Project description:We conducted RNA-seq analysis to identify genes that are differentially expressed in H3K27M and H3K36M oncohistones compared to wt and control eye tissue (eye discs), followed by smRNA-seq profiling based on our results and to confirm upregulation of piRNAs
Project description:Raw data from E-MTAB-1585 was normalized by using reads per million. https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1585/ Strand specific RNA-Seq data E-MTAB-1585 was normalized and subtracted control from knockdown to generate tracks that more clearly displayed the unusual pattern of RNA expression caused by knockdown of 7SK. The following wig files were generated from multiple samples (i.e.raw data files), as indicated in the 'readme.txt' file. 7sk_3p_KD_norm.wig: 7SK 3P Knockdown normalized 7sk_3p_KDF_norm.wig: 7SK 3P Knockdown normalized (Forward) 7sk_3p_KDR_norm.wig: 7SK 3P Knockdown normalized (Reverse) 7sk_5p_KD_norm.wig: 7SK 5P Knockdown normalized 7sk_5p_KDF_norm.wig: 7SK 5P Knockdown normalized (Forward) 7sk_5p_KDR_norm.wig: 7SK 5P Knockdown normalized (Reverse) 7sk_Control_norm.wig: 7SK Control normalized 7sk_ControlF_norm.wig: 7SK Control normalized (Forward) 7sk_ControlR_norm.wig: 7SK Control normalized (Reverse) 7sk_3p_KDF-ControlF.wig: 7SK 3P Knockdown-Control (Forward) 7sk_3p_KDR-ControlR.wig: 7SK 3P Knockdown-Control (Reverse) 7sk_5p_KDF-ControlF.wig: 7SK 5P Knockdown-Control (Forward) 7sk_5p_KDR-ControlR.wig: 7SK 5P Knockdown-Control (Reverse)
Project description:This project aims to explore a new system for genetic control of dibenzothiophene desulfurization in Gordonia alkanivorans strain 135 using integrated omics approaches. A quantitative protomics, RNA-Seq analysis was performed. RNA-seq results were further validated using qRT-PCR for differentially expressed genes.
Project description:We report genome-wide binding of the highly conserved TF Sine oculis (So), which is necessary for Drosophila eye development and has few previously known direct transcriptional targets. Our data identify novel putative targets of So-mediated regulation, including genes involved in multiple aspects of development. 2 biological replicates of ChIP-seq with anti-So antibody on chromatin from D. melanogaster third instar eye-antennal imaginal discs; negative control - same sample and ChIP-seq protocol without anti-So antibody
Project description:Genome control is operated by transcription factors (TF) controlling their target genes by binding to promoters and enhancers. Conceptually, the interactions between TFs, their binding sites, and their functional targets are represented by gene regulatory networks (GRN). Deciphering in vivo GRNs underlying organ development in an unbiased genome-wide setting involves identifying both functional TF-gene interactions and physical TF-DNA interactions. To reverse-engineer the GRN of eye development in Drosophila, we performed RNA-seq across 72 genetic perturbations and sorted cell types, and inferred a co-expression network. Next, we derived direct TF-DNA interactions using computational motif inference, ultimately connecting 241 TFs to 5632 direct target genes through 24926 enhancers. Using this network we found network motifs, cis-regulatory codes, and new regulators of eye development. We validate the predicted target regions of Grainyhead by ChIP-seq and identify this factor as a general co-factor in the eye network, being bound to thousands of nucleosome-free regions.
Project description:<p>Gene expression is a biological process regulated at different molecular levels, including chromatin accessibility, transcription, and RNA maturation and transport. In addition, these regulatory mechanisms have strong links with cellular metabolism. Here we present a multi-omics dataset that captures different aspects of this multi-layered process in yeast. We obtained RNA-seq, metabolomics, and H4K12Ac ChIP-seq data for wild-type and mip6delta strains during a heat-shock time course. Mip6 is an RNA-binding protein that contributes to RNA export during environmental stress and is informative of the contribution of post-transcriptional regulation to control cellular adaptations to environmental changes. The experiment was performed in quadruplicate, and the different omics measurements were obtained from the same biological samples, which facilitates the integration and analysis of data using covariance-based methods. We validate our dataset by showing that ChIP-seq, RNA-seq and metabolomics signals recapitulate existing knowledge about the response of ribosomal genes and the contribution of trehalose metabolism to heat stress.</p>
Project description:Retinoic acid (RA) is a transcriptional control agent that regulates several aspects of eye development including invagination of the optic vesicle to form the optic cup, although a target gene for this role has not been previously identified. As loss of RA synthesis in Rdh10 knockout embryos affects the expression levels of thousands of genes, a different approach is needed to identity genes that are directly regulated by RA. Here, we combined ChIP-seq for epigenetic marks with RNA-seq on eye tissue from wild-type embryos and Rdh10-/- embryos that exhibit failure in optic cup formation. We identified a small number of genes with decreased expression when RA is absent that also have decreased presence of a nearby epigenetic gene activation mark (H3K27ac). One such gene was Alx1 that also has an RA response element (RARE) located near the RA-regulated H3K27ac mark, providing strong evidence that RA directly activates Alx1. In situ hybridization studies showed that Rdh10-/- embryos exhibit a large decrease in eye Alx1 expression. CRISPR/Cas9 knockout of Alx1 resulted in a failure in optic cup formation, thus demonstrating that RA directly activates Alx1 in order to stimulate this stage of eye development.