Expression data from mouse proximal intestinal epithelial Lgr5(hi) stem cells and differentiated villus cells (enterocytes from Atoh1 conditional knockout)
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ABSTRACT: We used microarrays to detail the differentail gene expression between intestinal Lgr5(hi) stem cells and differentiated cells Assay the differential gene expression using total RNA from flow cytometry sorted Lgr5(hi) cells and EDTA isolated enterocytes from Atoh1 conditional knockout
Project description:This SuperSeries is composed of the following subset Series: GSE41541: Expression data from mouse proximal intestinal epithelial Lgr5(hi) stem cells and differentiated villus cells (enterocytes from Atoh1 conditional knockout) GSE41542: H3K79me2 ChIP-seq in mouse proximal intestinal Lgr5(hi) stem cells and villus cells GSE41710: Global gene expression analysis of Dot1l-deficient and control intestinal villus cells in mouse Refer to individual Series
Project description:We analyzed chromatin modifications, DNaseI-hypersensitive sites, and occupancy of a key secretory-lineage transcription factor, ATOH1. We found that lateral inhibition in the intestine occurs through ATOH1 exerting direct control within a broadly permissive chromatin state that is established in stem cells and is highly similar in specified progenitors of divergent potential. Mapping chromatin modifications (H3K4me2 and H3K27ac), DNaseI hypersensitivity (DHS), and ATOH1 binding sites in isolated intestinal crypt progenitors and mature intestinal villus cells.
Project description:Following neural tube closure at around E9.5, the rhombic lip within the rhombomere 1/isthmus region ("upper rhombic lip") produces a sequence of neuronal lineages that populate the brainstem and cerebellum. The transcription factor Atoh1 (Math1) is required for this specialized neurogenesis, although the genetic programs that delineate the temporal cell fate changes downstream of Atoh1 are not well characterized. We examined the gene expresion changes that take place within Atoh1 lineages We purified early (E10.5) and late (E13.5) born Atoh1 expressing cells from E14.5 embryos using a transgenic labeling strategy, and analyzed differences in gene expression across the two populations using the microarray data shown below.
Project description:To investigate the function of Atoh1 in colon cancer cells. We have employed whole genome microarray expression profiling as a discovery platform to iedntify the gene expression induced by Atoh1 in colon cancer cells. Mutated Atoh1 (5SA-Atoh1) replaced 5 serine residues to Alanin for the protein stabilization were expressed in human colon cancer cellline; DLD1 cells. Triplicated RNAs were generated from GFP expressing DLD1 cells and 5SA-Atoh1 expressing DLD1 cell, respectively.
Project description:Using EphB2 or the ISC marker Lgr5, we have FACS-purified and profiled intestinal stem cells (ISCs), crypt proliferative progenitors and late transient amplifying cells to define a gene expression program specific for normal ISCs. A frequent complication in colorectal cancer (CRC) is regeneration of the tumor after therapy. The intestinal stem cell signature predicts disease relapse in CRC and identifies a stem cell-like population that displays robust tumor- initiating capacity in immunodeficient mice as well as long-term self-renewal potential. We FACS purified mouse intestinal crypt cells according to their EphB2 or Lgr5 contents. We used Affymetrix chips to hybridize 2 samples from EphB2 high, 2 samples from EphB2 medium and 2 samples from EphB2 low cells (one sample from each group in a first hybridization on February 2009 plus an additional sample from each group on March 2009). Additionally, we hybridized one sample from Lgr5-EGFP high and one sample from Lgr5-EGFP low cells, obtained from Lgr5-EGFP knock-in mice (Barker et al., 2007).
Project description:Atoh1 is the master transcription factor of intestinal secretory cells. Lineage-tracing model of Atoh1+ve cells showed that the progeny of Atoh1+ve cells can develop into either LGR5+ve or LGR5-ve cells. Present analysis compared the gene expression profile of Atoh1+ve cell-derived LGR5+ve cells and LGR5-ve cells, compared to the resident LGR5+ve cell population of the mouse small intestine.
Project description:The identification of Lgr5 as an intestinal stem cell marker has made it possible to isolate and study primary intestinal stem cells. Applying quantitative mass spectrometry as well as transcriptomic analysis, we profiled the protein and gene changes between FACS-sorted Lgr5+ve stem cells and their immediate undifferentiated daughter cells. The overall comparison of mRNA and protein levels revealed a high level of correlation, implying that the initial control of intestinal stem cell biology occurs largely at the mRNA level. Taken together, our study presents a valuable resource for the study of intestinal stem cell biology. We used cell fractions of intestines from Lgr5-EGFP-ires-CreERT2 mice, expressing GFP under the control of the Lgr5 promoter. RNA was isolated from two FACS sorted cell populations, one expressing GFP at high levels (GFPhi) and the other expressing GFP at low levels (GFPlow). The gates set to sort cells for the expression profiling were the same as for the cells used for the mass spectrometry analysis. Differentially labelled cRNA from GFPhi and GFPlow cells from two different sorts (each combining three different mice) were hybridized on 4X44K Agilent Whole Mouse Genome dual colour Microarrays (G4122F) in two dye swap experiments, resulting in four individual arrays.
Project description:This SuperSeries is composed of the following subset Series: GSE23672: COMPARATIVE TRANSCRIPTOMIC AND PROTEOMIC ANALYSIS OF LGR5+ve STEM CELLS AND THEIR DAUGHTERS (AGILENT ARRAYS) GSE33948: COMPARATIVE TRANSCRIPTOMIC AND PROTEOMIC ANALYSIS OF LGR5+ve STEM CELLS AND THEIR DAUGHTERS (AFFYMETRIX ARRAYS) Refer to individual Series