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Table 1 Lymphocytes and myeloid cells with significant effects of the factors of Isolate, TVclass, or WUR genotype based on xCell enrichment scores

From: Gene expression in tonsils in swine following infection with porcine reproductive and respiratory syndrome virus

Full name

dLSMa

SE

p-value

Cell group

KS06-NVSL

 Isolate

Class-switched memory B-cells

0.013

0.006

0.032

Lymphocytes

CD4+ central memory T-cells

0.003

0.002

0.098

Lymphocytes

Basophils

0.042

0.017

0.016

Myeloid cells

Plasmacytoid dendritic cells

− 0.003

0.002

0.099

Myeloid cells

High-Low

 TVclass

B-cells

0.021

0.012

0.081

Lymphocytes

CD8+ T-cells

0.011

0.006

0.059

Lymphocytes

Class-switched memory B-cellsc

0.017

0.005

0.004

Lymphocytes

Memory B-cells

0.009

0.004

0.042

Lymphocytes

naive B-cells

−0.004

0.002

0.048

Lymphocytes

Plasma cells

0.008

0.003

0.028

Lymphocytes

Type 1 T-helper cells

0.007

0.003

0.027

Lymphocytes

CD8+ naive T-cells

0.005

0.002

0.033

Lymphocytes

CD8+ central memory T-cellsc

0.021

0.007

0.003

Lymphocytes

Basophilsc

0.046

0.016

0.006

Myeloid cells

Activated dendritic cells

0.016

0.008

0.048

Myeloid cells

Plasmacytoid dendritic cells

0.005

0.002

0.020

Myeloid cells

Immune scoreb

0.021

0.010

0.034

 

AA-AB

 WUR

Type 1 T-helper cells

0.007

0.004

0.082

Lymphocytes

Plasmacytoid dendritic cells

0.005

0.002

0.056

Myeloid cells

  1. a Differences of least squared means (dLSM) between factor levels for cell enrichment scores: LSM for KS06 minus LSM for NVSL isolates; High minus Low tonsil viral class; AA minus AB WUR genotypes. Only estimates of significance (p < 0.1) for lymphocytes and myeloid cells and their subsets are shown based on the library size of the RNA-seq data
  2. b Immune score, as determined by the xCell software, is an aggregated score that considers B cells, CD4+ T cells, CD8+ T cells, dendritic cells, eosinophils, macrophages, monocytes, mast-cells, neutrophils, and natural killer cells
  3. cSignificant after multiple test correction