Virus Expression Database

GSE53993

Comparative total RNA and mRNA sequencing and systems analysis reveals nascent transcriptional response to early HIV-1 infection in a CD4+ T cell line

Submitted by Michael Katze (University of Washington, USA) on Jan 10 2014

Platform: ngs – Illumina HiSeq 2000 (Homo sapiens)

Pubmed: 24850744

Summary To systematically investigate early host transcriptional response to HIV-1 infection, including polyadenylated and non-polyadenylated transcripts, we separately sequenced Total RNAs (Total RNA-seq) from HIV-1-infected SupT1 cells, a human CD4+ T cell line. We show many non-polyadenylated RNAs were also differentially expressed upon HIV-1 infection, as expected only detected by Total RNA-seq. Interestingly, we identified 8 times more differentially expressed genes at 12 hour post-infection by Total RNA-seq than by mRNA-seq, mostly protein-coding genes.

16 Samples

ID Title Cell Type Timepoint Reported Virus Virus Species Exclusion Reason
GSM1305142 HIV_12hr_rep1 helper T-lymphocyte  12 hrs HIV Human immunodeficiency virus 1
GSM1305143 HIV_12hr_rep2 helper T-lymphocyte  12 hrs HIV Human immunodeficiency virus 1
GSM1305144 HIV_12hr_rep3 helper T-lymphocyte  12 hrs HIV Human immunodeficiency virus 1
GSM1305145 HIV_24hr_rep1 helper T-lymphocyte  24 hrs HIV Human immunodeficiency virus 1
GSM1305146 HIV_24hr_rep2 helper T-lymphocyte  24 hrs HIV Human immunodeficiency virus 1
GSM1305147 HIV_24hr_rep3 helper T-lymphocyte  24 hrs HIV Human immunodeficiency virus 1
GSM1305148 Mock_12hr_rep1 helper T-lymphocyte  12 hrs Mock Uninfected
GSM1305149 Mock_12hr_rep2 helper T-lymphocyte  12 hrs Mock Uninfected
GSM1305150 Mock_12hr_rep3 helper T-lymphocyte  12 hrs Mock Uninfected
GSM1305151 Mock_24hr_rep1 helper T-lymphocyte  24 hrs Mock Uninfected
GSM1305152 Mock_24hr_rep3 helper T-lymphocyte  24 hrs Mock Uninfected
GSM1305153 UV_12hr_rep1 helper T-lymphocyte  12 hrs UV-inactivated virion Uninfected
GSM1305154 UV_12hr_rep2 helper T-lymphocyte  12 hrs UV-inactivated virion Uninfected
GSM1305155 UV_12hr_rep3 helper T-lymphocyte  12 hrs UV-inactivated virion Uninfected
GSM1305156 UV_24hr_rep1 helper T-lymphocyte  24 hrs UV-inactivated virion Uninfected
GSM1305157 UV_24hr_rep3 helper T-lymphocyte  24 hrs UV-inactivated virion Uninfected