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TranscriptomicsTranscription profiling of human cells expressing FoxM1-ER fusion protein
Experiment description To identify FoxM1-regulated genes, we carried out gene expression profile analysis after inducible activation of a FoxM1-ER fusion protein using high-density human cDNA microarrays. We constructed a stable line of U2OS cells expressing full-length HA-FoxM1 fused at its C-term...
ORGANISM(S): Homo sapiens 
2005-01-01 | E-MEXP-230 | biostudies-arrayexpress
TranscriptomicsNiche-Independent Expansion and Controlled Differentiation of Intestinal Stem Cells in vitro
While stem cells at the bottom of intestinal crypts have been isolated and expanded in vitro in the form of organoids, the self-renewal and differentiation of Lgr5+ stem cells in typical culture conditions cannot be easily controlled. Here we show that two small molecules, CHIR99021 and Valproic Aci...
ORGANISM(S): Mus musculus 
2014-04-02 | E-MTAB-1978 | biostudies-arrayexpress
ProteomicsProbing the Tumour Suppressor Function of BAP1 in CRISPR-engineered Human Liver Organoids
The deubiquitinating enzyme BAP1 is a tumour suppressor, amongst others involved in cholangiocarcinoma. BAP1 has many proposed molecular targets, while its Drosophila homolog is known to deubiquitinate Histone H2AK119. Here, we mutate BAP1 by CRISPR/Cas9 in normal human liver organoids. We find that...
ORGANISM(S): Homo sapiens (Human) 
2019-05-22 | PXD013353 | Pride
Bap1 Crispr-cas9 Multiomics Human cholangiocarcinoma Human tumor modelling Human liver organoids 
TranscriptomicsSingle intestinal stem cells build crypt-villus structures in vitro without a cellular niche
The intestinal epithelium is the most rapidly self-renewing tissue in adult mammals. We have recently demonstrated the presence of approximately six cycling Lgr5+ stem cells at the bottoms of small intestinal crypts1. We have now established long-term culture conditions under which single crypts und...
ORGANISM(S): Mus musculus 
2009-04-03 | E-GEOD-14594 | biostudies-arrayexpress
TranscriptomicsPaneth cells constitute the niche for Lgr5 stem cells in intestinal crypts
Homeostasis of self-renewing small intestinal crypts results from neutral competition between Lgr5 stem cells, small cycling cells located at crypt bottoms1, 2. Lgr5 stem cells are interspersed between terminally differentiated Paneth cells, that are known to produce bactericidal products such as ly...
ORGANISM(S): Mus musculus 
2010-11-29 | E-GEOD-25109 | biostudies-arrayexpress
TranscriptomicsLong-term in vitro expansion of epithelial organoids from human colon, adenoma, adenocarcinoma and Barrett's Esophagus
Background & Aims: We have recently established long-term culture conditions under which single crypts or stem cells derived from murine small intestine expand over long periods of time. Growing crypts undergo multiple crypt fission events, whilst simultaneously generating villus-like epithelial dom...
ORGANISM(S): Homo sapiens 
2011-12-07 | E-GEOD-28907 | biostudies-arrayexpress
TranscriptomicsGene expression profiling of Lgr5 positive cells within intestinal adenomas
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 a...
ORGANISM(S): Mus musculus 
2012-08-12 | E-GEOD-37926 | biostudies-arrayexpress
TranscriptomicsGene expression signature of fast and slow cycling intestinal crypt base columnar cell populations
The identification of Lgr5 as an intestinal stem cell marker has made it possible to isolate and study primary stem cells from small intestine. Using the cell cycle specific expression og the mKi67 gene, we generated a novel Ki67-RFP knock-in allele which identifies dividing cells. Using Lgr5-GFP;Ki...
ORGANISM(S): Mus musculus 
2014-09-08 | E-GEOD-52813 | biostudies-arrayexpress
TranscriptomicsRNA-seq of mouse small intestinal organoids with an intestinal-epithelial specific deletion of LSD1 compared to wild type
To assess the role of LSD1 in mouse small intestinal epithelium, we grew small intestinal organoids in vitro from mice with an epithelial specific deletion of LSD1 (Villin-Cre+; Lsd1f/f) and from wild type (Villin-Cre-; Lsd1f/f) mice. This experiment uses a new Cre strain with 100% recombination eff...
ORGANISM(S): Mus musculus 
2023-08-02 | E-MTAB-10500 | biostudies-arrayexpress
GenomicsIntegrated genome-wide analysis of transcription factor occupancy, RNA polymerase II binding and steady-state RNA levels identify differentially regulated functional gene classes
Routine methods for assaying steady-state mRNA levels such as RNA-seq and micro-arrays are commonly used as readouts to study the role of transcription factors (TFs) in gene expression regulation. However, cellular RNA levels do not solely depend on activity of TFs and subsequent transcription by RN...
ORGANISM(S): Homo sapiens 
2012-03-09 | E-GEOD-36349 | biostudies-arrayexpress
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