Adaptive immune response that restrains ALV
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA824028 | ENA |
REPOSITORIES: ENA
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2017-10-04 | E-MTAB-5135 | biostudies-arrayexpress
Project description:Purpose: The goals of this study are to investigate the differentially expressed mRNAs and lncRNAs between ALV-J infected MDM and uninfected MDM in chickens by Illumina deep sequencing. Methods: Total RNA from two ALV-J-infected MDM (designated: J3h_1, J3h_2, J36h_1 and J36h_2) and two uninfected MDM samples (designated: NC3h_1, NC3h_2, NC36h_1 and NC36h_2) was isolated by TRIzol following the manufacturer’s instruction at 3 h post infection (hpi) and 36 hpi. RNA samples were subjected to Illumina deep sequencing by Illumina Hiseq 2000. Results:Compared to the uninfected control, a total of 1568 and 550 up-regulated genes were identified in chicken MDM at 3 hpi and 36 hpi respectively, and 1227 and 397 down-regulated genes were identified at 3 hpi and 36 hpi, respectively.128 and 30 DE lncRNAs were identified in MDM at 3 hpi and 36 hpi, respectively. Conclusions: Strong immune response induced by ALV-J infection in MDM at 3 hpi. Many genes, lncRNAs involved in immune response such as PRRs signaling pathway and Jak-STAT signaling pathway at 3 hpi. Specifically, 78 ISGs expression significantly increased in ALV-J-infected MDM at 3 hpi. We speculated that host innate immune response could inhibit ALV-J replication in chicken MDM. These results provide valuable insights into the game of host antiviral immune response and ALV-J infection.
2017-08-29 | GSE103207 | GEO
Project description:Purpose: The goals of this study are to investigate the differentially expressed miRNAs between ALV-J-infected primary monocyte-derived macrophages (MDM) and uninfected control by Illumina deep sequencing. Methods:Total RNA from two ALV-J-infected MDM (designated: J3h_1, J3h_2, J36h_1 and J36h_2) and two uninfected MDM samples (designated: NC3h_1, NC3h_2, NC36h_1 and NC36h_2) was isolated by TRIzol following the manufacturer’s instruction at 3 h post infection (hpi) and 36 hpi. RNA samples of two individuals within each group were pooled with equal amounts, and then were subjected to Illumina deep sequencing by Illumina Hiseq 2000. Results: compared to the uninfected MDM, we identified 13 significant up-regulated miRNAs and 2 significant down-regulated miRNAs in ALV-J infected MDM at 3 hpi, and 6 significant up-regulated miRNAs and 2 significant down-regulated miRNAs in ALV-J infected MDM at 36 hpi. Conclusions: Our results suggest that DE miRNAs involved in the immune response induced by ALV-J infection in MDM at 3 hpi. In addition, only 25 miRNAs-target DEGs were identified in MDM with ALV-J infection at 36 hpi, and these target DEGs can’t be significantly enriched in any GO terms and KEGG pathway..
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Project description:Purpose: The goals of this study are to investigate the differentially expressed genes between ALV-J infected (WRR+) and uninfected (WRR-)chickens spleens by Illumina deep sequencing. Methods: 140-day-old female chickens of White Recessive Rock (WRR) were confirmed as J subgroup avian leukosis virus (ALV-J) infection. Total RNA from three ALV-J-infected spleens (designated: WRR1+, WRR2+, WRR3+) and three uninfected normal spleen samples (designated: WRR1-, WRR2-, WRR3-) was isolated by TRIzol following the manufacturer’s instruction (Invitrogen, CA, USA). RNA samples of three individuals within each group were pooled with equal amounts, and then were subjected to Illumina deep sequencing by Illumina Genome Analyzer IIx. Results: Through raw data processed, 49,979,648 and 43,704,401 clean reads with an average length of 101 bp, which represented total residues of 4,859,084,087 and 4,238,826,168 bp, were obtained for WRR- and WRR+ libraries, respectively. Subsequently, the clean reads in the two libraries were assembled. Altogether, 121,493 contigs were assembled with an average length of 927 bp (ranged from 300 bp to 23,402 bp), leading to generation of 82,829 unigenes. The length of unigenes varied from 351 bp to 28,928 bp, with an average length of 1,155 bp. Based on the FPKM value of each gene, 252 DEGs were identified by DEGseq package using Benjamini-q-value of 0.05 as a cut-off. In ALV-J infected spleens, 90 genes showed up-regulated and 162 showed down-regulated expression when compared to uninfected samples. Conclusions: Our study represents the first time to elucidate the ALV-J infected chickens’spleens at the transcription level by RNA-seq technology. A total of 252 genes were found to be differentially expressed in ALV-J infected spleens when compared to uninfected chickens. These genes can be considered as candidates for further study ALV-J invasion. Spleen mRNA profiles of 140-day-old ALV-J infected (WRR+) and uninfected (WRR-) female chickens of White Recessive Rock were generated by deep sequencing, using Illumina Genome Analyzer IIx.
2014-11-15 | E-GEOD-63226 | biostudies-arrayexpress
Project description:Purpose: The goals of this study are to investigate the differentially expressed genes between ALV-J infected (WRR+) and uninfected (WRR-)chickens spleens by Illumina deep sequencing. Methods: 140-day-old female chickens of White Recessive Rock (WRR) were confirmed as J subgroup avian leukosis virus (ALV-J) infection. Total RNA from three ALV-J-infected spleens (designated: WRR1+, WRR2+, WRR3+) and three uninfected normal spleen samples (designated: WRR1-, WRR2-, WRR3-) was isolated by TRIzol following the manufacturer’s instruction (Invitrogen, CA, USA). RNA samples of three individuals within each group were pooled with equal amounts, and then were subjected to Illumina deep sequencing by Illumina Genome Analyzer IIx. Results: Through raw data processed, 49,979,648 and 43,704,401 clean reads with an average length of 101 bp, which represented total residues of 4,859,084,087 and 4,238,826,168 bp, were obtained for WRR- and WRR+ libraries, respectively. Subsequently, the clean reads in the two libraries were assembled. Altogether, 121,493 contigs were assembled with an average length of 927 bp (ranged from 300 bp to 23,402 bp), leading to generation of 82,829 unigenes. The length of unigenes varied from 351 bp to 28,928 bp, with an average length of 1,155 bp. Based on the FPKM value of each gene, 252 DEGs were identified by DEGseq package using Benjamini-q-value of 0.05 as a cut-off. In ALV-J infected spleens, 90 genes showed up-regulated and 162 showed down-regulated expression when compared to uninfected samples. Conclusions: Our study represents the first time to elucidate the ALV-J infected chickens’spleens at the transcription level by RNA-seq technology. A total of 252 genes were found to be differentially expressed in ALV-J infected spleens when compared to uninfected chickens. These genes can be considered as candidates for further study ALV-J invasion.
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