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SRP063507
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- Homo sapiens
- 448 Downloadable Samples
Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
Genotypic differences greatly influence susceptibility and resistance to disease. Understanding genotype-phenotype relationships requires that phenotypes be viewed as manifestations of network properties, rather than simply as the result of individual genomic variations. Genome sequencing efforts have identified numerous germline mutations associated with cancer predisposition and large numbers of somatic genomic alterations. However, it remains challenging to distinguish between background, or passenger and causal, or driver cancer mutations in these datasets. Human viruses intrinsically depend on their host cell during the course of infection and can elicit pathological phenotypes similar to those arising from mutations. To test the hypothesis that genomic variations and tumour viruses may cause cancer via related mechanisms, we systematically examined host interactome and transcriptome network perturbations caused by DNA tumour virus proteins. The resulting integrated viral perturbation data reflects rewiring of the host cell networks, and highlights pathways that go awry in cancer, such as Notch signalling and apoptosis. We show that systematic analyses of host targets of viral proteins can identify cancer genes with a success rate on par with their identification through functional genomics and large-scale cataloguing of tumour mutations. These complementary approaches together result in increased specificity for cancer gene identification. Combining systems-level studies of pathogen-encoded gene products with genomic approaches will facilitate prioritization of cancer-causing driver genes so as to advance understanding of the genetic basis of human cancer.
Publication Title
Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins.
Sample Metadata Fields
Cell line
View Samples- Homo sapiens
- 11 Downloadable Samples
- IlluminaHiSeq2000
Description
The mitochondrial matrix is unique in that it must integrate folding and assembly of proteins derived from nuclear and mitochondrial genomes. In C. elegans, the mitochondrial unfolded protein response (UPRmt) senses matrix protein misfolding and induces a program of nuclear gene expression, including mitochondrial chaperonins, to promote mitochondrial proteostasis. While misfolded mitochondrial matrix-localized ornithine trans-carbamylase (OTC) induces chaperonin expression, our understanding of mammalian UPRmt is rudimentary, reflecting a lack of acute triggers for UPRmt activation. This limitation has prevented analysis of the cellular responses to matrix protein misfolding and the effects of UPRmt on mitochondrial translation to control protein folding loads. Here, we combine pharmacological inhibitors of matrix-localized HSP90/TRAP1 or LON protease, which promote chaperonin expression, with global transcriptional and proteomic analysis to reveal an extensive and acute response of human cells to UPRmt. This response involved widespread induction of nuclear genes, including matrix-localized proteins involved in folding, pre-RNA processing and translation. Functional studies revealed rapid but reversible translation inhibition in mitochondria occurring concurrently with defects in pre-RNA processing due to transcriptional repression and LON-dependent turnover of the mitochondrial pre-RNA processing nuclease MRPP3. This study reveals that acute mitochondrial protein folding stress activates both increased chaperone availability within the matrix and reduced matrix-localized protein synthesis through translational inhibition, and provides a framework for further dissection of mammalian UPRmt. Overall design: triplicate experiment of 2 conditions (untreated, GTPP treatment)
Publication Title
Mitochondrial unfolded protein response controls matrix pre-RNA processing and translation.
Sample Metadata Fields
No sample metadata fields
View Samples- Danio rerio
- 6 Downloadable Samples
- IlluminaGenomeAnalyzerIIx
Description
The zebrafish heart remarkably regenerates after a severe ventricular damage followed by inflammation, fibrotic tissue deposition and removal concomitant with cardiac muscle replacement. We have investigated the role of the endocardium in this regeneration process. 3D-whole mount imaging in injured hearts revealed that GFP-labelled endocardial cells in ET33mi-60A transgenic fish become rapidly activated and highly proliferative at 3 days post cryoinjury (dpci). Endocardial cells extensively expand within the injury site and organize to form a coherent structure at 9 dpci that persists throughout the regeneration process. Upon injury, endocardial cells strongly up-regulate the Notch pathway ligand delta like4 (dll4) and the Notch receptors notch1b, notch2 and notch3. Expression profiling showed that Notch signalling inhibition affects endocardial gene expression and genes related to extracellular matrix remodelling and inflammation. Gain- and loss-of-function experiments revealed that Notch is required for the organization of the endocardium, attenuation of the inflammatory response and cardiomyocyte proliferation. These results demonstrate a novel structural and signalling role for the endocardium during heart regeneration. Overall design: RNA was extracted from apical tip of heart ventricles 72h after cryoinjured adult zebrafish heart treated with DMSO (Controls) or RO gamma secretase inhibitor at 24 and 48h post injury.
