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Massively parallel reporter assay for programmed ribosomal frameshifting on designed sequence libraries

ABSTRACT: Massively parallel reporter assay for programmed ribosomal frameshifting on designed sequence libraries

PROVIDER: PRJNA607955 | ENA |

REPOSITORIES: ENA

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Massively parallel reporter assay for programmed ribosomal frameshifting on designed sequence libraries

Project description:We designed an oligonucleotide libraries containing a potential frameshifting site, cloned the library variants into a dedicated reporter construct, transfected and integrated these constructs in the genome of K562 cells, and performed FACSseq (as well as targeted RNA sequencing) to determine if and to what extent frameshifting occurs.

2020-02-22 | GSE145684 | GEO

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Massively parallel splicing reporter assay on designed sequence libraries

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Project description:programmed ribosomal frameshift Raw sequence reads

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Massively Parallel Reporter Assay for pluripotency factors in mESCs

Project description:A massively parallel reporter assay, MPRA, was conducted in mouse embryonic stem cells (mESC). Synthetic cis-regulatory elements comprised of binding sites for pluripotency transcription factors and genomic sequences with comparable binding sites configurations were used in the assay. Transcripts of dsRed were amplified via PCR from the end of the transcript to sequence 3' UTR barcodes.

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Genome-wide CRISPR screen for regulators of SARS-CoV-2 programmed ribosomal frameshifting

Project description:Genome-wide CRISPR-Cas9 knockout screens were performed in dual-fluorescent frameshifting reporter cell lines to identify human host factors for SARS-CoV-2 programmed ribosomal frameshfiting.

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Project description:We designed and assayed synthetic regulatory elements varying c-amp response element number, affinity, distance to the promoter, spacing between multiple CREs, and surrounding sequence content. Using 5 massively-parallel reporter assays, we measured the expression of 17,406 unique sequences when placed upstream of a minimal promoter using next-generation sequencing of barcodes associated with synthesized elements. We then determine how the varied c-amp response element architectures influence expression when these variants are assayed in an episomal and genomic context across a range of forskolin concentrations, an inducer of c-amp response element activity. Included here are all sequences designed and analyzed in the assay. Assay results from certain library designs were not insightful and not included in the main text but are additionally included here in the barcode-mapping and MPRA sequencing datasets.

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