Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Endogenous miRNA-200b/c activity and regulation explored by a functional dual fluorescence reporter

ABSTRACT: Endogenous miRNA-200b/c activity and regulation explored by a functional dual fluorescence reporter

PROVIDER: PRJNA646246 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR12218958.fastq.gz	Fastqsanger.gz
	SRR12218959.fastq.gz	Fastqsanger.gz
	SRR12218960.fastq.gz	Fastqsanger.gz
	SRR12218961.fastq.gz	Fastqsanger.gz
	SRR12218962.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 8

Similar Datasets

Endogenous miRNA-200b/c activity and regulation explored by a functional dual fluorescence reporter

Project description:Since their discovery, microRNAs (miRNA)s have been widely studied in almost every field of biology and medicine, leading to the identification of important gene regulation circuits and cellular mechanisms. However, investigations are generally focused on the analysis of their downstream targets and biological functions in overexpression and knockdown approaches, while miRNAs endogenous levels and activity remain poorly investigated. Here, we used the cellular plasticity-regulating process of epithelial-to-mesenchymal transition (EMT) as a model to show the efficacy of a plasmid-based fluorescent sensor to separate cells with distinct EMT signatures, based on miR-200b/c activity. The system was further combined with a CRISPR-Cas9 screening platform to unbiasedly identify miR-200b/c upstream regulating genes. The sensor allows to infer miRNAs fundamental biological properties, as profiling of sorted cells indicated miR-200b/c as a molecular switch between EMT differentiation and proliferation, and suggested a role for metabolic enzymes in miR-200/EMT regulation. Analysis of miRNAs’ endogenous levels and activity could lead to a better comprehension of their biological role in physiology and disease.

2020-12-01 | GSE154429 | GEO

Identifying human pre-mRNA cleavage and polyadenylation factors by genome-wide CRISPR screens in a dual fluorescence readthrough reporter (2)

Project description:The majority of messenger RNA precursor (pre-mRNA) undergoes 3' end cleavage and polyadenylation (CPA), termed as to 3’ end processing. This processing is specified by a polyadenylation site (PAS) and adjacent RNA sequences and regulated by a large variety of core and auxiliary CPA factors. To date, most of the CPA factors have been discovered through biochemical and proteomic studies. However, genome-wide genetic identification of CPA factors has been hampered by the lack of a reliable high-throughput method. Here, we developed a dual fluorescence readthrough reporter system with a PAS inserted between two fluorescent reporters, GFP and mCherry. This system enables the measurement of 3’ end processing in living cells via flow cytometry analysis. Using this system in combination with a human CRISPR library, we conducted a genome-wide screen for CPA factors. The screens identified most of the well-known CPA factors, including most components of the core CPA machineries (i.e. CPSF, CSTF, CFI, and CFII complexes), the CPA scaffold protein SYMPK, PPP1R10 in PNUTS-PP1 complex, as well as CBLL1 (a subunit of m6A RNA methyltransferase complex). Importantly, the screens also uncovered CCNK/CDK12 as a functional core CPA machinery. Furthermore, the screens identified RPRD1B, an RNA polymerase II (RNAP II) binding protein, as a CPA factor. Further characterization showed that RPRD1B binds RNA and regulates the release of RNAP II at the 3’ end of genes. Thus, this dual fluorescence reporter coupled with CRISPR screen provides a reliable tool for identifying bona fide CAP factors, offering a platform for investigating 3’ end processing in various contexts.

2024-04-11 | GSE243456 | GEO

Identifying human pre-mRNA cleavage and polyadenylation factors by genome-wide CRISPR screens in a dual fluorescence readthrough reporter (1)

2024-04-11 | GSE242480 | GEO

A nuclear-localized red fluorescence knock-in reporter allele for mouse pancreatic beta-cells

Project description:In this study, we generated a novel nuclear-localized red fluorescence knock-in reporter allele (Ins2.Apple) for mouse pancreatic beta-cells. Beta-cells were isolated by FACS from 60-day-old mice, segregated by sex, and RNA-sequencing was performed to assess sex-specific differences in beta-cell gene expression profiles. We also isolated beta-cells (by FACS) from MIP-GFP mice at 60 days of age. RNA-sequencing was performed, and was compared to that of Ins2.Apple beta cells, to assess gene expression changes brought on by the presence of the MIP-GFP transgene.

2018-12-15 | E-MTAB-6329 | biostudies-arrayexpress

A nuclear-localized red fluorescence knock-in reporter allele for mouse pancreatic beta-cells

Project description:A nuclear-localized red fluorescence knock-in reporter allele for mouse pancreatic beta-cells

| PRJEB24047 | ENA

Identifying human pre-mRNA cleavage and polyadenylation factors by genome-wide CRISPR screens in a dual fluorescence readthrough reporter

Project description:Identifying human pre-mRNA cleavage and polyadenylation factors by genome-wide CRISPR screens in a dual fluorescence readthrough reporter

| PRJNA1018528 | ENA

Juvenile Fluorescence

Project description:Juvenile Fluorescence Raw sequence reads

| PRJNA436185 | ENA

miR-200b is associated with cisplatin sensitivity in bladder cancer cells

Project description:We aimed to clarify the role of miR-200b in cisplatin (CDDP) sensitivity in bladder cancer (BCa). CDDP resistant T24 cells (T24RC) were transfected with a miR mimic negative control (NC) or a miR-200b mimic, after which cells were treated with or without CDDP. We found that ectopic miR-200b expression re-sensitized the T24RC cells to CDDP. Gene expression microarray analysis revealed that the combination of miR-200b and CDDP affected genes involved in CDDP sensitivity and cytotoxicity.

2018-05-31 | GSE103250 | GEO

Identifying human pre-mRNA cleavage and polyadenylation factors by genome-wide CRISPR screens in a dual fluorescence readthrough reporter (2)

Project description:Identifying human pre-mRNA cleavage and polyadenylation factors by genome-wide CRISPR screens in a dual fluorescence readthrough reporter (2)

| PRJNA1018532 | ENA

Identifying human pre-mRNA cleavage and polyadenylation factors by genome-wide CRISPR screens in a dual fluorescence readthrough reporter (1)

Project description:Identifying human pre-mRNA cleavage and polyadenylation factors by genome-wide CRISPR screens in a dual fluorescence readthrough reporter (1)

| PRJNA1013561 | ENA

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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