| Literature DB >> 24642186 |
Abstract
BACKGROUND: Feline immunodeficiency virus (FIV) is a widespread pathogen of the domestic cat and an important animal model for human immunodeficiency virus (HIV) research. In contrast to HIV, only limited information is available on the transcriptional host cell response to FIV infections. This study aims to identify FIV-induced gene expression changes in feline T-cells during the early phase of the infection. Illumina RNA-sequencing (RNA-seq) was used identify differentially expressed genes (DEGs) at 24 h after FIV infection.Entities:
Mesh:
Year: 2014 PMID: 24642186 PMCID: PMC3999937 DOI: 10.1186/1743-422X-11-52
Source DB: PubMed Journal: Virol J ISSN: 1743-422X Impact factor: 4.099
Figure 1Quantification of FIV provirus DNA in infected T-cells. Numbers of FIV DNA copies per cell at 8 and 24 hpi were determined by qPCR.
Numbers of Illumina sequencing reads per replicate sample
| 1 | Mock | 46,309,391 | 45,147,168 | 27,254,153 | 0 |
| 2 | Mock | 53,685,029 | 52,542,136 | 31,599,152 | 0 |
| 3 | Mock | 57,062,177 | 56,196,638 | 34,375,083 | 0 |
| 4 | Mock | 52,365,374 | 51,444,090 | 31,300,419 | 0 |
| 5 | FIV 24 hpi | 42,631,408 | 40,486,522 | 24,221,149 | 78,104 |
| 6 | FIV 24 hpi | 43,382,804 | 42,296,304 | 24,862,708 | 108,985 |
| 7 | FIV 24 hpi | 46,555,404 | 45,552,109 | 27,350,225 | 85,229 |
| 8 | FIV 24 hpi | 48,539,624 | 47,351,395 | 27,513,918 | 133,436 |
List of top 20 most significantly regulated genes
| OASL | 3.438 | 8.558 | 10.340 | 2.82E-07 | Yes |
| ACHE | 2.618 | 8.011 | 9.400 | 2.16E-06 | Yes |
| DHX58 | 2.578 | 11.431 | 12.797 | 4.98E-06 | No |
| DDX58 | 2.842 | 7.276 | 8.783 | 6.51E-06 | No |
| TGM2 | 5.425 | 4.792 | 7.231 | 8.45E-06 | Yes |
| HMGN2 | -2.061 | 12.013 | 10.969 | 9.68E-05 | Yes |
| CDKN1A | 2.083 | 9.092 | 10.152 | 1.40E-04 | Yes |
| ZFP36 | 2.040 | 7.806 | 8.834 | 2.98E-04 | Yes |
| BCL6 | 2.102 | 3.744 | 4.817 | 3.32E-04 | Yes |
| ASB2 | 5.465 | 3.050 | 5.500 | 3.72E-04 | No |
| CSF1 | 2.042 | 7.056 | 8.087 | 3.91E-04 | Yes |
| FITM1 | 2.082 | 2.227 | 3.286 | 4.69E-04 | No |
| IFI44 | 2.587 | 4.470 | 5.841 | 1.75E-03 | Yes |
| TP53INP1 | 2.226 | 4.988 | 6.143 | 1.77E-03 | No |
| BMF | 2.281 | 3.717 | 4.907 | 1.85E-03 | No |
| SPINK4 | -2.896 | 3.157 | 1.623 | 2.28E-03 | No |
| HSPE1 | 2.985 | 3.005 | 4.583 | 3.20E-03 | No |
| COA1 | -2.516 | 3.559 | 2.227 | 3.54E-03 | No |
| CXCL11 | 3.130 | 0.750 | 2.396 | 4.16E-03 | Yes |
| ERBB2 | 2.312 | 1.123 | 2.333 | 5.42E-03 | No |
Most significantly regulated genes in FIV infected cells at 24 hpi as detected by RNA-seq. Fold changes were obtained by comparison of the mean read counts of FIV vs. mock infected cells. Genes were ranked according to the p-values.
Figure 2Validation of 10 selected DEGs by RT-qPCR and comparison with RNA-sequencing. RT-qPCR gene expression levels at 8 and 24 hpi were compared to mock infected cells. Fold changes were obtained by merging the mean values of 4 replicates for each time point, previously normalized to the expression of the 3 reference genes ABL, B2M and RSP7. Stars indicate significant (p < 0.05) expression changes.