TOP TEN perturbations for 1553588_at (Homo sapiens)

Organism: Homo sapiens
Gene: 1553588_at
Selected probe(set): 224372_at
Platform: Affymetrix Human Genome U133 Plus 2.0 Array

Expression of 1553588_at (224372_at) across 6672 perturbations tested by GENEVESTIGATOR:

non-contractile lung myofibroblast study 1 (ribo. bound RNA) / non-contractile lung myofibroblast study 1 (total RNA)

Relative Expression (log2-ratio):-2.5398922
Number of Samples:6 / 6
Experimental non-contractile lung myofibroblast study 1 (ribo. bound RNA)
Primary lung myofibroblasts explanted from control individuals grown in a 3-dimensional type I collagen matrix and not allowed to contract. Tissues were obtained from cancer patients (age range 56-82 years) at the time of tumor resection. The analyzed lung resection was histologically normal and distant from tumor tissue. Primary cells outgrowth were cultured in DMEM growth medium (10% FCS) and passaged at a 1:4 split ratio until passage 4 to 9. Cells were considered myofibroblasts if they had a typical spindle morphology, if they were vimentin- and alpha smooth muscle actin-positive and factor VIII and surfactant C-negative. To simulate an aberrant, fibrotic environment, the 3-dimensional type I collagen gel was fixed at the border of the dish to not allow primary cells to freely contract (non-contractile matrices). Microarray was performed only with ribosome-bound RNA.
Control non-contractile lung myofibroblast study 1 (total RNA)
Primary lung myofibroblasts explanted from control individuals grown in a 3-dimensional type I collagen matrix and not allowed to contract. Tissues were obtained from cancer patients (age range 56-82 years) at the time of tumor resection. The analyzed lung resection was histologically normal and distant from tumor tissue. Primary cells outgrowth were cultured in DMEM growth medium (10% FCS) and passaged at a 1:4 split ratio until passage 4 to 9. Cells were considered myofibroblasts if they had a typical spindle morphology, if they were vimentin- and alpha smooth muscle actin-positive and factor VIII and surfactant C-negative. To simulate an aberrant, fibrotic environment, the 3-dimensional type I collagen gel was fixed at the border of the dish to not allow primary cells to freely contract (non-contractile matrices). Microarray was performed with total RNA.

LRPPRC depletion study 1 (9% resid. exp.) / control shRNA infected MCH58 cell sample

Relative Expression (log2-ratio):-2.291832
Number of Samples:2 / 2
Experimental LRPPRC depletion study 1 (9% resid. exp.)
MCH58 cells were infected with lentiviral-shRNA resulting in 9% residual expression of leucine-rich pentatricopeptide repeat motif-containing protein (LRPPRC). Decreased LRPPRC expression resulted in proportional impairment of mitochondrial OXPHOS (oxidative phosphorylation) system function. Mutated LRPPRC is associated with Leigh syndrome, French-Canadian type (LSFC).
Control control shRNA infected MCH58 cell sample
MCH58 cells were mock infected with off-target lentiviral-shRNA. The cells kept 100% expression of leucine-rich pentatricopeptide repeat motif-containing protein (LRPPRC).

sapphyrin PCI-2050 study 1 / mannitol treated A549 cell sample

Relative Expression (log2-ratio):-2.0611763
Number of Samples:3 / 3
Experimental sapphyrin PCI-2050 study 1
A549 human lung cancer cells were seeded eights days prior to treatment of non-cycling plateau phase cultures with drug. At four hours prior to RNA isolation, 1.25uM sapphyrin PCI-2050 (1.25uM final concentration) was added to the culture. ATC code:---
Control mannitol treated A549 cell sample
A549 human lung cancer cells were seeded eights days prior to treatment of non-cycling plateau phase cultures with drug. At four hours prior to RNA isolation, mannitol (5% final concentration) was added to the culture.

idiopathic pulmonary fibrosis study 9 (non-contractile; ribo. bound RNA) / idiopathic pulmonary fibrosis study 9 (non-contractile; total RNA)

Relative Expression (log2-ratio):-2.0100594
Number of Samples:6 / 6
Experimental idiopathic pulmonary fibrosis study 9 (non-contractile; ribo. bound RNA)
Primary lung myofibroblasts explanted from patients with idiopathic pulmonary fibrosis (IPF) grown in a 3-dimensional type I collagen matrix and not allowed to contract. Tissues were obtained from IPF patients (age range 57-68 years) at the time of biopsy, autopsy, lung resection or lung transplantation. Primary cells outgrowth were cultured in DMEM growth medium (10% FCS) and passaged at a 1:4 split ratio until passage 4 to 9. Cells were considered myofibroblasts if they had a typical spindle morphology, if they were vimentin- and alpha smooth muscle actin-positive and factor VIII and surfactant C-negative. To simulate an aberrant, fibrotic environment, the 3-dimensional type I collagen gel was fixed at the border of the dish to not allow primary cells to freely contract (non-contractile matrices). Microarray was performed only with ribosome-bound RNA.
Control idiopathic pulmonary fibrosis study 9 (non-contractile; total RNA)
Primary lung myofibroblasts explanted from patients with idiopathic pulmonary fibrosis (IPF) grown in a 3-dimensional type I collagen matrix and not allowed to contract. Tissues were obtained from IPF patients (age range 57-68 years) at the time of biopsy, autopsy, lung resection or lung transplantation. Primary cells outgrowth were cultured in DMEM growth medium (10% FCS) and passaged at a 1:4 split ratio until passage 4 to 9. Cells were considered myofibroblasts if they had a typical spindle morphology, if they were vimentin- and alpha smooth muscle actin-positive and factor VIII and surfactant C-negative. To simulate an aberrant, fibrotic environment, the 3-dimensional type I collagen gel was fixed at the border of the dish to not allow primary cells to freely contract (non-contractile matrices). Microarray was performed with total RNA.

