Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Massively parallel splicing reporter assay on designed sequence libraries

ABSTRACT: Massively parallel splicing reporter assay on designed sequence libraries

PROVIDER: PRJNA545827 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Massively parallel splicing reporter assay on designed sequence libraries

Project description:We designed 4 oligonucleotide libraries containing either a retained intron, a cassette exon, tandem 5' or tandem 3' splice sites, cloned them into dedicated reporter constructs, transfected and integrated these constructs in the genome of K562 cells, and performed targeted RNA sequencing to determine RNA splicing ratios and a FACSseq approach to determine protein isoform ratios.

2019-06-03 | GSE132064 | GEO

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

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

| PRJNA607955 | ENA

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

A massively parallel reporter assay for RNA localization in neurons

Project description:We performed a massively parallel reporter assay for RNA localization in two mouse neuronal cell lines, CAD and Neuro-2a. We transfected a library of around 50,000 different 3'UTR reporters (cloned downstream of GFP) into cells grown on transwell plates and collected soma and neurite fractions separately. RNA was extracted and cDNA synthesized, followed by targeted amplification of the reporter mRNA and Illumina sequencing.

2021-04-23 | GSE173098 | GEO

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.

2019-09-18 | GSE120240 | GEO

Characterization of maturational enhancer activity by massively parallel reporter assay [amplicon-Seq]

Project description:The activity of enhancers with dynamic P300 binding or mutagenized nuclear receptor motifs was assessed by massively parallel reporter assay during CM maturation.

2023-01-19 | GSE196346 | GEO

Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay

Project description:We apply a massively parallel reporter assay (MPRA) that relies on mRNA and plasmid tag sequencing (Tag-Seq) to compare the regulatory activities of more than 27,000 distinct variants of two inducible enhancers in human cells: a synthetic cAMP-regulated enhancer and the virus-inducible interferon beta enhancer. The resulting data define accurate maps of functional transcription factor binding sites in both enhancers at single-nucleotide resolution and can be used the to train quantitative sequence-activity models (QSAMs). Reporter Tag-Seq from HEK293 cells transfected with each of six MPRA plasmid pools, with and without stimulation (forskolin or Sendai virus). The reporter mRNAs contain unique 10 nucleotide tags that facilitates quantitation of their abundances. The same tags were also sequenced from each ransfected plasmid pool to facilitate normalization to plasmid copy numbers. The reporter constructs were designed according to two different mutagenesis strategies: 'single-hit scanning' and 'multi-hit sampling'. The specific variants are included in the processed data files.

2012-02-26 | E-GEOD-31982 | biostudies-arrayexpress

A single-cell massively parallel reporter assay detects cell type specific cis-regulatory activity

Project description:We developed a single-cell massively parallel reporter assay (scMPRA) to measure the activity of libraries of cis-regulatory sequences (CRSs) across multiple cell-types simultaneously. As a proof of concept, we assayed a library of core promoters in a mixture of HEK293 and K562 cells and showed that scMPRA is a reproducible, highly parallel, single-cell reporter gene assay. Our results show that housekeeping promoters and CpG island promoters have lower activity in K562 cells relative to HEK293, which likely reflects developmental differences between the cell lines. Within K562 cells, scMPRA identified a subset of developmental promoters that are upregulated in the CD34+/CD38- sub-state, confirming this state as more “stem-like.” Finally, we deconvolved the intrinsic and extrinsic components of cell-to-cell variability and found that developmental promoters have a higher proportion of extrinsic noise compared to housekeeping promoters. We anticipate scMPRA will be widely applicable for studying the role of CRSs across diverse cell types.

2021-11-11 | GSE188639 | GEO

Massively Parallel Reporter Assay of human-specific substitutions in neurodevelopmental enhancers

Project description:We performed a Massively Parallel Reporter Assay (MPRA) to screen >30,000 human-specific substitutions in ChIP-seq-identified Human Gain Enhancers (HGEs) and Human Accelerated Regions (HARs), highly conserved non-coding regions that show accelerated sequence evolution in humans. After comparing human and chimpanzee reference alleles, we used a second MPRA to deconvolute individual substitutions within differentially active enhancers from substitutions in the same fragment and from other variants (human segregating variants or chimpanzee-specific variants) to isolate their specific effects on enhancer activity.

2019-11-26 | GSE140983 | GEO

Systematic dissection of regulatory motifs in 2,000 predicted human enhancers using a massively parallel reporter assay

Project description:We employ a massively parallel reporter assay (MPRA) to measure the ex vivo activities of hundreds of K562 and HepG2 enhancers with known transcription factor motif instances. For seven selected motifs that correspond to known or predicted activators and repressors in the two cell types, we make directed modifications of the bases corresponding to these motifs and observe the changes in enhancer activity. Reporter mRNA-seq from HepG2 and K562 cells transfected with a ~55,000-plex MPRA plasmid pool containing 5,418 mutated human enhancer sequences, each linked to 10 distinct 10-nt tags. The reporter mRNA tags facilitate quantitation of their abundances. The same tags were also sequenced from the transfected MPRA plasmid pool to facilitate normalization to plasmid copy numbers.

2013-03-15 | E-GEOD-33367 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data