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Status |
Public on Jul 07, 2024 |
Title |
BHK-21 cells, repRNA-v4, bio_rep 1, 3h |
Sample type |
SRA |
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|
Source name |
kidney
|
Organism |
Mesocricetus auratus |
Characteristics |
tissue: kidney cell line: BHK-21 cell type: fibroblast cells genotype: BHK-21 WT, transfected with repRNA-v4 treatment: No
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Treatment protocol |
10 µg of repRNA-v4 RNA was transfected into 4 million wildtype BHK-21 cells via electroporation. Samples were collected at 1-hour, 3-hour, and 12-hour time points for subsequent RNA-seq analysis.
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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, and 1% MEM Non-Essential Amino Acids Solution (Gibco, #11140050) in a humidified 37℃ incubator with 5% CO2.
|
Extracted molecule |
total RNA |
Extraction protocol |
Each sample collected about 500,000 cells for RNA isolation using TRIzol™ Reagent (Thermo Fisher Scientific, #15596018). 1 μg RNA was used for the construction of sequencing libraries. RNA libraries for RNA-seq were prepared using a VAHTS Universal V6 RNA-seq Library Prep Kit for MGI (Vazyme, #NRM604-2) following manufacturer's user guide.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
DNBSEQ-T7 |
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|
Description |
no
|
Data processing |
Cleaned paired-end reads were aligned to the Mesocricetus auratus genome (GCF_017639785.1_BCM_Maur_2.0_genomic.fna) and the genome of the alphaviral RNA replication system using STAR 2.7.8a. Genome annotation file (GCF_017639785.1_BCM_Maur_2.0_genomic.gtf) was downloaded from NCBI and edited to add the annotation information of the alphaviral RNA replication system. Transcript abundances were estimated using featureCounts, then normalized to RPKM using in-house R scripts. 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-delimited text files include raw transcript abundances estimated using featureCounts.
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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 |
GPL32830 |
Series (2) |
GSE235339 |
Measurement of the degradation rate of alphaviral RNA in BHK-21 cells |
GSE235343 |
Replicative RNA enables directed evolution and Darwinian adaptation in mammalian cells |
|
Relations |
BioSample |
SAMN35807166 |
SRA |
SRX20728677 |