kidney transplantation study 15 (8 week) / normal monocyte (CD14+) sample

Relative Expression (log2-ratio):-1.9851017
Number of Samples:2 / 5
Experimental kidney transplantation study 15 (8 week)
CD14+ monocyte samples derived from kidney transplant patients 8 weeks post-transplantation. Samples were collected 8 week after transplantation and administration of immunosuppressive therapy (day 1-4: methylprednisolone (60 mg); 3 doses: rabbit polyclonal anti-thymocyte globulin (ThymoglobulinH; 6 mg/kg); mycophenolate mofetil (CellCeptH); and tacrolimus (PrografH).
Control normal monocyte (CD14+) sample
CD14+ monocyte samples derived from healthy control subjects.

idiopathic pulmonary fibrosis study 9 (contractile; ribo. bound RNA) / idiopathic pulmonary fibrosis study 9 (contractile; total RNA)

Relative Expression (log2-ratio):-1.8637085
Number of Samples:6 / 6
Experimental idiopathic pulmonary fibrosis study 9 (contractile; ribo. bound RNA)
Primary lung myofibroblasts explanted from patients with idiopathic pulmonary fibrosis (IPF) grown in a 3-dimensional type I collagen matrix and allowed to contract. Tissues were obtained from IPF patients (age range 57-68 years) at the time of biopsy, autopsy, lung resection or lung transplantation. Primary cells outgrowth were cultured in DMEM growth medium (10% FCS) and passaged at a 1:4 split ratio until passage 4 to 9. Cells were considered myofibroblasts if they had a typical spindle morphology, if they were vimentin- and alpha smooth muscle actin-positive and factor VIII and surfactant C-negative. To simulate the environment of physiological healing, the 3-dimensional type I collagen gel was released from the border of the dish to allow primary cells to freely contract (contractile matrices). Microarray was performed only with ribosome-bound RNA.
Control idiopathic pulmonary fibrosis study 9 (contractile; total RNA)
Primary lung myofibroblasts explanted from patients with idiopathic pulmonary fibrosis (IPF) grown in a 3-dimensional type I collagen matrix and allowed to contract. Tissues were obtained from IPF patients (age range 57-68 years) at the time of biopsy, autopsy, lung resection or lung transplantation. Primary cells outgrowth were cultured in DMEM growth medium (10% FCS) and passaged at a 1:4 split ratio until passage 4 to 9. Cells were considered myofibroblasts if they had a typical spindle morphology, if they were vimentin- and alpha smooth muscle actin-positive and factor VIII and surfactant C-negative. To simulate the environment of physiological healing, the 3-dimensional type I collagen gel was released from the border of the dish to allow primary cells to freely contract (contractile matrices). Microarray was performed with total RNA.

expO thyroid gland cancer study 1 (papillary carcinoma, NOS; primary) / expO thyroid gland cancer study 1 (follicular adenocarcinoma, NOS; primary)

Relative Expression (log2-ratio):1.8559189
Number of Samples:25 / 2
Experimental expO thyroid gland cancer study 1 (papillary carcinoma, NOS; primary)
Primary tumor tissue samples obtained from the thyroid gland of patients with papillary carcinoma (NOS).
Control expO thyroid gland cancer study 1 (follicular adenocarcinoma, NOS; primary)
Primary tumor tissue sample obtained from the thyroid gland of a patient with follicular adenocarcinoma (NOS).

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

Relative Expression (log2-ratio):1.6491051
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.

glioma study 16 (LN-215) / normal astrocyte sample

Relative Expression (log2-ratio):1.6235676
Number of Samples:2 / 3
Experimental glioma study 16 (LN-215)
Human glioma cell line LN215 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.

ARC study 1 / untreated MCF-7 cell sample

Relative Expression (log2-ratio):-1.5875988
Number of Samples:2 / 2
Experimental ARC study 1
MCF7 cells treated with 2uM ARC (4-amino-6-hydrazino-7-beta-d-ribofuranosyl-7H-pyrrolo-(2, 3-d)-pyrimidine-5-carboxamide, NSC 188491) for 24 hours. ATC code:---
Control untreated MCF-7 cell sample
MCF-7 cells untreated.

Organism: Homo sapiens
Gene: 1553588_at
Selected probe(set): 1553588_at
Platform: Affymetrix Human Genome U133 Plus 2.0 Array

Expression of 1553588_at (1553588_at) across 6672 perturbations tested by GENEVESTIGATOR:

HIF-1a/HIF-2a depletion study 1 (hypoxia; AB81) / hypoxia study 11 (AB81)

Relative Expression (log2-ratio):2.1322489
Number of Samples:3 / 3
Experimental HIF-1a/HIF-2a depletion study 1 (hypoxia; AB81)
Human podocyte cells AB81 with shRNA-mediated stable knock-down of HIF-1a and HIF-2a (Hypoxia-inducible factor 1-alpha and Hypoxia-inducible factor 2-alpha) 24 hours after treatment with hypoxia (1% O2). Conditionally immortalized human podocytes AB81 were cultured under permissive conditions (33 °C) in RPMI-1640 supplemented with 10% FBS, antibiotics, and 1% ITS. Differentiation was induced by thermoshift to 37 °C in 6-well plates.
Control hypoxia study 11 (AB81)
Human podocyte cell line AB81 treated with hypoxia (1% O2) for 24 hours. Conditionally immortalized human podocytes AB81 were cultured under permissive conditions (33 °C) in RPMI-1640 supplemented with 10% FBS, antibiotics, and 1% ITS. Differentiation was induced by thermoshift to 37 °C in 6-well plates.

idiopathic pulmonary fibrosis study 9 (non-contractile; ribo. bound RNA) / idiopathic pulmonary fibrosis study 9 (non-contractile; total RNA)

