TOP TEN perturbations for 1405_i_at (Homo sapiens)

Organism: Homo sapiens
Gene: 1405_i_at
Selected probe(set): 1555759_a_at
Platform: Affymetrix Human Genome U133 Plus 2.0 Array

Expression of 1405_i_at (1555759_a_at) across 6673 perturbations tested by GENEVESTIGATOR:

TNF-ɑ study 16 (12h) / rheumatoid arthritis study 10

Relative Expression (log2-ratio):7.641801
Number of Samples:3 / 6
Experimental TNF-ɑ study 16 (12h)
Synovial fibroblast samples isolated from affected knee of patients with rheumatoid factor positive rheumatoid arthritis (RA) were stimulated by 10 ng/ml of TNF-ɑ in serum-free DMEM for 12 hours. Synovial fibroblasts were isolated from surgically obtained synovial membrane by trypsin/collagenase digestion, followed by negative purification using CD-14 Dynabeads® M-450. Before the TNF-ɑ stimulation, fibroblasts were cultured for four passages in DMEM medium supplemented with antibiotics and 10% FCS. The RA was classified according to the criteria of the American College of Rheumatology. Average duration of RA: 11.5 ± 0.5 years. Patients were receiving non-steroidal antiinflammatory drugs. CRP: 38.1 ± 7.2 mg/l.
Control rheumatoid arthritis study 10
Synovial fibroblast samples isolated from affected knee of patients with rheumatoid factor positive rheumatoid arthritis (RA), classified according to the criteria of the American College of Rheumatology. Average duration of RA: 11.5 ± 0.5 years. Patients were receiving non-steroidal antiinflammatory drugs. CRP: 38.1 ± 7.2 mg/l. Synovial fibroblasts were isolated from surgically obtained synovial membrane by trypsin/collagenase digestion, followed by negative purification using CD-14 Dynabeads® M-450. The fibroblasts were than cultured for four passages in DMEM medium supplemented with antibiotics and 10% FCS. Prior RNA isolation, the fibroblasts were washed in serum free DMEM.

polyinosinic-polycytidylic acid study 1 (10ug/ml) / vehicle (DME) treated bronchial epithelial cell sample

Relative Expression (log2-ratio):7.176551
Number of Samples:3 / 17
Experimental polyinosinic-polycytidylic acid study 1 (10ug/ml)
Bronchial epithelial cells (NHBE) treated with polyinosinic-polycytidylic acid (Poly(I:C); 10ug/ml; vendor: InvivoGen / catalog number: tlrl-pic / catalog name: Poly(I:C) High Molecular Weight [31852-29-6]) for 6 hours. For treatment primary cells were seeded at a density of 50'000 cells/well in pre-coated rat tail collagen type I 96-well plates for 24 hours followed by 4 hours starvation. NHBE cells were isolated from different Caucasian, healthy and non-smoker donors from the airway located above the bifurcation of the lungs (tracheal/bronchial). ATC code:
Control vehicle (DME) treated bronchial epithelial cell sample
Bronchial epithelial cells (NHBE) treated with vehicle (DME) for 6 hours. For treatment primary cells were seeded at a density of 50'000 cells/well in pre-coated rat tail collagen type I 96-well plates for 24 hours followed by 4 hours starvation. NHBE cells were isolated from different Caucasian, healthy and non-smoker donors from the airway located above the bifurcation of the lungs (tracheal/bronchial).

rheumatoid arthritis study 69 (TNF; 20h; 1ng/ml) / rheumatoid arthritis study 69 (untreated)

Relative Expression (log2-ratio):6.7949543
Number of Samples:6 / 6
Experimental rheumatoid arthritis study 69 (TNF; 20h; 1ng/ml)
Joint synovial fibroblast samples from patients with rheumatoid arthritis after treatment with 1ng/ml TNF for 20 hours. Synovial fibroblasts were isolated from tissues discarded after synovectomy or joint replacement and isolated from digested synovial tissue and sorted for enriched CD45−, CD31−, CD235a−, Pdpn+ surface proteins. Cells were maintained in DMEM supplemented with 10% FBS, 2 mM L-glutamine, 50 uM 2-mercaptoethanol, antibiotics (penicillin and streptomycin), and essential and nonessential amino acids and used between passages 5 and 8 for treatment.
Control rheumatoid arthritis study 69 (untreated)
Joint synovial fibroblast samples from patients with rheumatoid arthritis. Synovial fibroblasts were isolated from tissues discarded after synovectomy or joint replacement and prepared from digested synovial tissue and sorted for enriched CD45−, CD31−, CD235a−, Pdpn+ surface proteins. Cells were maintained in DMEM supplemented with 10% FBS, 2 mM L-glutamine, 50 uM 2-mercaptoethanol, antibiotics (penicillin and streptomycin), and essential and nonessential amino acids and used between passages 5 and 8 for treatment.

