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Sample GSM4543942

Query DataSets for GSM4543942

Status

Public on May 12, 2020

Title

TP_B_12h

Sample type

SRA

Source name

LLC-PK1_TP_12h

Organism

Sus scrofa

Characteristics

cell line: LLC-PK1
cell type: porcine kidney cells
treatment: SVA-infected
time point: 12h

Extracted molecule

total RNA

Extraction protocol

Total RNAs from the SVA- and mock-infected groups were extracted using RNA extraction kit (#DR104-1) and the RNA of 4μg per sample was used in the construction of cDNA library using NEBNext® Ultra™ RNA Library Prep Kit for Illumina®.
RNA libraries were prepared for sequencing using standard Illumina protocols.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NovaSeq 6000

Data processing

Basecalls performed using Illumina Casava1.7 software
The raw sequencing reads are filtered by removing low quality reads, and clean reads were obtained. The clean reads was then mapped to the whole pig genome using HISAT2 software.
Expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced (FPKM) was used to evaluate the expression level of each gene and the fold-changes between different samples. The Pearson correlation coefficient (R2) was calculated to quantify the degree of correlation between repeated samples by using SPSS 19.0 software.
Genome_build: whole pig genome (https://www.ncbi.nlm.nih.gov/genome/?term=Sus+scrofa)
Supplementary_files_format_and_content: FPKM,expected number of Fragments Per Kilo base 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

Submission date

May 11, 2020

Last update date

May 13, 2020

Contact name

jing wang

E-mail(s)

wj229249720@126.com

Phone

13082565736

Organization name

Yangzhou university