Project description:In order to study the effect of transcription factor knockdown, we selectively depleted mRNA products from 483 different genes that are known or predicted to encode transcription factors. We treated Drosophila S2R+ tissue culture cells with double strand RNAs designed to be specific for these loci. Following RNAi treatment, we isolated poly A+ RNA from the cells, and performed stranded high-throughput RNA-Seq analyses to determine knockdown efficiency and propagating transcriptional consequences.
Project description:To understand how RNAi depletion of transcription factors impact the Drosophila transcriptome, we performed selective knockdown of 46 transcription factors in Drosophila S2R+ cell line. We treated cells with long double strand RNAs by bathing for 1 to 3 days. We purified polyA+ RNA and prepared strand-specific RNA-Seq libraries. We quantitatively measured transcriptomic responses using a time series analysis.
Project description:A probe of the coupling of gene expression and nuclear structure in Drosophila S2R+ cells was undertaken by a study of altered expression profile following a 6 day RNAi mediated genetic perturbation of Klaroid (CG18584), Lamin (CG6944) and Msp-300 (CG33715).
Project description:A probe of the coupling of gene expression and nuclear structure in Drosophila S2R+ cells was undertaken by a study of altered expression profile following a 6 day RNAi mediated genetic perturbation of Klaroid (CG18584), Lamin (CG6944) and Msp-300 (CG33715). Genotypic Technology designed Custom Gene Expression Drosophila 8x15k array ( Agilent-AMADID:020441)
Project description:Identifying putative transcription factor target genes by combining CRISPR/Cas9-based transcriptional activation with RNAseq in Drosophila S2R+ cells. This study focuses on the transcription factors Twist and Snail, singly and together. RNA from Drosophila cells following CRISPR/Cas9-based activation of Twist, Snail, or Twist and Snail together, compared with non-targeting sgRNA. Two biological replicates for each experiment
Project description:We identified 131 high affinity sites of the Drosophila DCC combining residual ChIP-chip profiles after differential crosslinking and RNAi-mediated knockdown of spreading factors Keywords: ChIP-chip
Project description:Identifying putative transcription factor target genes by combining CRISPR/Cas9-based transcriptional activation with RNAseq in Drosophila S2R+ cells. This study focuses on the transcription factors Twist and Snail, singly and together.
