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COMPARATIVE TRANSCRIPTOMIC AND PROTEOMIC ANALYSIS OF LGR5+ve STEM CELLS AND THEIR DAUGHTERS (AFFYMETRIX ARRAYS)

ABSTRACT: 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.

ORGANISM(S): Mus musculus

PROVIDER: GSE33948 | GEO | 2012/08/13

SECONDARY ACCESSION(S): PRJNA156463

REPOSITORIES: GEO

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COMPARATIVE TRANSCRIPTOMIC AND PROTEOMIC ANALYSIS OF LGR5+ve STEM CELLS AND THEIR DAUGHTERS (AGILENT ARRAYS)

2012-08-13 | GSE23672 | GEO

COMPARATIVE TRANSCRIPTOMIC AND PROTEOMIC ANALYSIS OF LGR5+ve STEM CELLS AND THEIR DAUGHTERS (AFFYMETRIX ARRAYS)

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 (GFPbright) and the other expressing GFP at low levels (GFPdim). The gates set to sort cells for the expression profiling were the same as for the cells used for the mass spectometry analysis. cRNA from GFPbright and GFPdim cells from three different sorts (each combining three to four mice) were hybridized on Affymetrix Mouse HT MG-430 PM plate arrays.

2012-08-12 | E-GEOD-33948 | biostudies-arrayexpress

COMPARATIVE TRANSCRIPTOMIC AND PROTEOMIC ANALYSIS OF LGR5+ve STEM CELLS AND THEIR DAUGHTERS (AGILENT ARRAYS)

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.

2012-08-12 | E-GEOD-23672 | biostudies-arrayexpress

COMPARATIVE TRANSCRIPTOMIC AND PROTEOMIC ANALYSIS OF LGR5+ve STEM CELLS AND THEIR DAUGHTERS

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

2012-08-12 | E-GEOD-33949 | biostudies-arrayexpress

Lgr5+ve stem cells in nephrogenesis

Project description:Multipotent stem cells and their lineage-restricted progeny drive nephron formation within the developing kidney. Validated markers of these early stem/progenitor populations are essential for deciphering their in vivo function and for evaluating their clinical potential for treating adult kidney disease. Here, we document expression of the adult stem cell marker Lgr5 in the developing kidney and assess the stem/progenitor identity of Lgr5+ve cells via in vivo lineage tracing. The appearance and localization of Lgr5+ve cells coincided with that of the S-shaped body around E14. Lgr5 expression remained restricted to cell clusters within developing nephrons in the cortex until P7, when expression was permanently silenced. In vivo lineage tracing identified Lgr5 as a marker of a novel progenitor population within nascent nephrons dedicated to generating the thick ascending limb of Henle's loop and distal convoluted tubule. The Lgr5 surface marker and experimental models described here will be invaluable for deciphering the contribution of early nephron stem cells to developmental defects and for isolating human nephron progenitors as a prerequisite to evaluating their therapeutic potential.

2012-09-04 | GSE39881 | GEO

Lgr5+ve stem cells in nephrogenesis

2012-09-04 | E-GEOD-39881 | biostudies-arrayexpress

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2013-04-25 | GSE46303 | GEO

Gene expression profile of intestinal stem cells (ISCs) and ATOH1+ve cells in mice

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.

2017-06-01 | GSE81451 | GEO

DNA Methylation Dynamics During Lgr5+ Intestinal Stem Cell Differentiation (Affymetrix Arrays)

Project description:The identification of Lgr5 as an intestinal stem cell marker has made it possible to isolate and study primary stem cells from small intestine and skins. Applying genome-wide resequencing of bisulfite-treated genomic DNA, we profiled the DNA methylation changes of FACS-sorted Lgr5+ve stem cells and their immediate undifferentiated daughter cells from small intestine and skin. In addition to this, we also analyzed terminally differentiated villus cells. We find that terminal differentiation of an adult solid-tissue stem cell does not require DNA methylation dynamics at transcriptional start sites, but is characterized by hypo-methylation of enhancer-like domains. 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 several FACS-sorted cell populations, one expressing GFP at high levels (GFPhi) and the other expressing GFP at low levels (GFPlow), both from small intestine and skin. We also isolated RNA from intestinal epithelial villus cells. Differentially labelled cRNA from GFPhi, GFPlow and villus cells from three different sorts (each combining three different mice) were hybridized on Affymetrix HT MG-430 PM arrays.

2013-04-25 | E-GEOD-46303 | biostudies-arrayexpress

Gene expression profiling of Lgr5 positive cells within intestinal adenomas

Project description:The generation of the Lgr5_EGFP_ires_CreERT2 knock-in mouse allows marking of Lgr5 positive cells of different tissues. Here we use these mice to sort Lgr5 positive cells and their daughter cells form intestinal adenomas and describe the expression profile of these two cell populations. Intestinal adenomas were generated by inducing Apc deletion through tamoxifen injection in Apc_fl/fl-Lgr5_EGFP_ires_CreERT2 mice. In these mice, GFP is expressed under the control of the Lgr5 promoter, leading to highest GFP levels in Lgr5 positive cells (GFP-high). Dividing GFP-high cells pass on Gfp two their daughter cells, thereby diluting the GFP. Daughter cells can therefore be isolated based on their lower GFP positivity (GFP-low). We sorted these two cell fractions (GFP-high and GFP-low) and compared them to each other on 4X44K Agilent Whole Mouse Genome dual colour Microarrays (G4122F). Three independent sorts were performed and RNA of GFP-high cells hybridized directly against RNA of GFP-low cells in three dye swap experiments, resulting in six individual arrays.

2012-08-12 | E-GEOD-37926 | biostudies-arrayexpress

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