TOP TEN perturbations for 11759760_s_at (Homo sapiens)

Organism: Homo sapiens
Gene: 11759760_s_at
Selected probe(set): 215779_s_at
Platform: Affymetrix Human Genome U133 Plus 2.0 Array

Expression of 11759760_s_at (215779_s_at) across 5880 perturbations tested by GENEVESTIGATOR:

formaldehyde study 3 (4500ug/ml) / vehicle (EtOH) treated bronchial epithelial cell sample

Relative Expression (log2-ratio):5.1379013
Number of Samples:3 / 3
Experimental formaldehyde study 3 (4500ug/ml)
Bronchial epithelial cells (NHBE) treated with 4500 ug/ml formaldehyde (within range of concentrations reported to induce toxicity in lung epithelial cells and other cell types) for 24 hours. NHBE cells were derived from a 60 year old male non-smoker. ATC code:---
Control vehicle (EtOH) treated bronchial epithelial cell sample
Bronchial epithelial cells (NHBE) treated with vehicle (ethanol) at a final concentration of 2% v/v (concentration that ensures >80% cell viability after 24 hours of exposure) for 24 hours. NHBE cells were derived from a 60 year old male non-smoker.

tumor supernatant activation study 3 / memory T-cell activation study 1

Relative Expression (log2-ratio):4.631653
Number of Samples:4 / 3
Experimental tumor supernatant activation study 3
Memory (CD45RA-) CD4+ T cells isolated from peripheral blood of female healthy donors were incubated for 24 hours in 1:1 mix of tumor supernatant from primary invasive breast ductal carcinoma and X-VIVO 20 medium supplemented with antiCD3/CD28 beads, before harvest for RNA isolation. The tumor supernatant was prepared as followed: fresh surgical specimen was dissociated in X-VIVO 20 medium by GentleMACS dissociator and the resulting suspension was clarified by centrifugation for 15min at 13'000 g. ATC code:---
Control memory T-cell activation study 1
Memory (CD45RA-) CD4+ T-cells isolated from peripheral blood of healthy female donors were activated with anti-CD3/CD28 beads for 24hrs.

tumor supernatant activation study 3 / untreated memory CD4 T-cell sample

Relative Expression (log2-ratio):4.5766716
Number of Samples:4 / 3
Experimental tumor supernatant activation study 3
Memory (CD45RA-) CD4+ T cells isolated from peripheral blood of female healthy donors were incubated for 24 hours in 1:1 mix of tumor supernatant from primary invasive breast ductal carcinoma and X-VIVO 20 medium supplemented with antiCD3/CD28 beads, before harvest for RNA isolation. The tumor supernatant was prepared as followed: fresh surgical specimen was dissociated in X-VIVO 20 medium by GentleMACS dissociator and the resulting suspension was clarified by centrifugation for 15min at 13'000 g. ATC code:---
Control untreated memory CD4 T-cell sample
Memory (CD45RA-) CD4+ T-cells were isolated from peripheral blood of healthy female donors and incubated in X-VIVO 20 medium for 24 hours, before harvest for RNA isolation.

breast cancer study 15 (inv. dc) / normal breast tissue

Relative Expression (log2-ratio):4.365406
Number of Samples:5 / 5
Experimental breast cancer study 15 (inv. dc)
Primary invasive ductal carcinoma tissue sample derived from the breasts of female patients after surgery.
Control normal breast tissue
Tissue samples of the breast from healthy female individuals after breast reduction surgery.

paracetamol (acetaminophen) study 5 (5000uM) / vehicle (medium) treated hepatocyte sample

Relative Expression (log2-ratio):3.9014578
Number of Samples:2 / 2
Experimental paracetamol (acetaminophen) study 5 (5000uM)
Hepatocytes treated with compound: acetaminophen (5000uM; CHEMBL112) for 8 hours. ATC code:
Control vehicle (medium) treated hepatocyte sample
Hepatocytes treated with vehicle (medium) for 8 hours.

prostate cancer study 8 (p. canc) / prostate cancer study 8 (ptasc)

Relative Expression (log2-ratio):3.8950539
Number of Samples:3 / 2
Experimental prostate cancer study 8 (p. canc)
CD26+ FACS sorted prostate neoplasm cell (p. canc) samples from patients with primary prostate cancer collected after radical prostatectomy.
Control prostate cancer study 8 (ptasc)
CD90+ FACS sorted prostate tumor-associated stromal cell (ptasc) samples from patients with primary prostate cancer collected after radical prostatectomy.

BPDE study 3 (0.5uM) / vehicle (DMSO) treated WI-38 fibroblast sample

Relative Expression (log2-ratio):3.7201767
Number of Samples:3 / 3
Experimental BPDE study 3 (0.5uM)
WI-38 normal fibroblast cells exposed to 0.5uM racemic anti-BPDE [(±)-7r, 8t-dihydroxy-9t, 10t-epoxy-7, 8, 9, 10-tetrahydro benzo[a]pyrene] (BPDE) for 24 hours. Cells were incubated with BPDE (added in 10 ul DMSO) for 20 min, the exposure medium was then replaced with fresh medium, and after 24 hours cells were washed with phosphate-buffered saline and harvested. ATC code:---
Control vehicle (DMSO) treated WI-38 fibroblast sample
WI-38 normal fibroblast cells exposed to 0.1% DMSO vehicle control for 24 hours.