Relative Expression (log2-ratio):-2.0026894
Number of Samples:6 / 6
Experimental idiopathic pulmonary fibrosis study 9 (non-contractile; ribo. bound RNA)
Primary lung myofibroblasts explanted from patients with idiopathic pulmonary fibrosis (IPF) grown in a 3-dimensional type I collagen matrix and not allowed to contract. Tissues were obtained from IPF patients (age range 57-68 years) at the time of biopsy, autopsy, lung resection or lung transplantation. Primary cells outgrowth were cultured in DMEM growth medium (10% FCS) and passaged at a 1:4 split ratio until passage 4 to 9. Cells were considered myofibroblasts if they had a typical spindle morphology, if they were vimentin- and alpha smooth muscle actin-positive and factor VIII and surfactant C-negative. To simulate an aberrant, fibrotic environment, the 3-dimensional type I collagen gel was fixed at the border of the dish to not allow primary cells to freely contract (non-contractile matrices). Microarray was performed only with ribosome-bound RNA.
Control idiopathic pulmonary fibrosis study 9 (non-contractile; total RNA)
Primary lung myofibroblasts explanted from patients with idiopathic pulmonary fibrosis (IPF) grown in a 3-dimensional type I collagen matrix and not allowed to contract. Tissues were obtained from IPF patients (age range 57-68 years) at the time of biopsy, autopsy, lung resection or lung transplantation. Primary cells outgrowth were cultured in DMEM growth medium (10% FCS) and passaged at a 1:4 split ratio until passage 4 to 9. Cells were considered myofibroblasts if they had a typical spindle morphology, if they were vimentin- and alpha smooth muscle actin-positive and factor VIII and surfactant C-negative. To simulate an aberrant, fibrotic environment, the 3-dimensional type I collagen gel was fixed at the border of the dish to not allow primary cells to freely contract (non-contractile matrices). Microarray was performed with total RNA.

non-contractile lung myofibroblast study 1 (ribo. bound RNA) / non-contractile lung myofibroblast study 1 (total RNA)

Relative Expression (log2-ratio):-1.9510403
Number of Samples:6 / 6
Experimental non-contractile lung myofibroblast study 1 (ribo. bound RNA)
Primary lung myofibroblasts explanted from control individuals grown in a 3-dimensional type I collagen matrix and not allowed to contract. Tissues were obtained from cancer patients (age range 56-82 years) at the time of tumor resection. The analyzed lung resection was histologically normal and distant from tumor tissue. Primary cells outgrowth were cultured in DMEM growth medium (10% FCS) and passaged at a 1:4 split ratio until passage 4 to 9. Cells were considered myofibroblasts if they had a typical spindle morphology, if they were vimentin- and alpha smooth muscle actin-positive and factor VIII and surfactant C-negative. To simulate an aberrant, fibrotic environment, the 3-dimensional type I collagen gel was fixed at the border of the dish to not allow primary cells to freely contract (non-contractile matrices). Microarray was performed only with ribosome-bound RNA.
Control non-contractile lung myofibroblast study 1 (total RNA)
Primary lung myofibroblasts explanted from control individuals grown in a 3-dimensional type I collagen matrix and not allowed to contract. Tissues were obtained from cancer patients (age range 56-82 years) at the time of tumor resection. The analyzed lung resection was histologically normal and distant from tumor tissue. Primary cells outgrowth were cultured in DMEM growth medium (10% FCS) and passaged at a 1:4 split ratio until passage 4 to 9. Cells were considered myofibroblasts if they had a typical spindle morphology, if they were vimentin- and alpha smooth muscle actin-positive and factor VIII and surfactant C-negative. To simulate an aberrant, fibrotic environment, the 3-dimensional type I collagen gel was fixed at the border of the dish to not allow primary cells to freely contract (non-contractile matrices). Microarray was performed with total RNA.

hypoxia study 11 (AB81) / control AB81 cell sample (normoxia)

Relative Expression (log2-ratio):-1.915616
Number of Samples:3 / 3
Experimental hypoxia study 11 (AB81)
Human podocyte cell line AB81 treated with hypoxia (1% O2) for 24 hours. Conditionally immortalized human podocytes AB81 were cultured under permissive conditions (33 °C) in RPMI-1640 supplemented with 10% FBS, antibiotics, and 1% ITS. Differentiation was induced by thermoshift to 37 °C in 6-well plates.
Control control AB81 cell sample (normoxia)
Human podocyte cell line AB81 treated with normoxia (20% O2) for 24 hours. Conditionally immortalized human podocytes AB81 were cultured under permissive conditions (33 °C) in RPMI-1640 supplemented with 10% FBS, antibiotics, and 1% ITS. Differentiation was induced by thermoshift to 37 °C in 6-well plates.

polycystic ovary syndrome study 6 / normal granulosa cell sample

Relative Expression (log2-ratio):1.7380733
Number of Samples:5 / 2
Experimental polycystic ovary syndrome study 6
Granulosa cell sample derived from women with polycystic ovary syndrome (PCOS) after controlled ovarian hyperstimulation, as a part of standard in vitro fertilization (IVF) protocol. The PCOS was diagnosed according to Rotterdam revised criteria. All subjects were < 35 years with normal prolactin levels and normal thyroid function.
Control normal granulosa cell sample
Granulosa cell sample derived from normal ovulatory women after controlled ovarian hyperstimulation, as a part of standard in vitro fertilization (IVF) protocol. The reason for IVF was male or tubal factor infertility. All subjects were < 35 years with normal prolactin levels, normal thyroid function, regular menstrual cycle, no clinical or biochemical evidence of hyperandrogenism, no polycystic ovaries and normal insulin sensitivity.

HIF-2a depletion study 1 (hypoxia; AB81) / hypoxia study 11 (AB81)

Relative Expression (log2-ratio):1.7332029
Number of Samples:3 / 3
Experimental HIF-2a depletion study 1 (hypoxia; AB81)
Human podocyte cells AB81 with shRNA-mediated stable knock-down of HIF-2a (Hypoxia-inducible factor 2-alpha) 24 hours after treatment with hypoxia (1% O2). Conditionally immortalized human podocytes AB81 were cultured under permissive conditions (33 °C) in RPMI-1640 supplemented with 10% FBS, antibiotics, and 1% ITS. Differentiation was induced by thermoshift to 37 °C in 6-well plates.
Control hypoxia study 11 (AB81)
Human podocyte cell line AB81 treated with hypoxia (1% O2) for 24 hours. Conditionally immortalized human podocytes AB81 were cultured under permissive conditions (33 °C) in RPMI-1640 supplemented with 10% FBS, antibiotics, and 1% ITS. Differentiation was induced by thermoshift to 37 °C in 6-well plates.

