TOP TEN perturbations for 1553450_s_at (Homo sapiens)

Organism: Homo sapiens
Gene: 1553450_s_at
Selected probe(set): 235823_at
Platform: Affymetrix Human Genome U133 Plus 2.0 Array

Expression of 1553450_s_at (235823_at) across 6673 perturbations tested by GENEVESTIGATOR:

stem cell differentiation study 50 (IRF2 shRNA; ASC; proerythroblast) / stem cell differentiation study 50 (mock shRNA; ASC; proerythroblast)

Relative Expression (log2-ratio):2.2918043
Number of Samples:3 / 4
Experimental stem cell differentiation study 50 (IRF2 shRNA; ASC; proerythroblast)
Proerythroblast differentiated from IRF2 (interferon regulatory factor 2) shRNA transduced hematopoietic stem/progenitor cells (CD34+). CD34+ hematopoietic stem/progenitor cells (HSC) were transduced with lentivirus expressing shRNA targeting IRF2 gene with following differentiation to the erythroid lineage. HSCs were obtained from magnetically sorted G-CSF mobilized peripheral blood mononuclear cells of healthy donors. Cells were expanded in StemSpan SFEM medium supplied with Flt-3 ligand (100 ng/ml), SCF (100 ng/ml), IL-3 (20 ng/ml), IL-6 (20 ng/ml) and penicillin/streptomycin. Cells were harvested for total RNA extraction at the proerythroblast stage of differentiation.
Control stem cell differentiation study 50 (mock shRNA; ASC; proerythroblast)
Proerythroblast differentiated from control shRNA transduced hematopoietic stem/progenitor cells (CD34+). CD34+ hematopoietic stem/progenitor cells (HSC) were transduced with lentivirus expressing control shRNA with following differentiation to the erythroid lineage. HSCs were obtained from magnetically sorted G-CSF mobilized peripheral blood mononuclear cells of healthy donors. Cells were expanded in StemSpan SFEM medium supplied with Flt-3 ligand (100 ng/ml), SCF (100 ng/ml), IL-3 (20 ng/ml), IL-6 (20 ng/ml) and penicillin/streptomycin. Cells were harvested for total RNA extraction at the proerythroblast stage of differentiation.

atopic dermatitis study 21 (lesional; whole skin) / normal skin tissue

Relative Expression (log2-ratio):2.2257957
Number of Samples:5 / 6
Experimental atopic dermatitis study 21 (lesional; whole skin)
Lesional full thickness skin samples isolated from patient with moderate-to-severe atopic dermatitis by laser capture microdissection. Patients' cohort characteristics: 3 males and 2 females; age 27-59 years (mean age: 39.4 years); SCORing of Atopic Dermatitis index (SCORAD) ranging from 45-65; total IgE: 14-1821 kU/l; eosinophilic count: 1.4-11.8 %.
Control normal skin tissue
Full thickness skin samples isolated from healthy subjects by laser capture microdissection.

stem cell differentiation study 50 (IRF6 shRNA; ASC; proerythroblast) / stem cell differentiation study 50 (mock shRNA; ASC; proerythroblast)

Relative Expression (log2-ratio):2.187086
Number of Samples:3 / 4
Experimental stem cell differentiation study 50 (IRF6 shRNA; ASC; proerythroblast)
Proerythroblast differentiated from IRF6 (interferon regulatory factor 6) shRNA transduced hematopoietic stem/progenitor cells (CD34+). CD34+ hematopoietic stem/progenitor cells (HSC) were transduced with lentivirus expressing shRNA targeting IRF6 gene with following differentiation to the erythroid lineage. HSCs were obtained from magnetically sorted G-CSF mobilized peripheral blood mononuclear cells of healthy donors. Cells were expanded in StemSpan SFEM medium supplied with Flt-3 ligand (100 ng/ml), SCF (100 ng/ml), IL-3 (20 ng/ml), IL-6 (20 ng/ml) and penicillin/streptomycin. Cells were harvested for total RNA extraction at the proerythroblast stage of differentiation.
Control stem cell differentiation study 50 (mock shRNA; ASC; proerythroblast)
Proerythroblast differentiated from control shRNA transduced hematopoietic stem/progenitor cells (CD34+). CD34+ hematopoietic stem/progenitor cells (HSC) were transduced with lentivirus expressing control shRNA with following differentiation to the erythroid lineage. HSCs were obtained from magnetically sorted G-CSF mobilized peripheral blood mononuclear cells of healthy donors. Cells were expanded in StemSpan SFEM medium supplied with Flt-3 ligand (100 ng/ml), SCF (100 ng/ml), IL-3 (20 ng/ml), IL-6 (20 ng/ml) and penicillin/streptomycin. Cells were harvested for total RNA extraction at the proerythroblast stage of differentiation.

