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Sample GSM4509253

Query DataSets for GSM4509253

Status

Public on Jun 19, 2020

Title

con-2

Sample type

SRA

Source name

PK-15 cell line

Organism

Sus scrofa

Characteristics

cell line: PK-15
cell type: Kidney cell line
infection: Mock

Extracted molecule

total RNA

Extraction protocol

Total RNA was isolated using the Mini Best Universal RNA Extraction kit (Takara, Dalian, China).
rRNAs were depleted with RNA sample purification beads, which employ an RNaseH-based method. Then, the RNA was fragmented and reverse transcribed. The cDNA library was subjected to end repair, poly(A)-tailing, adaptor ligation, and PCR amplification of 12–15 cycles for sequencing library construction.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

HiSeq X Ten

Description

Negative Control
processed data file: Normalized dataset.xls

Data processing

Reads were trimmed to remove the bases with low quality and adapter sequences.
The trimmed reads were aligned to the pig reference genome using Hisat2.
Gene expression levels were quantified using the featureCounts.
Differentially expressed genes between NC and PCV2 infection group were selected by DESeq2 with Padj. <0.05 and fold change (FC) of >1.2 or <0.0.83.
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: Normalized dataset.xls: Excel file includes FPKM for each sample.

Submission date

May 01, 2020

Last update date

Jun 19, 2020

Contact name

Jin He

E-mail(s)

hejin@zju.edu.cn

Organization name

Zhejiang University

Street address

Yuhangtang Road No.866