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Sample GSM6716704 Query DataSets for GSM6716704
Status Public on Jul 07, 2024
Title BHK-21 cells, expressing nsP4 in trans, biol rep 2
Sample type SRA
 
Source name kidney
Organism Mesocricetus auratus
Characteristics tissue: kidney
cell line: BHK-21
cell type: fibroblast cells
genotype: expressing nsP4 in trans
treatment: No
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 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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model DNBSEQ-T7
 
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.
 
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
 
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
Relations
BioSample SAMN31627067
SRA SRX18185085

Supplementary file Size Download File type/resource
GSM6716704_MCA187_nsP4_in_trans_biol_rep_2_transcripts.txt.gz 852.0 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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