osteoarthritis study 46 (TNF; 20h; 1ng/ml) / osteoarthritis study 46 (TNF; IL-17; baseline)

Relative Expression (log2-ratio):6.580513
Number of Samples:6 / 6
Experimental osteoarthritis study 46 (TNF; 20h; 1ng/ml)
Joint synovial fibroblast samples from patients with osteoarthritis after treatment with 1ng/ml TNF for 20 hours. Synovial fibroblasts were isolated from tissues discarded after synovectomy or joint replacement and isolated from digested synovial tissue and sorted for enriched CD45−, CD31−, CD235a−, Pdpn+ surface proteins. Cells were maintained in DMEM supplemented with 10% FBS, 2 mM L-glutamine, 50 uM 2-mercaptoethanol, antibiotics (penicillin and streptomycin), and essential and nonessential amino acids and used between passages 5 and 8 for treatment.
Control osteoarthritis study 46 (TNF; IL-17; baseline)
Joint synovial fibroblast samples at baseline from patients with osteoarthritis before treatment with 1ng/ml TNF and/or IL-17 for 20 hours. Synovial fibroblasts were isolated from tissues discarded after synovectomy or joint replacement and prepared from digested synovial tissue and sorted for enriched CD45−, CD31−, CD235a−, Pdpn+ surface proteins. Cells were maintained in DMEM supplemented with 10% FBS, 2 mM L-glutamine, 50 uM 2-mercaptoethanol, antibiotics (penicillin and streptomycin), and essential and nonessential amino acids and used between passages 5 and 8 for treatment.

rheumatoid arthritis study 69 (TNF; 20h; 1ng/ml) / rheumatoid arthritis study 69 (TNF; IL-17A; baseline)

Relative Expression (log2-ratio):6.3966866
Number of Samples:6 / 6
Experimental rheumatoid arthritis study 69 (TNF; 20h; 1ng/ml)
Joint synovial fibroblast samples from patients with rheumatoid arthritis after treatment with 1ng/ml TNF for 20 hours. Synovial fibroblasts were isolated from tissues discarded after synovectomy or joint replacement and isolated from digested synovial tissue and sorted for enriched CD45−, CD31−, CD235a−, Pdpn+ surface proteins. Cells were maintained in DMEM supplemented with 10% FBS, 2 mM L-glutamine, 50 uM 2-mercaptoethanol, antibiotics (penicillin and streptomycin), and essential and nonessential amino acids and used between passages 5 and 8 for treatment.
Control rheumatoid arthritis study 69 (TNF; IL-17A; baseline)
Joint synovial fibroblast samples at baseline from patients with rheumatoid arthritis before treatment with 1ng/ml TNF and/or IL-17 for 20 hours. Synovial fibroblasts were isolated from tissues discarded after synovectomy or joint replacement and prepared from digested synovial tissue and sorted for enriched CD45−, CD31−, CD235a−, Pdpn+ surface proteins. Cells were maintained in DMEM supplemented with 10% FBS, 2 mM L-glutamine, 50 uM 2-mercaptoethanol, antibiotics (penicillin and streptomycin), and essential and nonessential amino acids and used between passages 5 and 8 for treatment.

LPS study 1 / vehicle (DTT/polym. B) treated monocyte sample

Relative Expression (log2-ratio):6.293231
Number of Samples:3 / 3
Experimental LPS study 1
Monocytes were plated in 12-well plates and differentiated in RPMI 1640 containing 10% FBS plus 50 ng/ml (>500 U/ml) GM-CSF and 100 ng/ml (>500 U/ml) IL-4 for 5 days. At day 5, Lipopolysaccharide (LPS; 100 ng/ml) was added. At 18 h after treatment, total RNA was isolated. ATC code:---
Control vehicle (DTT/polym. B) treated monocyte sample
Monocytes were plated in 12-well plates and differentiated in RPMI 1640 containing 10% FBS plus 50 ng/ml (>500 U/ml) GM-CSF and 100 ng/ml (>500 U/ml) IL-4 for 5 days. At day 5, vehicle consisting of equivalent volume of 8 mM DTT (galectin-1 storage buffer) and 10 μg/ml polymyxin B was added. At 18 h after treatment, total RNA was isolated.

galectin-1 study 1 / vehicle (DTT/polym. B) treated monocyte sample

Relative Expression (log2-ratio):6.1918116
Number of Samples:3 / 3
Experimental galectin-1 study 1
Monocytes were plated in 12-well plates and differentiated in RPMI 1640 containing 10% FBS plus 50 ng/ml (>500 U/ml) GM-CSF and 100 ng/ml (>500 U/ml) IL-4 for 5 days. At day 5, galectin-1 (20 μM) in the presence of 10 μg/ml polymyxin B was added. At 18 h after treatment, total RNA was isolated.
Control vehicle (DTT/polym. B) treated monocyte sample
Monocytes were plated in 12-well plates and differentiated in RPMI 1640 containing 10% FBS plus 50 ng/ml (>500 U/ml) GM-CSF and 100 ng/ml (>500 U/ml) IL-4 for 5 days. At day 5, vehicle consisting of equivalent volume of 8 mM DTT (galectin-1 storage buffer) and 10 μg/ml polymyxin B was added. At 18 h after treatment, total RNA was isolated.

