|
| Status |
Public on Jul 07, 2024 |
| Title |
BHK-21 cells, expressing nsP4 in trans, harboring repRNA-v4 RNA, |
| Sample type |
SRA |
| |
|
| Source name |
kidney
|
| Organism |
Mesocricetus auratus |
| Characteristics |
tissue: kidney
cell line: BHK-21
cell type: fibroblast cells
genotype: harboring repRNA-v4 RNA and expressing nsP4 in trans
treatment: No
|
| Treatment protocol |
No treatment
|
| Growth protocol |
BHK-21 cells were cultivated in Minimum Essential Medium with Earle's Balanced Salts (MEM/EBSS) supplemented with 10% fetal bovine serum (FBS), 100 units/mL penicillin, 100 μg/ml streptomycin, 1% MEM Non-Essential Amino Acids Solution (Gibco, #11140050) and 10 μg/ml puromycin in a humidified 37℃ incubator with 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
After removing the culture medium, the cells were washed once with DPBS and then digested with trypsin for 3 minutes. The digestion was terminated by adding culture medium containing 10% serum, and the cells were then dispersed by pipetting. Subsequently, the cells were centrifuged at 1000 rpm for 3 minutes, and the pellet was washed twice with cold DPBS containing 0.05% BSA. Finally, the cells were resuspended in DPBS containing 0.05% BSA.
The library was constructed following the manufacturer's instructions for the Chromium Next GEM Single Cell 5' Kit v2 from 10x Genomics.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
10x Genomics
|
| Data processing |
Cleaned reads were demultiplexed, barcode processed, gene counted using the Cell Ranger software v4.0.0. against the Mesocricetus auratus genome (GCF_017639785.1_BCM_Maur_2.0_genomic.fna) and the genome of alphaviral RNA replication system. The genome annotation file (GCF_017639785.1_BCM_Maur_2.0_genomic.gff) was downloaded from NCBI and modified to include annotation about the genome of the alphaviral RNA replication system. Subsequent analyses were performed using the Seurat package with default or recommended parameters.
Assembly: Mesocricetus auratus genome (GCF_017639785.1_BCM_Maur_2.0_genomic.fna) and the genome of the alphaviral RNA replication system
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: fa and gtf files for the alphaviral RNA replication system
|
| |
|
| Submission date |
Jun 20, 2023 |
| Last update date |
Jul 07, 2024 |
| Contact name |
Yihan Lin |
| E-mail(s) |
yihan.lin@pku.edu.cn
|
| Organization name |
Peking University
|
| Street address |
No.5 Yiheyuan Road, Haidian
|
| City |
Beijing |
| ZIP/Postal code |
10087 |
| Country |
China |
| |
|
| Platform ID |
GPL28997 |
| Series (2) |
| GSE235341 |
Single cell RNA-seq of BHK-21 cells carrying alphaviral RNA replication system |
| GSE235343 |
Replicative RNA enables directed evolution and Darwinian adaptation in mammalian cells |
|
| Relations |
| BioSample |
SAMN35808184 |
| SRA |
SRX20728746 |
