Transcriptome profiling using RNA-seq of ß-TC3 cell, a mouse pancreatic cell line used in the study of novel Cis-regulatory elements for the Pax6 gene . Overall design: Total RNA was collected and a Illumina sequencing libraries prepared from two biological replicates of cultured ß-TC3 cells.
Functional characteristics of novel pancreatic Pax6 regulatory elements.
Cell line, Subject
View SamplesSamples were taken from colorectal cancers in surgically resected specimens in 35 colorectal cancer patients. The expression profiles were determined using Affymetrix Human Genome U133 Plus 2.0 arrays. Comparison between the sample groups allow to identify a set of discriminating genes that can be used for molecular markers for CIN phynotype.
Chromosomal instability (CIN) phenotype, CIN high or CIN low, predicts survival for colorectal cancer.
Specimen part
View SamplesSamples were taken from colorectal cancers in surgically resected specimens in 33 colorectal cancer patients. The expression profiles were determined using Affymetrix Human Genome U133 Plus 2.0 arrays. Comparison between the sample groups allow to identify a set of discriminating genes that can be used for molecular markers for CIN phynotype
Chromosomal instability (CIN) phenotype, CIN high or CIN low, predicts survival for colorectal cancer.
Specimen part
View SamplesSpecimens were obtained from non-neoplastic colorectal mucosa for RNA ayalysis. Samples were obtained either from surgically resected specimens or during surveillance coloscopy. The expression profiles were determined using Affymetrix Human Genome U133 Plus 2.0 arrays.The correlation between mtDNA CNV and mitochondria-related gene expressions were investigated.
Increased Copy Number Variation of mtDNA in an Array-based Digital PCR Assay Predicts Ulcerative Colitis-associated Colorectal Cancer.
Specimen part, Disease, Disease stage
View SamplesAnalysis of gene expression by RNA-seq upon siRNA mediated knockdown of scaffold attachment factor A (SAF-A) versus control siRNA in RPE1 cells at 24 hour and 48 hour time points post transfection reveals SAF-A loss does not impact on gene transcription Overall design: Two control RNA-seq libraries where produced (24h and 48h) to compare to the two SAF-A siRNA knockdown RNA-seq libraries, each was a single experimental replicate.
SAF-A Regulates Interphase Chromosome Structure through Oligomerization with Chromatin-Associated RNAs.
Cell line, Subject
View SamplesColon cancer invade to depper layer and the expression of major molecules at cancer front change. But the screening of expression changing at cancer front has not be adequtely clarified.
Microarray Analysis of Gene Expression at the Tumor Front of Colon Cancer.
No sample metadata fields
View Samplesc-Myc is one of key players that are crucially involved in maintaining the undifferentiated state and the self-renewal of ESCs. To understand the mechanism by which c-Myc helps preserve these prominent characteristics of ESCs, we generated null-ES cells for the Max gene, which encodes the best characterized partner protein for all Myc family proteins. Although Myc/Max complexes have been widely regarded as crucial regulators of the ESC status, our data reveal that ESCs do not absolutely require these complexes in so-called ground state or related conditons and that this requirement is restricted to conventional ES culture conditions without using a MAPK inhibitor.
Indefinite self-renewal of ESCs through Myc/Max transcriptional complex-independent mechanisms.
Sex, Specimen part
View SamplesAblation of expression of the Max gene encoding a Myc protein partner in ES cells provoked two major phenomena, i.e. loss of pluripotency and apoptotic cell death. We found that nicotinamide (Nam) significantly alleviates these Max expression ablation-coupled phenotypes in ES cells. To see the alleviation effect of Nam on the overall expression profile of Max-null ES cells whose Max expression is controlled by the tet-off system, we eliminated Max expression by adding doxycycline (Dox) in the presence of Nam.
Sirt1, p53, and p38(MAPK) are crucial regulators of detrimental phenotypes of embryonic stem cells with Max expression ablation.
Sex, Specimen part, Treatment
View SamplesEpithelia of small and large intestines differ in their structures and functions. Such heterogeneity between these two epithelial tissues might be controlled by both epithelium-intrinsic and -extrinsic programs. By employing the cell transplantation technique developed in our laboratory, we investigated how adult SI epithelial cells behave when heterotopically transplanted onto colon. Then the gene expression profiles of small intestinal epithelium heterotopically transplanted onto colon and control colonic epithelium were compared.
Small intestinal stem cell identity is maintained with functional Paneth cells in heterotopically grafted epithelium onto the colon.
Specimen part
View SamplesmRNA-seq and expression profile of mouse ES OS25 cells Overall design: Gene expression (mRNA-Seq) in mouse ES cells
Polycomb associates genome-wide with a specific RNA polymerase II variant, and regulates metabolic genes in ESCs.
Cell line, Subject
View Samples