GEO DataSets

(Submitter supplied) Homeostatic regulation of the intestinal enteroendocrine lineage hierarchy is a poorly understood process. We resolved transcriptional changes during enteroendocrine differentiation in real-time at single-cell level using a novel knock-in allele of Neurog3, the master regulator gene briefly expressed at the onset of enteroendocrine specification. A bi-fluorescent reporter, Neurog3Chrono, measures time from the onset of enteroendocrine differentiation and enables precise positioning of single-cell transcriptomes along an absolute time axis. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19057 GPL21103

45 Samples

Download data: CSV

(Submitter supplied) Analysis of FACS-sorted intestinal Neurog3+/+ and Neurog3+/- cells from Neurog3 fluorencent reporter mice carrying two-(+/+) or one- (+/-) Neurog3 alleles. In the intestine, Neurog3 is an enteroendocrine (EE) lineage determinating transcription factor that transiently expressed in early EEC progenitors. By comparison the molecular profiles of Neurog3+/+ and Neurog3+/- cells, we hypothesized that Neurog3 gene dosage regulates the allocation of EE progenitor fates towards EEC vs. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

6 Samples

Download data: TSV

(Submitter supplied) Sox4 is expressed in intestinal stem cells (ISCs) and early intestinal progenitors. The regulatory role for Sox4 in intestinal homeostasis is currently unknown. Here, we used RNA-seq to determine the role of Sox4 in the intestinal epithelium using a conditional knockout model.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

8 Samples

Download data: TXT

(Submitter supplied) Objective: Enteroendocrine cells (EECs) survey the gut luminal environment and co-ordinate hormonal, immune and neuronal responses to it. They exhibit well characterized physiological roles ranging from the control of local gut function to whole body metabolism, but little is known regarding the regulatory networks controlling their differentiation, especially in human gut. The small molecule Isoxazole-9 (ISX-9) has been shown to stimulate neuronal and pancreatic beta-cell differentiation, both closely related to EEC differentiation. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

2 Samples

Download data: PDF, TSV

(Submitter supplied) Aim: The mammalian gut is the largest endocrine organ. Dozens of hormones secreted by enteroendocrine cells regulate a variety of physiological functions of the gut but also of the pancreas and brain. Here, we examined the role of the helix-loop-helix transcription factor ID2 during the differentiation of intestinal stem cells along the enteroendocrine lineage. Methods: To assess the functions of ID2 in the adult mouse small intestine, we used single-cell RNA sequencing, genetically modified mice, and organoid assays. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

6 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

synthetic construct; Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other; Expression profiling by high throughput sequencing

Platforms:

GPL32628 GPL30173 GPL24676

20 Samples

Download data: BW, MTX, TSV, TXT

(Submitter supplied) Enteroendocrine cells (EECs) are hormone-producing cells residing in the epithelium of stomach, small intestine (SI) and colon. EECs regulate various aspects of metabolic activity including insulin levels, satiety, gastrointestinal secretion and motility. The generation of different EEC lineages of the SI is incompletely understood. We now report a TFome-wide CRISPR knockout screen in adult human intestinal organoids to identify dominant transcription factors controlling EEC differentiation. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

2 Samples

Download data: MTX, TSV

(Submitter supplied) Enteroendocrine cells (EECs) are hormone-producing cells residing in the epithelium of stomach, small intestine (SI) and colon. EECs regulate various aspects of metabolic activity including insulin levels, satiety, gastrointestinal secretion and motility. The generation of different EEC lineages of the SI is incompletely understood. We now report a TFome-wide CRISPR knockout screen in adult human intestinal organoids to identify dominant transcription factors controlling EEC differentiation. more...

Organism:

synthetic construct; Homo sapiens

Type:

Other

Platforms:

GPL30173 GPL32628

11 Samples

Download data: TXT

(Submitter supplied) Enteroendocrine cells (EECs) are hormone-producing cells residing in the epithelium of stomach, small intestine (SI) and colon. EECs regulate various aspects of metabolic activity including insulin levels, satiety, gastrointestinal secretion and motility. The generation of different EEC lineages of the SI is incompletely understood. We now report a TFome-wide CRISPR knockout screen in adult human intestinal organoids to identify dominant transcription factors controlling EEC differentiation. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL30173

7 Samples

Download data: BW

(Submitter supplied) Aim: Transcriptional analysis of the colon of adult Nkx2.2flox/flox;Villin-Cre (Nkx2.2int) mice versus control Methods: 2 cm of the colon (as measured after the caecum) of 6 week old control and mutant mice were dissected and total RNA extracted. Libraries were prepared from total RNA (RIN>8) with the TruSeq RNA prep kit (Illumina) and sequenced using the HiSeq2000 (Illumina) instrument. More than 20 million reads were mapped to the mouse genome (UCSC/mm9) using Tophat (version 2.0.4) with 4 mismatches and 10 maximum multiple hits. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

