TOP TEN perturbations for 39942_at (Homo sapiens)

Organism: Homo sapiens
Gene: 39942_at
Selected probe(set): 205965_at
Platform: Affymetrix Human Genome U133 Plus 2.0 Array

Expression of 39942_at (205965_at) across 6674 perturbations tested by GENEVESTIGATOR:

EBNA2 overexpr. study 1 (4h) / control virus transfected EREB2-5 cell sample (24h)

Relative Expression (log2-ratio):3.6417418
Number of Samples:3 / 3
Experimental EBNA2 overexpr. study 1 (4h)
EREB2-5 cell line stably transfected with the chimeric Epstein-Barr virus-encoded nuclear antigen 2 (EBNA2) and control expression plasmid coding for bacterial chloramphenicol acetyltransferase (CAT) gene and . CAT was used as a negative control. Briefly, before the CAT and EBNA2 induction, cells were maintained in RPMI media and deprived of estrogen for 3 days before doxycycline and estrogen was added. Expression of EBNA2 was induced after addition of estrogen and expression of CAT was induced by the addition of doxycycline to a final concentration of 100 ng/mL medium. Doxycycline induced cells were harvested 4 hours after induction. Because EBNA2 is essential for the proliferation of EBV-infected cells, EREB2-5 cells grow only in the presence of estrogen. Before the preparation of RNA, NGFR cells were purified by MACS separation to enrich the cells with a transcriptional response to doxycycline.
Control control virus transfected EREB2-5 cell sample (24h)
EREB2-5 cell line stably transfected with control expression plasmid coding for bacterial chloramphenicol acetyltransferase (CAT) gene. CAT was used as a negative control. Briefly, before the CAT induction, cells were maintained in RPMI media and deprived of estrogen for 3 days before doxycycline was added. Expression of CAT was induced by the addition of doxycycline to a final concentration of 100 ng/mL medium. Doxycycline induced cells were harvested 24 hours after induction. Estrogen withdrawal leads to the inactivation of EBNA2, resulting in cell cycle arrest. Before the preparation of RNA, NGFR cells were purified by MACS separation to enrich the cells with a transcriptional response to doxycycline.

dendritic cell study 6 (gardiquimod; RN486) / dendritic cell study 6 (CpG A; RN486)

Relative Expression (log2-ratio):3.637352
Number of Samples:4 / 4
Experimental dendritic cell study 6 (gardiquimod; RN486)
Plasmacytoid dendritic cells (pDCs) collected from blood of healthy donors and treated with gardiquimod (TLR7 agonist) and RN486 (Bruton’s tyrosine kinase; BTK inhibitor) for 3 hours. pDCs were sorted as CD303+, CD123+, CD45+, CD69+, CD40+, CD86+.
Control dendritic cell study 6 (CpG A; RN486)
Plasmacytoid dendritic cells (pDCs) collected from blood of healthy donors and treated with CpG-A ODN2216 Class A (TLR9 agonist) and RN486 (Bruton’s tyrosine kinase; BTK inhibitor) for 3 hours. pDCs were sorted as CD303+, CD123+, CD45+, CD69+, CD40+, CD86+.

dendritic cell study 6 (gardiquimod) / dendritic cell study 6 (untreated)

Relative Expression (log2-ratio):3.5478945
Number of Samples:7 / 8
Experimental dendritic cell study 6 (gardiquimod)
Plasmacytoid dendritic cells (pDCs) collected from blood of healthy donors and treated with gardiquimod (TLR7 agonist) for 3 hours. pDCs were sorted as CD303+, CD123+, CD45+, CD69+, CD40+, CD86+.
Control dendritic cell study 6 (untreated)
Plasmacytoid dendritic cells (pDCs) collected from blood of healthy donors. pDCs were sorted as CD303+, CD123+, CD45+, CD69+, CD40+, CD86+.

dendritic cell study 6 (gardiquimod; RN486) / dendritic cell study 6 (untreated)

Relative Expression (log2-ratio):3.4586544
Number of Samples:4 / 8
Experimental dendritic cell study 6 (gardiquimod; RN486)
Plasmacytoid dendritic cells (pDCs) collected from blood of healthy donors and treated with gardiquimod (TLR7 agonist) and RN486 (Bruton’s tyrosine kinase; BTK inhibitor) for 3 hours. pDCs were sorted as CD303+, CD123+, CD45+, CD69+, CD40+, CD86+.
Control dendritic cell study 6 (untreated)
Plasmacytoid dendritic cells (pDCs) collected from blood of healthy donors. pDCs were sorted as CD303+, CD123+, CD45+, CD69+, CD40+, CD86+.

monocyte activation study 1 (NOD2L/TLR/1L; 6h) / untreated monocyte sample (6h)

Relative Expression (log2-ratio):3.3908176
Number of Samples:5 / 5
Experimental monocyte activation study 1 (NOD2L/TLR/1L; 6h)
Monocytes were isolated from five healthy donors, cultured in RPMI with 10% vitamin D–sufficient (100 nM) human serum and activated for 6 hours with 1 ug/ml muramyl dipeptide (nucleotide-binding oligomerization domain-containing protein 2 ligand, NOD2L) and 1 ug/ml mycobacterial 19-kDa triacylated lipopeptide (TLR2/1 ligand, TLR2/1L). This type of activation is via nucleotide-binding oligomerization domain-containing protein 2 (NOD2) and heterodimeric Toll-like receptor 2 and Toll-like receptor 1 (TLR2/1).
Control untreated monocyte sample (6h)
Monocytes were isolated from five healthy donors, cultured in RPMI with 10% vitamin D–sufficient (100 nM) human serum and collected after 6 hours for RNA isolation.

monocyte activation study 1 (TLR/1L; 6h) / untreated monocyte sample (6h)

