TOP TEN perturbations for 39946_at (Homo sapiens)

Organism: Homo sapiens
Gene: 39946_at
Selected probe(set): 205815_at
Platform: Affymetrix Human Genome U133 Plus 2.0 Array

Expression of 39946_at (205815_at) across 6674 perturbations tested by GENEVESTIGATOR:

hepatoblastoma study 1 (crowded fetal) / normal liver tissue

Relative Expression (log2-ratio):9.668184
Number of Samples:3 / 5
Experimental hepatoblastoma study 1 (crowded fetal)
Liver tumor tissue samples from children with hepatoblastoma (epithelial type (E-HB); crowded fetal subtype). Tumors were integrase interactor 1–negative (INI1 or SMARCB1) as recommended by the International ConsensusHBClassification group.
Control normal liver tissue
Normal liver tissue samples.

hepatoblastoma study 1 (fetal) / normal liver tissue

Relative Expression (log2-ratio):9.14909
Number of Samples:4 / 5
Experimental hepatoblastoma study 1 (fetal)
Liver tumor tissue samples from children with hepatoblastoma (epithelial type (E-HB); fetal subtype). Tumors were integrase interactor 1–negative (INI1 or SMARCB1) as recommended by the International ConsensusHBClassification group.
Control normal liver tissue
Normal liver tissue samples.

colorectal cancer study 33 (adenocarcinoma; trans. colon) / normal transverse colon tissue

Relative Expression (log2-ratio):8.724121
Number of Samples:5 / 2
Experimental colorectal cancer study 33 (adenocarcinoma; trans. colon)
Primary tumor samples derived from the transverse colon of patients with adenocarcinoma.
Control normal transverse colon tissue
Normal transverse colon tissue samples.

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

Relative Expression (log2-ratio):-8.589153
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.

pancreatic islet study 3 (re-differentiated; PPRF; 4d) / normal pancreatic islet sample

Relative Expression (log2-ratio):-8.5454855
Number of Samples:2 / 7
Experimental pancreatic islet study 3 (re-differentiated; PPRF; 4d)
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 for 6 weeks and re-differentiated for 4 days according to Pharmaceutical Production Research Facility (PPRF) Protocol. Re-differentiation phase: For induction of expanded cells to differentiate into islet-like cell clusters, the cells were seeded into 60 mm ultra-low attachment dishes in serum-free CMRL-1066 supplemented with 4 mM L-glutamine, 1% BSA, insulin (10 g/ml), transferrin (5.5 g/ml), sodium selenite (6.7ng/ml), and 1% antibiotic antimycotic solution at a density of 6.0 x 10EXP6 cells per dish. The induction medium was further added with islet neogenesis-associated protein (INGAP) peptide at a concentration of 1.0ug/ml.
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.

pancreatic islet study 3 (re-differentiated; Whittier) / normal pancreatic islet sample

Relative Expression (log2-ratio):-8.53565
Number of Samples:2 / 7
Experimental pancreatic islet study 3 (re-differentiated; Whittier)
Human pancreatic islets were from 2 male donors (46 and 54 years old, body mass index 21kg/m2 and 31.6kg/m2). Islets cells were expanded for 4 weeks and re-differentiated for 1 week according to Whittier protocol. Re-differentiation phase: After four passages (1 month expansion), cells were dispersed with Versene and cultured in serum-free CMRL-1066 medium supplemented with insulin (10 g/ml), transferrin (5.5 g/ml), sodium selenite (6.7ng/ml). After 1 week of culture on HTB-9-coated plates, cells were harvested and forced to reaggregate overnight.
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.

pancreatic islet study 3 (re-differentiated; PPRF; 2d) / normal pancreatic islet sample

Relative Expression (log2-ratio):-8.484818
Number of Samples:2 / 7
Experimental pancreatic islet study 3 (re-differentiated; PPRF; 2d)
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 for 6 weeks and re-differentiated for 2 days according to Pharmaceutical Production Research Facility (PPRF) Protocol. Re-differentiation phase: For induction of expanded cells to differentiate into islet-like cell clusters, the cells were seeded into 60 mm ultra-low attachment dishes in serum-free CMRL-1066 supplemented with 4 mM L-glutamine, 1% BSA, insulin (10 g/ml), transferrin (5.5 g/ml), sodium selenite (6.7ng/ml), and 1% antibiotic antimycotic solution at a density of 6.0 x 10EXP6 cells per dish. The induction medium was further added with islet neogenesis-associated protein (INGAP) peptide at a concentration of 1.0ug/ml.
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.

pancreatic islet study 3 (re-differentiated; NIH) / normal pancreatic islet sample

Relative Expression (log2-ratio):-8.448603
Number of Samples:4 / 7
Experimental pancreatic islet study 3 (re-differentiated; NIH)
Pancreatic islet cells were expanded for 10 weeks and re-differentiated for 1 week according to National Institutes of Health (NIH) protocol. Re-differentiation phase: Expanded cells were cultured for 1 week in serum-free CMRL-1066 medium supplemented with insulin (10 g/ml), transferrin (5.5 g/ml), sodium selenite (6.7ng/ml).
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.

pancreatic islet study 3 (re-differentiated; PPRF; 8d) / normal pancreatic islet sample

Relative Expression (log2-ratio):-8.407543
Number of Samples:2 / 7
Experimental pancreatic islet study 3 (re-differentiated; PPRF; 8d)
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 for 6 weeks and re-differentiated for 8 days according to Pharmaceutical Production Research Facility (PPRF) Protocol. Re-differentiation phase: For induction of expanded cells to differentiate into islet-like cell clusters, the cells were seeded into 60 mm ultra-low attachment dishes in serum-free CMRL-1066 supplemented with 4 mM L-glutamine, 1% BSA, insulin (10 g/ml), transferrin (5.5 g/ml), sodium selenite (6.7ng/ml), and 1% antibiotic antimycotic solution at a density of 6.0 x 10EXP6 cells per dish. The induction medium was further added with islet neogenesis-associated protein (INGAP) peptide at a concentration of 1.0 ug/ml.
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.

pancreatic islet study 3 (expanded; Whittier; HGF) / normal pancreatic islet sample

Relative Expression (log2-ratio):-8.386121
Number of Samples:3 / 7
Experimental pancreatic islet study 3 (expanded; Whittier; HGF)
Human pancreatic islets cells were expanded according to Whittier protocol and treated with hepatocyte growth factor (HGF, 25 ng/ml) for 4 weeks. Expansion phase: 1000 islets of 50–150µm in diameter were purified by hand-picking after dithizone staining, partially dissociated using Versene to separate “outer” and “inner” populations, the outer population was removed. Cell clusters from the inner population were plated on HTB-9 matrix-coated dishes in RPMI-1640 supplemented with 2 mM L-glutamine, 10% FBS, and 25 ng/ml HGF. After confluence, cells were harvested using Versene containing 0.025% trypsin and subcultured (1:2).
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.