GEO DataSets

(Submitter supplied) We profiled genome-wide accesssible chromatin data and RNA-seq from four species (zebrafish, stickleback, mouse, and human) to identify commonly regulated genes and regulatory metods in intestinal epithelial cells (IECs). We identify a group genes that are commonly expressed in IECs and genes that are commonly expressed along the length of the intestine in fish and mammals. Using accessible chromatin data we identified enriched transcription factor binding site motifs In IECs and sites that are commonly accessible in IECs in all species. more...

Organism:

Danio rerio

Type:

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

Platform:

GPL14875

7 Samples

Download data: BED, BW, TXT

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

Organism:

Homo sapiens; Danio rerio; Gasterosteus aculeatus

Type:

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

Platforms:

GPL14875 GPL11154 GPL18463

21 Samples

Download data: BED, BW, TXT

(Submitter supplied) We profiled genome-wide accesssible chromatin data and RNA-seq from four species (zebrafish, stickleback, mouse, and human) to identify commonly regulated genes and regulatory metods in intestinal epithelial cells (IECs). We identify a group genes that are commonly expressed in IECs and genes that are commonly expressed along the length of the intestine in fish and mammals. Using accessible chromatin data we identified enriched transcription factor binding site motifs In IECs and sites that are commonly accessible in IECs in all species. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL11154

10 Samples

Download data: BED, BW, TXT

(Submitter supplied) We profiled genome-wide accesssible chromatin data and RNA-seq from four species (zebrafish, stickleback, mouse, and human) to identify commonly regulated genes and regulatory metods in intestinal epithelial cells (IECs). We identify a group genes that are commonly expressed in IECs and genes that are commonly expressed along the length of the intestine in fish and mammals. Using accessible chromatin data we identified enriched transcription factor binding site motifs In IECs and sites that are commonly accessible in IECs in all species. more...

Organism:

Gasterosteus aculeatus

Type:

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

Platform:

GPL18463

4 Samples

Download data: BED, BW, TXT

(Submitter supplied) We profiled transcriptome and accessible chromatin landscapes in intestinal epithelial cells (IECs) from mice reared in the presence or absence of microbiota. We show that regional differences in gene transcription along the intestinal tract were accompanied by major alterations in chromatin organization. Surprisingly, we discovered that microbiota modify host gene transcription in IECs without significantly impacting the accessible chromatin landscape. more...

Organism:

Mus musculus

Type:

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

Platform:

GPL13112

39 Samples

Download data: BIGWIG, TXT

(Submitter supplied) In order to test the development of gastrointestinal tract (GIT) in pre-weaned cavles, the GIT tissues were collected from day 0, day 7, day 21 and day 42 calves. RNA-seq was used to measure the transcriptome profiles. The RNA-seq analysis revealed the fast development of small intestine and rumen tissue during the first week after birth.

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15749

71 Samples

Download data: TXT

(Submitter supplied) 8 week-old male Hsd:ICR(CD-1) mice were fed ad libitum a standard chow (Harlan Teklad diet 2018S) and housed in groups of five. Animals were then divided into 3 pools (n=10) and sacrificed. The small intestine was extracted and divided into three sections, where the first 2-3 cm after the stomach comprised the duodenum, the middle third the jejunum, and the section before the ileo-ceco-colic junction comprised the ileum. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Datasets:

GDS521 GDS522 GDS524

Platforms:

GPL82 GPL83 GPL81

36 Samples

Download data

Analysis of regional differences in gene expression profiles along the intestinal tract. Duodenum, jejunum, ileum, and colon of 8 week-old male Hsd:ICR(CD-1) mice examined.

Organism:

Mus musculus

Type:

Expression profiling by array, count, 4 tissue sets

Platform:

GPL83

Series:

GSE849

12 Samples

Download data

Analysis of regional differences in gene expression profiles along the intestinal tract. Duodenum, jejunum, ileum, and colon of 8 week-old male Hsd:ICR(CD-1) mice examined.

Organism:

Mus musculus

Type:

Expression profiling by array, count, 4 tissue sets

Platform:

GPL82

Series:

GSE849

12 Samples

Download data

Analysis of regional differences in gene expression profiles along the intestinal tract. Duodenum, jejunum, ileum, and colon of 8 week-old male Hsd:ICR(CD-1) mice examined.