Relative Expression (log2-ratio):2.9687386
Number of Samples:5 / 5
Experimental monocyte activation study 1 (TLR/1L; 6h)
Monocytes were isolated from five healthy donors, cultured in RPMI with 10% vitamin D–sufficient (100 nM) human serum and activated for 6 hours with 1 ug/ml mycobacterial 19-kDa triacylated lipopeptide (TLR2/1 ligand, TLR2/1L). This type of activation is via heterodimeric Toll-like receptor 2 and Toll-like receptor 1 (TLR2/1).
Control untreated monocyte sample (6h)
Monocytes were isolated from five healthy donors, cultured in RPMI with 10% vitamin D–sufficient (100 nM) human serum and collected after 6 hours for RNA isolation.

dendritic cell study 7 (IL-4 mddc) / dendritic cell study 7 (IL-15 mddc)

Relative Expression (log2-ratio):-2.8459167
Number of Samples:3 / 3
Experimental dendritic cell study 7 (IL-4 mddc)
Mature IL-4 dendritic cells differentiated from CD14+ monocytes obtained from healthy donors. Monocytes were seeded in RPMI and supplemented with 2.5 % heat-inactivated human AB serum. Monocytes were cultured with 800 IU/mL granulocyte macrophage colony-stimulating factor and 20 ng/mL IL-4 in order to generate immature IL-4 DCs. Conventional maturation cocktail, comprising 10 ng/mL tumor necrosis factor-α, 10 ng/mL interleukin-1β, 15 ng/ml interleukin-6 and 1 µg/mL prostaglandin E2 was added for 48 hours. CD14+ monocytes were isolated from peripheral blood mononuclear cells (PBMC) by Ficoll density gradient centrifugation and purified by positive magnetic cell selection.
Control dendritic cell study 7 (IL-15 mddc)
Mature IL-15 dendritic cells differentiated from CD14+ monocytes obtained from healthy donors. Monocytes were seeded in RPMI and supplemented with 2.5 % heat-inactivated human AB serum. Differentiation was induced with 800 IU/mL granulocyte macrophage colony-stimulating factor and 200 ng/mL IL-15 to obtain immature IL-15 DCs. A TLR-activating maturation cocktail, comprising 3 µg/mL R848, 2.5 ng/mL tumor necrosis factor-α, 250 ng/mL interferon-γ and 1 µg/mL prostaglandin E2 was added after 24-48 hours of differentiation for 18-20 hours. CD14+ monocytes were isolated from peripheral blood mononuclear cells (PBMC) by Ficoll density gradient centrifugation and purified by positive magnetic cell selection.

E. coli study 2 / unstimulated, normal monocyte-derived macrophage sample

Relative Expression (log2-ratio):2.8071308
Number of Samples:5 / 7
Experimental E. coli study 2
Monocyte-derived macrophage samples derived from healthy control subjects cultured for 4 hours with 2.5 × 105 heat-killed E. coli.
Control unstimulated, normal monocyte-derived macrophage sample
Monocyte-derived macrophage samples derived from healthy control subjects cultured for 4 hours unstimulated.

EBNA2 overexpr. study 1 (24h) / control virus transfected EREB2-5 cell sample (24h)

Relative Expression (log2-ratio):2.7117872
Number of Samples:3 / 3
Experimental EBNA2 overexpr. study 1 (24h)
EREB2-5 cell line stably transfected with the chimeric Epstein-Barr virus-encoded nuclear antigen 2 (EBNA2) and control expression plasmid coding for bacterial chloramphenicol acetyltransferase (CAT) gene and . CAT was used as a negative control. Briefly, before the CAT and EBNA2 induction, cells were maintained in RPMI media and deprived of estrogen for 3 days before doxycycline and estrogen was added. Expression of EBNA2 was induced after addition of estrogen and expression of CAT was induced by the addition of doxycycline to a final concentration of 100 ng/mL medium. Doxycycline induced cells were harvested 24 hours after induction. Because EBNA2 is essential for the proliferation of EBV-infected cells, EREB2-5 cells grow only in the presence of estrogen. Before the preparation of RNA, NGFR cells were purified by MACS separation to enrich the cells with a transcriptional response to doxycycline.
Control control virus transfected EREB2-5 cell sample (24h)
EREB2-5 cell line stably transfected with control expression plasmid coding for bacterial chloramphenicol acetyltransferase (CAT) gene. CAT was used as a negative control. Briefly, before the CAT induction, cells were maintained in RPMI media and deprived of estrogen for 3 days before doxycycline was added. Expression of CAT was induced by the addition of doxycycline to a final concentration of 100 ng/mL medium. Doxycycline induced cells were harvested 24 hours after induction. Estrogen withdrawal leads to the inactivation of EBNA2, resulting in cell cycle arrest. Before the preparation of RNA, NGFR cells were purified by MACS separation to enrich the cells with a transcriptional response to doxycycline.

rheumatoid arthritis study 31 / IFNa-2a study 1

Relative Expression (log2-ratio):-2.575944
Number of Samples:4 / 7
Experimental rheumatoid arthritis study 31
Monocyte samples isolated from patients with rheumatoid arthritis (RA). Monocytes from whole blood were depleted from granulocytes by CD15 MACS beads, and afterwards they were sorted from remaining peripheral blood leukocytes by CD14 labeling. Patients fulfilled the revised American College of Rheumatology criteria (ACR) for RA.
Control IFNa-2a study 1
Monocyte samples isolated from healthy donors and stimulated in vitro by 100 ng/ml IFNα2a in whole blood for 1.5 hour. Following stimulation, monocytes were depleted from granulocytes using CD15 MACS beads, and they were sorted from remaining peripheral blood leukocytes by CD14 labeling.