Background
Methods
Birds and viruses
Experiment design
RNA extraction and purification
cDNA library construction and sequencing
Data analysis
Confirmation of RNA-Seq data by quantitative real-time PCR
Primer | Sequence | Reference |
---|---|---|
VP2 | Sense: 5-AGACCCCATTCCCGCTAT-3 Anti-sense: 5-GCCTTGGACGCTTGTTTG-3 | - |
CCR2 | Sense: 5- ATGCCAACAACAACGTTTGA-3 Anti-sense: 5- TGTTGCCTATGAAGCCAAA-3 | [47] |
CCR4 | Sense: 5- CCTGGTCATTGTGGTCCTCT-3 Anti-sense: 5- TCCCACTGTAGAACCCAACC-3 | [47] |
IL-6 | Sense: 5-AAATCCCTCCTCGCCAATCTG-3 Anti-sense: 5-CCTCACGGTCTTCTCCATAAACG-3 | - |
IFN-γ | Sense: 5-ATCATACTGAGCCAGATTGTTTCG-3 Anti-sense: 5-CTTTCACCTTCTTCACGCCATC-3 | - |
MHC-I | Sense: 5-CTTCATTGCCTTCGACAAAG-3 Anti-sense: 5-GCCACTCCACGCAGGT-3 | [26] |
IL-15 | Sense: 5- ATGCTGGGGATGGCACA-3 Anti-sense: 5- GCACATAGGAAGAAGATGGTTAGT-3 | [46] |
Actin | Sense: 5-TTCACCACCACAGCCGAGAG-3 Anti-sense: 5-ACCACAGGACTCCATACCCAAG-3 | - |
Results
VP2 gene expression during IBDV infection in chickens
Identification of differentially expressed genes between the mock group and the infection group on day 1 and day 3
The host mainly displayed strong immune responses in the early stage of virus infection
Type | Term ID | Description | FDR |
---|---|---|---|
Biological process | GO:0044319 | wound healing, spreading of cells | 0.003661 |
Biological process | GO:0090504 | epiboly | 0.003661 |
Biological process | GO:0090505 | epiboly involved in wound healing | 0.003661 |
Molecular function | GO:0005544 | calcium-dependent phospholipid binding | 0.043024 |
Biological process | GO:0002237 | response to molecule of bacterial origin | 0.007461 |
Biological process | GO:0032496 | response to lipopolysaccharide | 0.041095 |
Biological process | GO:0051607 | defense response to virus | 0.012681 |
Molecular function | GO:0005125 | cytokine activity | 0.000213 |
Biological process | GO:0009615 | response to virus | 0.029828 |
Biological process | GO:0002252 | immune effector process | 0.001041 |
Biological process | GO:0098542 | defense response to other organism | 6.04E-05 |
Biological process | GO:0043207 | response to external biotic stimulus | 6.81E-05 |
Biological process | GO:0051707 | response to other organism | 6.81E-05 |
Biological process | GO:0009607 | response to biotic stimulus | 0.000108 |
Biological process | GO:0006955 | immune response | 3.68E-05 |
Biological process | GO:0006952 | defense response | 1.19E-05 |
Biological process | GO:0051704 | multi-organism process | 0.006676 |
Biological process | GO:0002376 | immune system process | 0.000423 |
Biological process | GO:0009605 | response to external stimulus | 0.028338 |
Biological process | GO:0006950 | response to stress | 0.004792 |
Molecular function | GO:0005488 | binding | 0.027882 |
ID | Description | Gene ID |
P-value |
---|---|---|---|
gga00480 | Glutathione metabolism | GPX2, ANPEP, HPGDS, GSTA, GSTA3, GGT1, MGST1, GSTK1, RRM2B, IDH1, GPX7, GPX8, GPX3, GSTT1L, MGST2, TXNDC12 | 1.69E-05 |
gga00982 | Drug metabolism - cytochrome P450 | ALDH1A3, HPGDS, GSTA, GSTA3, MGST1, GSTK1, MAOB,MAOA, GSTT1L, MGST2 | 0.023815 |
gga00520 | Amino sugar and nucleotide sugar metabolism | CHIA, GMPPB, GALK1, CMAS, GFPT1, GALE, TSTA3, PGM3, GNPNAT1, UAP1, PGM1, NANS, GNE, GMPPA | 0.001888 |
gga00030 | Pentose phosphate pathway | RGN, RBKS, RPIA, PGM1, ALDOB, IDNK, PFKL | 0.003885 |
gga00980 | Metabolism of xenobiotics by cytochrome P450 | ALDH1A3, HPGDS, GSTA, GSTA3, MGST1, GSTK1, EPHX1, GSTT1L, MGST2 | 0.0264181 |
gga04520 | Adherens junction | SMAD2, IGF1R, CTNNB1, ACTN4, YES1, SRC, EGFR, FGFR1, TJP1, CDH1, PVRL3, LMO7, INSR, MLLT4, BAIAP2, ERBB2, CTNND1, SNAI2 | 0.004207 |
gga00051 | Fructose and mannose metabolism | AKR1B10, SORD, GMPPB, AKR1B1, TSTA3, ALDOB, GMPPA, PFKL | 0.008313 |
gga04512 | ECM-receptor interaction | DAG1, LAMB2, VTN, ITGA6, COL1A2, LAMB1, LAMC2, ITGB4, COL4A5, ITGB6, LAMA5, LAMB3, LAMA3 | 0.0186877 |
gga04530 | Tight junction | CLDN5, CLDN3, CLDN4, CTNNB1, ACTN4, OCLN, MYH11, MYL9, YES1, YBX3, SRC, CTTN, MYH10, TJP1, IGSF5, SHROOM2, CLDN10, EPB41L1, JAM3, TJP3, MLLT4, LLGL2, SHROOM3, RAB3B, INADL, PARD6G | 0.00391 |
gga04510 | Focal adhesion | LAMB2, CAV1, KDR, IGF1R, VTN, CAPN2, CTNNB1, ACTN4, MYL9, ITGA6, COL1A2, BCL2, SRC, MYLK, LAMB1, EGFR, LAMC2, BCAR1, ITGB4, CAV2, COL4A2, PAK1, LAMA4, COL4A5, PARVA, DOCK1, ITGB6, ERBB2, LAMA5, LAMB3, LAMA3 | 0.0065603 |