CAR T cell study 4 (PSCA-28t28Z; post-infusion) / CAR T cell study 4 (PSCA-28t28Z; pre-infusion)

Relative Expression (log2-ratio):1.674427
Number of Samples:3 / 3
Experimental CAR T cell study 4 (PSCA-28t28Z; post-infusion)
CD8+ T cells transduced with PSCA-28t28Z (second generation CAR) and isolated 30 days after adoptive transfer into mice bearing HPAC-derived pancreatic tumor. Human peripheral blood mononuclear cells were stimulated with anti-CD3 antibody (OKT3) in presence of IL-2. Two days post-stimulation, T cells were transduced with retroviral vectors encoding PSCA-28t28Z. Cells were cultured for 2 weeks in presence of IL-2 and then transfered into 4-5-week-old male NSG mice. Subcutaneous xenografts were generated by injection of HPAC cells. Once tumors became palpable, mice were treated with CD8+ T cells expressing PSCA-28t28Z. Untransduced CD4+ cells from the same donor were given to each mouse for cytokine support. Spleen-resident human CD8+ T cells were isolated 30 days later using the CD8 MicroBeads (post-infusion samples).
Control CAR T cell study 4 (PSCA-28t28Z; pre-infusion)
Primary human CD8+ T cells stimulated ex vivo and transduced to express PSCA-28t28Z (second generation CAR). Human peripheral blood mononuclear cells were stimulated with anti-CD3 antibody (OKT3) in presence of IL-2. Two days post-stimulation, T cells were transduced with retroviral vectors encoding PSCA-28t28Z. Cells were cultured for 2 weeks in presence of IL-2, until collection of samples (pre-infusion samples).

LRPPRC depletion study 1 (9% resid. exp.) / control shRNA infected MCH58 cell sample

Relative Expression (log2-ratio):-1.6359844
Number of Samples:2 / 2
Experimental LRPPRC depletion study 1 (9% resid. exp.)
MCH58 cells were infected with lentiviral-shRNA resulting in 9% residual expression of leucine-rich pentatricopeptide repeat motif-containing protein (LRPPRC). Decreased LRPPRC expression resulted in proportional impairment of mitochondrial OXPHOS (oxidative phosphorylation) system function. Mutated LRPPRC is associated with Leigh syndrome, French-Canadian type (LSFC).
Control control shRNA infected MCH58 cell sample
MCH58 cells were mock infected with off-target lentiviral-shRNA. The cells kept 100% expression of leucine-rich pentatricopeptide repeat motif-containing protein (LRPPRC).

plicamycin study 2 (100 nM) / vehicle (PBS) treated TC-71 cell sample

Relative Expression (log2-ratio):-1.6105022
Number of Samples:3 / 3
Experimental plicamycin study 2 (100 nM)
TC-71 Ewing´s sarcoma cells treated with compound: plicamycin (mithramycin, 100 nM) for 6 hours. ATC code:
Control vehicle (PBS) treated TC-71 cell sample
TC-71 Ewing´s sarcoma cells treated with 0.01% phosphate-buffered saline (PBS) in growth medium for 6 hours.

HIF-1a/HIF-2a depletion study 1 (hypoxia; AB81) / HIF-1a depletion study 2 (hypoxia; AB81)

Relative Expression (log2-ratio):1.5773325
Number of Samples:3 / 3
Experimental HIF-1a/HIF-2a depletion study 1 (hypoxia; AB81)
Human podocyte cells AB81 with shRNA-mediated stable knock-down of HIF-1a and HIF-2a (Hypoxia-inducible factor 1-alpha and Hypoxia-inducible factor 2-alpha) 24 hours after treatment with hypoxia (1% O2). Conditionally immortalized human podocytes AB81 were cultured under permissive conditions (33 °C) in RPMI-1640 supplemented with 10% FBS, antibiotics, and 1% ITS. Differentiation was induced by thermoshift to 37 °C in 6-well plates.
Control HIF-1a depletion study 2 (hypoxia; AB81)
Human podocyte cells AB81 with shRNA-mediated stable knock-down of HIF-1a (Hypoxia-inducible factor 1-alpha) 24 hours after treatment with hypoxia (1% O2). Conditionally immortalized human podocytes AB81 were cultured under permissive conditions (33 °C) in RPMI-1640 supplemented with 10% FBS, antibiotics, and 1% ITS. Differentiation was induced by thermoshift to 37 °C in 6-well plates.

Organism: Homo sapiens
Gene: 1553588_at
Selected probe(set): 1553588_at
Platform: Affymetrix Human Genome U133 Plus 2.0 Array

Expression of 1553588_at (1553588_at) across 6672 perturbations tested by GENEVESTIGATOR:

HIF-1a/HIF-2a depletion study 1 (hypoxia; AB81) / hypoxia study 11 (AB81)

Relative Expression (log2-ratio):2.1322489
Number of Samples:3 / 3
Experimental HIF-1a/HIF-2a depletion study 1 (hypoxia; AB81)
Human podocyte cells AB81 with shRNA-mediated stable knock-down of HIF-1a and HIF-2a (Hypoxia-inducible factor 1-alpha and Hypoxia-inducible factor 2-alpha) 24 hours after treatment with hypoxia (1% O2). Conditionally immortalized human podocytes AB81 were cultured under permissive conditions (33 °C) in RPMI-1640 supplemented with 10% FBS, antibiotics, and 1% ITS. Differentiation was induced by thermoshift to 37 °C in 6-well plates.
Control hypoxia study 11 (AB81)
Human podocyte cell line AB81 treated with hypoxia (1% O2) for 24 hours. Conditionally immortalized human podocytes AB81 were cultured under permissive conditions (33 °C) in RPMI-1640 supplemented with 10% FBS, antibiotics, and 1% ITS. Differentiation was induced by thermoshift to 37 °C in 6-well plates.

