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TranscriptomicsscRNA-seq of human fetal duodenal enteroids grown in EGF and/or NRG1
The purpose of this study was to interrogate the role of EGF-family ligands, in particular Epidermal Growth Factor (EGF) and Neuregulin 1 (NRG1), as human intestinal stem cell niche factors. An established duodenal enteroid line derived from a 20.2 week post conception biological specimen was expose...
ORGANISM(S): Homo sapiens 
2020-12-10 | E-MTAB-9720 | biostudies-arrayexpress
TranscriptomicsMultiomic (Joint snRNA/snATAC) sequencing data of intestinal crypts and epithelial only organoids derived from human fetal duodenum
Here, we used joint single-nuclei RNA-sequencing (snRNA-seq) and single-nuclei ATAC sequencing (scATAC) to profile freshly isolated crypts from the human fetal intestine and matched intestinal epithelial only organoids (also known as enteroids) derived from these crypts after one passage of in vitro...
ORGANISM(S): Homo sapiens 
2022-07-16 | E-MTAB-11908 | biostudies-arrayexpress
TranscriptomicsscRNA-seq of intestinal epithelial organoids derived from human fetal duodenum
Here, we used single-cell RNA-sequencing (scRNA-seq) to profile intestinal epithelial only organoids (also known as enteroids) from human fetal duodenum after one passage of in vitro growth. Organoids were grown in the standard 25% LWRN media with either 100 ng/ml of EGF or 1 ng/ml of EREG added.
ORGANISM(S): Homo sapiens 
2022-07-17 | E-MTAB-11912 | biostudies-arrayexpress
TranscriptomicsEpithelial maturation of human intestinal organoids from pluripotency entirely in vitro
In vitro human pluripotent stem cell derived intestinal organoids (HIOs) are immature and lack for diverse differentiated secretory cell types. We would like to test the hypothesis whether addition of a mesenchyme secreting ligand which is depleted in canonical organoid culture media could increase ...
ORGANISM(S): Homo sapiens 
2022-12-31 | E-MTAB-10876 | biostudies-arrayexpress
TranscriptomicsscRNA-seq of human fetal intestine tissue
Here, we performed single cell RNA sequencing (scRNA-seq) of human fetal duodenal tissue samples from 8 individual biological specimens across 7-21 weeks of gestation. The data set is composed of over 37,000 cells (between 3,000-9,000 cells per time point) from diverse intestinal lineages. Lineages ...
ORGANISM(S): Homo sapiens 
2020-12-12 | E-MTAB-9489 | biostudies-arrayexpress
TranscriptomicsscRNA-seq of pluripotent stem cell derived human intestinal organoids
Here, we used single cell RNA-sequencing (scRNA-seq) to profile pluripotent stem cell derived human intestinal organoids (HIOs) grown in matrigel or a non-adhesive alginate hydrogel after 28 days of in vitro growth. Additionally, we used scRNA-seq to profile HIOs derived in the presence of Neureguli...
ORGANISM(S): Homo sapiens 
2021-05-21 | E-MTAB-10268 | biostudies-arrayexpress
TranscriptomicsTranscription profiling of XX and XY sorted mouse somatic support cells and XX and XY mouse whole gonads to identify potential new mammalian gonadal sex determining genes.
Gonadal sex determining (GSD) genes that initiate fetal ovarian and testicular development and differentiation are expressed in the cells of the urogenital ridge that differentiate as somatic support cells (SSCs), i.e., granulosa cells of the ovary and Sertoli cells of the testis. To identify potent...
ORGANISM(S): Mus musculus 
2007-11-30 | E-GEOD-4928 | biostudies-arrayexpress
TranscriptomicsGene expression profiles induced by overexpression of PDEF in MCF10A mammary epithelial cell line
Recent studies suggest that PDEF is required for secretory cell differentiation in several epithelial tissues. To investigate PDEF in the mammary gland, we examined the effect of this transcription factor on gene expression using microarray based profiling of MCF-10A cells. These cells are non-trans...
ORGANISM(S): Homo sapiens 
2014-03-29 | E-GEOD-40986 | biostudies-arrayexpress
TranscriptomicsTranscriptomic Classification of Genetically Engineered Mouse Models of Breast Carcinoma Identifies Human Subtype Counterparts
Background: Human breast cancer is a heterogeneous disease consisting of multiple molecular subtypes. Genetically engineered mouse models (GEMMs) are useful resources for studying breast cancers in vivo under genetically controlled and immune competent conditions. Identifying murine models with cons...
ORGANISM(S): Mus musculus 
2013-11-04 | E-GEOD-42640 | biostudies-arrayexpress
TranscriptomicsComparison of Expression Profiles for Agrobacterium tumefaciens visR mutant to wild-type strain.
Many bacteria colonize surfaces and transition to a sessile mode of growth. The plant pathogen Agrobacterium tumefaciens produces a unipolar polysaccharide (UPP) adhesin at single cell poles that contact surfaces. Here we report that elevated levels of the intracellular signal cyclic diguanosine mon...
ORGANISM(S): Agrobacterium tumefaciens 
2014-08-21 | E-GEOD-60565 | biostudies-arrayexpress
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