Impact of EBV infection on B cells from tonsils cord blood and peripheral blood
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Michele Bernasconi
PROVIDER: E-MEXP-3582 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:We next sought to identify the transcriptional program that differentiates IL-9+Th2 cells from “conventional” Th2 cells. To this end, we selected representative Th1, Th17, Th2, and IL-9+Th2 clones (Figure 5A) and determined their transcriptome in the resting state and at different time points after activation using RNAseq. Peripheral Blood Mononuclear Cells (PBMC) were isolated by Ficoll-Plaque Plus (GE Healthcare, UK) density gradient centrifugation. Human CD4+ T cells were isolated from PBMC by EasySep positive selection kit (Stemcell Technologies) according to manufacturer’s instruction. Positively selected CD4+ T cells were washed with PBS and stained for subsequent Th cell subset sorting. Memory Th cell subsets were sorted to over 90% purity according to their expression of chemokine receptors from CD45RA-CD25-CD8-CD3+ cells: Th1(CXCR3+CCR8-CCR6-CCR4-), Th2 (CXCR3-CCR8-CCR6-CCR4+), Th17 (CXCR3-CCR8-CCR6+CCR4+), Th9 (CXCR3-CCR8+CCR6-CCR4+). Single cell Th subset clones were directly sorted into 96well plate according to their expression of chemokine receptors (see above). Single cell clones were expanded and maintained by periodic restimulation with PHA (phytohaemaglutinine, 1 µg/ml, Sigma-Chemicals) and irradiated allogenic feeder cells (5x104/well) in culture medium. T cells were polyclonally activated using beads coated with antibodies against CD3, CD2, and CD28 (T cell/bead = 2:1, human T cell activation/expansion Kit, Miltenyi). Cell cultures were sampled before activation (time 0h) and 2, 4, 6, 9, 12, 24, and 48 hours after activation.
2017-11-10 | E-MTAB-5739 | biostudies-arrayexpress
Project description:To investigate the role of PPAR-γ in human TH cells, transcriptional response of activated “TH9” clones to treatment with GW9662, a potent PPAR-γ antagonist was assessed. “TH9” cell clones were incubated with GW9662 for 48h and activated with αCD3/2/28 for 12 h. Transcriptomic profiling was performed by bulk RNA-seq. To generate TH9 clones, Peripheral Blood Mononuclear Cells (PBMC) were isolated by Ficoll-Plaque Plus (GE Healthcare, UK) density gradient centrifugation. Human CD4+ T cells were isolated from PBMC by EasySep positive selection kit (Stemcell Technologies) according to manufacturer’s instruction. Positively selected CD4+ T cells were washed with PBS and stained for subsequent TH cell subset sorting. Effector memory “TH9” cells (CXCR3-CCR8+CCR6-CCR4+) were sorted to over 90% purity according to their expression of chemokine receptors from CD45RA-CD25-CD8-CD3+ cells. Single cell “TH9” clones were directly sorted into 96well plate according to their expression of chemokine receptors (see above). Single cell clones were expanded and maintained by periodic restimulation with PHA (1 µg/ml, Sigma-Chemicals) and irradiated allogenic feeder cells (5x104/well) in culture medium.
2022-10-31 | E-MTAB-12197 | biostudies-arrayexpress
Project description:STAT3 is an immidiate regulator of Th17 differentiation. STAT3 difieciency downmodulate Th17 specific genes and Th17 responses. Therefore, we intend to identify genome wide targets of STAT3. We used microarrays to profile gene expression of STAT3 regulated genes during Th17 polarization. Total RNA was extracted from non-targeting and STAT3 siRNA treated Thp, Th0 and Th17 cell samples from different time points. Total RNA subjected to poly-A selection and hybridization on Affymetrix microarrays.
2017-05-03 | E-GEOD-67185 | biostudies-arrayexpress
Project description:Nine heterogeneous melanoma cell lines including D10 and WM115 were studied for cancer stem cell characteristics in vitro. D10 cell line was the only cell line expressing the cancer stem cell marker CD133. Thus, gene expression profiling on CD133+ and CD133- D10 cells was carried out using Affymetrix GeneChips Human Genome U133A 2.0.
2013-01-17 | E-MEXP-3542 | biostudies-arrayexpress
Project description:To study the effect of paracrine interleukin-9 (IL-9) on T helper cells, we incubated IL-9R+ T helper cells isolated from blood (5 samples) and skin (3 samples) with or without IL-9 for 12h and the transcriptome was analyzed by bulk RNA-seq.
2022-10-31 | E-MTAB-12204 | biostudies-arrayexpress
Project description:To test whether human in vitro primed Th9 cells recapitulate the core pathogenic Th2 cell phenotype, we differentiated naïve T cells into Th1 (IL-12), Th2 (IL-4), Th9 (IL-4+TGF-β), and iTreg (TGF-β). After 7 days transcriptomic profiling by bulk RNA-seq was performed.