idiopathic pulmonary fibrosis study 9 (non-contractile; ribo. bound RNA) / idiopathic pulmonary fibrosis study 9 (non-contractile; total RNA)

Relative Expression (log2-ratio):-2.0026894
Number of Samples:6 / 6
Experimental idiopathic pulmonary fibrosis study 9 (non-contractile; ribo. bound RNA)
Primary lung myofibroblasts explanted from patients with idiopathic pulmonary fibrosis (IPF) grown in a 3-dimensional type I collagen matrix and not allowed to contract. Tissues were obtained from IPF patients (age range 57-68 years) at the time of biopsy, autopsy, lung resection or lung transplantation. Primary cells outgrowth were cultured in DMEM growth medium (10% FCS) and passaged at a 1:4 split ratio until passage 4 to 9. Cells were considered myofibroblasts if they had a typical spindle morphology, if they were vimentin- and alpha smooth muscle actin-positive and factor VIII and surfactant C-negative. To simulate an aberrant, fibrotic environment, the 3-dimensional type I collagen gel was fixed at the border of the dish to not allow primary cells to freely contract (non-contractile matrices). Microarray was performed only with ribosome-bound RNA.
Control idiopathic pulmonary fibrosis study 9 (non-contractile; total RNA)
Primary lung myofibroblasts explanted from patients with idiopathic pulmonary fibrosis (IPF) grown in a 3-dimensional type I collagen matrix and not allowed to contract. Tissues were obtained from IPF patients (age range 57-68 years) at the time of biopsy, autopsy, lung resection or lung transplantation. Primary cells outgrowth were cultured in DMEM growth medium (10% FCS) and passaged at a 1:4 split ratio until passage 4 to 9. Cells were considered myofibroblasts if they had a typical spindle morphology, if they were vimentin- and alpha smooth muscle actin-positive and factor VIII and surfactant C-negative. To simulate an aberrant, fibrotic environment, the 3-dimensional type I collagen gel was fixed at the border of the dish to not allow primary cells to freely contract (non-contractile matrices). Microarray was performed with total RNA.

non-contractile lung myofibroblast study 1 (ribo. bound RNA) / non-contractile lung myofibroblast study 1 (total RNA)

Relative Expression (log2-ratio):-1.9510403
Number of Samples:6 / 6
Experimental non-contractile lung myofibroblast study 1 (ribo. bound RNA)
Primary lung myofibroblasts explanted from control individuals grown in a 3-dimensional type I collagen matrix and not allowed to contract. Tissues were obtained from cancer patients (age range 56-82 years) at the time of tumor resection. The analyzed lung resection was histologically normal and distant from tumor tissue. Primary cells outgrowth were cultured in DMEM growth medium (10% FCS) and passaged at a 1:4 split ratio until passage 4 to 9. Cells were considered myofibroblasts if they had a typical spindle morphology, if they were vimentin- and alpha smooth muscle actin-positive and factor VIII and surfactant C-negative. To simulate an aberrant, fibrotic environment, the 3-dimensional type I collagen gel was fixed at the border of the dish to not allow primary cells to freely contract (non-contractile matrices). Microarray was performed only with ribosome-bound RNA.
Control non-contractile lung myofibroblast study 1 (total RNA)
Primary lung myofibroblasts explanted from control individuals grown in a 3-dimensional type I collagen matrix and not allowed to contract. Tissues were obtained from cancer patients (age range 56-82 years) at the time of tumor resection. The analyzed lung resection was histologically normal and distant from tumor tissue. Primary cells outgrowth were cultured in DMEM growth medium (10% FCS) and passaged at a 1:4 split ratio until passage 4 to 9. Cells were considered myofibroblasts if they had a typical spindle morphology, if they were vimentin- and alpha smooth muscle actin-positive and factor VIII and surfactant C-negative. To simulate an aberrant, fibrotic environment, the 3-dimensional type I collagen gel was fixed at the border of the dish to not allow primary cells to freely contract (non-contractile matrices). Microarray was performed with total RNA.

hypoxia study 11 (AB81) / control AB81 cell sample (normoxia)

Relative Expression (log2-ratio):-1.915616
Number of Samples:3 / 3
Experimental hypoxia study 11 (AB81)
Human podocyte cell line AB81 treated with hypoxia (1% O2) for 24 hours. Conditionally immortalized human podocytes AB81 were cultured under permissive conditions (33 °C) in RPMI-1640 supplemented with 10% FBS, antibiotics, and 1% ITS. Differentiation was induced by thermoshift to 37 °C in 6-well plates.
Control control AB81 cell sample (normoxia)
Human podocyte cell line AB81 treated with normoxia (20% O2) for 24 hours. Conditionally immortalized human podocytes AB81 were cultured under permissive conditions (33 °C) in RPMI-1640 supplemented with 10% FBS, antibiotics, and 1% ITS. Differentiation was induced by thermoshift to 37 °C in 6-well plates.

polycystic ovary syndrome study 6 / normal granulosa cell sample

Relative Expression (log2-ratio):1.7380733
Number of Samples:5 / 2
Experimental polycystic ovary syndrome study 6
Granulosa cell sample derived from women with polycystic ovary syndrome (PCOS) after controlled ovarian hyperstimulation, as a part of standard in vitro fertilization (IVF) protocol. The PCOS was diagnosed according to Rotterdam revised criteria. All subjects were < 35 years with normal prolactin levels and normal thyroid function.
Control normal granulosa cell sample
Granulosa cell sample derived from normal ovulatory women after controlled ovarian hyperstimulation, as a part of standard in vitro fertilization (IVF) protocol. The reason for IVF was male or tubal factor infertility. All subjects were < 35 years with normal prolactin levels, normal thyroid function, regular menstrual cycle, no clinical or biochemical evidence of hyperandrogenism, no polycystic ovaries and normal insulin sensitivity.