allyl alcohol study 3 (70uM) / vehicle (medium) treated hepatocyte sample

Relative Expression (log2-ratio):3.7132874
Number of Samples:2 / 2
Experimental allyl alcohol study 3 (70uM)
Hepatocytes treated with compound: allyl alcohol (70uM; CHEMBL234926) for 24 hours. ATC code:---
Control vehicle (medium) treated hepatocyte sample
Hepatocytes treated with vehicle (medium) for 24 hours.

colchicine study 7 (4000uM) / vehicle (medium) treated hepatocyte sample

Relative Expression (log2-ratio):3.6989708
Number of Samples:2 / 2
Experimental colchicine study 7 (4000uM)
Hepatocytes treated with compound: colchicine (4000uM; CHEMBL107) for 24 hours. ATC code:
Control vehicle (medium) treated hepatocyte sample
Hepatocytes treated with vehicle (medium) for 24 hours.

wound healing study 2 (ex vivo; DMSO) / normal skin tissue (ex vivo)

Relative Expression (log2-ratio):3.5987492
Number of Samples:3 / 3
Experimental wound healing study 2 (ex vivo; DMSO)
Ex vivo skin samples obtained from healthy donors following reduction surgery of abdomen, and incubated in culture medium containing DMSO for 4 days. To make sure that mainly epidermis was present in the samples, as much dermal tissue as possible was removed by dissection. Skin was sliced into 1x10 mm slices and incubated in keratinocyte medium for four days with 1:1000 fold dilution of DMSO. The cultivation was performed in serum-free keratinocyte medium supplemented with transferrin, hEGF (0.15 ng/mL), 0.5 mg/mL hydrocortisone, gentamicin, amphotericin B, and epinephrine but without insulin.
Control normal skin tissue (ex vivo)
Normal skin samples obtained from healthy donors following reduction surgery of abdomen. To make sure that mainly epidermis was present in the samples, as much dermal tissue as possible was removed by dissection.

Organism: Homo sapiens
Gene: 11759760_s_at
Selected probe(set): 208523_x_at
Platform: Affymetrix Human Genome U133 Plus 2.0 Array

Expression of 11759760_s_at (208523_x_at) across 5880 perturbations tested by GENEVESTIGATOR:

wound healing study 2 (ex vivo; DMSO) / normal skin tissue (ex vivo)

Relative Expression (log2-ratio):3.4953232
Number of Samples:3 / 3
Experimental wound healing study 2 (ex vivo; DMSO)
Ex vivo skin samples obtained from healthy donors following reduction surgery of abdomen, and incubated in culture medium containing DMSO for 4 days. To make sure that mainly epidermis was present in the samples, as much dermal tissue as possible was removed by dissection. Skin was sliced into 1x10 mm slices and incubated in keratinocyte medium for four days with 1:1000 fold dilution of DMSO. The cultivation was performed in serum-free keratinocyte medium supplemented with transferrin, hEGF (0.15 ng/mL), 0.5 mg/mL hydrocortisone, gentamicin, amphotericin B, and epinephrine but without insulin.
Control normal skin tissue (ex vivo)
Normal skin samples obtained from healthy donors following reduction surgery of abdomen. To make sure that mainly epidermis was present in the samples, as much dermal tissue as possible was removed by dissection.

wound healing study 2 (ex vivo; AG1478) / normal skin tissue (ex vivo)

Relative Expression (log2-ratio):3.3511324
Number of Samples:3 / 3
Experimental wound healing study 2 (ex vivo; AG1478)
Ex vivo skin samples obtained from healthy donors following reduction surgery of abdomen, and incubated in culture medium containing AG1478 for 4 days. To make sure that mainly epidermis was present in the samples, as much dermal tissue as possible was removed by dissection. Skin was sliced into 1x10 mm slices and incubated in keratinocyte medium for four days with 10 micromolar AG1478 (dissolved in DMSO). The cultivation was performed in serum-free keratinocyte medium supplemented with transferrin, hEGF (0.15 ng/mL), 0.5 mg/mL hydrocortisone, gentamicin, amphotericin B, and epinephrine but without insulin. AG1478 is EGFR kinase inhibitor. ATC code:---
Control normal skin tissue (ex vivo)
Normal skin samples obtained from healthy donors following reduction surgery of abdomen. To make sure that mainly epidermis was present in the samples, as much dermal tissue as possible was removed by dissection.

tumor supernatant activation study 3 / memory T-cell activation study 1

Relative Expression (log2-ratio):3.290472
Number of Samples:4 / 3
Experimental tumor supernatant activation study 3
Memory (CD45RA-) CD4+ T cells isolated from peripheral blood of female healthy donors were incubated for 24 hours in 1:1 mix of tumor supernatant from primary invasive breast ductal carcinoma and X-VIVO 20 medium supplemented with antiCD3/CD28 beads, before harvest for RNA isolation. The tumor supernatant was prepared as followed: fresh surgical specimen was dissociated in X-VIVO 20 medium by GentleMACS dissociator and the resulting suspension was clarified by centrifugation for 15min at 13'000 g. ATC code:---
Control memory T-cell activation study 1
Memory (CD45RA-) CD4+ T-cells isolated from peripheral blood of healthy female donors were activated with anti-CD3/CD28 beads for 24hrs.

