The goal of the study was to understand how integrin beta1 expressed in epithelial cells directs developmental angiogenesis. Integrin beta1 was deleted specifically in the pituitary glands of embryonic mice. RNA was isolated from knockout and WT control pituitaries dissected at e12.5, one day prior to the initiation of developmental angiogenesis. Overall design: RNA from the e12.5 pituitaries of 3 WT and 2 KO littermate embryos was profiled.
Epithelial cell integrin β1 is required for developmental angiogenesis in the pituitary gland.
Specimen part, Subject
View SamplesPurpose: We tested global gene transcriptome changes by RNA-sequencing analysis in the offspring breast tumors of SV40 transgenic mice to further identify key epigenetic-controlled genes in regulation of the prenatal/maternal BSp diet-mediated early breast cancer prevention. Method: Mouse offspring mammary tumor mRNA from control and maternal BSp treatment were generated by deep sequencing, in duplicate or triplicate, using Illumina NextSeq500 platform (GPL19057). The sequence reads that passed quality filters were analyzed. We utilized the R/Bioconductor package DESeq to evaluate differential gene expression for sequence count data by the use of negative binomial distributio. qRT–PCR validation was performed using TaqMan and SYBR Green assays. Conclusions: Our data showed differential transcriptome distribution in the breast tumors of mouse offspring between the control and prenatal/maternal BSp treatment groups. Overall design: Total RNA obtained from the offspring breast tumors of SV40 transgenic mice with mothers fed either control or BSp diets, and analyzed by Illumina NextSeq500 platform (GPL19057).
Temporal Efficacy of a Sulforaphane-Based Broccoli Sprout Diet in Prevention of Breast Cancer through Modulation of Epigenetic Mechanisms.
Age, Cell line, Treatment, Subject
View Samplestranscriptome profiling of miR-92a inhibitor treated and control cells with the aim of measuring miR-92a influence on its mRNA targets
Mapping the human miRNA interactome by CLASH reveals frequent noncanonical binding.
Cell line, Treatment
View SamplesHESC-H9 and iPSC lines 3.5, 3.6 and 3.12 were analyzed using Affymetrix microarray before and after Definitive Endoderm (DE) formation. DE was induced using the ActivinA differentiation protocol described by D'Amour et al., 2006 (PMID: 16258519) Clustering analysis of transcripts that were differentially regulated during DE formation indicated that iPSC lines 3.5 and 3.12 differentiate in manner that is highly similar to HESC-H9 cells iPSC line 3.6 had a more divergent transcriptional profile.
Directed differentiation of human pluripotent stem cells into intestinal tissue in vitro.
No sample metadata fields
View SamplesWe performed gene expression profiling of 26 colorectal tumors and matched histologically normal adjacent colonic tissue samples using the Illumina Ref-8 whole-genome expression BeadChip. We performed an integrated analysis of promoter DNA methylation and gene expression data to investigate the effects of DNA hypermethylation on gene expression.
Genome-scale analysis of aberrant DNA methylation in colorectal cancer.
Sex, Disease, Disease stage
View SamplesActinic keratosis is a common skin disease that may progress to invasive squamous cell carcinoma. Ingenol mebutate has demonstrated efficacy in field treatment of actinic keratosis. However, molecular mechanisms on ingenol mebutate response are not yet fully understood.
Identification of differentially expressed genes in actinic keratosis samples treated with ingenol mebutate gel.
Specimen part, Disease, Disease stage, Subject
View SamplesThis SuperSeries is composed of the SubSeries listed below.
Transcriptome and cytogenetic profiling analysis of matched in situ/invasive cutaneous squamous cell carcinomas from immunocompetent patients.
Sex, Age, Specimen part, Disease stage, Subject
View SamplesAlthough most cutaneous squamous cell carcinomas (cSCC) develop from actinic keratoses (AK), the key events for this evolution remain unclear. We have combined the results of different genomic and expression array platforms on matched samples of sun-exposed skin, AK and cSCC from ten immunocompetent patients, with the objective of better understanding the mechanisms involved in this progression. Gene expression analysis and copy number alterations were assessed using GeneChip Human Gene 2.0 ST Array (Affymetrix) and CytoScan HD Cytogenetics Solution (Affymetrix) platforms, respectively. Integration of genome and transcriptome results was evaluated using the DR-Integrator tool. Additional studies (qPCR, immunohistochemistry and Western blot) were performed for selected genes. Twenty-two genes showed a progressive expression spectrum from clinically normal sun-exposed skin samples to cSCC. FOSL1 and BNC1 encode transcription factors whose expression was increased in cSCC in the expression array and the qPCR. By immunohistochemistry, FOSL1 showed an intense staining at the invasive front of cSCC samples and BNC1 expression varied from a nuclear location (sun-exposed skin) to a cytoplasmic location (cSCC). Western blot analyses confirmed the enhancement of FOSL1 and BNC1 expression. Additionally, the smallest overlapping regions of genomic imbalance (SORIs) involving at least 3 of the samples of each group (sun-exposed skin, AK or cSCC) were selected. One of the SORIs was a deletion in the p24.1 band of chromosome 3, shared by 7 of the cSCC. A strong correlation in the integration analysis was found for NEK10, a gene contained in the previously mentioned SORI. Loss of NEK10 expression in cSCC was confirmed by immunohistochemistry and western blot analyses. In conclusion, our findings suggest that FOSL1 may play a role in promoting the cSCC invasion ability. We have also identified two additional genes, NEK10 and BNC1, which could also act as tumor drivers.
Transcriptome and cytogenetic profiling analysis of matched in situ/invasive cutaneous squamous cell carcinomas from immunocompetent patients.
Sex, Age, Specimen part, Disease stage, Subject
View SamplesIt is unclear how nanosecond electrical pulses affect gene expression.
Evaluation of the Genetic Response of U937 and Jurkat Cells to 10-Nanosecond Electrical Pulses (nsEP).
Specimen part, Cell line
View SamplesIt is unclear how nanosecond electrical pulses affect gene expression.
Evaluation of the Genetic Response of U937 and Jurkat Cells to 10-Nanosecond Electrical Pulses (nsEP).
Specimen part, Cell line
View Samples