HIF-2a depletion study 1 (hypoxia; AB81) / hypoxia study 11 (AB81)

Relative Expression (log2-ratio):1.7332029
Number of Samples:3 / 3
Experimental HIF-2a depletion study 1 (hypoxia; AB81)
Human podocyte cells AB81 with shRNA-mediated stable knock-down of HIF-2a (Hypoxia-inducible factor 2-alpha) 24 hours after treatment with hypoxia (1% O2). Conditionally immortalized human podocytes AB81 were cultured under permissive conditions (33 °C) in RPMI-1640 supplemented with 10% FBS, antibiotics, and 1% ITS. Differentiation was induced by thermoshift to 37 °C in 6-well plates.
Control hypoxia study 11 (AB81)
Human podocyte cell line AB81 treated with hypoxia (1% O2) for 24 hours. Conditionally immortalized human podocytes AB81 were cultured under permissive conditions (33 °C) in RPMI-1640 supplemented with 10% FBS, antibiotics, and 1% ITS. Differentiation was induced by thermoshift to 37 °C in 6-well plates.

CAR T cell study 4 (PSCA-28t28Z; post-infusion) / CAR T cell study 4 (PSCA-28t28Z; pre-infusion)

Relative Expression (log2-ratio):1.674427
Number of Samples:3 / 3
Experimental CAR T cell study 4 (PSCA-28t28Z; post-infusion)
CD8+ T cells transduced with PSCA-28t28Z (second generation CAR) and isolated 30 days after adoptive transfer into mice bearing HPAC-derived pancreatic tumor. Human peripheral blood mononuclear cells were stimulated with anti-CD3 antibody (OKT3) in presence of IL-2. Two days post-stimulation, T cells were transduced with retroviral vectors encoding PSCA-28t28Z. Cells were cultured for 2 weeks in presence of IL-2 and then transfered into 4-5-week-old male NSG mice. Subcutaneous xenografts were generated by injection of HPAC cells. Once tumors became palpable, mice were treated with CD8+ T cells expressing PSCA-28t28Z. Untransduced CD4+ cells from the same donor were given to each mouse for cytokine support. Spleen-resident human CD8+ T cells were isolated 30 days later using the CD8 MicroBeads (post-infusion samples).
Control CAR T cell study 4 (PSCA-28t28Z; pre-infusion)
Primary human CD8+ T cells stimulated ex vivo and transduced to express PSCA-28t28Z (second generation CAR). Human peripheral blood mononuclear cells were stimulated with anti-CD3 antibody (OKT3) in presence of IL-2. Two days post-stimulation, T cells were transduced with retroviral vectors encoding PSCA-28t28Z. Cells were cultured for 2 weeks in presence of IL-2, until collection of samples (pre-infusion samples).

LRPPRC depletion study 1 (9% resid. exp.) / control shRNA infected MCH58 cell sample

Relative Expression (log2-ratio):-1.6359844
Number of Samples:2 / 2
Experimental LRPPRC depletion study 1 (9% resid. exp.)
MCH58 cells were infected with lentiviral-shRNA resulting in 9% residual expression of leucine-rich pentatricopeptide repeat motif-containing protein (LRPPRC). Decreased LRPPRC expression resulted in proportional impairment of mitochondrial OXPHOS (oxidative phosphorylation) system function. Mutated LRPPRC is associated with Leigh syndrome, French-Canadian type (LSFC).
Control control shRNA infected MCH58 cell sample
MCH58 cells were mock infected with off-target lentiviral-shRNA. The cells kept 100% expression of leucine-rich pentatricopeptide repeat motif-containing protein (LRPPRC).

plicamycin study 2 (100 nM) / vehicle (PBS) treated TC-71 cell sample

Relative Expression (log2-ratio):-1.6105022
Number of Samples:3 / 3
Experimental plicamycin study 2 (100 nM)
TC-71 Ewing´s sarcoma cells treated with compound: plicamycin (mithramycin, 100 nM) for 6 hours. ATC code:
Control vehicle (PBS) treated TC-71 cell sample
TC-71 Ewing´s sarcoma cells treated with 0.01% phosphate-buffered saline (PBS) in growth medium for 6 hours.

HIF-1a/HIF-2a depletion study 1 (hypoxia; AB81) / HIF-1a depletion study 2 (hypoxia; AB81)

Relative Expression (log2-ratio):1.5773325
Number of Samples:3 / 3
Experimental HIF-1a/HIF-2a depletion study 1 (hypoxia; AB81)
Human podocyte cells AB81 with shRNA-mediated stable knock-down of HIF-1a and HIF-2a (Hypoxia-inducible factor 1-alpha and Hypoxia-inducible factor 2-alpha) 24 hours after treatment with hypoxia (1% O2). Conditionally immortalized human podocytes AB81 were cultured under permissive conditions (33 °C) in RPMI-1640 supplemented with 10% FBS, antibiotics, and 1% ITS. Differentiation was induced by thermoshift to 37 °C in 6-well plates.
Control HIF-1a depletion study 2 (hypoxia; AB81)
Human podocyte cells AB81 with shRNA-mediated stable knock-down of HIF-1a (Hypoxia-inducible factor 1-alpha) 24 hours after treatment with hypoxia (1% O2). Conditionally immortalized human podocytes AB81 were cultured under permissive conditions (33 °C) in RPMI-1640 supplemented with 10% FBS, antibiotics, and 1% ITS. Differentiation was induced by thermoshift to 37 °C in 6-well plates.