tumor supernatant activation study 3 / untreated memory CD4 T-cell sample

Relative Expression (log2-ratio):3.264533
Number of Samples:4 / 3
Experimental tumor supernatant activation study 3
Memory (CD45RA-) CD4+ T cells isolated from peripheral blood of female healthy donors were incubated for 24 hours in 1:1 mix of tumor supernatant from primary invasive breast ductal carcinoma and X-VIVO 20 medium supplemented with antiCD3/CD28 beads, before harvest for RNA isolation. The tumor supernatant was prepared as followed: fresh surgical specimen was dissociated in X-VIVO 20 medium by GentleMACS dissociator and the resulting suspension was clarified by centrifugation for 15min at 13'000 g. ATC code:---
Control untreated memory CD4 T-cell sample
Memory (CD45RA-) CD4+ T-cells were isolated from peripheral blood of healthy female donors and incubated in X-VIVO 20 medium for 24 hours, before harvest for RNA isolation.

DN-GRHL2 overexpression study 2 (high TER) / control H2B-GFP transfected bronchial epithelial cell sample (high TER)

Relative Expression (log2-ratio):-3.159402
Number of Samples:3 / 3
Experimental DN-GRHL2 overexpression study 2 (high TER)
Primary human bronchial epithelial (HBE) cells from donors without pre-existing lung disease infected with lentivirus containing a dominant negative mutant form of grainyheadlike family member 2 (DN-GRHL2). HBE cells (passage 0) were cultured in air-liquid interface. HBE cells (passage 0) were seeded in collagen-coated dishes. At 40% confluence, cell cultures were infected with lentivirus and 48 hours post infection they were selected with 1 ug/ml puromycin. To induce the DN-GRHL2 overexpression 0.5 ug/ml doxycycline was added for 48 hours when transepithelial resistance (TER) reached a maximum level (between day 14 – 18, depending on the donors). To construct an inducible Tet-on GFP-labeled dominant-negative mutant of GRHL2, DNA encoding a truncated version of mouse Grhl2 in which amino acids 1-232 were replaced with EGFP was cloned into pTRIPZ inducible lentiviral vector.
Control control H2B-GFP transfected bronchial epithelial cell sample (high TER)
Primary human bronchial epithelial (HBE) cells from donors without pre-existing lung disease infected with control H2B-GFP lentivirus. HBE cells (passage 0) were cultured in air-liquid interface. Cells were seeded in collagen-coated dishes. At 40% confluence, cell cultures were infected with lentivirus and 48 hours post infection they were selected with 1 ug/ml puromycin. To induce the H2B-GFP expression, 0.5 ug/ml doxycycline was added for 48 hours when transepithelial resistance (TER) reached a maximum level (between day 14 – 18, depending on the donors). To construct a Tet-on GFP labeled control vector, nuclear H2B-GFP was cloned into pTRIPZ inducible lentiviral vector.

cutaneous T-cell lymphoma study 1 (tumor phase) / normal skin tissue

Relative Expression (log2-ratio):2.6043873
Number of Samples:4 / 8
Experimental cutaneous T-cell lymphoma study 1 (tumor phase)
Lesional skin biopsies from patients with cutaneous T-cell lymphoma in the tumor phase (extranodal).
Control normal skin tissue
Skin biopsies from healthy individuals.

NGFR depletion study 1 / normal SW-480 cell sample

Relative Expression (log2-ratio):2.5773296
Number of Samples:6 / 3
Experimental NGFR depletion study 1
RNAi-mediated gene knockdown of NGFR in colorectal cancer cell line SW-480.
Control normal SW-480 cell sample
Non-transduced SW-480 colorectal cell line sample.

breast cancer study 15 (inv. dc) / normal breast tissue

Relative Expression (log2-ratio):2.504304
Number of Samples:5 / 5
Experimental breast cancer study 15 (inv. dc)
Primary invasive ductal carcinoma tissue sample derived from the breasts of female patients after surgery.
Control normal breast tissue
Tissue samples of the breast from healthy female individuals after breast reduction surgery.

formaldehyde study 3 (4500ug/ml) / vehicle (EtOH) treated bronchial epithelial cell sample

Relative Expression (log2-ratio):2.2963724
Number of Samples:3 / 3
Experimental formaldehyde study 3 (4500ug/ml)
Bronchial epithelial cells (NHBE) treated with 4500 ug/ml formaldehyde (within range of concentrations reported to induce toxicity in lung epithelial cells and other cell types) for 24 hours. NHBE cells were derived from a 60 year old male non-smoker. ATC code:---
Control vehicle (EtOH) treated bronchial epithelial cell sample
Bronchial epithelial cells (NHBE) treated with vehicle (ethanol) at a final concentration of 2% v/v (concentration that ensures >80% cell viability after 24 hours of exposure) for 24 hours. NHBE cells were derived from a 60 year old male non-smoker.

glioma study 16 (LN-18) / normal astrocyte sample

Relative Expression (log2-ratio):2.2609196
Number of Samples:2 / 3
Experimental glioma study 16 (LN-18)
Human glioma cell line LN018 was cultured in DMEM supplemented with 10% FCS (fetal calf serum) and antibiotics at 37C and 5% CO2.
Control normal astrocyte sample
Normal brain astrocytes. Clonetics normal human astrocytes (NHA) from Cambrex (primary-derived cultures) and cultured according to the manufacturer's recommendations.

