TOP TEN perturbations for 1384_at (Homo sapiens)

Organism: Homo sapiens
Gene: 1384_at
Selected probe(set): 213849_s_at
Platform: Affymetrix Human Genome U133 Plus 2.0 Array

Expression of 1384_at (213849_s_at) across 6672 perturbations tested by GENEVESTIGATOR:

atypical teratoid/rhabdoid tumor study 1 / non-tumor brain tissue

Relative Expression (log2-ratio):-4.25879
Number of Samples:20 / 9
Experimental atypical teratoid/rhabdoid tumor study 1
Primary tumor tissue sample from the brain of pediatric patients with atypical teratoid/rhabdoid tumor (AT/RT).
Control non-tumor brain tissue
Histologically normal brain tissue at rapid autopsy from patients who died from atypical teratoid/rhabdoid tumor.

TC-71 / TC-32

Relative Expression (log2-ratio):4.0475655
Number of Samples:6 / 6
Experimental TC-71
Human primary cancer cell line derived from the humerus of a patient with Ewing sarcoma. Synonyms:TC71; GM11654 Cellosaurus code:
Control TC-32
Human primary cancer cell line derived from the unspecified origin of a patient with Ewing’s sarcoma. Synonyms:TC32 Cellosaurus code:

Langerhans cell histiocytosis study 1 / normal plasmocytoid dendritic cell sample

Relative Expression (log2-ratio):3.98635
Number of Samples:7 / 3
Experimental Langerhans cell histiocytosis study 1
Langerhans cell histiocytes (LCH) were isolated from LCH lesions of patients undergoing surgery. All patients had single system disease, five patients had bone lesion, one had skin lesion and one had mucosal manifestation. Langerhans cells histiocytes were purified by FACS as CD1a+ / CD270 + population with > 95% purity.
Control normal plasmocytoid dendritic cell sample
Normal plasmocytoid dendritic cells were isolated from peripheral blood of healthy adult donors. Plasmocytoid dendritic cells were defined as HLA-DR+ / CD45RAhi / CD11c- / BDCA2+ population.

stem cell differentiation study 46 (BMP4, inhibitors) / normal embryonic stem cell sample (WA09)

Relative Expression (log2-ratio):-3.9238777
Number of Samples:3 / 3
Experimental stem cell differentiation study 46 (BMP4, inhibitors)
Extraembryonic cells differentiated from WA09 cells in chemically defined medium supplemented with BMP4 and inhibitors of activin and FGF2. Differentiation was performed in the absence of feeders cells and serum. Cells were first grown on fibronection-coated plates in CDM supplemented with activin (10 ng/ml) and FGF2 (12 ng/ml) for two days and then in CDM supplemented with BMP4 (10 ng/ml), an inhibitor of Alk4/5/7 receptors (type I Activin receptor-like kinase), SB431542 (10uM), and an inhibitor of FGF receptors, SU5402 (10uM), for 3-4 days.
Control normal embryonic stem cell sample (WA09)
WA09 embryonic stem cells cultivated in chemically defined medium (CDM). Cells were first grown on fibronection-coated plates in CDM supplemented with activin (10 ng/ml) and FGF2 (12 ng/ml) for two days and then further cultivated in CDM alone for 3-4 days. CDM consists of 50% Iscove’s Modified Dulbecco’s Medium and 50% F12 Ham´s nutrient mixture. It is devoid of serum and supplemented with insulin (7 ug/ml), transferrin (15 ug/ml), monothioglycerol (450 uM) and serum albumin (5 mg/ml).

atypical teratoid/rhabdoid tumor study 1 / primitive neuroectodermal tumor study 1

Relative Expression (log2-ratio):-3.8487177
Number of Samples:20 / 9
Experimental atypical teratoid/rhabdoid tumor study 1
Primary tumor tissue sample from the brain of pediatric patients with atypical teratoid/rhabdoid tumor (AT/RT).
Control primitive neuroectodermal tumor study 1
Primary tumor tissue sample from the supratentorial brain of pediatric patients with primitive neuroectodermal tumor.

