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Sample GSM7500630 Query DataSets for GSM7500630
Status Public on Jul 07, 2024
Title BHK-21 cells, repRNA-v4, bio_rep 1, 1h
Sample type SRA
 
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
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.
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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model DNBSEQ-T7
 
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.
 
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 SAMN35807167
SRA SRX20728676

Supplementary file Size Download File type/resource
GSM7500630_RNAde1-1h_transcripts.txt.gz 853.0 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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