Organism: Homo sapiens
Gene: 11759760_s_at
Selected probe(set): 208527_x_at
Platform: Affymetrix Human Genome U133 Plus 2.0 Array

Expression of 11759760_s_at (208527_x_at) across 5880 perturbations tested by GENEVESTIGATOR:

HIV-associated neurocognitive disorder study 7 (normal) / HIV-associated neurocognitive disorder study 6 (normal)

Relative Expression (log2-ratio):-3.4785404
Number of Samples:2 / 2
Experimental HIV-associated neurocognitive disorder study 7 (normal)
Postmortem brain samples of the centrum semiovale (deep white matter) at the coronal level of the genu of the corpus callosum from patients with normal brain pathology. The patients received antiretroviral therapy (ART).
Control HIV-associated neurocognitive disorder study 6 (normal)
Postmortem brain samples of the centrum semiovale (deep white matter) at the coronal level of the genu of the corpus callosum from patients with normal brain pathology. The patients did not receive any antiretroviral therapy (ART).

zalypsis study 2 / untreated OPM1 cell sample

Relative Expression (log2-ratio):3.2579956
Number of Samples:2 / 2
Experimental zalypsis study 2
OPM1 multiple myeloma cells treated in vitro with zalypsis (5 nM), a novel marine-derived compound with potent antimyeloma activity. Cells were harvested at the beginning of induction of cell death (15-20% cell death as assessed by Annexin V-FITC staining). ATC code:---
Control untreated OPM1 cell sample
OPM1 multiple myeloma cells untreated.

colorectal cancer study 43 (metastase; brain) / colorectal cancer study 43 (metastase; liver)

Relative Expression (log2-ratio):-2.9684925
Number of Samples:2 / 25
Experimental colorectal cancer study 43 (metastase; brain)
Metastatic tumor tissue obtained from the brain of patients with primary colorectal adenocarcinoma.
Control colorectal cancer study 43 (metastase; liver)
Metastatic tumor tissue obtained from the liver of patients with primary colon adenocarcinoma.

NGFR depletion study 1 / normal SW-480 cell sample

Relative Expression (log2-ratio):2.7016478
Number of Samples:6 / 3
Experimental NGFR depletion study 1
RNAi-mediated gene knockdown of NGFR in colorectal cancer cell line SW-480.
Control normal SW-480 cell sample
Non-transduced SW-480 colorectal cell line sample.

connective/soft tissue cancer study 1 (PDX; connective and soft tissue, sarcoma, NOS; metastatic) / connective/soft tissue cancer study 1 (PDX; connective and soft tissue, leiomyosarcoma, NOS; metastatic)

Relative Expression (log2-ratio):2.6550827
Number of Samples:3 / 2
Experimental connective/soft tissue cancer study 1 (PDX; connective and soft tissue, sarcoma, NOS; metastatic)
Patient-derived xenograft (PDX) samples generated in female athymic nude mice from a metastasis of patients with primary connective and soft tissue, sarcoma, NOS of the soft tissue (subcutaneously implanted). Metastatic site of patient tumor sample is not reported.
Control connective/soft tissue cancer study 1 (PDX; connective and soft tissue, leiomyosarcoma, NOS; metastatic)
Patient-derived xenograft (PDX) samples generated in female athymic nude mice from a metastasis of patients with primary connective and soft tissue, leiomyosarcoma, NOS of the soft tissue (subcutaneously implanted). Metastatic site of patient tumor sample is not reported.

colorectal cancer study 43 (metastase; brain) / colorectal cancer study 43 (metastase; lung)

Relative Expression (log2-ratio):-2.6548424
Number of Samples:2 / 5
Experimental colorectal cancer study 43 (metastase; brain)
Metastatic tumor tissue obtained from the brain of patients with primary colorectal adenocarcinoma.
Control colorectal cancer study 43 (metastase; lung)
Metastatic tumor tissue obtained from the lung of patients with primary colon adenocarcinoma.

HIVGFP(G); SIVVLP(G) study 1 / uninfected monocyte-derived dendritic cell sample

Relative Expression (log2-ratio):2.554844
Number of Samples:2 / 2
Experimental HIVGFP(G); SIVVLP(G) study 1
Monocyte-derived dendritic cell samples (MDDC) from isolated and stimulated CD14+ monocytes (GM-CSF and IL-4 for dendritic cell differentiation) of adult peripheral blood. MDDC were infected with GFP-encoding HIV-1 pseudotyped with VSV-G [HIVGFP(G)] and VSV-G-pseudotyped SIVmac239 virus-like particles [SIVVLP(G)] for 48 hours.
Control uninfected monocyte-derived dendritic cell sample
Monocyte-derived dendritic cell samples (MDDC) from isolated and stimulated CD14+ monocytes (GM-CSF and IL-4 for dendritic cell differentiation) of adult peripheral blood. MDDC were treated with lipopolysaccharide (LPS) for 48 hours.

wound healing study 2 (ex vivo; DMSO) / normal skin tissue (ex vivo)

Relative Expression (log2-ratio):2.5296202
Number of Samples:3 / 3
Experimental wound healing study 2 (ex vivo; DMSO)
Ex vivo skin samples obtained from healthy donors following reduction surgery of abdomen, and incubated in culture medium containing DMSO for 4 days. To make sure that mainly epidermis was present in the samples, as much dermal tissue as possible was removed by dissection. Skin was sliced into 1x10 mm slices and incubated in keratinocyte medium for four days with 1:1000 fold dilution of DMSO. The cultivation was performed in serum-free keratinocyte medium supplemented with transferrin, hEGF (0.15 ng/mL), 0.5 mg/mL hydrocortisone, gentamicin, amphotericin B, and epinephrine but without insulin.
Control normal skin tissue (ex vivo)
Normal skin samples obtained from healthy donors following reduction surgery of abdomen. To make sure that mainly epidermis was present in the samples, as much dermal tissue as possible was removed by dissection.

