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GSE65343
Homo sapiens
20 Downloadable Samples
Affymetrix Human Gene 2.1 ST Array (hugene21st)
Description
used to identify differences between tissues from patients undergoing surgery for BPH with unresolved symptoms compared to incidental BPH from patients with prostate cancer
Publication Title
Surgical intervention for symptomatic benign prostatic hyperplasia is correlated with expression of the AP-1 transcription factor network.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 10 Downloadable Samples
Illumina HiSeq 2000
Description
While skeletal myogenesis is tightly coordinated by myogenic regulatory factors including MyoD and myogenin, chromatin modifications have emerged as vital mechanisms of myogenic regulation. We have previously established that bexarotene, a clinically approved agonist of retinoid X receptor, promotes the specification and differentiation of skeletal muscle lineage. Here, we examine a genome-wide impact of rexinoids on myogenic differentiation through integral RNA-seq and ChIP-seq analyses. We found that bexarotene promotes myoblast differentiation through the coordination of exit from the cell cycle and the activation of muscle-related genes. We uncovered a new mechanism of rexinoid action which is mediated by the nuclear receptor and largely reconciled through a direct regulation of MyoD gene expression. In addition, we determined a rexinoid-responsive residue-specific histone acetylation at a distinct chromatin state associated to MyoD and myogenin. Thus, we provide novel molecular insights into the interplay between retinoid X receptor signaling and chromatin states pertinent to myogenic programs in early myoblast differentiation. Overall design: We have profiled the global effect of bexarotene, a selective agonist of retinoid X receptor on myoblast gene expression by RNA-seq analysis using RNA isolated from C2C12 myoblasts following 12 or 24 hours of differentiation in the presence and absence of 50 nM bexarotene, with 2 biological replicates. Proliferating myoblasts were used as controls.
Publication Title
Insights into interplay between rexinoid signaling and myogenic regulatory factor-associated chromatin state in myogenic differentiation.
Sample Metadata Fields
Cell line, Subject
View Samples- Mus musculus
- 8 Downloadable Samples
- Illumina HiSeq 2500
Description
CTSK-mGFP positive cells from Day 6 old mouse femurs were sorted as single cells into 384 well plates pre-loaded with unique barcoded RT-primers. After sorting, cells were snap frozen on dry ice before being submitted to the New York Genome Center (NYGC) for cDNA synthesis and library preparation. The FACS profile for all the sored cells were collected to co-relate with gene expression. Overall design: Mouse femur was obtained from mice within the same litter. Femur samples was subjected to collagenase digestion, and single cell suspension was obtained. The samples were stained for FACS antibodies and single cell sorting was performed into two individual 384 well plates. The experiment has two replicates from two independant animals. The samples were always kept discrete.
Publication Title
Discovery of a periosteal stem cell mediating intramembranous bone formation.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Mus musculus
- 9 Downloadable Samples
- Affymetrix Mouse Gene 2.0 ST Array (mogene20st)
Description
AZD1208 is a novel PIM kinase inhibitor that we have shown inhibits tumorigenesis in tissue recombination models, Myc-CaP allograft models, and human prostate cancer xenografts. We sought to determine the intracellular pathways that are responsible for the anti-tumor effect. To this end we used the tissue recombination protocol to implant MYCCaP cells into castrated mice. MYCCaP cells are an androgen-dependent mouse cell line that overexpresses the oncogene MYC. The mice used for implantation were castrated, so any tumors that result from the grafting procedure are androgen-independent. The grafted mice were divided into a control population receiving vehicle, and a test population receiving AZD1208. The tumors were harvested and in vitro cell lines were made. The new cell lines have been perpetuated in androgen-depleted media.
Publication Title
PIM kinase inhibitor AZD1208 for treatment of MYC-driven prostate cancer.
Sample Metadata Fields
Cell line
View Samples- Homo sapiens
- 43 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
GS-5759 is a bifunctional ligand composed of a quinolinone-containing pharmacophore found in several 2-adrenoceptor agonists linked covalently to a phosphodiesterase 4 inhibitor (PDE4) related to GSK 256066 by a pent-1-yn-1-ylbenzene spacer. The object of the study was to detemine if gene expression changes induced by GS-5759 were replicated by a 2-adrenoceptor agonist (indacaterol; Ind) and a PDE4 inhibitor (GSK 256066; GSK) in combination.
Publication Title
GS-5759, a Bifunctional β2-Adrenoceptor Agonist and Phosphodiesterase 4 Inhibitor for Chronic Obstructive Pulmonary Disease with a Unique Mode of Action: Effects on Gene Expression in Human Airway Epithelial Cells.
