E-GEOD-53514
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: PRJNA232183
PROVIDER: E-GEOD-53514 | ExpressionAtlas | 2025-01-24
REPOSITORIES: ExpressionAtlas
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| E-GEOD-53514-analysis-methods.tsv | Tabular | |||
| E-GEOD-53514-atlasExperimentSummary.Rdata | Rdata | |||
| E-GEOD-53514-configuration.xml | Xml | |||
| E-GEOD-53514-percentile-ranks.tsv | Tabular | |||
| E-GEOD-53514.condensed-sdrf.tsv | Tabular |
Items per page: 5 1 - 5 of 107 |
Similar Datasets
Project description:Coexpression of CD49b and LAG-3 identifies human and mouse T regulatory type 1 cells
| PRJNA232183 | ENA
Project description:This SuperSeries is composed of the following subset Series: GSE19622: Individual-specific and allele-specific chromatin signatures in diverse human populations GSE25416: High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells (ChIP-seq) GSE30226: Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity [ChIP_seq]. GSE32692: Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells [new ChIP-Seq samples] For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Refer to individual Series
2011-10-17 | E-GEOD-32883 | biostudies-arrayexpress
Project description:Cellular decision-making is mediated by a complex interplay of external stimuli with the intracellular environment, in particular transcription factor regulatory networks. Here we have determined the expression of a network of 18 key haematopoietic transcription factors (TFs) in 597 single primary blood stem and progenitor cells isolated from mouse bone marrow. We demonstrate that different stem/progenitor populations are characterised by distinctive TF expression states, and through comprehensive bioinformatic analysis reveal positively and negatively correlated TF pairings, including previously unrecognised relationships between Gata2, Gfi1 and Gfi1b. Validation using transcriptional and transgenic assays confirmed direct regulatory interactions consistent with a novel regulatory triad in immature blood stem cells, where Gata2 may function to modulate cross-inhibition between Gfi1 and Gfi1b. Single cell expression profiling therefore identifies network states and allows reconstruction of network hierarchies involved in controlling stem cell fate choices, and provides a blueprint for studying both normal development and human disease. Examination of Gata2 and Gfi1 binding patterns in murine mast cells
2013-04-24 | E-GEOD-42518 | biostudies-arrayexpress
Project description:To gain insights into the interplay between DNA methylation and gene regulation we generated a basepair resolution reference map of the mouse methylome in stem cells and neurons. High genome coverage allowed for a novel quantitative analysis of local methylation states, which identified Low Methylated Regions (LMR) with an average methylation of 30%. These regions are evolutionary conserved, reside outside of CpG islands and distal to promoters. They represent regulatory regions evidenced by their DNaseI hypersensitivity and chromatin marks of enhancer elements. LMRs are occupied by transcription factors (TF) and their reduced methylation requires TF binding while introduction of TF binding sites creates LMRs de novo. This dependency on TF activity is further evident when comparing the methylomes of embryonic stem cells and derived neuronal cells. LMRs present in both cell types are occupied by broadly expressed factors, while LMRs present at only one state are occupied by cell-type specific TFs. Methylome data can thus enhance the prediction of occupied TF binding sites and identification of active regulatory regions genome-wide. Our study provides reference methylomes for the mouse at two cell states, identifies a novel and highly dynamic feature of the epigenome that defines distal regulatory elements and shows that transcription factor binding dynamically shapes mammalian methylomes. Whole genome shotgun bisulfite sequencing of mouse embryonic stem (ES) cells and derived neuronal progenitors (NP). CTCF ChIP sequencing in mouse ES and Dnmt1/3a/3b triple knock-out ES (TKO) cells. H3K4me1, H3K4me2 and H3K27me3 ChIP sequencing in mouse ES cells. Pax6 ChIP-chip in mouse ES cells.
2011-12-09 | E-GEOD-30203 | biostudies-arrayexpress
Project description:ChIP-seq of H3K27ac was performed in regulatory T cells (resting and activated) and conventional T cells (naïve, effector, memory) in mouse and human. A small number of regulatory elements were lineage specific in both mouse and human and represented the 'core' lineage specification program. Regulatory element acetylation levels were associated with genetic variation in humans and lineage-specific loci were enriched for autoimmune risk-alleles (especially type 1 diabetes) identified in classic and fine-resolution genome-wide association studies.