HS-27A / HS-5

Relative Expression (log2-ratio):2.524373
Number of Samples:4 / 4
Experimental HS-27A
Human bone marrow stromal cell line derived from a male Caucasian patient. Cells were immortalized by transduction with the human papilloma virus E6/E7 genes. HS-27a supports obblestone area formation by early hematopoietic progenitors. Synonyms:HS27A; HS27a; HS-27a; HS 27a Cellosaurus code:
Control HS-5
Human bone marrow stromal cell line of a 30 yeas old male Caucasian immortalized by transduction with the human papilloma virus E6/E7 genes. HS-5 secretes multiple cytokines that support the proliferation of committed progenitors. Synonyms:HS5; HS 5 Cellosaurus code:

tumor supernatant activation study 3 / untreated memory CD4 T-cell sample

Relative Expression (log2-ratio):2.5048914
Number of Samples:4 / 3
Experimental tumor supernatant activation study 3
Memory (CD45RA-) CD4+ T cells isolated from peripheral blood of female healthy donors were incubated for 24 hours in 1:1 mix of tumor supernatant from primary invasive breast ductal carcinoma and X-VIVO 20 medium supplemented with antiCD3/CD28 beads, before harvest for RNA isolation. The tumor supernatant was prepared as followed: fresh surgical specimen was dissociated in X-VIVO 20 medium by GentleMACS dissociator and the resulting suspension was clarified by centrifugation for 15min at 13'000 g. ATC code:---
Control untreated memory CD4 T-cell sample
Memory (CD45RA-) CD4+ T-cells were isolated from peripheral blood of healthy female donors and incubated in X-VIVO 20 medium for 24 hours, before harvest for RNA isolation.

Organism: Homo sapiens
Gene: 11759760_s_at
Selected probe(set): 214455_at
Platform: Affymetrix Human Genome U133 Plus 2.0 Array

Expression of 11759760_s_at (214455_at) across 5880 perturbations tested by GENEVESTIGATOR:

HIVGFP(G); SIVVLP(G) study 1 / SIVVLP(G) study 1

Relative Expression (log2-ratio):4.899021
Number of Samples:2 / 2
Experimental HIVGFP(G); SIVVLP(G) study 1
Monocyte-derived dendritic cell samples (MDDC) from isolated and stimulated CD14+ monocytes (GM-CSF and IL-4 for dendritic cell differentiation) of adult peripheral blood. MDDC were infected with GFP-encoding HIV-1 pseudotyped with VSV-G [HIVGFP(G)] and VSV-G-pseudotyped SIVmac239 virus-like particles [SIVVLP(G)] for 48 hours.
Control SIVVLP(G) study 1
Monocyte-derived dendritic cell samples (MDDC) from isolated and stimulated CD14+ monocytes (GM-CSF and IL-4 for dendritic cell differentiation) of adult peripheral blood. MDDC were infected with VSV-G-pseudotyped SIVmac239 virus-like particles [SIVVLP(G)] for 48 hours.

HIVGFP(G); SIVVLP(G) study 1 / uninfected monocyte-derived dendritic cell sample

Relative Expression (log2-ratio):4.891226
Number of Samples:2 / 2
Experimental HIVGFP(G); SIVVLP(G) study 1
Monocyte-derived dendritic cell samples (MDDC) from isolated and stimulated CD14+ monocytes (GM-CSF and IL-4 for dendritic cell differentiation) of adult peripheral blood. MDDC were infected with GFP-encoding HIV-1 pseudotyped with VSV-G [HIVGFP(G)] and VSV-G-pseudotyped SIVmac239 virus-like particles [SIVVLP(G)] for 48 hours.
Control uninfected monocyte-derived dendritic cell sample
Monocyte-derived dendritic cell samples (MDDC) from isolated and stimulated CD14+ monocytes (GM-CSF and IL-4 for dendritic cell differentiation) of adult peripheral blood. MDDC were treated with lipopolysaccharide (LPS) for 48 hours.

HIVGFP(G); SIVVLP(G) study 1 / HIVGFP(G) study 1

Relative Expression (log2-ratio):4.1920176
Number of Samples:2 / 2
Experimental HIVGFP(G); SIVVLP(G) study 1
Monocyte-derived dendritic cell samples (MDDC) from isolated and stimulated CD14+ monocytes (GM-CSF and IL-4 for dendritic cell differentiation) of adult peripheral blood. MDDC were infected with GFP-encoding HIV-1 pseudotyped with VSV-G [HIVGFP(G)] and VSV-G-pseudotyped SIVmac239 virus-like particles [SIVVLP(G)] for 48 hours.
Control HIVGFP(G) study 1
Monocyte-derived dendritic cell samples (MDDC) from isolated and stimulated CD14+ monocytes (GM-CSF and IL-4 for dendritic cell differentiation) of adult peripheral blood. MDDC were infected with GFP-encoding HIV-1 pseudotyped with VSV-G [HIVGFP(G)] for 48 hours.