atopic dermatitis study 21 (non-lesional; whole skin) / normal skin tissue

Relative Expression (log2-ratio):2.0030794
Number of Samples:5 / 6
Experimental atopic dermatitis study 21 (non-lesional; whole skin)
Non-lesional full thickness skin samples isolated from patient with moderate-to-severe atopic dermatitis by laser capture microdissection. Patients' cohort characteristics: 3 males and 2 females; age 27-59 years (mean age: 39.4 years); SCORing of Atopic Dermatitis index (SCORAD) ranging from 45-65; total IgE: 14-1821 kU/l; eosinophilic count: 1.4-11.8 %.
Control normal skin tissue
Full thickness skin samples isolated from healthy subjects by laser capture microdissection.

Burkitt lymphoma study 2 (immunodeficiency-associated) / Burkitt lymphoma study 1 (endemic)

Relative Expression (log2-ratio):1.896101
Number of Samples:2 / 13
Experimental Burkitt lymphoma study 2 (immunodeficiency-associated)
Tumor tissue samples from the lymph node of children with immunodeficiency-associated Burkitt lymphoma (ID-BL).
Control Burkitt lymphoma study 1 (endemic)
Tumor tissue samples from the lymph node of children with endemic Burkitt lymphoma (eBL).

HCC827 / A-549

Relative Expression (log2-ratio):1.7628765
Number of Samples:6 / 6
Experimental HCC827
Human primary cancer cell line derived from the lung of a patient with non-small-cell lung cancer. Synonyms:HCC-827; HCC0827 Cellosaurus code:
Control A-549
Human primary cancer cell line derived from the lung of a patient with carcinoma. Synonyms:A 549; A549; NCI-A549; A549/ATCC; hA549 Cellosaurus code:

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

Relative Expression (log2-ratio):-1.7504492
Number of Samples:7 / 8
Experimental dendritic cell study 6 (gardiquimod)
Plasmacytoid dendritic cells (pDCs) collected from blood of healthy donors and treated with gardiquimod (TLR7 agonist) for 3 hours. pDCs were sorted as CD303+, CD123+, CD45+, CD69+, CD40+, CD86+.
Control dendritic cell study 6 (untreated)
Plasmacytoid dendritic cells (pDCs) collected from blood of healthy donors. pDCs were sorted as CD303+, CD123+, CD45+, CD69+, CD40+, CD86+.

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

Relative Expression (log2-ratio):-1.7395115
Number of Samples:4 / 4
Experimental dendritic cell study 6 (gardiquimod; RN486)
Plasmacytoid dendritic cells (pDCs) collected from blood of healthy donors and treated with gardiquimod (TLR7 agonist) and RN486 (Bruton’s tyrosine kinase; BTK inhibitor) for 3 hours. pDCs were sorted as CD303+, CD123+, CD45+, CD69+, CD40+, CD86+.
Control dendritic cell study 6 (CpG A; RN486)
Plasmacytoid dendritic cells (pDCs) collected from blood of healthy donors and treated with CpG-A ODN2216 Class A (TLR9 agonist) and RN486 (Bruton’s tyrosine kinase; BTK inhibitor) for 3 hours. pDCs were sorted as CD303+, CD123+, CD45+, CD69+, CD40+, CD86+.