Langerhans cell histiocytosis study 1 / normal myeloid dendritic cell sample

Relative Expression (log2-ratio):3.8469782
Number of Samples:7 / 3
Experimental Langerhans cell histiocytosis study 1
Langerhans cell histiocytes (LCH) were isolated from LCH lesions of patients undergoing surgery. All patients had single system disease, five patients had bone lesion, one had skin lesion and one had mucosal manifestation. Langerhans cells histiocytes were purified by FACS as CD1a+ / CD270 + population with > 95% purity.
Control normal myeloid dendritic cell sample
Normal myeloid dendritic cells were isolated from peripheral blood of healthy adult donors. Myeloid dendritic cells were defined as HLA-DR+ / CD11c + / BDCA1+ / BDCA3- population.

CAR T cell study 4 (GFP; post-infusion) / CAR T cell study 4 (GFP; pre-infusion)

Relative Expression (log2-ratio):3.732934
Number of Samples:3 / 3
Experimental CAR T cell study 4 (GFP; post-infusion)
CD8+ T cells transduced with GFP 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 GFP as a control. 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 GFP (control group). 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 (GFP; pre-infusion)
Primary human CD8+ T cells stimulated ex vivo and transduced to express GFP. 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 GFP as a control. Cells were cultured for 2 weeks in presence of IL-2, until collection of samples (pre-infusion samples).

pancreatic islet study 3 (expanded; PPRF) / normal pancreatic islet sample

Relative Expression (log2-ratio):-3.7085161
Number of Samples:2 / 7
Experimental pancreatic islet study 3 (expanded; PPRF)
Human pancreatic islets were isolated from a cadaveric donor. The population was 70% pure in mature islets, which was determined by dithizone staining. Islets cells were expanded according to Pharmaceutical Production Research Facility Protocol (PPRF) for 6 weeks. Expansion phase: Approximately 2,500 islet equivalents were seeded onto 75-cm2 fibronectin-coated tissue culture-treated flasks in a proprietary serum-free medium (PPRF medium). The serum-free PPRF medium was supplemented with 30% serum-free mesenchymal-conditioned medium. When the cell migration resulted in the formation of large-size colonies, the cells were harvested by trypsinization and replated into new tissue culture flasks. Once the cells reached near confluence (80–90%) in monolayer, they were trypsinized, counted, and subcultured at a density of 5,000 cells per cm2. Thereafter, cells were serially passaged using the same protocol.
Control normal pancreatic islet sample
Pancreatic islets were obtained from seven donors aged between 37 and 70 years and body mass index between 22 and 27. Functional islets were cultured in CMRL 1066 supplemented with 10% FCS, 1% glutamine, 5.6 mM glucose, 1 mM HEPES, 110 U/ml penicillin, and 110 g/ml streptomycin for 7 days or immediately processed after isolation.

stem cell differentiation study 59 (iDRG; 9d) / normal embryonic stem cell sample (WA09)

Relative Expression (log2-ratio):-3.6614637
Number of Samples:4 / 4
Experimental stem cell differentiation study 59 (iDRG; 9d)
Immature dorsal root ganglia neurons (iDRGs) obtained by differentiation of WA09 embryonic stem cells. WA09 cells were differentiated for 8 days and subsequently cryopreserved. After thawing, cells were further differentiated for 1 day. Further details are described in the paper.
Control normal embryonic stem cell sample (WA09)
Undifferentiated WA09 embryonic stem cell samples.

stem cell differentiation study 46 (BMP4) / normal embryonic stem cell sample (WA09)

Relative Expression (log2-ratio):-3.6025543
Number of Samples:3 / 3
Experimental stem cell differentiation study 46 (BMP4)
Mesendoderm cells differentiated from WA09 cells in chemically defined medium (CDM) supplemented with BMP4. Differentiation was performed in the absence of feeders cells and serum. Cells were first grown on fibronection-coated plates in CDM supplemented with activin (10 ng/ml) and FGF2 (12 ng/ml) for two days and then in CDM supplemented with BMP4 (10 ng/ml) for 3-4 days.
Control normal embryonic stem cell sample (WA09)
WA09 embryonic stem cells cultivated in chemically defined medium (CDM). Cells were first grown on fibronection-coated plates in CDM supplemented with activin (10 ng/ml) and FGF2 (12 ng/ml) for two days and then further cultivated in CDM alone for 3-4 days. CDM consists of 50% Iscove’s Modified Dulbecco’s Medium and 50% F12 Ham´s nutrient mixture. It is devoid of serum and supplemented with insulin (7 ug/ml), transferrin (15 ug/ml), monothioglycerol (450 uM) and serum albumin (5 mg/ml).