Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Space-time logic of liver gene expression

ABSTRACT: Space-time logic of liver gene expression

PROVIDER: PRJNA606289 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR11074441.fastq.gz	Fastqsanger.gz
	SRR11074442.fastq.gz	Fastqsanger.gz
	SRR11074443.fastq.gz	Fastqsanger.gz
	SRR11074444.fastq.gz	Fastqsanger.gz
	SRR11074445.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 40

Similar Datasets

Space-time logic of liver gene expression

Project description:We molecularly characterized thousands of liver hepatocytes cells at different time points around the circadian clock. This enable us to reconstruct mRNA expression profiles in space and time.

2020-11-01 | GSE145197 | GEO

Space-time logic of liver gene expression at sub-lobular scale.

Project description:The mammalian liver is a central hub for systemic metabolic homeostasis. Liver tissue is spatially structured, with hepatocytes operating in repeating lobules, and sub-lobule zones performing distinct functions. The liver is also subject to extensive temporal regulation, orchestrated by the interplay of the circadian clock, systemic signals and feeding rhythms. However, liver zonation has previously been analysed as a static phenomenon, and liver chronobiology has been analysed at tissue-level resolution. Here, we use single-cell RNA-seq to investigate the interplay between gene regulation in space and time. Using mixed-effect models of messenger RNA expression and smFISH validations, we find that many genes in the liver are both zonated and rhythmic, and most of them show multiplicative space-time effects. Such dually regulated genes cover not only key hepatic functions such as lipid, carbohydrate and amino acid metabolism, but also previously unassociated processes involving protein chaperones. Our data also suggest that rhythmic and localized expression of Wnt targets could be explained by rhythmically expressed Wnt ligands from non-parenchymal cells near the central vein. Core circadian clock genes are expressed in a non-zonated manner, indicating that the liver clock is robust to zonation. Together, our scRNA-seq analysis reveals how liver function is compartmentalized spatio-temporally at the sub-lobular scale.

| S-EPMC7116850 | biostudies-literature

Cis-regulatory elements control gene expression in time and space

Project description:Cis-regulatory elements control gene expression in time and space

| PRJNA748047 | ENA

Space-time Mapping Identifies Concerted Multicellular Patterns and Gene Programs in Healing Wounds and their Conservation in Cancers.

Project description:Tissue repair responses in metazoans are highly coordinated by different cell types over space and time. However, comprehensive single-cell based characterization covering this coordination is lacking. Here, we captured transcriptional states of single cells over space and time during skin wound closure, revealing choreographed gene expression profiles. We identified shared and prominent space-time patterns of cellular and gene expression enrichment: which we call multicellular ‘movements’ and which spanned multiple cell types. We validated some of the discovered space-time movements using large volume imaging of cleared wounds and demonstrated the value of this analysis to predict gene products made by macrophages or fibroblasts, which activated gene programs in the opposite cell type. Finally, using two different tumor models, we tested the hypothesis that tumors are like ‘wounds that never heal’ finding conserved wound healing movements in the tumor space, wherein some movements were preferentially used in one tumor versus another.

2022-05-28 | GSE204777 | GEO

Mapping cells thorugh time and space - pancreatic endocrinogenesis multiome

Project description:Mapping cells thorugh time and space - pancreatic endocrinogenesis multiome

| PRJNA1151677 | ENA

Miswired enhancer logic drives translocation positive rhabdomyosarcoma

Project description:Core regularity transcription factors (CR TFs) define cell identity and lineage through an exquisitely precise and logical order during embryogenesis and development. These CR TFs regulated one another in three-dimensional space via distal enhancers that serve as logic gates embedded in their TF recognition sequences. Aberrant chromatin organization resulting in miswired circuitry of enhancer logic is a newly recognized feature in many cancers. Here, we report that PAX3-FOXO1 expression is driven by a translocated FOXO1 distal super enhancer (SE). ChIP-seq in tumors bearing rare PAX translocations implicate enhancer miswiring is a pervasive feature across all FP-RMS tumors. Therefore, our data reveal a mechanism of a translocated hijacked enhancer which disrupts the normal CR TF logic during skeletal muscle development (PAX3 to MYOD to MYOG), replacing it with an infinite loop logic that makes rhabdomyosarcoma cells unable to exit the undifferentiated proliferating stage.

2019-12-25 | GSE136799 | GEO

A sexually dimorphic hepatic cycle of very low density lipoprotein uptake and assembly

Project description:Single-cell transcriptomes can reveal spatiotemporal programmes of liver function on the sublobular scale. However, how sexual dimorphism affects this space-time logic remains poorly understood. To address this, we performed single-cell RNA-seq in the mouse liver, which allowed us to model how lobular position, circadian time and sex shape the transcriptome.

2024-09-04 | GSE244392 | GEO

Cis-regulatory elements control gene expression in time and space

Project description:Cis-regulatory elements control gene expression in time and space and their disruption can lead to pathologies. Reporter assays allow the functional validation of enhancers and other regulatory elements, and transgenic mice provide a powerful tool to study gene regulation in vivo. However, these experiments are time-consuming and inefficient. Here, we increase the throughput of transgenic reporter assays by using a piggyBac transposon-based system, and use it to decode the regulatory landscape of atrial fibrillation, a prevalent cardiac arrhythmia. We systematically interrogated ten human atrial fibrillation associated loci, finding five new cardiac-specific enhancers. We also connected novel genes to atrial fibrillation through genome editing and three-dimensional chromatin structure analysis. Of note, we identified a bivalent regulatory element in the second intron of the CAV1 gene at the 7q31 locus, differentially acting upon four genes. Our approach also detected negative regulatory elements such as an ubiquitous silencer in the 16q22 locus that regulates ZFHX3 and can outcompete heart enhancers. Our study characterizes the function of new genetic elements that might be of relevance for the better understanding of gene regulation in cardiac arrhythmias. Thus, we have established a new framework for the efficient dissection of the genetic contribution to common human diseases.

2024-10-31 | GSE180396 | GEO

Effects of a Closed Space Environment on Gene Expression in Hair Follicles of Astronauts in the International Space Station

Project description:In recent times, long-term stay has become a common occurrence in the International Space Station (ISS). However, adaptation to the space environment can sometimes pose physiological problems to the astronauts after their return. Therefore, it is important to develop healthcare technologies for astronauts. In this study, hair, an easy-to-obtain sample, was identified as the candidate. In order to investigate the genetic changes in human hair during space flight, the hair follicles of 10 astronauts were analyzed by DNA microarray and real time q-PCR analyses. Space environment induced gene expression of hair follicles of astronaut was measured 6 differnent times included 2 in flight on orbit. Ten independent experiments were performed on differing astronauts. and the sampling day was differed for each astronaut because of their schedules.

2016-03-31 | E-GEOD-74708 | biostudies-arrayexpress

Effects of a Closed Space Environment on Gene Expression in Hair Follicles of Astronauts in the International Space Station

2016-03-31 | GSE74708 | GEO