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

Relative Expression (log2-ratio):1.4767761
Number of Samples:4 / 7
Experimental dendritic cell study 6 (CpG A; RN486)
Plasmacytoid dendritic cells (pDCs) collected from blood of healthy donors and treated with CpG-A ODN2216 Class A (TLR9 agonist) and RN486 (Bruton’s tyrosine kinase; BTK inhibitor) for 3 hours. pDCs were sorted as CD303+, CD123+, CD45+, CD69+, CD40+, CD86+.
Control dendritic cell study 6 (CpG A)
Plasmacytoid dendritic cells (pDCs) collected from blood of healthy donors and treated with CpG-A ODN2216 Class A (TLR9 agonist) for 3 hours. pDCs were sorted as CD303+, CD123+, CD45+, CD69+, CD40+, CD86+.

DLBCL study 7 (ABC; plasmablast-like) / DLBCL study 7 (ABC; naive-like)

Relative Expression (log2-ratio):-1.4742804
Number of Samples:11 / 2
Experimental DLBCL study 7 (ABC; plasmablast-like)
Primary tumor samples from patients with diffuse large B-cell lymphoma (activated B-cell like type). Samples were also classified based on subset-specific B-cell-associated gene signature (BAGS) and assigned to plasmablast-like group. Patients were treated according to standard protocols, and comparable doses of RCHOP- like regimens were used. No patient was treated with stem cell transplantation.
Control DLBCL study 7 (ABC; naive-like)
Primary tumor samples from patients with diffuse large B-cell lymphoma (activated B-cell like type). Samples were also classified based on subset-specific B-cell-associated gene signature (BAGS) and assigned to naive-like group. Patients were treated according to standard protocols, and comparable doses of RCHOP- like regimens were used. No patient was treated with stem cell transplantation.

Organism: Homo sapiens
Gene: 1553450_s_at
Selected probe(set): 1553449_at
Platform: Affymetrix Human Genome U133 Plus 2.0 Array

Expression of 1553450_s_at (1553449_at) across 6673 perturbations tested by GENEVESTIGATOR:

smoking study 57 (24 hrs) / smoking study 57 (4 hrs)

Relative Expression (log2-ratio):-3.9270592
Number of Samples:3 / 3
Experimental smoking study 57 (24 hrs)
Nasal epithelium organotypic tissue culture harvested 24 hours (recovery phase) after 4 repetitive exposures to 16% (vol/vol) mainstream cigarette smoke (one 3R4F reference cigarette pro exposure), with 1 hour rest between each treatment. Exposure was performed directly at the air/liquid interface and culture medium was replaced immediately after treatment. The 3D tissue model was generated from primary human nasal epithelial cells derived from a 54 years old Caucasian non-smoking female donor co-cultured with primary human airway fibroblasts.
Control smoking study 57 (4 hrs)
Nasal epithelium organotypic tissue culture harvested 4 hours after 4 repetitive exposures to 16% (vol/vol) mainstream cigarette smoke (one 3R4F reference cigarette pro exposure), with 1 hour rest between each treatment. Exposure was performed directly at the air/liquid interface and culture medium was replaced immediately after treatment. The 3D tissue model was generated from primary human nasal epithelial cells derived from a 54 years old Caucasian non-smoking female donor co-cultured with primary human airway fibroblasts.

smoking study 80 (nasal epith; 3R4F; 4h; 0.15mg/l) / air exposed organotypic nasal epithelium culture sample (4h; 3R4F)