2015-10-05 | GSE73418 | GEO
Project description:Integrated multiomics profiling identifies the differentiation program of regulatory T cells in human tumors [mouse bulk ATAC-seq]
| PRJNA868754 | ENA
Project description:Distal cell-type-specific regulatory elements may be located at very large distances from the genes that they control and are often hidden within intergenic regions or in introns of other genes. The development of methods that enable mapping of regions of open chromatin genome wide has greatly advanced the identification and characterisation of these elements. Here we use DNase I hypersensitivity mapping followed by deep sequencing (DNase-seq) to generate a map of open chromatin in primary human tracheal epithelial (HTE) cells and use bioinformatic approaches to characterise the distribution of these sites within the genome and with respect to gene promoters, intronic and intergenic regions. Genes with THE-selective open chromatin at their promoters were associated with multiple pathways of epithelial function and differentiation. The data predict novel cell-type-specific regulatory elements for genes involved in HTE cell function, such as structural proteins and ion channels, and the transcription factors that may interact with them to control gene expression. Moreover, the map of open chromatin can identify the location of potentially critical regulatory elements in genome-wide association studies (GWAS) in which the strongest association is with single nucleotide polymorphisms in non-coding regions of the genome. We demonstrate its relevance to a recent GWAS that identifies modifiers of cystic fibrosis lung disease severity. Since HTE cells have many functional similarities with bronchial epithelial cells and other differentiated cells in the respiratory epithelium, these data are of direct relevance to elucidating the molecular basis of normal lung function and lung disease. To identify cis-regulatory elements for genes expressed in human tracheal epithelial cells we generated genome-wide maps of open chromatin by DNase-seq. HTE cells were isolated from these trachea and grown as described previously (Davis P.B. et al.1990).
2013-11-08 | E-GEOD-52179 | biostudies-arrayexpress
Project description:Despite their enormous importance, the molecular circuits that control the differentiation of Th17 cells remain largely unknown. Recent studies have reconstructed regulatory networks in mammalian cells, but have focused on short-term responses and relied on perturbation approaches that cannot be applied to primary T cells. Here, we develop a systematic strategy – combining transcriptional profiling at high temporal resolution, novel computational algorithms, and innovative nanowire-based tools for performing gene perturbations in primary T cells – to derive and experimentally validate a temporal model of the dynamic regulatory network that controls Th17 differentiation. The network is arranged into two self-reinforcing and mutually antagonistic modules that either suppress or promote Th17 differentiation. The two modules contain 12 novel regulators with no previous implication in Th17 differentiation, which may be essential to maintain the appropriate balance of Th17 and other CD4+ T cell subsets. Overall, our study identifies and validates 39 regulatory factors that are embedded within a comprehensive temporal network and identifies novel drug targets and organizational principles for the differentiation of Th17 cells. DNA binding of TSC22D3 in Th17 cells compared to WCE
2013-03-07 | E-GEOD-43949 | biostudies-arrayexpress
Project description:Background; Mouse and rat models are mainstays in pharmacology, toxicology and drug development â but differences between strains and between species complicate data interpretation and application to human health. Dioxin-like polyhalogenated aromatic hydrocarbons represent a major class of environmentally and economically relevant toxicants. In mammals dioxin exposure leads to a broad spectrum of adverse affects, including hepatotoxicity of varying severity. Several studies have shown that dioxins extensively alter hepatic mRNA levels. Surprisingly, though, analysis of a limited portion of the transcriptome revealed that rat and mouse responses diverge greatly (Boverhof et al. Toxicol Sci 94:398â416, 2006). Results; We employed oligonucleotide arrays to compare the response of 8,125 rat and mouse orthologs. We confirmed that there is limited inter-species overlap in dioxin-responsive genes. Rat-specific and mouse-specific genes are enriched for specific functional groups which differ between species, conceivably accounting for species-specificities in liver histopathology. While no evidence for the involvement of copy-number variation was found, extensive inter-species variation in the transcriptional-regulatory network was identified; Nr2f1 and Fos emerged as candidates to explain species-specific and species-independent responses, respectively. Conclusion; Our results suggest that a small core of genes is responsible for mediating the similar features of dioxin hepatotoxicity in rats and mice but non-overlapping pathways are simultaneously at play to result in distinctive histopathological outcomes. The extreme divergence between mouse and rat transcriptomic responses appears to reflect divergent transcriptional-regulatory networks. Taken together, these data suggest that both rat and mouse models should be used to screen the acute hepatotoxic effects of drugs and toxic compounds. Experiment Overall Design: Wild-type Long-Evans(Kuopio) rats were treated with 100 ug/kg TCDD (n=4) or with cornoil vehicle as control (n=4) for 19 hours. Their livers were then excised, RNA extracted, and the resulting samples hybridized to Affymetrix RAE230A arrays to survey changes in the transcriptome profile.
2008-10-25 | E-GEOD-10770 | biostudies-arrayexpress
Project description:An appendix to the published Gaulton et al. work (PMID: 20118932; E-GEOD-17616). In the original paper, the authors note that samples 1 and 2 are not as pure as the third sample. This appendix provides FAIRE-Seq data obtained from a purified islet sample to replace the problematic published data. The goal of the original experiment was to identify active regulatory DNA in human pancreatic islets. This was accomplished using high-throughput sequencing of genomic regions isolated using FAIRE from three purified pancreatic islet samples to identify sites of open chromatin.
2014-12-23 | E-MTAB-3199 | biostudies-arrayexpress