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Sequencing of the STARR-seq transfection plasmid library

ABSTRACT: Sequencing of the STARR-seq transfection plasmid library

PROVIDER: PRJEB87672 | ENA |

REPOSITORIES: ENA

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Sequencing of the STARR-seq transfection plasmid library

Project description:The STARR-seq plasmid library used for transfection was sequenced to enable input normalization. The sequencing library was generated with the NEBNext Ultra II FS DNA Library Prep Kit (New England Biolabs) and sequenced on the Illumina iSeq 100

2025-08-08 | E-MTAB-14972 | biostudies-arrayexpress

STARR-seq enhancer activity determined following hydrodynamic delivery of STARR-seq plasmid library to mouse liver using three different STARR-seq promoters: Super Core promoter, ORI promoter, and minimal Albumin promoter [G173]

Project description:Massively parallel reporter assays (MPRA) are widely used to discover functional enhancers but have largely been limited to transfected cell models. Here, we combine hydrodynamic injection with a modified STARR-seq-based MPRA to determine condition-specific enhancer activity in mouse liver at scale, and we examine how different promoters affect STARR-seq reporter activity. Strong liver enhancer activity was observed with STARR-seq libraries containing an Albumin minimal promoter but not when using a Super Core promoter or an origin of replication (ORI) promoter. This work is part of a larger study where we prepare a global STARR-seq library, comprised of ~50,000 genomic sequences released by DNase-I digestion of mouse liver nuclei, and where we identify condition-specific enhancers with strong correlations between liver enhancer activity and the chromatin state of the corresponding endogenous genomic regions.

2024-06-17 | GSE267075 | GEO

The functional enhancer repertoire of human embryonic stem cells [plasmid DNA-seq]

Project description:We combined Self-Transcribing Active Regulatory Region Sequencing (STARR-seq) with an enrichment step using chromatin immunoprecipitation in a massively parallel reporter assay. We applied this assay, termed ChIP-STARR-seq, to normal (primed) and naive human embryonic stem cells, building up a comprehensive catalogue of functional enhancers. This database record describes the DNA-seq component from plasmid libraries prior to transfection.

2017-07-05 | GSE99629 | GEO

Project description:STARR-seq enhancer activity determined following hydrodynamic delivery of STARR-seq plasmid library to mouse liver using three different STARR-seq promoters: Super Core promoter, ORI promoter, and minimal Albumin promoter [G173]

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DNA-Diffusion STARR-Seq Validation

Project description:To test how DNA-Diffusion sequences can induce transcription, we select 2150 sequences, including DNA-Diffusion synthetic and natural occurring DHS sites for each cell type (K562, HepG2, and GM12878) and insert them into STARR-Seq plasmids (N= 6450 sequences). all synthetic and naturally occurring sequences were combined into a single library, and this same library was experimentally tested using STARR-Seq in different cell lines (K562, HepG2, GM12878).

2025-10-07 | GSE293971 | GEO

Functional definition of thyroid hormone response elements based on a synthetic Starr-seq screen

Project description:We performed an original protocol called synthetic STARR-seq (PMID: 30427832) in which a library of putative response elements are tested for their capacity to bind thyroid hormone (T3) nuclear receptors and convey T3 transactivation More than 10 000 putative T3 response elements (T3RE) were cloned in the hSTARR-seq-ORI vector with a minimal promoter, in the 3' end of the transcribed sequence. These are variant of the consensus T3RE (5'NGGTCANNNNRGGNNA3') Therefore the most active T3RE are over-represented in the RNA of cells transfected with the plasmid library and treated with T3.

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Analysis of diversity in barcoded plasmid library

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STARR-seq library profiling 100 defined open chromatin regions (‘focused library’) in livers of male and female mice treated with the nuclear receptor CAR (Nr1i3) agonist ligand TCPOBOP.

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Integrative transcriptomic and proteomic analysis unveils dynamic molecular responses to single, dual, and triple plasmid transfection of HEK293 cells for recombinant adeno-associated virus vector production

Project description:Despite clinical success, scalable and high-titer manufacturing of recombinant adeno-associated virus (rAAV) remains challenging, partially due to a limited understanding of the underlying cellular mechanisms and regulatory factors that govern production. We systemically investigate single, dual and the prevailing triple plasmid transfection process for rAAV production in human embryonic kidney (HEK293) cells and subsequently elucidate cellular molecular impacts of each approach through integrative transcriptomics, proteomics and chemometrics. Using a ‘high concentration, H’ single plasmid transfection process yielded increased rAAV titer (3-12-fold) compared to dual or triple transfection with 1556 differentially expressed genes (DEGs) identified. Single plasmid transfection activated fundamental processes intrinsic to transient transfection, including immune and defense response of the host cells, in addition to regulation of viral processes. Key pathways correlating with improved rAAV productivity were identified, including MYC targets, interferon responses, E2F targets, oxidative phosphorylation, G2M checkpoint, mitotic spindle, and WNT beta catenin signalling. The top 25 signature genes correlating with rAAV productivity and top 30 hub genes were also identified, which collectively serve as targeted genome and pathway engineering points for improved rAAV production. The data provides a rich repository of knowledge for the rational optimization of transient transfection strategies for tangible improvements in rAAV manufacturing.

2026-08-02 | PXD081880 | Pride

Sequence determinants of human gene regulatory elements, STARR-seq motif library experiments

Project description:Sequence determinants of human gene regulatory elements, STARR-seq motif library experiments

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