Relative Expression (log2-ratio):3.8281517
Number of Samples:9 / 9
Experimental smoking study 80 (nasal epith; 3R4F; 4h; 0.15mg/l)
Organotypic human nasal epithelium culture 4 hours after exposure to diluted mainstream cigarette smoke (0.15 mg nicotine/l) from 3R4F reference cigarettes. Organotypic nasal MucilAirTM cultures were consisted of nasal epithelial cells derived from a healthy non-smoker 41-year old female, fully differentiated and cultured at the air-liquid interface (37°C, 5% CO2, 90% humidity) and maintained in the respective culture medium in 12-well culture plates (0.7 ml/well), with a medium change every 2 – 3 days, for a maximum of 12 days before exposure. After exposure, the medium was not changed until it was collected. The smoke was generated according to the Health Canada Intense smoking protocol (a 55-mL puff over 2s, twice per minute with an 8-s pump exhaust time). Each 3R4F cigarette was smoked to a defined standard butt length (approximately 35 mm), yielding approximately 10 – 11 puffs per stick. The cultures were exposed to smoke continuously for 28 minutes in smoking machine and 4 hours after smoke exposure the cells were collected for RNA extraction.
Control air exposed organotypic nasal epithelium culture sample (4h; 3R4F)
Organotypic human nasal epithelium culture 4 hours after exposure to conditioned fresh air. Organotypic nasal MucilAirTM cultures were consisted of nasal epithelial cells derived from a healthy non-smoker 41-year old female, fully differentiated and cultured at the air-liquid interface (37°C, 5% CO2, 90% humidity) and maintained in the respective culture medium in 12-well culture plates (0.7 ml/well), with a medium change every 2 – 3 days, for a maximum of 12 days before exposure. After exposure, the medium was not changed until it was collected. The cultures were exposed to conditioned fresh air continuously for 28 minutes. These samples represented control samples for 3R4F smoke exposure at timepoint 4 hours after exposure.

smoking study 65 (4h) / normal sham-exposed bronchial organotypic tissue

Relative Expression (log2-ratio):3.7977962
Number of Samples:3 / 3
Experimental smoking study 65 (4h)
Human bronchial organotypic tissue culture exposed at the air-liquid interface to 16.7% (vol/vol) mainstream cigarette smoke of 4 cigarettes (3R4F, 6-7 minutes each) followed by fresh culture medium incubation for 4 hours. Cigarettes were smoked on a 30-port carousel smoking machine according to health Canada regimen with 1 hour rest between each cigarette. Organotypic culture consisted in a co-culture of primary bronchial respiratory epithelial cells derived from a healthy nonsmoking 67-year-old Caucasian female and primary airway fibroblasts derived from a healthy nonsmoking 61-year-old Caucasian male.
Control normal sham-exposed bronchial organotypic tissue
Human bronchial organotypic tissue culture exposed at the air-liquid interface to 60% humidified air (4 exposure with 1 hour rest between each treatment) followed by fresh culture medium incubation for 4 hours. Organotypic culture consisted in a co-culture of primary bronchial respiratory epithelial cells derived from a healthy nonsmoking 67-year-old Caucasian female and primary airway fibroblasts derived from a healthy nonsmoking 61-year-old Caucasian male.

smoking study 57 (4 hrs) / normal sham-exposed nasal epithelial cell sample

Relative Expression (log2-ratio):3.7393847
Number of Samples:3 / 3
Experimental smoking study 57 (4 hrs)
Nasal epithelium organotypic tissue culture harvested 4 hours after 4 repetitive exposures to 16% (vol/vol) mainstream cigarette smoke (one 3R4F reference cigarette pro exposure), with 1 hour rest between each treatment. Exposure was performed directly at the air/liquid interface and culture medium was replaced immediately after treatment. The 3D tissue model was generated from primary human nasal epithelial cells derived from a 54 years old Caucasian non-smoking female donor co-cultured with primary human airway fibroblasts.
Control normal sham-exposed nasal epithelial cell sample
Nasal epithelium organotypic tissue culture harvested 4 hours after 4 single exposures to 100% humidified air (with 60% humidity), with 1 hour rest between each treatment. Exposure was performed directly at the air/liquid interface and culture medium was replaced immediately after treatment. The 3D tissue model was generated from primary human nasal epithelial cells derived from a 54 years old Caucasian non-smoking female donor co-cultured with primary human airway fibroblasts. The organotypic tissue culture model was maintained for 14 days at 37°C and culture medium replaced every 2 days.

