Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

CIGAR-seq, a CRISPR/Cas-based method for unbiased screening of novel mRNA modification regulators II

ABSTRACT: Cellular RNA is decorated with over 160 types of chemical modifications. Many modifications in mRNA, including m6A and m5C, have been associated with critical cellular functions under physiological and/or pathological conditions. To understand the biological functions of these modifications, it is vital to identify the regulators that could modulate the modification rate. However, a high-throughput method for unbiased screening of these regulators is so far lacking. Here, we report such a method combining pooled CRISPR screen and reporters with RNA modification readout, termed CRISPR integrated gRNA and reporter sequencing (CIGAR-seq).

ORGANISM(S): Homo sapiens

PROVIDER: GSE157367 | GEO | 2020/11/04

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

CIGAR-seq, a CRISPR/Cas-based method for unbiased screening of novel mRNA modification regulators I

Project description:Cellular RNA is decorated with over 160 types of chemical modifications. Many modifications in mRNA, including m6A and m5C, have been associated with critical cellular functions under physiological and/or pathological conditions. To understand the biological functions of these modifications, it is vital to identify the regulators that could modulate the modification rate. However, a high-throughput method for unbiased screening of these regulators is so far lacking. Here, we report such a method combining pooled CRISPR screen and reporters with RNA modification readout, termed CRISPR integrated gRNA and reporter sequencing (CIGAR-seq).

2020-11-04 | GSE157366 | GEO

CIGAR-seq, a CRISPR/Cas-based method for unbiased screening of novel mRNA modification regulators

Project description:CIGAR-seq, a CRISPR/Cas-based method for unbiased screening of novel mRNA modification regulators

| PRJNA661064 | ENA

CIGAR-seq, a CRISPR/Cas-based method for unbiased screening of novel mRNA modification regulators I

Project description:CIGAR-seq, a CRISPR/Cas-based method for unbiased screening of novel mRNA modification regulators I

| PRJNA661069 | ENA

CIGAR-seq, a CRISPR/Cas-based method for unbiased screening of novel mRNA modification regulators II

Project description:CIGAR-seq, a CRISPR/Cas-based method for unbiased screening of novel mRNA modification regulators II

| PRJNA661068 | ENA

Generation of corrected hiPSC clones from a Cornelia de Lange Syndrome (CdLS) patient through CRISPR-Cas based technology

Project description:Cornelia de Lange syndrome (CdLS) is an autosomal dominant disease mainly caused by mutations in the Nipped-B-like protein (NIPBL) gene resulting in the alteration of the cohesin pathway. Here, we generated human induced pluripotent stem cells (hiPSCs) from a CdLS patient carrying a mutation in the NIPBL gene, c.5483G>A, and tested CRISPR-Cas based approaches to repair the genetic defect. We applied an efficient and precise method of gene correction through CRISPR-Cas induced homology directed repair (HDR), which allowed the generation of hiPSC clones with regular karyotype and preserved stemness. The efficient and precise gene replacement strategy developed in this study can be extended to the modification of other genomic loci in hiPSCs. Isogenic wild-type and mutated hiPSCs produced with the CRISPR-Cas technology are fundamental CdLS cellular models to study the disease molecular determinants and identifying therapeutic targets.

2023-03-17 | E-MTAB-11604 | biostudies-arrayexpress

Simultaneous identification of m6A and m5C reveals coordinated RNA modification at single-molecule resolution [mouse frontal cortex]

Project description:The expanding field of epitranscriptomics might rival the epigenome in the diversity of biological processes impacted. However, the identification of multiple modification types in individual RNA molecules remains challenging. We present CHEUI, a new method that detects N6-methyladenosine (m6A) and 5-methylcytidine (m5C) in individual transcript molecules in a single condition as well as differential methylation between two conditions, using nanopore signals. CHEUI processes observed and expected signals with convolutional neural networks to achieve high single-molecule accuracy and outperform other methods in detecting m6A and m5C sites and quantifying their stoichiometry. Moreover, CHEUI’s unique capability to identify different modifications in the same signal data reveals a non-random co-occurrence of m6A and m5C in transcripts in human cell lines and during mouse embryonic brain development. CHEUI unlocks the capability of studying links between multiple RNA modifications and phenotypes, enabling the discovery of new epitranscriptome functions. Furthermore, CHEUI's training and testing protocols are adaptable to other modifications, making it a versatile RNA technology.

2022-10-31 | GSE211760 | GEO

Simultaneous identification of m6A and m5C reveals coordinated RNA modification at single-molecule resolution [HeLa cells]

2022-10-31 | GSE211759 | GEO

Prediction of m6A and m5C at single-molecule resolution reveals a transcriptome-wide co-occurrence of RNA modifications

2024-01-16 | GSE253150 | GEO

Transfer learning enables identification of multiple types of RNA modification using nanopore direct RNA sequencing

Project description:RNA internal modifications play critical role in development of multicellular organisms and their response to environmental cues. Using nanopore direct RNA sequencing (DRS), we constructed a large in vitro epitranscriptome (IVET) resource from plant cDNA library labeled with m6A, m1A and m5C respectively. Furthermore, after transfer learning, the pre-trained model was used to detect additional RNA internal modification such as m1A, hm5C, m7G and Ψ modification. Finally, we illustrated a global view of epitranscriptome with m6A, m1A, m5C, m7G and Ψ modification in rice seedlings under normal and high salinity environment. In summary, we provided a strategy for creating IVET resource from cDNA library and developed a computational method that use IVET-based transfer learning termed TandemMod for profiling epitranscriptome landscape with co-occupancy of multiple types of RNA modification in plants responsive to environmental signal.

2024-03-28 | GSE227087 | GEO

Comprehensive analysis of mRNA 5-methylcytosine modification in Eimeria tenella oocysts

Project description:5-methylcytosine (m5C) is a type of RNA modifications reported to regulate diverse biological processes. However, the distribution and biological functions of m5C in E. tenella mRNAs remain largely unknown. Herein, we report transcriptome-wide profiling of mRNA m5C in E. tenella by applying m5C RNA immunoprecipitation followed by a deep-sequencing approach (m5C-RIP-seq). Our data showed that m5C peaks were distributed across the whole mRNA body. There were 2813 hypermethylated and 1850 hypomethylated m5C peaks in sporulated oocysts compared with unsporulated oocysts. Further joint analysis showed a positive correlation between m5C modification and gene expression levels. The mRNA sequencing and m5C-RIP-seq data were consistent with the results of the quantitative reverse transcription PCR (RT-qPCR) and m5C-RIP-qPCR, respectively. Gene ontology (GO) and pathway enrichment analysis predicated diverse biological functions and pathways, including microtubule motor activity, helicase activity, cGMP-PKG signaling pathway, aminoacyl-tRNA biosynthesis, glycolysis/gluconeogenesis and spliceosome. Meanwhile, stage-specific gene expression signatures of m5C-related enzymes were observed. Altogether, our findings revealed the transcriptional significance of m5C modification in E. tenella oocysts, providing clues for in-depth research.

2023-12-19 | GSE249232 | GEO

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