{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Norbert Perrimon"],"organism":["Drosophila melanogaster"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-GEOD-71430"],"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"],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - Total RNA extracted with TRIZOL, followed by purification using Qiagen Rneasy MinElute Cleanup Kit, including on-column DNAse treatment. Standard multiplexing mRNA sequencing library following Illumina protocol","Sample Treatment - Cells were transfected with Actin:dCas9-VPR, together with a non-targeting sgRNA (negative control), or a pool of 5 sgRNAs targeting either Twist, Snail, or a combination of both pools."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - align to genome with tophat v2 using default parameters, with self built bowtie2 genome database according to drosophila melanogaster genome assembly r5.51. read number counts obtained with Htseq, with --mode=union, --stranded=no data normalization and identifying DEG with Deseq package with built in functions Genome_build: Drosophila genome r5.51 from flybase Supplementary_files_format_and_content: tab deliminated .txt file with gene name and read number count for each gene"],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"pubmed_abstract":["A number of approaches for Cas9-mediated transcriptional activation have recently been developed, allowing target genes to be overexpressed from their endogenous genomic loci. However, these approaches have thus far been limited to cell culture, and this technique has not been demonstrated in vivo in any animal. The technique involving the fewest separate components, and therefore the most amenable to in vivo applications, is the dCas9-VPR system, where a nuclease-dead Cas9 is fused to a highly active chimeric activator domain. In this study, we characterize the dCas9-VPR system in Drosophila cells and in vivo. We show that this system can be used in cell culture to upregulate a range of target genes, singly and in multiplex, and that a single guide RNA upstream of the transcription start site can activate high levels of target transcription. We observe marked heterogeneity in guide RNA efficacy for any given gene, and we confirm that transcription is inhibited by guide RNAs binding downstream of the transcription start site. To demonstrate one application of this technique in cells, we used dCas9-VPR to identify target genes for Twist and Snail, two highly conserved transcription factors that cooperate during Drosophila mesoderm development. In addition, we simultaneously activated both Twist and Snail to identify synergistic responses to this physiologically relevant combination. Finally, we show that dCas9-VPR can activate target genes and cause dominant phenotypes in vivo, providing the first demonstration of dCas9 activation in a multicellular animal. Transcriptional activation using dCas9-VPR thus offers a simple and broadly applicable technique for a variety of overexpression studies."],"study_type":["RNA-seq of coding RNA"],"species":["Drosophila melanogaster"],"pubmed_title":["In Vivo Transcriptional Activation Using CRISPR-Cas9 in Drosophila."],"pubmed_authors":["Nobert Perrimon","Norbert Perrimon","Xiaochun Ni","Lin S, Ewen-Campen B, Ni X, Housden BE, Perrimon N"],"additional_accession":[]},"is_claimable":false,"name":"In vivo transcriptional activation using CRISPR-Cas9 in Drosophila","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","dates":{"release":"2015-08-10T00:00:00Z","modification":"2023-09-22T01:33:16.754Z","creation":"2022-02-23T18:54:21.794Z"},"accession":"E-GEOD-71430","cross_references":{"pubmed":["26245833"],"ENA":["SRP061691"],"EFO":["EFO_0003738"],"doi":["10.1534/genetics.115.181065"]}}