| Organism |
Mus musculus |
| Characteristics |
mouse strain: C57BL/6
genotype: Arid1af/f
tissue: liver
|
| Treatment protocol |
AB17 cells were infected with Ad-GFP or Ad-Cre, respectively. 48 hours after infection, GFP-positive cells were sorted by flow cytometer (BD FACSJazz).
|
| Growth protocol |
Primary hepatocytes were first isolated from Arid1af/f mice. Isolated cells were then immortalized with SV40LT-expressing lentivirus and then transformed by HrasV12D-expressing lentivirus to generate a cell line named AB17. The AB17 cells were cultured in DMEM medium supplied with 10% fetal bovin serum (FBS) and 100 µg/ml penicillin-streptomycin at 37℃ in a humidified incubator with 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Single cell was captured by the 10-17 µm C1 Single-Cell Auto Prep System (Fluidigm).
Sequencing libraries were constructed using SMARTer (Clontech) whole-transcriptome amplification (WTA) on 73 Ad-GFP infected cells and 76 Ad-Cre infected cells, according to the manufacturer’s instruction. An ERCC Spike-in mix (Ambion) was used as the technical control.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
infected with Ad-GFP
|
| Data processing |
Raw sequencing reads were trimmed by Trimmomatic (v0.36) to remove adapters and low quality sequences.
The filtered reads were aligned to the Mus musculus genome GRCm38 UCSC annotated transcripts via Tophat (v2.1.0) with default parameters.
HTSeq (v0.8.0.) was used for transcripts counting for the subsequent statistical analyses were based on negative binomial distribution which requires integer counts. ERCC expressions were used to remove unwanted variation using R Bioconductor package RUVSeq (v1.16.0).
Genome_build: GRCm38
Supplementary_files_format_and_content: counts
|
| |
|
| Submission date |
Nov 25, 2019 |
| Last update date |
Jul 23, 2023 |
| Contact name |
Ze-guang Han |
| E-mail(s) |
hanzg@sjtu.edu.cn
|
| Organization name |
Shanghai Jiao Tong University
|
| Department |
Shanghai Center for Systems Biomedicine
|
| Street address |
800 Dongchuan Road
|
| City |
Shanghai |
| ZIP/Postal code |
200240 |
| Country |
China |
| |
|
| Platform ID |
GPL21273 |
| Series (2) |
| GSE140924 |
Identification of the dedifferentiation trajectory of the cells without Arid1a using single cell RNA-seq |
| GSE140925 |
Arid1a in mouse embryonic cells |
|
| Relations |
| BioSample |
SAMN13382239 |
| SRA |
SRX7212858 |