smoking study 57 (48 hrs) / smoking study 57 (4 hrs)

Relative Expression (log2-ratio):-3.7056427
Number of Samples:3 / 3
Experimental smoking study 57 (48 hrs)
Nasal epithelium organotypic tissue culture harvested 48 hours (recovery phase) after 4 repetitive exposures to 16% (vol/vol) mainstream cigarette smoke (one 3R4F reference cigarette pro exposure), with 1 hour rest between each treatment. Exposure was performed directly at the air/liquid interface and culture medium was replaced immediately after treatment. The 3D tissue model was generated from primary human nasal epithelial cells derived from a 54 years old Caucasian non-smoking female donor co-cultured with primary human airway fibroblasts.
Control smoking study 57 (4 hrs)
Nasal epithelium organotypic tissue culture harvested 4 hours after 4 repetitive exposures to 16% (vol/vol) mainstream cigarette smoke (one 3R4F reference cigarette pro exposure), with 1 hour rest between each treatment. Exposure was performed directly at the air/liquid interface and culture medium was replaced immediately after treatment. The 3D tissue model was generated from primary human nasal epithelial cells derived from a 54 years old Caucasian non-smoking female donor co-cultured with primary human airway fibroblasts.

smoking study 6 brand cig. (intermediate) / air exposed bronchial epithelial cell sample

Relative Expression (log2-ratio):3.617343
Number of Samples:3 / 3
Experimental smoking study 6 brand cig. (intermediate)
Normal human bronchial epithelial cells exposed to smoke from a typical "full flavor" American brand of cigarettes for 15 min. Afterwards cells were re-fed with fresh media and incubated for 4h.
Control air exposed bronchial epithelial cell sample
Normal human bronchial epithelial cells exposed to air for 15 min. Afterwards cells were fed with fresh media and incubated for 4h.

smoking study 80 (nasal epith; CHTP1.2; 4h; 0.51mg/l) / air exposed organotypic nasal epithelium culture sample (4h; CHTP1.2)

Relative Expression (log2-ratio):3.5742512
Number of Samples:9 / 9
Experimental smoking study 80 (nasal epith; CHTP1.2; 4h; 0.51mg/l)
Organotypic human nasal epithelium culture 4 hours after exposure to 0.51 mg nicotine/l aerosol from a potential modified-risk tobacco product, carbon-heated tobacco product 1.2 (CHTP1.2). Organotypic nasal MucilAirTM cultures were consisted of nasal epithelial cells derived from a healthy non-smoker 41-year old female, fully differentiated and cultured at the air-liquid interface (37°C, 5% CO2, 90% humidity) and maintained in the respective culture medium in 12-well culture plates (0.7 ml/well), with a medium change every 2 – 3 days, for a maximum of 12 days before exposure. After exposure, the medium was not changed until it was collected. The aerosol was generated according to the Health Canada Intense smoking protocol (a 55-mL puff over 2s, twice per minute with an 8-s pump exhaust time). Each CHTP1.2 stick was used for a total of 12 puffs per stick. The cultures were exposed to aerosol continuously for 28 minutes in smoking machine and 4 hours after aerosol exposure the cells were collected for RNA extraction.
Control air exposed organotypic nasal epithelium culture sample (4h; CHTP1.2)
Organotypic human nasal epithelium culture 4 hours after exposure to conditioned fresh air. Organotypic nasal MucilAirTM cultures were consisted of nasal epithelial cells derived from a healthy non-smoker 41-year old female, fully differentiated and cultured at the air-liquid interface (37°C, 5% CO2, 90% humidity) and maintained in the respective culture medium in 12-well culture plates (0.7 ml/well), with a medium change every 2 – 3 days, for a maximum of 12 days before exposure. After exposure, the medium was not changed until it was collected. The cultures were exposed to conditioned fresh air continuously for 28 minutes. These samples represented control samples for CHTP1.2 aerosol exposure (carbon-heated tobacco product 1.2) at timepoint 4 hours after exposure.