Organism:

Mus musculus

Type:

Expression profiling by array, count, 4 tissue sets

Platform:

GPL81

Series:

GSE849

12 Samples

Download data

(Submitter supplied) Super-enhancers (SEs) are key transcriptional drivers of cellular, developmental and disease states in mammals, yet the conservational and regulatory features of these enhancer elements in non-mammalian vertebrates are unknown. To define SEs in zebrafish and enable sequence and functional comparisons to mouse and human SEs, we used genome-wide histone H3 lysine 27 acetylation (H3K27ac) occupancy as a primary SE delineator. more...

Organism:

Danio rerio

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18413

18 Samples

Download data: BED, WIG

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

Organism:

Danio rerio; Mus musculus

Type:

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

Platforms:

GPL17021 GPL18413 GPL13112

45 Samples

Download data: BIGWIG, TXT

(Submitter supplied) We profiled transcriptome and chromatin landscapes in jejunal mouse intestinal epithelial cells (IECs) from mice reared in the absence (Germ Free or GF) or presence (Conventionalized or CV) of microbiota. We show that microbiota colonization results in changes in histone modifications at hundreds of enhancers that are associated with microbiota-regulated genes. Furthermore, we show that microbiota colonization is associated with a drastic genome-wide reduction in Hnf4a and Hnf4g binding.

Organism:

Mus musculus

Type:

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

Platforms:

GPL13112 GPL17021

35 Samples

Download data: BIGWIG, TXT

(Submitter supplied) We performed RNA-seq from 6 days post fertilization hnf4a-/- and hnf4a+/+ zebrafish larval digestive tracts raised in the absence (Germ Free, GF) or presence (Conventionalized, CV) of microbiota. We found that zebrafish hnf4a activates almost half of the microbiota-suppressed genes, indicating that the microbiota supress Hnf4a trans-activity. We also provide evidence suggesting that microbial suppression of Hnf4a may contribute to IBD pathogenesis.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18413

10 Samples

Download data: BIGWIG

(Submitter supplied) Differentiation and specialisation of epithelial cells in the small intestine is regulated in two ways. First, there is differentiation along the crypt-villus axis of the intestinal stem cells into absorptive enterocytes, Paneth, goblet, tuft, enteroendocrine or M-cells, which is mainly regulated by WNT. Second, there is specialization along the cephalocaudal axis with different absorptive and digestive functions in duodenum, jejunum and ileum that is controlled by several transcription factors such as GATA4. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18061

12 Samples

Download data: TXT

(Submitter supplied) Our genome-wide gene expression data indicate that, despite the lack of crypts, the rostral, mid, and caudal portions of the zebrafish intestine have distinct functions analogous to the mammalian small and large intestine, respectively. Organization of ridge structures represents a unique feature of zebrafish intestine, though they produce similar cross sections to mammalian intestines. Evolutionary lack of stomach, crypts, Paneth cells and submucosal glands has shaped the zebrafish intestine into a simpler but unique organ in vertebrate intestinal biology.

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL10182

30 Samples

Download data: TXT

(Submitter supplied) An oligonucleotide microarray study of 42,000 new and predicted mouse genes across a comprehensive set of 55 tissues Keywords: other

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1537

55 Samples

Download data

(Submitter supplied) Single-cell mRNA sequencing (scRNA-seq) technologies are reshaping the current cell-type classification system. In previous studies, we built the mouse cell atlas (MCA) and human cell landscape (HCL) to catalog all cell types by collecting scRNA-seq data. However, systematically study for zebrafish (Danio rerio), fruit fly (Drosophila melanogaster) and earthworm (Eisenia andrei) are still lacking. Here, we construct the zebrafish, Drosophila and earthworm cell atlas with Microwell-seq protocols, which provides valuable resources for characterization of diverse cell populations of zebrafish, Drosophila and earthworm, and studying difference between vertebrates and Invertebrates at single cell level.

Organism:

Eisenia andrei

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL30479 GPL30478

28 Samples

Download data: TXT

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

Organism:

Drosophila melanogaster; Eisenia andrei; Danio rerio

Type:

Expression profiling by high throughput sequencing

5 related Platforms

151 Samples

Download data: TXT

(Submitter supplied) Single-cell mRNA sequencing (scRNA-seq) technologies are reshaping the current cell-type classification system. In previous studies, we built the mouse cell atlas (MCA) and human cell landscape (HCL) to catalog all cell types by collecting scRNA-seq data. However, systematically study for zebrafish (Danio rerio) and fruit fly (Drosophila melanogaster) are still lacking. Here, we construct the zebrafish and Drosophila cell atlas with Microwell-seq protocols, which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila, and studying difference between vertebrates and Invertebrates at single cell level.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL30277 GPL23085

106 Samples

Download data: TXT