2022-10-31 | E-MTAB-12199 | biostudies-arrayexpress
Project description:Studies correlating genetic variation to gene expression facilitate the interpretation of common human phenotypes and disease. As functional variants may be operating in a tissue-dependent manner, we performed gene expression profiling and association with genetic variants (SNPs) on three cell types of 85 individuals. After excluding 10 outlier individuals detected through principal component analysis, we detected cell type-specific genetic effects, with 69 - 80% of regulatory variants operating in a cell type-specific manner and identified multiple eQTLs per gene, unique or shared among cell types and positively correlated with the number of transcripts per gene. Cell type specific eQTLs were found at larger distances from genes and lower effect size similar to known enhancers. These data suggest that the complete regulatory variant repertoire can only be uncovered in the context of cell type specificity. Total RNA was extracted from fibroblasts, LCLs, and T-cells of the 85 unrelated individuals of the GenCord. Two one-quarter scale Message Amp II reactions (Ambion, Foster City, CA) were performed for each RNA extraction with 200 ng of total RNA. 1.5 μg of cRNA was hybridized to a commercial whole-genome expression array (WG-6 v3 Expression BeadChip, Illumina) to quantify transcript abundance. In total there were two technical replicates (labeling and hybridization) for each RNA sample.
2010-08-20 | E-GEOD-17080 | biostudies-arrayexpress
Project description:We investigated the mechanism of action of the HDAC inhibitor Givinostat in JAK2V617F cells. We confirm that the drug inhibits colony formation and proliferation and induces apoptosis at doses 2-3 fold lower in JAK2V617F (HEL, UKE1 and SET2) compared to JAK2 wild type cell lines (K562, KU812, THP1 and KG1). By global gene expression analysis, we observed 293 common genes in HEL and UKE1 modulated at 6 hour by Givinostat (179 up and 114 down), of which 8/8 were validated by RTQ-PCR. 25, 28 and 33 modulated genes are implicated in the regulation of proliferation, apoptosis and hematopoiesis, respectively. Interestingly, 9 genes, known to be deregulated in MPN (myeloproliferative neoplasms) patients cells, were normalized by Givinostat. The hematopoietic transcription factors NFE2 and C-MYB were downmodulated by the drug specifically in JAK2V617F cells, and ETS1 was upregulated in all cell lines, at both the RNA and protein levels. Modulation of NFE2 and C-MYB was JAK2 dependent, as shown by use of the JAK2 inhibitor AG490. Finally, we suggest that the inhibition of NFE2 and induction of ETS1, also observed in freshly isolated CD34+ cells from MPN patients, may be at least in part responsible for the observed inhibition of erythroid differentiation by the drug. Gene expression profiling, JAK2V617F cell lines, ITF2357. This series of microarray experiments contains the gene expression profiles of independent triplicates of HEL and UKE1 erythroleukemia cell lines bearing the JAK2V617F mutation, before and after ITF2357 treatment. 100 nanograms of total RNA were processed, and fragmented biotin-labelled single-stranded DNA target was hybridized to the GeneChip® Gene 1.0 ST array following the Affymetrix manufacturer's instructions.
2012-07-16 | E-GEOD-27615 | biostudies-arrayexpress
Project description:Time course of mRNA after 30 minutes of endurance exercise at simulated altitude of 4000 m in an untrained or six weeks trained state of six subjects. Time course of mRNA after 30 minutes of endurance exercise at simulated altitude of 4000 m in an untrained (1) or six weeks trained state (2) of six subjects (Hoxxx) Ho981: (1) GSM343213, GSM343214, GSM343215, GSM343216; (2) GSM343217, GSM343218, GSM343219, GSM343220 Ho982: (1) GSM343221, GSM343222, GSM343223, GSM343224; (2) GSM343225, GSM343226, GSM343227, GSM343228 Ho984: (1) GSM343229, GSM343230, GSM343231, GSM343232; (2) GSM343233, GSM343234, GSM343235, GSM343236 Ho994: (1) GSM343237, GSM343238, GSM343239, GSM343240; (2) GSM343241, GSM343242, GSM343243, GSM343244 Ho998: (1) GSM343245, GSM343246, GSM343247, GSM343248; (2) GSM343249, GSM343250, GSM343251, GSM343252 Ho996: (1) GSM343253, GSM343254, GSM343255, GSM343256 Keywords: time-course
2009-11-15 | E-GEOD-13623 | biostudies-arrayexpress
Project description:Global transcriptional analysis was used in order to understand functionality and applicability of in vitro DC models.
2013-03-15 | E-MEXP-3787 | biostudies-arrayexpress