T. cruzi study 1 (VSMC; 48h) / mock infected vascular smooth muscle cell sample (48h)

Relative Expression (log2-ratio):6.092783
Number of Samples:3 / 3
Experimental T. cruzi study 1 (VSMC; 48h)
Human vascular smooth muscle cells (VSMCs) infected with Trypanosoma cruzi trypomastigotes for 2 hours (10exp8/ml) and harvested 48 hours post infection. Cells were maintained in Ham’s F12K medium with 2 mM L-glutamine, 1.5 g/L sodium bicarbonate, 10 mM HEPES, 10 mM TES, 0.05 mg/ml ascorbic acid, 0.001 mg/ml insulin, 0.01 mg/ml transferrin, 10ng/ml sodium selenite, 0.03 mg/ml endothelial cell growth supplement (ECGS) and 10% FBS.
Control mock infected vascular smooth muscle cell sample (48h)
Human vascular smooth muscle cells (VSMCs) mock-infected and harvested 48 hours post mock infection with 2% FBS medium. Cells were maintained in Ham’s F12K medium with 2 mM L-glutamine, 1.5 g/L sodium bicarbonate, 10 mM HEPES, 10 mM TES, 0.05 mg/ml ascorbic acid, 0.001 mg/ml insulin, 0.01 mg/ml transferrin, 10ng/ml sodium selenite, 0.03 mg/ml endothelial cell growth supplement (ECGS) and 10% FBS.

osteoarthritis study 46 (TNF; 20h; 1ng/ml; IL-17A; 20h; 1ng/ml) / osteoarthritis study 46 (TNF; IL-17; baseline)

Relative Expression (log2-ratio):6.0473347
Number of Samples:6 / 6
Experimental osteoarthritis study 46 (TNF; 20h; 1ng/ml; IL-17A; 20h; 1ng/ml)
Joint synovial fibroblast samples from patients with osteoarthritis after treatment with 1ng/ml TNF and 1ng/ml IL-17 for 20 hours. Synovial fibroblasts were isolated from tissues discarded after synovectomy or joint replacement and isolated from digested synovial tissue and sorted for enriched CD45−, CD31−, CD235a−, Pdpn+ surface proteins. Cells were maintained in DMEM supplemented with 10% FBS, 2 mM L-glutamine, 50 uM 2-mercaptoethanol, antibiotics (penicillin and streptomycin), and essential and nonessential amino acids and used between passages 5 and 8 for treatment.
Control osteoarthritis study 46 (TNF; IL-17; baseline)
Joint synovial fibroblast samples at baseline from patients with osteoarthritis before treatment with 1ng/ml TNF and/or IL-17 for 20 hours. Synovial fibroblasts were isolated from tissues discarded after synovectomy or joint replacement and prepared from digested synovial tissue and sorted for enriched CD45−, CD31−, CD235a−, Pdpn+ surface proteins. Cells were maintained in DMEM supplemented with 10% FBS, 2 mM L-glutamine, 50 uM 2-mercaptoethanol, antibiotics (penicillin and streptomycin), and essential and nonessential amino acids and used between passages 5 and 8 for treatment.

osteoarthritis study 46 (TNF; 20h; 1ng/ml) / osteoarthritis study 46 (untreated)

Relative Expression (log2-ratio):5.9449368
Number of Samples:6 / 6
Experimental osteoarthritis study 46 (TNF; 20h; 1ng/ml)
Joint synovial fibroblast samples from patients with osteoarthritis after treatment with 1ng/ml TNF for 20 hours. Synovial fibroblasts were isolated from tissues discarded after synovectomy or joint replacement and isolated from digested synovial tissue and sorted for enriched CD45−, CD31−, CD235a−, Pdpn+ surface proteins. Cells were maintained in DMEM supplemented with 10% FBS, 2 mM L-glutamine, 50 uM 2-mercaptoethanol, antibiotics (penicillin and streptomycin), and essential and nonessential amino acids and used between passages 5 and 8 for treatment.
Control osteoarthritis study 46 (untreated)
Joint synovial fibroblast samples from patients with osteoarthritis. Synovial fibroblasts were isolated from tissues discarded after synovectomy or joint replacement and prepared from digested synovial tissue and sorted for enriched CD45−, CD31−, CD235a−, Pdpn+ surface proteins. Cells were maintained in DMEM supplemented with 10% FBS, 2 mM L-glutamine, 50 uM 2-mercaptoethanol, antibiotics (penicillin and streptomycin), and essential and nonessential amino acids and used between passages 5 and 8 for treatment.