4 Samples

Download data: CSV

(Submitter supplied) Aim: Transcriptional analysis of the duodenum of adult Nkx2.2flox/TN;Villin-Cre (TNint) mice versus control Methods: 2 cm of the duodenum (as measured from the stomach) of 6 week old control and mutant mice were dissected and total RNA extracted. Libraries were prepared from total RNA (RIN>8) with the TruSeq RNA prep kit (Illumina) and sequenced using the HiSeq2000 (Illumina) instrument. More than 20 million reads were mapped to the mouse genome (UCSC/mm9) using Tophat (version 2.0.4) with 4 mismatches and 10 maximum multiple hits. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

6 Samples

Download data: CSV

(Submitter supplied) Aim: Transcriptional analysis of the duodenum of adult Nkx2.2flox/SD;Villin-Cre (SDint) mice versus control Methods: 2 cm of the duodenum (as measured from the stomach) of 6 week old control and mutant mice were dissected and total RNA extracted. Libraries were prepared from total RNA (RIN>8) with the TruSeq RNA prep kit (Illumina) and sequenced using the HiSeq2000 (Illumina) instrument. More than 20 million reads were mapped to the mouse genome (UCSC/mm9) using Tophat (version 2.0.4) with 4 mismatches and 10 maximum multiple hits. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

6 Samples

Download data: CSV, TXT

(Submitter supplied) Aim: Transcriptional analysis of the duodenum of adult Nkx2.2flox/flox;Villin-Cre (Nkx2.2int) mice versus control Methods: 2 cm of the duodenum (as measured from the stomach) of 6 week old control and mutant mice were dissected and total RNA extracted. Libraries were prepared from total RNA (RIN>8) with the TruSeq RNA prep kit (Illumina) and sequenced using the HiSeq2000 (Illumina) instrument. More than 20 million reads were mapped to the mouse genome (UCSC/mm9) using Tophat (version 2.0.4) with 4 mismatches and 10 maximum multiple hits. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

6 Samples

Download data: CSV, TXT

(Submitter supplied) We performed 7 single-cell RNAseq experiments to identify progenitor cell populations in the small intestine. To also capture rare intestinal cell populations such as stem cells and secretory cells we not only analyzed crypt cells from wildtype mice but also used two reporter mouse lines: i) the FltpZV/+ mouse line of which we mixed live crypt cells with Fltp Venus reporter (FVR) positive cells at different ratios and ii) Foxa2-Venus fusion (FVF) reporter mice. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

14 Samples

Download data: H5AD, MTX, TSV

(Submitter supplied) Enteroendocrine cells (EECs) secrete serotonin (enterochromaffin [EC] cells) or specific peptide hormones (non-EC cells) that serve vital metabolic functions. The basis for terminal EEC diversity remains obscure. By forcing activity of the transcription factor (TF) NEUROG3 in 2D cultures of human intestinal stem cells, we replicated physiologic EEC differentiation and examined transcriptional and cis-regulatory dynamics that culminate in discrete cell types. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Other

Platforms:

GPL20795 GPL24676

101 Samples

Download data: BED, BW, MTX, TBI, TSV

(Submitter supplied) To investigate the regulation of human enteroendocrine cell differentiation, we established Neurog3ER inducible cell lines. We then performed simultaneous gene expression profiling and chromatin analysis at single cell level using data obtained from Multiome-seq at various time points.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

28 Samples

Download data: BED, MTX, TBI, TSV, TXT

(Submitter supplied) To investigate the regulation of human enteroendocrine cell differentiation, we established Neurog3ER inducible cell lines. We then performed gene expression profiling analysis at single cell level using data obtained from single cell RNA-seq of at various time points.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

6 Samples

Download data: MTX, TSV, TXT

(Submitter supplied) To investigate the regulation of human enteroendocrine cell differentiation, we established Neurog3ER inducible cell lines. We then analyzed ASCL1 and NEUROD1 binding using data obtained from CUT&RUN of at 96h.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL20795

12 Samples

Download data: BW, TXT

(Submitter supplied) To investigate the regulation of human enteroendocrine cell differentiation, we established Neurog3ER inducible cell lines. We then analysed active histone marks using data obtained from H3K27ac ChIP-seq at various time points.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20795

4 Samples

Download data: BW

(Submitter supplied) To investigate the regulation of human enteroendocrine cell differentiation, we established Neurog3ER inducible cell lines. We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 independent human lines at various time points.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20795

24 Samples

Download data: TXT