prostate cancer study 8 (p. canc) / prostate cancer study 8 (ptasc)

Relative Expression (log2-ratio):4.0720224
Number of Samples:3 / 2
Experimental prostate cancer study 8 (p. canc)
CD26+ FACS sorted prostate neoplasm cell (p. canc) samples from patients with primary prostate cancer collected after radical prostatectomy.
Control prostate cancer study 8 (ptasc)
CD90+ FACS sorted prostate tumor-associated stromal cell (ptasc) samples from patients with primary prostate cancer collected after radical prostatectomy.

tumor supernatant activation study 3 / memory T-cell activation study 1

Relative Expression (log2-ratio):4.0137405
Number of Samples:4 / 3
Experimental tumor supernatant activation study 3
Memory (CD45RA-) CD4+ T cells isolated from peripheral blood of female healthy donors were incubated for 24 hours in 1:1 mix of tumor supernatant from primary invasive breast ductal carcinoma and X-VIVO 20 medium supplemented with antiCD3/CD28 beads, before harvest for RNA isolation. The tumor supernatant was prepared as followed: fresh surgical specimen was dissociated in X-VIVO 20 medium by GentleMACS dissociator and the resulting suspension was clarified by centrifugation for 15min at 13'000 g. ATC code:---
Control memory T-cell activation study 1
Memory (CD45RA-) CD4+ T-cells isolated from peripheral blood of healthy female donors were activated with anti-CD3/CD28 beads for 24hrs.

bronchial epithelial cell differentiation study 1 (day28) / bronchial epithelial cell differentiation study 1 (subconfluent)

Relative Expression (log2-ratio):4.007642
Number of Samples:3 / 3
Experimental bronchial epithelial cell differentiation study 1 (day28)
Differentiated normal human bronchial epithelial cell (NHBE) cultured for 28 days in an air-liquid interface (ALI) system. At this time point cells were fully differentiated and formed a polarized, pseudostratified mucociliary epithelium. In order to generate the ALI culture, undifferentiated cells were grown under submerged conditions in bronchial air-liquid interface (B-ALI) growth basal medium supplemented with expansion media. When cells reached confluency (after 3-5 days), an air-liquid interface culture (ALI system) was created by removing the apical medium and replacing the medium of the basal compartment with B-ALI differentiation medium. During the 28 days culture medium was replaced every 48 hour.
Control bronchial epithelial cell differentiation study 1 (subconfluent)
Subconfluent undifferentiated normal human bronchial epithelial cell (NHBE) cultured for 1-2 days under submerged conditions in bronchial air-liquid interface (B-ALI) growth basal medium supplemented with expansion media. At this time point cells still grew dispersed in the culture insert and covered 70% of the insert.

tumor supernatant activation study 3 / untreated memory CD4 T-cell sample

Relative Expression (log2-ratio):3.9572625
Number of Samples:4 / 3
Experimental tumor supernatant activation study 3
Memory (CD45RA-) CD4+ T cells isolated from peripheral blood of female healthy donors were incubated for 24 hours in 1:1 mix of tumor supernatant from primary invasive breast ductal carcinoma and X-VIVO 20 medium supplemented with antiCD3/CD28 beads, before harvest for RNA isolation. The tumor supernatant was prepared as followed: fresh surgical specimen was dissociated in X-VIVO 20 medium by GentleMACS dissociator and the resulting suspension was clarified by centrifugation for 15min at 13'000 g. ATC code:---
Control untreated memory CD4 T-cell sample
Memory (CD45RA-) CD4+ T-cells were isolated from peripheral blood of healthy female donors and incubated in X-VIVO 20 medium for 24 hours, before harvest for RNA isolation.

esophagus cancer study 1 (PDX; squamous cell carcinoma, NOS; metastatic) / esophagus cancer study 1 (PDX; squamous cell carcinoma, NOS; primary)

Relative Expression (log2-ratio):-3.9052362
Number of Samples:2 / 3
Experimental esophagus cancer study 1 (PDX; squamous cell carcinoma, NOS; metastatic)
Patient-derived xenograft (PDX) samples generated in female athymic nude mice from a metastasis of patients with primary squamous cell carcinoma, NOS of the oesophagus (subcutaneously implanted). Metastatic site of patient tumor sample is not reported.
Control esophagus cancer study 1 (PDX; squamous cell carcinoma, NOS; primary)
Patient-derived xenograft (PDX) samples generated in female athymic nude mice from patients with primary squamous cell carcinoma, NOS of the oesophagus (subcutaneously implanted).

