Transcriptome Analysis Reveals the Multiple Functions of pBD2 in IPEC-J2 Cells against E. coli
Abstract
:1. Introduction
2. Results
2.1. Analysis of Bactericidal Activity
2.2. Transcriptome Profiling
2.3. Characterization of Differentially Expressed Genes by RNA Sequencing
2.4. KEGG Analysis Revealed That Immune Responses of Cells Were Trigger by E. coli
2.5. KEGG Pathway Analysis Revealed That pBD2 Has Multiple Functions in IEPC-J2 Cells against E. coli
2.6. Comparison of pBD2 Effect with E. coli-Induced Transcriptome Changes
2.7. Validation of RNA-seq Data by qRT-PCR
3. Discussion
4. Materials and Methods
4.1. Strains and Cells
4.2. Preparation for pBD2
4.3. Bactericidal Activity
4.4. Cell Culture and Treatment
4.5. Library Preparation and Quality Control
4.6. Analysis of DEGs
4.7. qRT-PCR
4.8. Statistical Analysis
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Samples | Clean Reads | Clean Bases | GC Content | %≥Q30 |
---|---|---|---|---|
Control-1 | 35,369,943 | 10,533,069,694 | 52.27% | 94.10% |
Control-2 | 32,617,012 | 9,703,386,646 | 52.26% | 94.14% |
Control-3 | 31,534,327 | 9,375,721,120 | 52.35% | 94.31% |
E. coli-1 | 24,055,348 | 7,170,857,754 | 52.64% | 93.23% |
E. coli-2 | 25,929,754 | 7,718,143,996 | 52.37% | 93.55% |
E. coli-3 | 22,754,029 | 6,773,668,654 | 52.28% | 93.90% |
pBD2-1 | 20,721,673 | 6,176,881,268 | 51.76% | 93.46% |
pBD2-2 | 23,894,463 | 7,107,703,946 | 52.28% | 94.16% |
pBD2-3 | 21,228,755 | 6,327,976,062 | 51.94% | 93.67% |
Samples | Mapped Reads | Unique Mapped Reads | Multiple Map Reads |
---|---|---|---|
Control-1 | 67,898,715 (95.98%) | 66,065,506 (93.39%) | 1,833,209 (2.59%) |
Control-2 | 62,849,152 (96.34%) | 61,097,600 (93.66%) | 1,751,552 (2.69%) |
Control-3 | 60,714,671 (96.27%) | 59,081,017 (93.68%) | 1,633,654 (2.59%) |
E. coli-1 | 46,168,875 (95.96%) | 44,891,836 (93.31%) | 1,277,039 (2.65%) |
E. coli-2 | 49,843,598 (96.11%) | 48,508,765 (93.54%) | 1,334,833 (2.57%) |
E. coli-3 | 43,776,016 (96.19%) | 42,624,022 (93.66%) | 1,151,994 (2.53%) |
pBD2-1 | 39,790,781 (96.01%) | 38,760,294 (93.53%) | 1,030,487 (2.49%) |
pBD2-2 | 46,057,704 (96.38%) | 44,834,945 (93.82%) | 1,222,759 (2.56%) |
pBD2-3 | 40,692,378 (95.84%) | 39,483,201 (92.99%) | 1,209,177 (2.85%) |
KEGG Pathway | ID | Gene Name | Corrected p-Value |
---|---|---|---|
NF-kappa B signaling pathway | ko04064 | TNFAIP3, BIRC3, CXCL8, TICAM1, NFKBIA, ICAM1, PTGS2, BCL10, PLAU, NFKB1, RELB, NFKB2 | 0.00000127 |
TNF signaling pathway | ko04668 | TNFAIP3, MAP3K8, BIRC3, EDN1, NFKBIA, ICAM1, PTGS2, ENSSSCG00000008954, CXCL2, NFKB1, CCL20, BCL3 | 0.00000233 |