Sample Metadata Fields
Cell line, Treatment
View Samples- Mus musculus
- 78 Downloadable Samples
- Illumina HiSeq 2500
Description
To determine the role of Mbd3/NuRD in lymphopoiesis, gene expression in purified populations of Mbd3-deleted and control lymphoid progenitor cells was analysed using RNA-seq. Overall design: Mbd3-deficient and control lymphoid progenitors were isolated from mouse bone marrow by flow cytometry, including haematopoietic stem cells (HSCs), lymphoid-primed multipotent progenitors (LMPPs), all-lymphoid progenitors (ALPs) and B cell-biased lymphoid progenitors (BLPs). RNA-seq was performed on 100 HSCs or 150 cells from the other populuations, using the previously described smartseq2 protocol for RNA-seq of small numbers of cells (Picelli et al. (2014) Nature protocols 9:171).
Publication Title
Mbd3/NuRD controls lymphoid cell fate and inhibits tumorigenesis by repressing a B cell transcriptional program.
Sample Metadata Fields
Sex, Age, Specimen part, Cell line, Subject
View Samples- Saccharomyces cerevisiae
- 7 Downloadable Samples
- Affymetrix Yeast Genome 2.0 Array (yeast2)
Description
Hmt1p is the predominant arginine methyltransferase in Saccharomyces cerevisiae. Its substrate proteins are involved in transcription, transcriptional regulation, nucleocytoplasmic transport and RNA splicing. Functionally, Hmt1p-catalysed methylation can also modulate protein-protein interactions. Despite Hmt1p being well-characterised, the effects of its knockout on the proteome and transcriptome have not been reported. SILAC-based analyses of the hmt1 proteome, in mid-log exponential growth, revealed a decreased abundance of phosphate-associated proteins including Pho84p (phosphate transporter), Pho8p (vacuolar alkaline phosphatase), Pho3p (acid phosphatase) along with Vtc1p, Vtc3p and Vtc4p (subunits of the vacuolar transporter chaperone complex). RNA-Seq and microarray analysis revealed a downregulation of phosphate-responsive genes in hmt1, including PHO5, PHO11 and PHO12 (acid phosphatases), PHO84 and PHO89 (phosphate transporters) and VTC3 (vacuolar transporter chaperone). Consistent with these observations, we observed a dysregulation of phosphate homeostasis in hmt1, with a general decrease in extracellular phosphatase production and a decrease in total Pi in phosphate replete medium. We show that the transcription factor Pho4p, responsible for activation of the PHO pathway, can be methylated by Hmt1p at Arg-241 and is the likely cause of phosphate dysregulation in hmt1. However, the methylation of Pho4p does not affect its nucleocytoplasmic localisation. We propose that the methylation of Pho4p may affect either its capacity to multimerise, its capacity to interact with Pho2p or target DNA, or may affect Pho4p phosphorylation at Ser-242 and/or Ser 243. Our study highlights a previously unknown function of Hmt1p in the regulation of phosphate homeostasis and suggests a means by which sensing of AdoMet may affect intracellular phosphate concentration.
Publication Title
Knockout of the Hmt1p Arginine Methyltransferase in <i>Saccharomyces cerevisiae</i> Leads to the Dysregulation of Phosphate-associated Genes and Processes.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 11 Downloadable Samples
- Illumina HiSeq 2500
Description
Mononuclear phagocytes are a diverse cell family that occupy all tissues and assume numerous functions to support tissue and systemic homeostasis. Our ability to investigate the roles of individual subsets is limited by an absence of approaches to ablate gene function within specific sub-populations. Using Nr4a1-dependent Ly6Clow monocytes as a representative cell type we show that enhancer deletion addresses these limitations. Combining ChIP-Seq and molecular approaches we identify a single, conserved, sub-domain within the Nr4a1 enhancer that is essential for Ly6Clow monocyte development. Mice lacking this enhancer lack Ly6Clow monocytes but retain Nr4a1 gene expression in macrophages during steady state and in response to LPS. Nr4a1 is a key negative regulator of inflammatory gene expression and decoupling these processes allows Ly6Clow monocytes to be studied without confounding influences. Enhancer targeting possesses greater specificity than cre recombinase-mediated gene deletion, providing a route to generate loss-of-function models in closely related cell types. Overall design: Paired End mRNA sequencing of FACS purified primary murine MDP, cMoP, Ly6Chi and Ly6Clow monocytes from the bone marrow and Ly6Chi and Ly6Clow monocytes from the peripheral blood
Publication Title
Deleting an Nr4a1 Super-Enhancer Subdomain Ablates Ly6C<sup>low</sup> Monocytes while Preserving Macrophage Gene Function.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Mus musculus
- 18 Downloadable Samples
- Illumina HiSeq 2500
Description
The goal of this study is to understand the alterations in transcriptome induced by histone H3K36M mutations Overall design: Transcritome profiling of 3 cell lines cultured in vitro and 6 murine tumors
Publication Title
Histone H3K36 mutations promote sarcomagenesis through altered histone methylation landscape.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 52 Downloadable Samples
- Illumina HumanRef-8 v3.0 expression beadchip, Illumina HumanHT-12 V4.0 expression beadchip
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Immunopathology of childhood celiac disease-Key role of intestinal epithelial cells.
Sample Metadata Fields
Specimen part, Cell line, Treatment
View Samples