PMA study 8 (0.0001 uM; Hep-G2) / vehicle (DMSO) treated Hep-G2 cell sample

Relative Expression (log2-ratio):3.9045906
Number of Samples:3 / 9
Experimental PMA study 8 (0.0001 uM; Hep-G2)
Hep-G2 cells exposed to 0.0001 uM PMA (dissolved in 0.5% v/v DMSO) for 72 hours. Synonyms: phorbol-12-myristat-13-acetate (PMA), tetradecanoylphorbol-acetate (TPA), tetradecanoyl phorbol acetate, 12-O-tetradecanoylphorbol-13-acetate. Cells were exposed to the chemical when 80% confluence was reached. Cells were treated with the IC10 determined by a 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide test (number of replicates, n = 3). ATC code:---
Control vehicle (DMSO) treated Hep-G2 cell sample
Hep-G2 cells treated with vehicle (DMSO 0.5% v/v) for 72 hours. Cells were exposed to the vehicle when 80% confluence was reached.

bronchial epithelial cell differentiation study 1 (day28) / bronchial epithelial cell differentiation study 1 (confluent)

Relative Expression (log2-ratio):3.7933798
Number of Samples:3 / 3
Experimental bronchial epithelial cell differentiation study 1 (day28)
Differentiated normal human bronchial epithelial cell (NHBE) cultured for 28 days in an air-liquid interface (ALI) system. At this time point cells were fully differentiated and formed a polarized, pseudostratified mucociliary epithelium. In order to generate the ALI culture, undifferentiated cells were grown under submerged conditions in bronchial air-liquid interface (B-ALI) growth basal medium supplemented with expansion media. When cells reached confluency (after 3-5 days), an air-liquid interface culture (ALI system) was created by removing the apical medium and replacing the medium of the basal compartment with B-ALI differentiation medium. During the 28 days culture medium was replaced every 48 hour.
Control bronchial epithelial cell differentiation study 1 (confluent)
Confluent undifferentiated normal human bronchial epithelial cell (NHBE) cultured for 3-5 days under submerged conditions in bronchial air-liquid interface (B-ALI) growth basal medium supplemented with expansion media. At this time point cells formed a monolayer covering the whole surface of the insert.

Organism: Homo sapiens
Gene: 11759760_s_at
Selected probe(set): 208490_x_at
Platform: Affymetrix Human Genome U133 Plus 2.0 Array

Expression of 11759760_s_at (208490_x_at) across 5880 perturbations tested by GENEVESTIGATOR:

DN-GRHL2 overexpression study 2 (high TER) / control H2B-GFP transfected bronchial epithelial cell sample (high TER)

Relative Expression (log2-ratio):-3.9597807
Number of Samples:3 / 3
Experimental DN-GRHL2 overexpression study 2 (high TER)
Primary human bronchial epithelial (HBE) cells from donors without pre-existing lung disease infected with lentivirus containing a dominant negative mutant form of grainyheadlike family member 2 (DN-GRHL2). HBE cells (passage 0) were cultured in air-liquid interface. HBE cells (passage 0) were seeded in collagen-coated dishes. At 40% confluence, cell cultures were infected with lentivirus and 48 hours post infection they were selected with 1 ug/ml puromycin. To induce the DN-GRHL2 overexpression 0.5 ug/ml doxycycline was added for 48 hours when transepithelial resistance (TER) reached a maximum level (between day 14 – 18, depending on the donors). To construct an inducible Tet-on GFP-labeled dominant-negative mutant of GRHL2, DNA encoding a truncated version of mouse Grhl2 in which amino acids 1-232 were replaced with EGFP was cloned into pTRIPZ inducible lentiviral vector.
Control control H2B-GFP transfected bronchial epithelial cell sample (high TER)
Primary human bronchial epithelial (HBE) cells from donors without pre-existing lung disease infected with control H2B-GFP lentivirus. HBE cells (passage 0) were cultured in air-liquid interface. Cells were seeded in collagen-coated dishes. At 40% confluence, cell cultures were infected with lentivirus and 48 hours post infection they were selected with 1 ug/ml puromycin. To induce the H2B-GFP expression, 0.5 ug/ml doxycycline was added for 48 hours when transepithelial resistance (TER) reached a maximum level (between day 14 – 18, depending on the donors). To construct a Tet-on GFP labeled control vector, nuclear H2B-GFP was cloned into pTRIPZ inducible lentiviral vector.

wound healing study 2 (ex vivo; AG1478) / normal skin tissue (ex vivo)

Relative Expression (log2-ratio):3.3020477
Number of Samples:3 / 3
Experimental wound healing study 2 (ex vivo; AG1478)
Ex vivo skin samples obtained from healthy donors following reduction surgery of abdomen, and incubated in culture medium containing AG1478 for 4 days. To make sure that mainly epidermis was present in the samples, as much dermal tissue as possible was removed by dissection. Skin was sliced into 1x10 mm slices and incubated in keratinocyte medium for four days with 10 micromolar AG1478 (dissolved in DMSO). The cultivation was performed in serum-free keratinocyte medium supplemented with transferrin, hEGF (0.15 ng/mL), 0.5 mg/mL hydrocortisone, gentamicin, amphotericin B, and epinephrine but without insulin. AG1478 is EGFR kinase inhibitor. ATC code:---
Control normal skin tissue (ex vivo)
Normal skin samples obtained from healthy donors following reduction surgery of abdomen. To make sure that mainly epidermis was present in the samples, as much dermal tissue as possible was removed by dissection.