NOD-like receptor signaling pathway | ko04621 | TNFAIP3, BIRC3, CXCL8, NFKBIA, NFKBIB, NFKB1 | 0.014302364 |
Chemokine signaling pathway | ko04062 | FOXO3, RAC1, CXCL8, NFKBIA, NFKBIB, ENSSSCG00000008954, CXCL2, NFKB1, GNAI1, CCL20 | 0.014397446 |
Genes | Sequence (5′ → 3′) | Size (bp) | GenBank Number | |
---|---|---|---|---|
MX1 | Forward | GTTACCGGGACAGCGAGATT | 105 | NM_214061.2 |
Reverse | CATGACTGATTCCCACGCCT | |||
EGFR | Forward | AGGACGAAGCAACATGGTCA | 132 | NM_214007.1 |
Reverse | TGCATAGCACAGGTTTCGGT | |||
EIF2AK2 | Forward | CCCTGCACTTCTAGCCATCT | 121 | NM_214319.1 |
Reverse | CGACCACTGGCCATTTCTTTC | |||
PIK3R1 | Forward | CTTGAGTCGGGTGCTGGAAC | 164 | XM_021076847.1 |
Reverse | AACGCGTCCCTAACCGATTC | |||
PTEN | Forward | TGCAATCCTCAGTTTGTGGT | 224 | NM_001143696.1 |
Reverse | TCCTCTGGTCCTGGTATGAAG | |||
OAS2 | Forward | AGCCAGAGCAATGGGAAACT | 228 | NM_001031796.1 |
Reverse | GAGTTGCCCCTCAAGACTGT | |||
ATP6VOB | Forward | AACCCCAGCCTCTTCGTAAA | 100 | XM_021096834.1 |
Reverse | TCACTCTGGAGGTCTGAAGG | |||
RPL30 | Forward | GACAAGGTCCAATGTTCCCA | 110 | NM_001190178.1 |
Reverse | CCAACCTCTTTTGTAGCCGT | |||
NDUFA2 | Forward | TGCTAAGTGGCAAAGCCTG | 167 | XM_003124046.4 |
Reverse | GGTAGAGGGTGGAACAAGGAA | |||
NR4A1 | Forward | TGAGAAGGTTCCCGGCTTTG | 196 | ENSSSCG00000031321 |
Reverse | GATGCTGTCGATCCAGTCCC | |||
TUBA1B | Forward | TACTCACCTCGACTCTTAGC | 103 | NM_001044544.1 |
Reverse | GATGCACTCACGCATGG |
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Lian, S.; Lin, X.; Zhan, F.; Shen, X.; Liang, Y.; Li, C. Transcriptome Analysis Reveals the Multiple Functions of pBD2 in IPEC-J2 Cells against E. coli. Int. J. Mol. Sci. 2022, 23, 9754. https://doi.org/10.3390/ijms23179754
Lian S, Lin X, Zhan F, Shen X, Liang Y, Li C. Transcriptome Analysis Reveals the Multiple Functions of pBD2 in IPEC-J2 Cells against E. coli. International Journal of Molecular Sciences. 2022; 23(17):9754. https://doi.org/10.3390/ijms23179754
Chicago/Turabian StyleLian, Shaoqiang, Xiaqing Lin, Fengting Zhan, Xiaoyang Shen, Yu Liang, and Chunli Li. 2022. "Transcriptome Analysis Reveals the Multiple Functions of pBD2 in IPEC-J2 Cells against E. coli" International Journal of Molecular Sciences 23, no. 17: 9754. https://doi.org/10.3390/ijms23179754
APA StyleLian, S., Lin, X., Zhan, F., Shen, X., Liang, Y., & Li, C. (2022). Transcriptome Analysis Reveals the Multiple Functions of pBD2 in IPEC-J2 Cells against E. coli. International Journal of Molecular Sciences, 23(17), 9754. https://doi.org/10.3390/ijms23179754