sbPBS study 2 (direct treatment) / PBS study 2 (direct treatment)

Relative Expression (log2-ratio):3.5528383
Number of Samples:3 / 3
Experimental sbPBS study 2 (direct treatment)
Human coronary artery endothelial cell (HCAEC) treated for 4 hours with smoke-bubbled PBS (sbPBS). Cells were cultured as monolayer on collagen A-coated cell culture plates, in standard endothelial growth culture medium. 1 day after confluency cells were starved overnight in endothelial growth medium containing 0.5% FCS and exposed to sbPBS for 4 hours. The aqueous cigarette smoke extract was produced from mainstream smoke (generated by a 20-port Borgwaldt smoking machine according to ISO standard 3308) from reference 3R4F cigarette bubbled through PBS (10 cigarettes/32 ml PBS). sbPBS was freshly prepared before experiment and was diluted in RPMI 1640 starving medium (0.5% FCS) to a final concentration of 0.09 puffs/ml. ATC code:---
Control PBS study 2 (direct treatment)
Human coronary artery endothelial cell (HCAEC) treated for 4 hours with PBS. Cells were cultured as monolayer on collagen A-coated cell culture plates, in standard endothelial growth culture medium. 1 day after confluency cells were starved overnight in endothelial growth medium containing 0.5% FCS and exposed for 4 hours to PBS (vehicle) diluted in RPMI 1640 starving medium (0.5% FCS). ATC code:---

smoking study 66 (4h) / normal sham-exposed nasal organotypic tissue

Relative Expression (log2-ratio):3.5314941
Number of Samples:3 / 3
Experimental smoking study 66 (4h)
Human nasal organotypic tissue culture exposed at the air-liquid interface to 16.7% (vol/vol) mainstream cigarette smoke of 4 cigarettes (3R4F, 6-7 minutes each) followed by fresh culture medium incubation for 4 hours. Cigarettes were smoked on a 30-port carousel smoking machine according to health Canada regimen with 1 hour rest between each cigarette. Organotypic culture consisted in a co-culture of primary nasal respiratory epithelial cells derived from a healthy nonsmoking 65-year-old Caucasian male and primary airway fibroblasts derived from a healthy nonsmoking 61-year-old Caucasian male.
Control normal sham-exposed nasal organotypic tissue
Human nasal organotypic tissue culture exposed at the air-liquid interface to 60% humidified air (4 exposure with 1 hour rest between each treatment) followed by fresh culture medium incubation for 4 hours. Organotypic culture consisted in a co-culture of primary nasal respiratory epithelial cells derived from a healthy nonsmoking 65-year-old Caucasian male and primary airway fibroblasts derived from a healthy nonsmoking 61-year-old Caucasian male.

smoking study 58 (48 hrs) / smoking study 58 (4 hrs)

Relative Expression (log2-ratio):-3.5293121
Number of Samples:3 / 3
Experimental smoking study 58 (48 hrs)
Nasal epithelium organotypic tissue culture harvested 48 hours (recovery phase) after 4 repetitive exposures to 10% (vol/vol) mainstream cigarette smoke (one 3R4F reference cigarette pro exposure), with 1 hour rest between each treatment. Exposure was performed directly at the air/liquid interface and culture medium was replaced immediately after treatment. The 3D tissue model was generated from primary human nasal epithelial cells derived from a 54 years old Caucasian non-smoking female donor co-cultured with primary human airway fibroblasts.
Control smoking study 58 (4 hrs)
Nasal epithelium organotypic tissue culture harvested 4 hours after 4 repetitive exposures to 10% (vol/vol) mainstream cigarette smoke (one 3R4F reference cigarette pro exposure), with 1 hour rest between each treatment. Exposure was performed directly at the air/liquid interface and culture medium was replaced immediately after treatment. The 3D tissue model was generated from primary human nasal epithelial cells derived from a 54 years old Caucasian non-smoking female donor co-cultured with primary human airway fibroblasts.