Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptomic landscapes provide a framework of native gene expression from which to imagine new connections in cell biology

ABSTRACT: Transcriptomic landscapes provide a framework of native gene expression from which to imagine new connections in cell biology

PROVIDER: PRJNA517591 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR8501312.fastq.gz	Fastqsanger.gz
	SRR8501313.fastq.gz	Fastqsanger.gz
	SRR8501314.fastq.gz	Fastqsanger.gz
	SRR8501315.fastq.gz	Fastqsanger.gz
	SRR8501316.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 8

Similar Datasets

Transcriptomic landscapes provide a framework of native gene expression from which to imagine new connections in cell biology

Project description:The Poly(A)-Test RNA-seq, ( PAT-seq ) approach was utilized to determine gene expression and poly(A)-site change in S. cerevisiae during colony maturation.

2019-06-24 | GSE125804 | GEO

Genetic Framework for GATA Factor Function in Vascular Biology

Project description:Vascular endothelial dysfunction underlies the genesis and progression of numerous diseases. Whereas the GATA transcription factor GATA-2 is expressed in endothelial cells and is implicated in coronary heart disease, it has been studied predominantly as a master regulator of hematopoiesis. As many questions remain unanswered regarding GATA-2 function in the vascular biology realm, we used ChIP-seq and loss-of-function strategies to define the GATA-2-instigated genetic network in human endothelial cells. By contrast to erythroid cells, GATA-2 occupied a unique target gene ensemble, consisting of genes encoding key determinants of endothelial cell identity and inflammation. GATA-2-occupied sites characteristically contained motifs that bind Activator Protein-1 (AP-1), a pivotal regulator of inflammatory genes. GATA-2 frequently occupied the same chromatin sites as c-JUN and c-FOS, heterodimeric components of AP-1. Though all three components were required for maximal AP-1 target gene expression, GATA-2 was not required for AP-1 chromatin occupancy. GATA-2 conferred maximal phosphorylation of chromatin-bound c-JUN at Ser 73, which stimulates AP-1-dependent transactivation, in a chromosomal context-dependent manner. This work establishes a link between a GATA factor and inflammation, mechanistic insights underlying GATA-2-AP-1 cooperativity, and a rigorous genetic framework for understanding GATA-2 function in normal and pathophysiological vascular states. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Examination of GATA2 ChIP-seq in HUVEC cells.

2011-08-11 | E-GEOD-29531 | biostudies-arrayexpress

Circadian clock, carcinogenesis, chronochemotherapy connections

Project description:Circadian clock, carcinogenesis, chronochemotherapy connections

| PRJNA739695 | ENA

Genetic Framework for GATA Factor Function in Vascular Biology

2011-08-11 | GSE29531 | GEO

An organoid screening framework to engineer intestinal epithelial composition

Project description:Barrier epithelia are essential to organismal homeostasis, and changes in their cellular composition are observed in human diseases. Within the small intestine, adult stem cells establish tissue cellularity, and may provide a means to control the abundance and quality of specialized epithelial cells. Nevertheless, we lack suitable approaches to identify biological targets and small molecules to modulate them. Here, we develop an extendable framework utilizing a physiologically-inspired organoid model to identify unknown, druggable regulators of intestinal stem cell differentiation that translate to intended manipulations in vivo. Specifically, we miniaturize and adapt an organoid model of Paneth cell differentiation to enable multiplexed phenotypic screening on the scale of thousands of samples, and employ longitudinal single-cell RNA-sequencing to understand hit biology. Strikingly, we identify that inhibitors of the nuclear exporter XPO1 modulate stem cell fate commitment, significantly increasing the abundance of Paneth cells independent of known differentiation cues. Our framework elucidates small molecules which modulate tissue stem cell biology and their underlying targets without the need for a priori knowledge of in vivo pathway biology.

2021-09-16 | GSE148524 | GEO

Human iPSC-derived glomeruli provide an advanced model to interrogate podocyte biology and accurately recapitulate podocytopathy

Project description:Human iPSC-derived glomeruli provide an advanced model to interrogate podocyte biology and accurately recapitulate podocytopathy

| PRJNA438893 | ENA

Comparative proteomic landscapes provide insights into mammalian preimplantation development

Project description:Understanding mammalian preimplantation development, particularly in humans, at the proteomic level remains limited. Here, we applied our Comprehensive Solution of Ultrasensitive Proteome Technology to measure the proteomic profiles of oocytes and early embryos, and identified nearly 8,000 proteins in humans and over 6,300 proteins in mice. We observed distinct proteomic dynamics before and around zygotic genome activation (ZGA) between the two species. Integrative analysis with translatome data revealed extensive divergence between translation activation and protein accumulation. Multi-omic analysis indicated that ZGA transcripts contribute to protein accumulation in blastocysts. Consequently, we identified several transcriptional regulators critical for early development in mice, thereby linking ZGA to the first lineage specification. Furthermore, single-embryo proteomics of poor quality embryos from over 100 patient-couples provided insights into preimplantation development failure. Our study may contribute to reshaping the framework of mammalian preimplantation development and opening new avenues for addressing human infertility.

2024-12-04 | GSE283213 | GEO

PSC-IBD mucosal biology

Project description:PSC-IBD mucosal biology

| PRJEB32359 | ENA

Human iPSC-derived glomeruli provide an advanced model to interrogate podocyte biology and accurately recapitulate podocytopathy

Project description:Podocytes are highly specialised cells within the glomeruli of the kidney that maintain the filtration barrier by forming interdigitating foot processes and slit-diaphragms. Disruption to these features result in proteinuria and glomerulosclerosis. Studies into podocyte biology and disease have previously relied on conditionally immortalised cell lines due to the non- proliferative nature of this cell type. Here we describe an advanced model to study both podocyte and glomerular biology using isolated glomeruli from kidney organoids derived from human pluripotent stem cells.

2018-12-04 | GSE111992 | GEO

A framework for performing single-cell spatial metabolomics with cell-type specific protein profiling for tissue systems biology

Project description:Metabolic reprogramming in cancer and immune cells occurs to support their increasing energy needs in biological tissues. Here we propose Single Cell SPAtially resolved METabolic (scSpaMet) framework for joint protein-metabolite profiling of single immune and cancer cells in male human tissues by incorporating untargeted spatial metabolomics and targeted multiplexed protein imaging in a single pipeline. We utilized the scSpaMet pipeline to profile cell types and spatial metabolomic maps of 19507, 31156, and 8215 single cells in human lung cancer, tonsil and endometrium tissues, respectively. ScSpaMet analysis revealed cell type-dependent metabolite profiles and local metabolite competition of neighboring single cells in human tissues. Deep learning-based joint embedding revealed unique metabolite states within cell types. Trajectory inference showed metabolic patterns along cell differentiation paths. Here we show scSpaMet’s ability to quantify and visualize the cell-type specific and spatially resolved metabolic-protein mapping as an emerging tool for systems-level understanding of tissue biology.

2023-10-02 | PXD045840 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data