RNA-seq characterizing a clonal human T cell line stably expressing doxycycline (dox)-inducbible constitutively active version of HSF1 (cHSF1). This cell line was treated with 1ug/mL dox or vehicle (water) for 18 hours (in biological quadruplicate) to modulate the proteostasis environment in a stress-independent manner.

CD4 T cells were isolated from PBMCs using Easy-SepTM Rosette Human CD4+ T cell enrichment kit (Stemcell Technologies, Canada). Isolated cells were activated with IL-2 and PHA for 5-7 days according to standard protocols. To minimize donor effects, activated T cells from four donors were pooled and activated CD4+ T cell-pools were treated either with 1.95 mM sodium butyrate or 0.04 mM bufexamac and cultured for 48 h. Untreated T cell-pools served as control. Subsequently, cells were harvested, washed with PBS, and RNA was isolated from trizol lysates of cells using Direct-zol RNA Miniprep Kit (Zymo Research) following manufacturer's instructions. Isolated RNA was additionally purified using Agencourt RNAClean XP beads (Beckman Coulter) following manufacturer's instructions. In total 3 independent samples of untreated, sodium butyrate treated , and bufexamac treated cells were generated. After quantification (Nanodrop), the RNA was quality controlled using a Bioanalyzer (Agilent Technologies). Good quality RNA (RIN > 7) was used to generate sequencing libraries by using 500 ng total RNA in a Sense mRNA Seq Libarary Prep Kit V2 for Illumina platforms (Lexogen) following manufacture's instructions. Libraries were quantified and subsequently sequenced on an Illumina HiSeq 1500 (sequencing mode: 100 nt, single-end). The sequencing data was preprocessed on a Galaxy server (hosted by LAFUGA, Gene Center, Munich). After demultiplexing, the data was trimmed according to Lexogen. The output was mapped to the human genome (hg19) using STAR (v. 2.5.2b-0). Abundant reads were further analyzed using HTSeq-count (v. 1.0.0) and a differential gene expression analysis was performed using DESeq (v. 1.0.19) setting the FDR < 0.01.

Non-naïve, resting CD4+ T cells were isolated from four HIV-1 infected individuals. The cells were treated with one of 5 different latency reversal agents or left unstimulated for 24 hurs. The RNA was extracted and used for RNAseq and CaptureSeq library generation. CaptureSeq was performed using custom designed probes from Arbor Biosciences.

RNA-seq of HIV-infected MDM and CD4 cells.

SupT1 cells were either infected with 1 µg/10^6 cells p24 equivalent of HIV_GFP virus or left uninfected, divided into aliquots of 5*106 cells/ tube and spinoculated for 90 minutes at 1500 g and 20°C to allow nearly universal infection. Cells were then resuspended at a concentration of 10^6 cells/ml and further incubated. At 12, 24 and 36h post–infection, RNA was extracted from each cellular sample and virus-containing supernatant and further processed for RNA-Seq to investigate gene expression, MeRIP-Seq and BS-Seq to investigate m6A and m5C epitranscriptomic marks.

mRNA profiles of from HIV+ Elite controller, HIV+ antiretroviral therapy (ART), HIV+ ART-naïve (or treatment-Naïve) and healthy control

Comparison of transcriptomic differences among monocyte-derived macrophages isolated from people without HIV and differentiated in the presence of PrEP (FTC and TDF)

Analysis of the behaviour of monocytes (as a compartment of innate immune system) from healthy volunteers and HIV positive donors in RPMI cell culture.

NGS transcriptome profiling using RNA-seq of PBMC speciments from a phase 1b trial in HIV-1 uninfected South Africans (HVTN 097), at baseline and days 1,3, and 7 post vaccination.

mRNA profiles of wildtype (WT), TNFα-stimulated (TNFα) and CHAF1A knockout (KO) J-Lat 10.6 cells. Wildtype J-Lat 10.6 cells were treated as control samples. Each group included replicates.

Primary CD4+ T cells from two healthy donors were mock treated with DMSO, with 2uM DDX3 inhibitor RK-33 or 1uM DDX3 inhibitor FH-1321. Cells were lysed and RNA was collected 4 hours and 18 hours post treatment and subjected to RNA-seq. The goal was to check what genes were differentially expressed upon DDX3 inhibition.

8 samples, 2 replicates each

RNA-seq characterizing a clonal SupT1 cell line stably expressing both the gene encoding XBP1s under control of the tetracycline repressor (tetR) and the gene encoding E. coli dihydrofolate reductase (DHFR) destabilizing domain fused to the active form of ATF6 (amino acid residues 1-373). These cells were treated with small molecules for 24 hours in quadruplicate to modulate the proteostasis environment in a stress-independent manner. The cells were treated with: 1) 0.1% DMSO for vehicle treatment condition, 2) 2 ug/mL doxycycline (dox) to activate XBP1s, 3) 10 uM trimethoprim (TMP) to activate ATF6, and 4) 2 ug/mL dox and 10 uM TMP to induce both XBP1s and ATF6 concomitantly.

Jurkat E6-1 & JLat9.2 CD4+ T cells were treated with 100IU/mL IFNb and sampled at 4 hours, 8 hours, and 12 hours post-treatment. An untreated "Mock" group for both Jurkat E6-1 & JLat9.2 CD4+ T cells were sampled at 4 hours.

Primary human CD4+ T cells (i.e., target cells) were isolated and infected with HI.fate (reporter) viruses. Cell populations were sorted by flow cytometry according to those supporting viral latency, active viral transcription, or control uninfected cells and their transcriptome was analyzed.

MRNA profiles of MDMs with or without HIV-1 infection