Organism: Homo sapiens
Gene: 1553588_at
Selected probe(set): 1553588_at
Platform: Affymetrix Human Genome U133 Plus 2.0 Array

Expression of 1553588_at (1553588_at) across 6672 perturbations tested by GENEVESTIGATOR:

HIF-1a/HIF-2a depletion study 1 (hypoxia; AB81) / hypoxia study 11 (AB81)

Relative Expression (log2-ratio):2.1322489
Number of Samples:3 / 3
Experimental HIF-1a/HIF-2a depletion study 1 (hypoxia; AB81)
Human podocyte cells AB81 with shRNA-mediated stable knock-down of HIF-1a and HIF-2a (Hypoxia-inducible factor 1-alpha and Hypoxia-inducible factor 2-alpha) 24 hours after treatment with hypoxia (1% O2). Conditionally immortalized human podocytes AB81 were cultured under permissive conditions (33 °C) in RPMI-1640 supplemented with 10% FBS, antibiotics, and 1% ITS. Differentiation was induced by thermoshift to 37 °C in 6-well plates.
Control hypoxia study 11 (AB81)
Human podocyte cell line AB81 treated with hypoxia (1% O2) for 24 hours. Conditionally immortalized human podocytes AB81 were cultured under permissive conditions (33 °C) in RPMI-1640 supplemented with 10% FBS, antibiotics, and 1% ITS. Differentiation was induced by thermoshift to 37 °C in 6-well plates.

idiopathic pulmonary fibrosis study 9 (non-contractile; ribo. bound RNA) / idiopathic pulmonary fibrosis study 9 (non-contractile; total RNA)

Relative Expression (log2-ratio):-2.0026894
Number of Samples:6 / 6
Experimental idiopathic pulmonary fibrosis study 9 (non-contractile; ribo. bound RNA)
Primary lung myofibroblasts explanted from patients with idiopathic pulmonary fibrosis (IPF) grown in a 3-dimensional type I collagen matrix and not allowed to contract. Tissues were obtained from IPF patients (age range 57-68 years) at the time of biopsy, autopsy, lung resection or lung transplantation. Primary cells outgrowth were cultured in DMEM growth medium (10% FCS) and passaged at a 1:4 split ratio until passage 4 to 9. Cells were considered myofibroblasts if they had a typical spindle morphology, if they were vimentin- and alpha smooth muscle actin-positive and factor VIII and surfactant C-negative. To simulate an aberrant, fibrotic environment, the 3-dimensional type I collagen gel was fixed at the border of the dish to not allow primary cells to freely contract (non-contractile matrices). Microarray was performed only with ribosome-bound RNA.
Control idiopathic pulmonary fibrosis study 9 (non-contractile; total RNA)
Primary lung myofibroblasts explanted from patients with idiopathic pulmonary fibrosis (IPF) grown in a 3-dimensional type I collagen matrix and not allowed to contract. Tissues were obtained from IPF patients (age range 57-68 years) at the time of biopsy, autopsy, lung resection or lung transplantation. Primary cells outgrowth were cultured in DMEM growth medium (10% FCS) and passaged at a 1:4 split ratio until passage 4 to 9. Cells were considered myofibroblasts if they had a typical spindle morphology, if they were vimentin- and alpha smooth muscle actin-positive and factor VIII and surfactant C-negative. To simulate an aberrant, fibrotic environment, the 3-dimensional type I collagen gel was fixed at the border of the dish to not allow primary cells to freely contract (non-contractile matrices). Microarray was performed with total RNA.

non-contractile lung myofibroblast study 1 (ribo. bound RNA) / non-contractile lung myofibroblast study 1 (total RNA)

Relative Expression (log2-ratio):-1.9510403
Number of Samples:6 / 6
Experimental non-contractile lung myofibroblast study 1 (ribo. bound RNA)
Primary lung myofibroblasts explanted from control individuals grown in a 3-dimensional type I collagen matrix and not allowed to contract. Tissues were obtained from cancer patients (age range 56-82 years) at the time of tumor resection. The analyzed lung resection was histologically normal and distant from tumor tissue. Primary cells outgrowth were cultured in DMEM growth medium (10% FCS) and passaged at a 1:4 split ratio until passage 4 to 9. Cells were considered myofibroblasts if they had a typical spindle morphology, if they were vimentin- and alpha smooth muscle actin-positive and factor VIII and surfactant C-negative. To simulate an aberrant, fibrotic environment, the 3-dimensional type I collagen gel was fixed at the border of the dish to not allow primary cells to freely contract (non-contractile matrices). Microarray was performed only with ribosome-bound RNA.
Control non-contractile lung myofibroblast study 1 (total RNA)
Primary lung myofibroblasts explanted from control individuals grown in a 3-dimensional type I collagen matrix and not allowed to contract. Tissues were obtained from cancer patients (age range 56-82 years) at the time of tumor resection. The analyzed lung resection was histologically normal and distant from tumor tissue. Primary cells outgrowth were cultured in DMEM growth medium (10% FCS) and passaged at a 1:4 split ratio until passage 4 to 9. Cells were considered myofibroblasts if they had a typical spindle morphology, if they were vimentin- and alpha smooth muscle actin-positive and factor VIII and surfactant C-negative. To simulate an aberrant, fibrotic environment, the 3-dimensional type I collagen gel was fixed at the border of the dish to not allow primary cells to freely contract (non-contractile matrices). Microarray was performed with total RNA.

hypoxia study 11 (AB81) / control AB81 cell sample (normoxia)

Relative Expression (log2-ratio):-1.915616
Number of Samples:3 / 3
Experimental hypoxia study 11 (AB81)
Human podocyte cell line AB81 treated with hypoxia (1% O2) for 24 hours. Conditionally immortalized human podocytes AB81 were cultured under permissive conditions (33 °C) in RPMI-1640 supplemented with 10% FBS, antibiotics, and 1% ITS. Differentiation was induced by thermoshift to 37 °C in 6-well plates.
Control control AB81 cell sample (normoxia)
Human podocyte cell line AB81 treated with normoxia (20% O2) for 24 hours. Conditionally immortalized human podocytes AB81 were cultured under permissive conditions (33 °C) in RPMI-1640 supplemented with 10% FBS, antibiotics, and 1% ITS. Differentiation was induced by thermoshift to 37 °C in 6-well plates.

polycystic ovary syndrome study 6 / normal granulosa cell sample

Relative Expression (log2-ratio):1.7380733
Number of Samples:5 / 2
Experimental polycystic ovary syndrome study 6
Granulosa cell sample derived from women with polycystic ovary syndrome (PCOS) after controlled ovarian hyperstimulation, as a part of standard in vitro fertilization (IVF) protocol. The PCOS was diagnosed according to Rotterdam revised criteria. All subjects were < 35 years with normal prolactin levels and normal thyroid function.
Control normal granulosa cell sample
Granulosa cell sample derived from normal ovulatory women after controlled ovarian hyperstimulation, as a part of standard in vitro fertilization (IVF) protocol. The reason for IVF was male or tubal factor infertility. All subjects were < 35 years with normal prolactin levels, normal thyroid function, regular menstrual cycle, no clinical or biochemical evidence of hyperandrogenism, no polycystic ovaries and normal insulin sensitivity.

