Spatially restricted immune and microbiota-driven adaptation of the gut
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1027812 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR26374800.fastq.gz | Fastqsanger.gz | |||
| SRR26379000.fastq.gz | Fastqsanger.gz | |||
| SRR26374801.fastq.gz | Fastqsanger.gz | |||
| SRR26379001.fastq.gz | Fastqsanger.gz | |||
| SRR26374802.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 200 |
Similar Datasets
Project description:Spatially restricted immune and microbiota-driven adaptation of the gut [Spatial Transcriptomics]
| PRJNA1027702 | ENA
Project description:Spatially restricted immune and microbiota-driven adaptation of the gut [scRNA-seq]
| PRJNA1027816 | ENA
Project description:The intestine is characterized by an environment where host requirements for efficient nutrient and water absorption are consequently paired with the requirement to establish and maintain tolerance to the outside environment. The organ is anatomically organized into the small intestine (SI) which specializes in nutrient absorption and the colon which specializes in water resorption. The transcriptional and cellular circuits that define intestinal regionalization and their robustness, adaptability, and resilience to changes in the local environment are not well characterized. Here, we generated a comprehensive survey of the spatial and cellular landscape of the murine intestine to demonstrate the steady state transcriptional landscape of the murine intestine is robust, adaptable, and resilient to perturbation. We characterized the transcriptional landscape of the full length of the intestine and show it is established independently of the microbiota and is not under circadian regulation. In the colon, these regional circuits were characterized by unique subsets of structural cells. Moreover, we identified a spatial adaptation to the microbiota in the colon characterized by the emergence of unique structural cell subsets including an enterocyte, fibroblast, and goblet cell, with the later two co-occurring in space. Employing a model of acute spatiotemporal damage allowed us to show the spatial landscape and adaptations we identified are both resilient to inflammation. Our results demonstrate that intestinal circuits are under host control and spatial adaptations in the steady state as well as in the process of recovery from tissue damage in the inflamed state are primarily characterized by changes to structural cell types such as epithelial and stromal cells.
2024-11-26 | GSE245274 | GEO
Project description:The intestine is characterized by an environment where host requirements for efficient nutrient and water absorption are consequently paired with the requirement to establish and maintain tolerance to the outside environment. The organ is anatomically organized into the small intestine (SI) which specializes in nutrient absorption and the colon which specializes in water resorption. The transcriptional and cellular circuits that define intestinal regionalization and their robustness, adaptability, and resilience to changes in the local environment are not well characterized. Here, we generated a comprehensive survey of the spatial and cellular landscape of the murine intestine to demonstrate the steady state transcriptional landscape of the murine intestine is robust, adaptable, and resilient to perturbation. We characterized the transcriptional landscape of the full length of the intestine and show it is established independently of the microbiota and is not under circadian regulation. In the colon, these regional circuits were characterized by unique subsets of structural cells. Moreover, we identified a spatial adaptation to the microbiota in the colon characterized by the emergence of unique structural cell subsets including an enterocyte, fibroblast, and goblet cell, with the later two co-occurring in space. Employing a model of acute spatiotemporal damage allowed us to show the spatial landscape and adaptations we identified are both resilient to inflammation. Our results demonstrate that intestinal circuits are under host control and spatial adaptations in the steady state as well as in the process of recovery from tissue damage in the inflamed state are primarily characterized by changes to structural cell types such as epithelial and stromal cells.
2024-11-26 | GSE245315 | GEO
Project description:This SuperSeries is composed of the SubSeries listed below.
2024-11-26 | GSE245316 | GEO
Project description:Interactions between the nuclear lamina (NL) and chromatin are thought to occur through large lamin association domains (LADs) and correlate with gene repression in these domains. We show that binding of lamin A/C (LMNA) to promoters occurs on discrete domains that are associated with distinct transcriptional outputs. Chromatin immunoprecipitation identifies thousands of LMNA-bound promoters, primarily linked to signaling functions. LMNA often occupies narrow domains on promoters, yet LMNA-bound promoters are often contiguous. LMNA-bound genes are overall repressed, but repression correlates with co-enrichment in repressive histone marks rather than LMNA occupancy per se. Genes marked by LMNA and H3K4me3 escape LMNA-associated repression in the absence of repressive histone marks. Positioning of LMNA on promoters relative to the TSS correlates with distinct transcriptional outputs: whereas upstream-distal binding can be transcriptionally permissive, TSS occupancy is associated with promoter inactivity. Perturbation in NL organization causes reorganization of lamin promoter occupancy and uncouples LMNA binding from promoter inactivity. Our results show the existence of many spatially restricted LMNA binding events on promoter regions, with distinct position-dependent transcriptional outputs. Total RNA obtained from ASCs and ASCs depleted of LMNA (LMNA-KD) and processed for microarray hybridization.
