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Total RNA sequencing of APC mutant and wt colonic organoids

ABSTRACT: We report elevated expression levels of genes involved in colon cancer in samples that carry mutations in the APC gene. Mutated skin fibroblasts were reprogrammed to iPSCs and then differentiated to colonigc organoids, where the total RNA was extracted from.

ORGANISM(S): Homo sapiens

PROVIDER: GSE77250 | GEO | 2017/06/19

SECONDARY ACCESSION(S): PRJNA309855

REPOSITORIES: GEO

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The effect of TGF-beta in Apc-mutated mouse intestinal organoids

Project description:Intestinal crypts isolated from Apcflox/flox; villin-CreERT mice were treated with Tamoxifen to induce the deletion of Apc. Tamoxifen-treated organoids were selected in the absence of Wnt agonists and then treated with TGF-beta. Total RNA obtained from Tamoxifen-treated, Apc-deleted intestinal organoids in the absence or presence of 3 ng/ml TGF-beta (18h).

2014-04-18 | E-GEOD-35093 | biostudies-arrayexpress

Gene expression changes in Apc-mutant mouse intestinal organoids with and without deleting the Prox1 transcription factor

Project description:We isolated and selected intestinal adenoma organoids from villin-CreER; Apcflox/flox and villin-CreER; Apcflox/flox; Prox1flox/flox mice and added tamoxifen to induce the deletion of the Apc and Prox1 genes in the intestinal epitheliul ex vivo. Microarray experiments were carried out 7 days after the addition of tamoxifen. Total RNA obtained from villin-CreER; Apcflox/flox and villin-CreER; Apcflox/flox; Prox1flox/flox organoids were compared 7 days after the addition of tamoxifen and 5 days after the selection for Apc-mutant organoids in the absence of the Wnt-agonist R-Spondin1.

2014-08-15 | E-GEOD-47568 | biostudies-arrayexpress

Molecular pathology of Usher 1B patient-derived retinal organoids at single cell resolution

Project description:Compare single cell transcriptomes of control and USH1B patient iPSC-derived retinal organoids to elucidate disease mechanisms of Usher syndrome type IB (USH1B). USH1B patient fibroblasts were collected at Great Ormond Street Hospital (GOSH) and reprogrammed to iPSCs. Control and patient iPSCs differentiated in vitro to generate retinal organoids and collected at 35wks. Sequencing was performed at GENEWIZ (Azenta life sciences) on a Illumina NovaSeq system. Data aligned to the human genome UCSC hg38 using cellranger package.

2023-03-27 | E-MTAB-11990 | biostudies-arrayexpress

scRNAseq of mouse colorectal organoids in FOLFIRI treatment

Project description:The aim of the experiment is to elucidate changes in tumor heterogeneity upon chemotherapy treatment. The experiment includes non-treated samples, samples right after chemotherapy treatment (FOLFIRI) and organoids recovered from FOLFIRI. It was conducted in two different genetic backgrounds, AKP (Apc KO, KrasG12D and P53 KO) and APS (Apc KO, P53 and Smad4KO). In addition to that, the organoids carry an inducible Cre-ERT2 knock-in allele in the mex3a locus. Upon 4-OH-Tamoxifen induction, Mex3a cells will recombine the tracing allele stop-TdTomato, enabling the tracing of this subpopulation. To understand the fate of the traced cells, samples right after chemotherapy and in the recovery setting were sorted based on their tomato expression. This enables a single cell tracing experiment.

2022-05-13 | E-MTAB-11145 | biostudies-arrayexpress

Gene expression changes in Apc-mutant mouse intestinal organoids 7 and 20 days after the induction of the Apc deletion

Project description:We isolated and selected intestinal adenoma organoids from Lgr5-EGFP-IRES-CreER; Apcflox/flox mice and added tamoxifen to induce the deletion of the Apc gene in the intestinal stem cells. Gene expressions on day7 and day20 after the addition of tamoxifen were compared, representing two stages with different colorectal cancer stem cell content. Total RNA obtained from Lgr5-EGFP-IRES-CreER; Apcflox/flox organoids were compared 7 days and 20 days after the addition of tamoxifen, cultured without the Wnt-agonist R-Spondin1.