Publication Title
Notch signalling restricts inflammation and <i>serpine1</i> expression in the dynamic endocardium of the regenerating zebrafish heart.
Sample Metadata Fields
No sample metadata fields
View Samples- Arabidopsis thaliana
- 28 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Effects of loss-of-function of AtMIKC* MADS-box genes on the mature Arabidopsis pollen transcriptome.
Publication Title
MADS-complexes regulate transcriptome dynamics during pollen maturation.
Sample Metadata Fields
Age, Specimen part
View Samples- Danio rerio
- 12 Downloadable Samples
- IlluminaHiSeq2500
Description
We use the Tlr2 mutant of zebrafish embryos model to study the transcriptome response to Mycobacterium marinum infection. We injected M.marinum into the caudal vein at 28 hours post fertilization and took samples at 4 days post infection. Overall design: This deep sequence study was designed to determine the gene expression profile in the Tlr2 mutant and heterozygote by M.marinum infection. RNA was isolated at 4 days post infection. Tlr2 mutants and heterozygotes zebrafish embryos were micro-injected into the caudal vein with 150CFU M.marinum, or PBS as a control at 28 hours post fertilization. After injections embryso were transerred into fresh egg water and incubated at 28 degree. At 4 days post infection triplicateds of 10 embryos per condition were snapfrozen in liquid nitogen, and total RNA was isolated using TRIZOL reagent.
Publication Title
Infection and RNA-seq analysis of a zebrafish tlr2 mutant shows a broad function of this toll-like receptor in transcriptional and metabolic control and defense to Mycobacterium marinum infection.
Sample Metadata Fields
No sample metadata fields
View Samples- Drosophila melanogaster
- 36 Downloadable Samples
- Illumina HiSeq 2500
Description
The goal of this project was to assess differential gene expression in the Ventral Nerve Cord (VNC) of adult Drosophila 5 hours after severing of the legs, wings and head. Overall design: Gene expression was assessed in 2 conditions (No Injury and 5-hrs after Injury) in the w1118 strain of Drosophila melanogaster. 5 independent biological replicates were used for each condition. RNA was isolated from the adult Ventral Nerve Cord (VNC) for the gene expression analysis (RNAseq).
Publication Title
A novel <i>Drosophila</i> injury model reveals severed axons are cleared through a Draper/MMP-1 signaling cascade.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Homo sapiens
- 14 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
Human testicular cells were isolated mechanically and enzymatically from testis of braindead donors and from urological samples. The expression of genes was studied at baseline and 1,25(OH)2D treated conditions.
Publication Title
Testicular synthesis and vitamin D action.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 6 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
To characterize LICs in ALL irrespective of surface markers expression, we investigated leukemia initiating activities of cellular subfractions of patient-derived xenograft BCP-ALL cells sorted according to different cell cycle phases (i.e. G0/G1 and G2/M) followed by transplantation onto NOD/SCID mice. All cell fractions led to leukemia engraftment indicating LIC activity irrespective of cell cycle stage. Most importantly, cells isolated from G0/G1 cell cycle phases led to early leukemia engraftment in contrast to cells from late cell cycle (G2/M). To further characterize cells with different engraftment potential in vivo, we analyzed the gene expression profiles of early (G1b early) and late (G2/M) engrafting cells.
Publication Title
Leukemia reconstitution <i>in vivo</i> is driven by cells in early cell cycle and low metabolic state.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 18 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
CNS leukemia is still the major obstacle in treating childhood acute lymphoblastic leukemia (ALL). We have used our NOD/SCID/huALL xenotransplantation model to identify molecular pathways leading to the infiltration of leukemic cells into the CNS compartment.
Publication Title
Central nervous system involvement in acute lymphoblastic leukemia is mediated by vascular endothelial growth factor.
Sample Metadata Fields
No sample metadata fields
View Samples