TOP TEN perturbations for NM_000413 (Homo sapiens)

Organism: Homo sapiens
Gene: NM_000413
Selected probe(set): 205829_at
Platform: Affymetrix Human Genome U133 Plus 2.0 Array

Expression of NM_000413 (205829_at) across 5339 perturbations tested by GENEVESTIGATOR:

TC-71 / TC-32

Relative Expression (log2-ratio):3.2855034
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:

gestational age study 1 (term) / elective termination placenta (1st trim.) tissue

Relative Expression (log2-ratio):1.9690952
Number of Samples:4 / 4
Experimental gestational age study 1 (term)
Term human placenta samples obtained from scheduled uncomplicated C-sections.
Control elective termination placenta (1st trim.) tissue
First trimester placenta samples (45-59 days) obtained from uncomplicated elective termination.

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

Relative Expression (log2-ratio):1.9387102
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; PPRF; 2d) / normal pancreatic islet sample

Relative Expression (log2-ratio):1.9384737
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.

transwell differentiation study 1 (TEER plateau) / untreated MCF10A cell sample

Relative Expression (log2-ratio):1.9145117
Number of Samples:4 / 3
Experimental transwell differentiation study 1 (TEER plateau)
MCF10A cells were plated onto polyester permeable supports (Transwells) at a density of 10^5 cells/cm^2. Plateau represents those plates with a plateau trans-epithelial electrical resistance (TEER) of 3000-3200 Ohms x cm^2.
Control untreated MCF10A cell sample
MCF10A cells grown to confluency on sterile plastic.

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

Relative Expression (log2-ratio):1.8668432
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.

Li-Fraumeni syndrome study 2 / normal breast stromal cell sample

Relative Expression (log2-ratio):-1.8279295
Number of Samples:8 / 4
Experimental Li-Fraumeni syndrome study 2
Morphologically normal breast stromal cells were isolated from non-involved tissue of Li-Fraumeni syndrome patients with breast cancer. Li-Fraumeni syndrome is cancer predisposing syndrome caused by germline mutation of the p53. Clinical characteristics of patient (50): 31-years old female with breast cancer and p53 mutation at codon 133 in exon 5, in one of the two alleles (Met133Thr). The donor had also family history of breast cancer and p53 mutations through at least last three generations. Clinical characteristic of patient (IUSM): 29-years old Caucasian female with non-invasive ductal carcinoma and bilateral Paget disease of the nipples; with heterozygous p53 12141delG germline frameshift mutation. The donor had also a maternal aunt with bilateral breast cancer in her 30's and a male sibling with osteogenic sarcoma of a leg at age 13, who later died of a brain tumor at age 19.
Control normal breast stromal cell sample
Normal breast stromal cells were isolated from donor with no history of cancer and wild-type p53.

Barrett's esophagus study 3 / esophageal squamous cell carcinoma study 1

Relative Expression (log2-ratio):-1.8124723
Number of Samples:17 / 8
Experimental Barrett's esophagus study 3
Esophageal epithelium samples from areas with Barrett's esophagus metaplasia which were recovered by laser capture microdissection.
Control esophageal squamous cell carcinoma study 1
Esophageal squamous cell carcinoma (ESCC) biopsy samples from chemotherapy-naive patients with histological grading G1 (well differentiated) and UICC stage II and III, which undergone esophagectomy.

transwell differentiation study 1 (TEER mid) / untreated MCF10A cell sample

Relative Expression (log2-ratio):1.7974682
Number of Samples:3 / 3
Experimental transwell differentiation study 1 (TEER mid)
MCF10A cells were plated onto polyester permeable supports (Transwells) at a density of 10^5 cells/cm^2. Midpoint represents those plates with a mid trans-epithelial electrical resistance (TEER) of 1400-1600 Ohms x cm^2.
Control untreated MCF10A cell sample
MCF10A cells grown to confluency on sterile plastic.

SDF study 4 / untreated MDA Mb231 cell sample

Relative Expression (log2-ratio):1.7849941
Number of Samples:3 / 6
Experimental SDF study 4
MDA Mb231 cells treated with 75nM stromal derived factor (SDF; Cxcl12) for 6h.
Control untreated MDA Mb231 cell sample
Untreated MDA Mb231 cells harvested after 6h.