Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome-wide enhancer identification by massively parallel reporter assay in Arabidopsis

ABSTRACT: Genome-wide enhancer identification by massively parallel reporter assay in Arabidopsis

PROVIDER: PRJNA659905 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR12539150_1.fastq.gz	Fastqsanger.gz
	SRR12539150_2.fastq.gz	Fastqsanger.gz
	SRR12539151_1.fastq.gz	Fastqsanger.gz
	SRR12539151_2.fastq.gz	Fastqsanger.gz
	SRR12539152_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 36

Similar Datasets

Quantification of mouse retinal enhancer activity by massively parallel reporter assay

Project description:Quantification of mouse retinal enhancer activity by massively parallel reporter assay

| PRJNA415987 | ENA

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

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

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

| PRJNA804494 | ENA

Massively parallel splicing reporter assay on designed sequence libraries

Project description:Massively parallel splicing reporter assay on designed sequence libraries

| PRJNA545827 | ENA

Massively parallel reporter assay for identification of RNA switches

Project description:Massively parallel reporter assay for identification of RNA switches

| PRJNA1105614 | ENA

Long-range massively parallel reporter assay reveals rules of distal enhancer-promoter interactions

Project description:Long-range massively parallel reporter assay reveals rules of distal enhancer-promoter interactions

| PRJNA1249097 | ENA

Long-range massively parallel reporter assay reveals rules of distal enhancer-promoter interactions

Project description:Long-range activation is an essential property of enhancers, yet the features determining long-range enhancer activities have not been systematically investigated due to a lack of high-throughput methods to measure long-range enhancer activities efficiently. To address this gap, we present a long-range massively parallel reporter assay (long-range MPRA), a genome-integrated assay allowing the measurement of hundreds of enhancers at multiple distances away from a promoter in parallel. The long-range MPRA assay features two independent landing pads, which allow for modular control over the genome-integrated promoter and enhancer libraries. We showcased the capability of long-range MPRA by testing over 300 K562 enhancers, as well as a set of enhancer combinations, at distances up to 100kb. We found that enhancers’ long-range activities are primarily determined by their intrinsic strength, with strong enhancers retaining more activity over long distances, while weak enhancers rapidly lose activity. Additionally, we found that GATA1-bound enhancers are more resistant to distance-dependent loss of activity, suggesting that TF binding also modulates long-range function. Finally, testing long-range enhancer activities with three different promoters (HBE, HBG and GAPDH) revealed that long-range E-P interactions rely on not only enhancer properties but also promoter responsiveness.

2025-04-15 | GSE294367 | 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

Genome-wide enhancer identification by massively parallel reporter assay in Arabidopsis

Project description:Enhancers are critical cis-regulatory elements controlling gene expression during cell development and differentiation. However, genome-wide enhancer characterization has been challenging due to the lack of a well-defined relationship between enhancers and genes. Here, we applied a massively parallel reporter assay on Arabidopsis to measure enhancer activities across the genome. We identified 4327 enhancers with various combinations of epigenetic modifications distinctively different from animal enhancers. Furthermore, we showed that enhancers differ from promoters in their preference for transcription factors. Although some enhancers are not conserved and overlap with transposable elements forming clusters, enhancers are generally conserved across thousand Arabidopsis species, suggesting they are selected under evolution pressure and could play critical roles in the regulation of important genes. Moreover, comparison analysis reveals that enhancers identified by different strategies do not overlap, suggesting these methods are complementary in nature. In sum, our work provides an additional catalog of enhancers and lays the foundation for further investigation into enhancers’ functional mechanisms in plants.

2020-10-13 | GSE157030 | GEO

A massively parallel reporter assay for RNA localization in neurons

Project description:A massively parallel reporter assay for RNA localization in neurons

| PRJNA723817 | ENA