HIF-2a depletion study 1 (hypoxia; AB81) / hypoxia study 11 (AB81)

Relative Expression (log2-ratio):1.7332029
Number of Samples:3 / 3
Experimental HIF-2a depletion study 1 (hypoxia; AB81)
Human podocyte cells AB81 with shRNA-mediated stable knock-down of HIF-2a (Hypoxia-inducible factor 2-alpha) 24 hours after treatment with hypoxia (1% O2). Conditionally immortalized human podocytes AB81 were cultured under permissive conditions (33 °C) in RPMI-1640 supplemented with 10% FBS, antibiotics, and 1% ITS. Differentiation was induced by thermoshift to 37 °C in 6-well plates.
Control hypoxia study 11 (AB81)
Human podocyte cell line AB81 treated with hypoxia (1% O2) for 24 hours. Conditionally immortalized human podocytes AB81 were cultured under permissive conditions (33 °C) in RPMI-1640 supplemented with 10% FBS, antibiotics, and 1% ITS. Differentiation was induced by thermoshift to 37 °C in 6-well plates.

CAR T cell study 4 (PSCA-28t28Z; post-infusion) / CAR T cell study 4 (PSCA-28t28Z; pre-infusion)

Relative Expression (log2-ratio):1.674427
Number of Samples:3 / 3
Experimental CAR T cell study 4 (PSCA-28t28Z; post-infusion)
CD8+ T cells transduced with PSCA-28t28Z (second generation CAR) and isolated 30 days after adoptive transfer into mice bearing HPAC-derived pancreatic tumor. Human peripheral blood mononuclear cells were stimulated with anti-CD3 antibody (OKT3) in presence of IL-2. Two days post-stimulation, T cells were transduced with retroviral vectors encoding PSCA-28t28Z. Cells were cultured for 2 weeks in presence of IL-2 and then transfered into 4-5-week-old male NSG mice. Subcutaneous xenografts were generated by injection of HPAC cells. Once tumors became palpable, mice were treated with CD8+ T cells expressing PSCA-28t28Z. Untransduced CD4+ cells from the same donor were given to each mouse for cytokine support. Spleen-resident human CD8+ T cells were isolated 30 days later using the CD8 MicroBeads (post-infusion samples).
Control CAR T cell study 4 (PSCA-28t28Z; pre-infusion)
Primary human CD8+ T cells stimulated ex vivo and transduced to express PSCA-28t28Z (second generation CAR). Human peripheral blood mononuclear cells were stimulated with anti-CD3 antibody (OKT3) in presence of IL-2. Two days post-stimulation, T cells were transduced with retroviral vectors encoding PSCA-28t28Z. Cells were cultured for 2 weeks in presence of IL-2, until collection of samples (pre-infusion samples).

LRPPRC depletion study 1 (9% resid. exp.) / control shRNA infected MCH58 cell sample

Relative Expression (log2-ratio):-1.6359844
Number of Samples:2 / 2
Experimental LRPPRC depletion study 1 (9% resid. exp.)
MCH58 cells were infected with lentiviral-shRNA resulting in 9% residual expression of leucine-rich pentatricopeptide repeat motif-containing protein (LRPPRC). Decreased LRPPRC expression resulted in proportional impairment of mitochondrial OXPHOS (oxidative phosphorylation) system function. Mutated LRPPRC is associated with Leigh syndrome, French-Canadian type (LSFC).
Control control shRNA infected MCH58 cell sample
MCH58 cells were mock infected with off-target lentiviral-shRNA. The cells kept 100% expression of leucine-rich pentatricopeptide repeat motif-containing protein (LRPPRC).

plicamycin study 2 (100 nM) / vehicle (PBS) treated TC-71 cell sample

Relative Expression (log2-ratio):-1.6105022
Number of Samples:3 / 3
Experimental plicamycin study 2 (100 nM)
TC-71 Ewing´s sarcoma cells treated with compound: plicamycin (mithramycin, 100 nM) for 6 hours. ATC code:
Control vehicle (PBS) treated TC-71 cell sample
TC-71 Ewing´s sarcoma cells treated with 0.01% phosphate-buffered saline (PBS) in growth medium for 6 hours.

HIF-1a/HIF-2a depletion study 1 (hypoxia; AB81) / HIF-1a depletion study 2 (hypoxia; AB81)

Relative Expression (log2-ratio):1.5773325
Number of Samples:3 / 3
Experimental HIF-1a/HIF-2a depletion study 1 (hypoxia; AB81)
Human podocyte cells AB81 with shRNA-mediated stable knock-down of HIF-1a and HIF-2a (Hypoxia-inducible factor 1-alpha and Hypoxia-inducible factor 2-alpha) 24 hours after treatment with hypoxia (1% O2). Conditionally immortalized human podocytes AB81 were cultured under permissive conditions (33 °C) in RPMI-1640 supplemented with 10% FBS, antibiotics, and 1% ITS. Differentiation was induced by thermoshift to 37 °C in 6-well plates.
Control HIF-1a depletion study 2 (hypoxia; AB81)
Human podocyte cells AB81 with shRNA-mediated stable knock-down of HIF-1a (Hypoxia-inducible factor 1-alpha) 24 hours after treatment with hypoxia (1% O2). Conditionally immortalized human podocytes AB81 were cultured under permissive conditions (33 °C) in RPMI-1640 supplemented with 10% FBS, antibiotics, and 1% ITS. Differentiation was induced by thermoshift to 37 °C in 6-well plates.