HIV-associated neurocognitive disorder study 7 (normal) / HIV-associated neurocognitive disorder study 6 (normal)

Relative Expression (log2-ratio):-3.2796373
Number of Samples:2 / 2
Experimental HIV-associated neurocognitive disorder study 7 (normal)
Postmortem brain samples of the centrum semiovale (deep white matter) at the coronal level of the genu of the corpus callosum from patients with normal brain pathology. The patients received antiretroviral therapy (ART).
Control HIV-associated neurocognitive disorder study 6 (normal)
Postmortem brain samples of the centrum semiovale (deep white matter) at the coronal level of the genu of the corpus callosum from patients with normal brain pathology. The patients did not receive any antiretroviral therapy (ART).

wound healing study 2 (ex vivo; DMSO) / normal skin tissue (ex vivo)

Relative Expression (log2-ratio):3.2551737
Number of Samples:3 / 3
Experimental wound healing study 2 (ex vivo; DMSO)
Ex vivo skin samples obtained from healthy donors following reduction surgery of abdomen, and incubated in culture medium containing DMSO for 4 days. To make sure that mainly epidermis was present in the samples, as much dermal tissue as possible was removed by dissection. Skin was sliced into 1x10 mm slices and incubated in keratinocyte medium for four days with 1:1000 fold dilution of DMSO. The cultivation was performed in serum-free keratinocyte medium supplemented with transferrin, hEGF (0.15 ng/mL), 0.5 mg/mL hydrocortisone, gentamicin, amphotericin B, and epinephrine but without insulin.
Control normal skin tissue (ex vivo)
Normal skin samples obtained from healthy donors following reduction surgery of abdomen. To make sure that mainly epidermis was present in the samples, as much dermal tissue as possible was removed by dissection.

tumor supernatant activation study 3 / memory T-cell activation study 1

Relative Expression (log2-ratio):3.2229223
Number of Samples:4 / 3
Experimental tumor supernatant activation study 3
Memory (CD45RA-) CD4+ T cells isolated from peripheral blood of female healthy donors were incubated for 24 hours in 1:1 mix of tumor supernatant from primary invasive breast ductal carcinoma and X-VIVO 20 medium supplemented with antiCD3/CD28 beads, before harvest for RNA isolation. The tumor supernatant was prepared as followed: fresh surgical specimen was dissociated in X-VIVO 20 medium by GentleMACS dissociator and the resulting suspension was clarified by centrifugation for 15min at 13'000 g. ATC code:---
Control memory T-cell activation study 1
Memory (CD45RA-) CD4+ T-cells isolated from peripheral blood of healthy female donors were activated with anti-CD3/CD28 beads for 24hrs.

tumor supernatant activation study 3 / untreated memory CD4 T-cell sample

Relative Expression (log2-ratio):3.163642
Number of Samples:4 / 3
Experimental tumor supernatant activation study 3
Memory (CD45RA-) CD4+ T cells isolated from peripheral blood of female healthy donors were incubated for 24 hours in 1:1 mix of tumor supernatant from primary invasive breast ductal carcinoma and X-VIVO 20 medium supplemented with antiCD3/CD28 beads, before harvest for RNA isolation. The tumor supernatant was prepared as followed: fresh surgical specimen was dissociated in X-VIVO 20 medium by GentleMACS dissociator and the resulting suspension was clarified by centrifugation for 15min at 13'000 g. ATC code:---
Control untreated memory CD4 T-cell sample
Memory (CD45RA-) CD4+ T-cells were isolated from peripheral blood of healthy female donors and incubated in X-VIVO 20 medium for 24 hours, before harvest for RNA isolation.

colorectal cancer study 43 (metastase; brain) / colorectal cancer study 43 (metastase; liver)

Relative Expression (log2-ratio):-3.1052122
Number of Samples:2 / 25
Experimental colorectal cancer study 43 (metastase; brain)
Metastatic tumor tissue obtained from the brain of patients with primary colorectal adenocarcinoma.
Control colorectal cancer study 43 (metastase; liver)
Metastatic tumor tissue obtained from the liver of patients with primary colon adenocarcinoma.

zalypsis study 2 / untreated OPM1 cell sample

Relative Expression (log2-ratio):2.76194
Number of Samples:2 / 2
Experimental zalypsis study 2
OPM1 multiple myeloma cells treated in vitro with zalypsis (5 nM), a novel marine-derived compound with potent antimyeloma activity. Cells were harvested at the beginning of induction of cell death (15-20% cell death as assessed by Annexin V-FITC staining). ATC code:---
Control untreated OPM1 cell sample
OPM1 multiple myeloma cells untreated.

glioma study 16 (BS-149) / normal astrocyte sample

Relative Expression (log2-ratio):2.7295828
Number of Samples:2 / 3
Experimental glioma study 16 (BS-149)
Human glioma cell line BS149 was cultured in DMEM supplemented with 10% FCS (fetal calf serum) and antibiotics at 37°C and 5% CO2.
Control normal astrocyte sample
Normal brain astrocytes. Clonetics normal human astrocytes (NHA) from Cambrex (primary-derived cultures) and cultured according to the manufacturer's recommendations.

HS-27A / HS-5

Relative Expression (log2-ratio):2.6343565
Number of Samples:4 / 4
Experimental HS-27A
Human bone marrow stromal cell line derived from a male Caucasian patient. Cells were immortalized by transduction with the human papilloma virus E6/E7 genes. HS-27a supports obblestone area formation by early hematopoietic progenitors. Synonyms:HS27A; HS27a; HS-27a; HS 27a Cellosaurus code:
Control HS-5
Human bone marrow stromal cell line of a 30 yeas old male Caucasian immortalized by transduction with the human papilloma virus E6/E7 genes. HS-5 secretes multiple cytokines that support the proliferation of committed progenitors. Synonyms:HS5; HS 5 Cellosaurus code: