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SRP041515
Mus musculus
9 Downloadable Samples
Illumina HiSeq 2000
Description
Here we show that the histone methyltransferase MLL4 (Kmt2d) is required for stem cell activity and an aggressive form of acute myeloid leukemia (AML) harboring the MLL-AF9 oncogene. MLL4 exerts its function by regulating transcriptional programs associated with the anti-oxidant response. Overall design: The role of Mll4 (Kmt2d) in regulating the transcriptome of primary and transformed hematopoietic stem cells was studied.
Publication Title
DNA-damage-induced differentiation of leukaemic cells as an anti-cancer barrier.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 8 Downloadable Samples
- Illumina HiSeq 2500
Description
IL-10 is a prototypical anti-inflammatory cytokine, which is fundamental to the maintenance of immune homeostasis, especially in the intestine. There is an assumption that cells producing IL-10 have an immunoregulatory function. However, here we report that IL-10-producing CD4+ T cells are phenotypically and functionally heterogeneous. By combining single cell transcriptome and functional analyses, we identified a subpopulation of IL-10-producing Foxp3Neg CD4+ T cells that displays regulatory activity unlike other IL-10-producing CD4+ T cells, which are unexpectedly pro-inflammatory. The combinatorial expression of co-inhibitory receptors is sufficient to discriminate IL-10-producing CD4+ T cells with regulatory function from others and to identify them across different tissues and disease models in mice and humans. These regulatory IL-10-producing Foxp3Neg CD4+ T cells have a unique transcriptional program, which goes beyond the regulation of IL-10 expression. Finally, we found that patients with Inflammatory Bowel Disease (IBD), demonstrate a deficiency in this specific regulatory T-cell subpopulation. Overall design: We carried out high troughput RNA sequencing of RNA isolated from IL-10 producing Foxp3- CD4+ T-cells, which were isolated from the spleen of mice treated with anti-CD3 antibody.
Publication Title
Molecular and functional heterogeneity of IL-10-producing CD4<sup>+</sup> T cells.
Sample Metadata Fields
Subject
View Samples- Homo sapiens
- 6 Downloadable Samples
Affymetrix Human Gene 2.0 ST Array (hugene20st)
Description
The conditioned media from Bifidobacterium infantis (BCM) and Lactobacillus acidophilus (LCM) were reported to promote maturation of innate immune response gene expression, which explained the protective effects of probiotics in clinical necrotizing enterocolitis. We used microarray analysis to investigate the expression of genes involved in regulation of BCM and LCM in IL-1 stimulated immature human enterocytes.
Publication Title
Secreted Metabolites of Bifidobacterium infantis and Lactobacillus acidophilus Protect Immature Human Enterocytes from IL-1β-Induced Inflammation: A Transcription Profiling Analysis.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Rattus norvegicus
- 6 Downloadable Samples
- Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
Goals of the study:
Publication Title
Global gene expression changes in rat retinal ganglion cells in experimental glaucoma.
Sample Metadata Fields
No sample metadata fields
View Samples- Vitis vinifera
- 24 Downloadable Samples
- Affymetrix Vitis vinifera (Grape) Genome Array (vitisvinifera)
Description
Grapevine rootstock 1616C shoots were sterilized and cultured on Murashige & Skoog (MS) medium containing 2% sucrose (w/v). Plantlets were grown in a growth chamber with a 16-h light/8-h dark cycle for 10 weeks at 25 °C.
Publication Title
Salt stress induces endoplasmic reticulum stress-responsive genes in a grapevine rootstock.
Sample Metadata Fields
Specimen part, Time
View Samples- Drosophila melanogaster
- 6 Downloadable Samples
- Illumina HiSeq 2000
Description
Chromatin in eukaryotic nuclei is organized at multiple scales, from individual nucleosomes to specific loops between regulatory sequences, to the folding of large genomic regions into topological domains and segregation of whole chromosomes into territories. Many of the chromatin proteins that regulate this architecture, including the essential Polycomb Group (PcG) proteins, are themselves organized into subnuclear structures. Deciphering mechanistic links between protein organization and genome architecture requires precise description and mechanistic perturbations of both. Using super-resolution microscopy, we characterized the nanoscale organization of PcG proteins in Drosophila cells and find hundreds of small protein clusters, distinct from the large PcG bodies present in just a few copies per cell that have been the focus of previous investigations. We manipulated PcG clusters either by disrupting the polymerization activity of the conserved Sterile Alpha Motif (SAM) of the PcG protein Polyhomeotic (Ph) or increasing Ph levels in Drosophila S2 cells. Disrupting clustering using Ph SAM mutations disrupts chromatin interactions on scales from 50kb to 13Mb while increasing Ph levels increases both cluster number and long range chromatin interactions. RNA-seq and qPCR indicate that both perturbations also alter expression levels of many genes. Molecular simulations suggest a model in which PcG cluster formation on chromatin is governed by the kinetics of association between Ph SAMs and PcG cluster size is bounded by the affinity and occupancy of chromatin binding sites. Our results suggest that nanoscale organization of PcG proteins into small, abundant clusters on chromatin through the polymerization activity of Ph SAM shapes genome architecture by mediating numerous long-range chromatin interactions. Overall design: Two biological replicates of three RNA-seq samples from S2 cells, cells overexpresing wild-type Ph, and cells overexpressing polymerization defective Ph-ML
Publication Title
Chromatin topology is coupled to Polycomb group protein subnuclear organization.
Sample Metadata Fields
Cell line, Subject
View Samples- Mus musculus
- 4 Downloadable Samples
- Affymetrix Mouse Gene 2.0 ST Array (mogene20st)
Description
Effects of treatment with Nimodipine on N9 cells
Publication Title
Nimodipine fosters remyelination in a mouse model of multiple sclerosis and induces microglia-specific apoptosis.
Sample Metadata Fields
Treatment
View Samples- Mus musculus
- 60 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
A multiply redundant genetic switch 'locks in' the transcriptional signature of regulatory T cells.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Mus musculus
- 33 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
The transcription factor FoxP3 partakes dominantly in the specification and function of FoxP3+ CD4+ T regulatory cells (Tregs), but is neither strictly necessary nor sufficient to determine the characteristic Treg transcriptional signature. Computational network inference and experimental testing assessed the contribution of several other transcription factors (TFs). Enforced expression of Helios or Xbp1 elicited specific signatures, but Eos, Irf4, Satb1, Lef1 and Gata1 elicited exactly the same outcome, synergizing with FoxP3 to activate most of the Treg signature, including key TFs, and enhancing FoxP3 occupancy at its genomic targets. Conversely, the Treg signature was robust to inactivation of any single cofactor. A redundant genetic switch thus locks-in the Treg phenotype, a model which accounts for several aspects of Treg physiology, differentiation and stability.
Publication Title
A multiply redundant genetic switch 'locks in' the transcriptional signature of regulatory T cells.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Mus musculus
- 12 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
The transcription factor FoxP3 partakes dominantly in the specification and function of FoxP3+ CD4+ T regulatory cells (Tregs), but is neither strictly necessary nor sufficient to determine the characteristic Treg transcriptional signature. Computational network inference and experimental testing assessed the contribution of several other transcription factors (TFs). Enforced expression of Helios or Xbp1 elicited specific signatures, but Eos, Irf4, Satb1, Lef1 and Gata1 elicited exactly the same outcome, synergizing with FoxP3 to activate most of the Treg signature, including key TFs, and enhancing FoxP3 occupancy at its genomic targets. Conversely, the Treg signature was robust to inactivation of any single cofactor. A redundant genetic switch thus locks-in the Treg phenotype, a model which accounts for several aspects of Treg physiology, differentiation and stability.
Publication Title
A multiply redundant genetic switch 'locks in' the transcriptional signature of regulatory T cells.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples