Unknown,Transcriptomics,Genomics,Proteomics

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High-Throughput mapping of the regulatory DNA


ABSTRACT: We introduce the Multiplexed Editing Regulatory Assay (MERA), a high-throughput CRISPR/Cas9-based approach that analyzes the regulatory genome for function in its native context. By tiling thousands of mutations across ~40 kb of cis-regulatory genomic space and using knock-in GFP reporters to read out gene activity, we obtain quantitative information on the contribution of cis-regulatory regions to gene expression. In addition, we performed a deep-sequencing strategy to find basepair-resolution functional motifs involved in regulation of the gene by sequencing thousands of functional and non-functional genotypes at genomic locations perturbed by specific guide RNAs. Design of 3908 gRNAs to perturb regulatory regions associated with the genes Tdgf1,Nanog,Zfp42 and Rpp25 as well as 10 GFP-targetting positive controls. Also, deep-sequencing of genomic regions mutated by 6 selected gRNAs after sorting the electroporated cells into GFP-positive and GFP-negative populations.

ORGANISM(S): Mus musculus

SUBMITTER: Nisha Rajagopal 

PROVIDER: E-GEOD-76318 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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