2013-07-14 | E-GEOD-42523 | biostudies-arrayexpress
Project description:The sensation of light is initiated in photoreceptor cells by the photoisomerization of a chromophore molecule from 11-cis to all-trans retinal. Continuous visual perception requires recycling of the spent chromophore back to the 11-cis form through the visual cycle, a series of reactions in the retinal pigmented epithelium (RPE). Light-driven chromophore consumption by photoreceptors is greater in daytime compared to night time, suggesting that correspondingly higher activity of the visual cycle may be required. On the other hand, as rod photoreceptors are saturated in bright light, the continuous turnover of their chromophore through the visual cycle during daytime would unnecessarily utilize precious energy and produce toxic byproducts. Here, we sought to determine whether the recycling of chromophore and the dark adaptation of rods is regulated by the circadian clock and light exposure. We demonstrate that in melatonin-proficient C3H/f+/+ mice, rod dark adaptation is slower during the day or after light exposure. This surprising daytime downregulation of the RPE visual cycle was further demonstrated by gene analysis, which revealed light-driven reduction in the expression of Rpe65, which encodes a key enzyme of the RPE visual cycle. In contrast, rods in melatonin-deficient strains (C57BL6/J and 129/Sv) were not affected by this daily visual cycle modulation. Our results demonstrate that the circadian clock and light exposure regulate the recycling of chromophore in the RPE visual cycle. This daily modulation of rod dark adaptation is mediated by melatonin and could potentially protect the retina from light-induced damage during the day. mRNA-seq of murine eyes (lens removed) in objective day (OD) vs. subjective day (SD) conditions (2 biological replicates per condition). Each biological replicate consisted of 4 eyes (from 1 female and 1 male).
2015-11-19 | E-GEOD-68470 | biostudies-arrayexpress
Project description:Interactions between the nuclear lamina (NL) and chromatin are thought to occur through large lamin association domains (LADs) and correlate with gene repression in these domains. We show that binding of lamin A/C (LMNA) to promoters occurs on discrete domains that are associated with distinct transcriptional outputs. Chromatin immunoprecipitation identifies thousands of LMNA-bound promoters, primarily linked to signaling functions. LMNA often occupies narrow domains on promoters, yet LMNA-bound promoters are often contiguous. LMNA-bound genes are overall repressed, but repression correlates with co-enrichment in repressive histone marks rather than LMNA occupancy per se. Genes marked by LMNA and H3K4me3 escape LMNA-associated repression in the absence of repressive histone marks. Positioning of LMNA on promoters relative to the TSS correlates with distinct transcriptional outputs: whereas upstream-distal binding can be transcriptionally permissive, TSS occupancy is associated with promoter inactivity. Perturbation in NL organization causes reorganization of lamin promoter occupancy and uncouples LMNA binding from promoter inactivity. Our results show the existence of many spatially restricted LMNA binding events on promoter regions, with distinct position-dependent transcriptional outputs. ChIPs were done from cultured untreated and LMNA-downregulated adipose stem cell (ASC) chromatin. MeDIPs were done from LMNA-downregulated ASCs. ChIP and MeDIP DNA was hybridized onto the aforementioned HG-18 Nimbegen promoter arrays.
2013-07-14 | E-GEOD-42522 | biostudies-arrayexpress
Project description:Development of specialized cell types and structures in the vertebrate heart is regulated by spatially-restricted molecular pathways. Disruptions in these pathways can cause severe congenital cardiac malformations or functional defects. To better understand these pathways and how they regulate cardiac development and function we used tomo-seq, combining high-throughput RNA sequencing with tissue sectioning, to establish a genome-wide expression dataset with high spatial resolution for the developing zebrafish heart. Analysis of the dataset revealed over 1100 genes differentially expressed in sub-compartments. Pacemaker cells in the sinoatrial region induce heart contractions, but little is known about the mechanisms underlying their development and function. Using our transcriptome map, we identified spatially restricted Wnt/β-catenin signaling activity in pacemaker cells, which was controlled by Islet-1 activity. Moreover, Wnt/β-catenin signaling at a specific developmental stage in the myocardium controls heart rate by regulating pacemaker cellular response to parasympathetic stimuli. Thus, this high-resolution transcriptome map incorporating all cell types in the embryonic heart can expose spatially-restricted molecular pathways critical for specific cardiac functions.
2018-02-06 | GSE104057 | GEO
Project description:Metabolic incorporation of electron-rich ribonucleosides enhances APEX-seq for profiling spatially restricted nascent transcriptome
| PRJNA793004 | ENA