2015-12-31 | E-GEOD-47569 | biostudies-arrayexpress

Lipid Profiling of Mouse Intestinal Organoids for studying APC Mutations

Project description:Inactivating mutations including both germline and somatic mutations in the adenomatous polyposis coli (APC) gene drives most familial and sporadic colorectal cancers. Understanding the metabolic implications of this mutation will aid to establish its wider impact on cellular behaviour and potentially inform clinical decisions. However, to date, alterations in lipid metabolism induced by APC mutations remain unclear. Intestinal organoids have gained widespread popularity in studying colorectal cancer and chemotherapies, because their three-dimensional structure more accurately mimics an in vivo environment. Here, we aimed to investigate intra-cellular lipid disturbances induced by APC gene mutations in intestinal organoids using a reversed-phase ultra-high-performance liquid chromatography mass spectrometry (RP-UHPLC-MS)-based lipid profiling method. Lipids of the organoids grown from either wildtype (WT) or mice with Apc mutations (Lgr5–EGFP-IRES-CreERT2 Apcfl/fl) were extracted and analysed using RP-UHPLC-MS. Concentrations of phospholipids (e.g. PC(16:0/16:0), PC(18:1/20:0), PC(38:0), PC(18:1/22:1)), ceramides (e.g. Cer(d18:0/22:0), Cer(d42:0), Cer(d18:1/24:1)) and hexosylceramide (e.g. HexCer(d18:1/16:0), HexCer(d18:1/22:0)) were higher in Apcfl/fl organoids, whereas levels of sphingomyelins (e.g. SM(d18:1/14:0), SM(d18:1/16:0) ) were lower compared to WT. These observations indicate that cellular metabolism of sphingomyelin was upregulated, resulting in the cellular accumulation of ceramides and production of HexCer due to the absence of Apcfl/fl in the organoids. Our observations demonstrated lipid profiling of organoids and provided an enhanced insight into the effects of the APC mutations on lipid metabolism, making for a valuable addition to screening options of the organoid lipidome.

2021-02-17 | ST001707 | MetabolomicsWorkbench

microRNAs differentially regulated in organoids derived from tumors of Apc-deficient mice

Project description:microRNA expression profiles were investigated in organoids derived from tumors of Apc-deficient mice and normal intestinal epitehlia of wild-type mice.

2016-12-01 | GSE75482 | GEO

The effect of TGF-beta in Apc-mutated mouse intestinal organoids

2014-04-18 | GSE35093 | GEO

Human pluripotent stem cell-derived kidney organoids reveal tubular epithelial pathobiology of heterozygous HNF1B-associated dysplastic kidney malformations - cell line dataset

Project description:Hepatocyte nuclear factor 1B (HNF1B) encodes a transcription factor expressed in developing human kidney epithelia. Heterozygous HNF1B mutations are the commonest monogenic cause of dysplastic kidney malformations (DKMs). To understand their pathobiology, we generated heterozygous HNF1B mutant kidney organoids from CRISPR-Cas9 gene-edited human ESCs and iPSCs reprogrammed from a family with HNF1B-asscociated DKMs. Mutant organoids contained enlarged malformed tubules and displayed deregulated cell turnover. This submission is RNAseq of organoids from MAN13 embryonic stem cells.

2024-04-29 | E-MTAB-12824 | biostudies-arrayexpress

Human pluripotent stem cell-derived kidney organoids reveal tubular epithelial pathobiology of heterozygous HNF1B-associated dysplastic kidney malformations

2024-04-29 | E-MTAB-12822 | biostudies-arrayexpress

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