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Sample GSM6643107

Query DataSets for GSM6643107

Status

Public on Oct 01, 2023

Title

Vero cells, Group2, 0h, rep1

Sample type

SRA

Source name

kidney

Organism

Chlorocebus aethiops

Characteristics

tissue: kidney
cell line: Vero
cell type: epithelial cells
genotype: WT
treatment: 37℃ TrypLE treatment

Growth protocol

Vero cells were cultured in MEM medium supplemented with 10% fetal bovine serum at 37 °C in a humidified atmosphere with 5% CO2, and passaged when the cells were cultured to 90% density.

Extracted molecule

total RNA

Extraction protocol

RNA is extracted from cells using standard extraction methods, followed by strict quality control of RNA samples, mainly by Agilent 2100 bioanalyzer: precise detection of RNA integrity
RNA libraries for RNA-seq were prepared using NEBNext RNA Library Prep Kit for Illumina following manufacturer's protocols.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NovaSeq 6000

Data processing

Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/015/252/025/GCF_015252025.1_Vero_WHO_p1.0/GCF_015252025.1_Vero_WHO_p1.0_genomic.fna.gz
Supplementary files format and content: Excel files for Group 1 and Group 2 samples analysis

Submission date

Oct 15, 2022

Last update date

Oct 01, 2023

Contact name

Yunchao Huang

E-mail(s)

ychaohuang@bjmu.edu.cn

Organization name

Beijing Institute of Biological Products Company Limited

Street address

Boxing 2nd Road