Project description:In this study we show that ascorbate (vitamin C) shifts the hydroxymethylome and transcriptome in RPE cells, and downregulates expression of VEGF. Overall design: Examination of transcriptome and hydroxymethylome in vitamin C treated or control ARPE-19 cells
Project description:Proteome and transcriptome often show poor correlation, hindering the system-wide analysis of post-transcriptional regulation. Here, the authors study proteome and transcriptome dynamics during Drosophila embryogenesis and present basic mathematical models describing the temporal regulation of most protein-RNA pairs. Overall design: S2R+ drosophila cell lines with Hrb98de knock down
Project description:Our data showed that ENT broadly impacted multiple populations of immune cells within the TME. Thus, we performed general immune transcriptome profiling on whole tumors isolated from the neu-N model using a PanCancer immune-profiling gene panel for the NanoString platform. Overall design: To identify all immune cell types infiltrating the tumors and associated functions, we utilized NanoString transcript profiling to evaluate broad changes in the transcriptome of whole tumors following treatment with various different drug combinations.
Project description:Proteome and transcriptome often show poor correlation, hindering the system-wide analysis of post-transcriptional regulation. Here, the authors study proteome and transcriptome dynamics during Drosophila embryogenesis and present basic mathematical models describing the temporal regulation of most protein-RNA pairs. Overall design: Whole embryos of Drosophila melanogaster measured at 14 time points during the first 20h of development (0h, 1h, 2h, 3h, 4h, 5h, 6h, 8h, 10h, 12h, 14h, 16h, 18h, 20h). Each sample was measured in biological quadruplicates. RNAseq samples correspond to proteome measurements deposited in ProteomeXchange as PXD005713.
Project description:Transcriptome profiling using RNA-seq of MV+, a mouse lens epithelium cell line expressing Pax6 and RAG renal adenocarcinoma cell line which does not express Pax6. Overall design: Total RNA was collected and a Illumina sequencing libraries prepared from three biological replicates of cultured MV+ and RAG cells.
Project description:This SuperSeries is composed of the SubSeries listed below. We analyze the transcriptomes of healthy donor and CD46 deficieint patients with and without in vitro activation by microarray and RNA-seq Overall design: Refer to individual Series Freshly isolated CD8 cells were either activated or not in vitro before RNA extraction and transcriptome analysis
Project description:Myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML) are diseases of abnormal hematopoietic differentiation with aberrant epigenetic alterations. Azacitidine (AZA) is a DNA methyltransferase inhibitor (DNMTi) widely used to treat MDS and AML, yet the impact of AZA on the cell surface proteome has not been defined. To identify potential therapeutic targets for use in combination with AZA in AML patients, we investigated the effects of AZA treatment on four AML cell lines representing different stages of differentiation. The effect of AZA treatment on these cell lines was characterized at three levels: the DNA methylome, the transcriptome, and the cell surface proteome. Untreated AML cell lines showed substantial overlap at all three omics level; however, while AZA treatment globally reduced DNA methylation in all cell lines, changes in the transcriptome and surface proteome were subtle and differed among the cell lines. Transcriptome analysis identified five commonly upregulated coding genes upon AZA treatment in all four cell lines, TRPM4 being the only gene encoding a surface protein, and surface proteomics analysis found no commonly regulated proteins. Gene Set Enrichment Analysis (GSEA) of differentially-regulated RNA and surface proteins showed a decrease in metabolism pathways and an increase in immune defense response pathways. As such, AZA treatmentled to diverse effects at the individual gene and protein level but converged to common responses at the pathway level. Given the heterogeneous responses in the four cell lines, the potential therapeutic strategies for AML in combinations with AZA are discussed. Overall design: To study the effects of AZA treatment on the regulation of DNA methylation, each of the four cell lines was treated with AZA (0.5 μM) for 3 days, followed by a four-day drug holiday
Project description:The functions of human PUM1 and PUM2 are considered to be redundant given that both PUF1 and PUF2 recognize the same PBE motif UGUANAUA. However pools of mRNAs published so far for PUM1 and PUM2 do not overlap. Therefore we sought to investigate the issue of redundancy in human cells. The both PUM proteins are less conserved in the region that is outside the PUM domain. We sought that interactors could be different. We identified mRNA pools binding separately PUM1 and PUM2 by RIP-Seq approach, normalized them using the whole TCam-2 cells transcriptome and aligned them with mRNA pools activated or repressed as tested by siRNA PUM1 and PUM2 knockdown. Overall design: PUM1 and PUM2-regulated RNAs were studied by RIP-Seq and siRNA-mediated PUM1 or PUM2 knockdown followed by RNA-Seq in TCam-2 cell line. RIP-Seq with non-immunized serum and TCam-2 transcriptome or control non-target siRNA were used as controls for RIP-Seq and RNA-Seq respectively. Each experiment was performed in 3 biological replicates.
Project description:The RNA binding protein Dazl is essential for gametogenesis, but its direct in vivo functions, RNA targets, and the molecular basis for germ cell loss in DAZL null mice are unknown. Here, we mapped transcriptome-wide Dazl-RNA interactions in vivo, revealing Dazl binding to thousands of mRNAs via polyA-proximal 3?UTR interactions. In parallel, fluorescence activated cell sorting and RNA-Seq identified mRNAs sensitive to Dazl deletion in male germ cells. Despite binding a broad set of mRNAs, integrative analyses indicate that Dazl post-transcriptionally controls only a subset of its mRNA targets, namely those corresponding to a network of genes critical for germ cell proliferation and survival. Additionally, we provide evidence that polyA sequences have key roles in specifying Dazl-RNA interactions across the transcriptome. Altogether, our results reveal a mechanism for Dazl-RNA binding, and illustrate that Dazl functions as a master regulator of a post-transcriptional mRNA program essential for germ cell survival. Overall design: Ribosome Profiling and RNA-seq libraries from monoclonal cell line with doxycyline inducible Dazl expression (GC-1-spg parental line)