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Status |
Public on Jul 07, 2024 |
Title |
BHK-21 cells, expressing nsP4 in trans, biol rep 2 |
Sample type |
SRA |
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Source name |
kidney
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Organism |
Mesocricetus auratus |
Characteristics |
tissue: kidney cell line: BHK-21 cell type: fibroblast cells genotype: expressing nsP4 in trans treatment: No
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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.
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Extracted molecule |
total RNA |
Extraction protocol |
Each sample collected 300,000 cells for RNA isolation using TRIzol™ Reagent (Thermo Fisher Scientific, #15596018). All the 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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Data processing |
Cleaned paired-end 150 bp reads were aligned to the Mesocricetus auratus genome (GCF_017639785.1_BCM_Maur_2.0_genomic.fna) and the alphaviral RNA replication system genome using STAR 2.7.8a. Genome annotation (GCF_017639785.1_BCM_Maur_2.0_genomic.gtf) was downloaded from NCBI and edited to add the information of the alphaviral RNA replication system. Transcript abundances were estimated using featureCounts, and then normalized and statistically compared using DESeq2. Assembly: BCM_Maur_2.0 Supplementary files format and content: tab-delimited text files include raw transcript abundances estimated using featureCounts.
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Submission date |
Nov 06, 2022 |
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 |
|
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Platform ID |
GPL32830 |
Series (2) |
GSE217397 |
RNA sequencing of BHK-21 cells carrying alphaviral RNA replication system |
GSE235343 |
Replicative RNA enables directed evolution and Darwinian adaptation in mammalian cells |
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Relations |
BioSample |
SAMN31627067 |
SRA |
SRX18185085 |