Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

MiCLIP analysis of m6A sites in LNCaP and RWPE cells

ABSTRACT: miCLIP analysis of m6A sites in LNCaP and RWPE cells

PROVIDER: PRJNA676163 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR13036640.fastq.gz	Fastqsanger.gz
	SRR13036641.fastq.gz	Fastqsanger.gz
	SRR13036642_1.fastq.gz	Fastqsanger.gz
	SRR13036642_2.fastq.gz	Fastqsanger.gz
	SRR13036643_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 6

Similar Datasets

miCLIP analysis of m6A sites in LNCaP and RWPE cells

Project description:Genomic and transcriptomic alterations are insufficient to explain the variance in protein expression seen in cancer. Recent evidence has highlighted the role of N6-methyladenosine (m6A) in the regulation of mRNA expression, stability and translation, supporting a potential role for post-transcriptional regulation mediated by m6A in cancer. Here we explore prostate cancer as an exemplar cancer and generate the first prostate m6A maps, and further examined how low levels of N6-adenosine-methyltransferase (METTL3) associates with advanced prostate cancer and results in altered expression at the level of transcription, translation, and protein. In particular extracellular matrix proteins have a high number of m6A sites and show significant changes in expression with METTL3 knock-down. We also discovered the upregulation of a hepatocyte nuclear factor-driven gene signature that is associated with therapy resistance in prostate cancer. Significantly, METTL3 knock-down rendered the cells resistant to androgen receptor antagonists, implicating changes in m6A as a mechanism for therapy resistance in metastatic prostate cancer.

2021-06-07 | GSE161303 | GEO

m6A modification in effector CD4+ T cells [m6A-miCLIP-seq]

Project description:GP61-primed effector CD4+ T cells were isolated from Ctrl or Mettl3-deficient SMARTA mice. Total RNAs were extracted with TRIzol reagent, and mRNAs were then isolated with Dynabeads® mRNA purification kit, followed by stardard m6A-miCLIP-SMARTer-seq with some modifications. Raw sequencing reads were aligned to the mouse genome (mm10) with BWA, and then m6A sites were determined.

2021-01-19 | GSE129649 | GEO

Nuclear miCLIP and Nuclear NKAP iCLIP

Project description:To identify m6A sites on endogenous nuclear RNAs, we performed miCLIP to identify m6A sites in PANC-1 cells. To identify NKAP binding sites on endogenous nuclear RNAs, we performed iCLIP for flag-tag NKAP to analyze the nuclear RNA binding with NKAP in the same cells.

2019-03-24 | GSE116425 | GEO

Analysis of m6A in NB cell line (miCLIP)

Project description:Analysis of m6A in NB cell line (miCLIP)

| PRJNA772285 | ENA

Single-nucleotide resolution profiling of N6-methyladenosine in SETD2 knockdown HepG2 cells [m6A miCLIP-seq]

Project description:To understand the global effect of H3K36me3 on m6A modification, we compared the m6A profiling in SETD2 knockdown and control HepG2 cells by miCLIP-seq, and found the depletion of H3K36me3 by SETD2 silencing globally reduced m6A in the human transcriptome.

2019-02-21 | GSE121942 | GEO

m6A modification in effector CD4+ T cells [m6A-miCLIP-seq]

Project description:m6A modification in effector CD4+ T cells [m6A-miCLIP-seq]

| PRJNA532394 | ENA

Analysis of m6A in NB cell line (miCLIP)

Project description:miCLIP of control, METTL14-overexpressed and ALKBH5-rescued CHP-212 cells

2024-06-30 | GSE186073 | GEO

miCLIP profiling of m6A sites in human CD8⁺ T cells during activation, with Input and noUV controls

Project description:miCLIP profiling of m6A sites in human CD8⁺ T cells during activation, with Input and noUV controls

| PRJEB98450 | ENA

Deep and accurate detection of m6A RNA modifications in human and mouse cells using miCLIP2 and m6Aboost machine learning [c]

Project description:N6-methyladenosine (m6A) is the most abundant internal RNA modification in eukaryotic mRNAs and influences many aspects of RNA processing, such as RNA stability and translation. miCLIP (m6A individual-nucleotide resolution UV crosslinking and immunoprecipitation) is an antibody-based approach to map m6A sites in the transcriptome with single-nucleotide resolution. However, due to broad antibody reactivity, reliable identification of m6A sites from miCLIP data remains challenging. Here, we present several experimental and computational innovations that significantly improve transcriptome-wide detection of m6A sites. Based on the recently developed iCLIP2 protocol, the optimised miCLIP2 results in high-complexity libraries using less input material, leading to a more comprehensive representation of m6A sites. Next, we established a robust computational pipeline to identify true m6A sites from our miCLIP2 data. The analyses are calibrated with data from Mettl3 knockout cells to learn the characteristics of m6A deposition, including a significant number of m6A sites outside of DRACH motifs. In order to make these results universally applicable, we trained a machine learning model, m6Aboost, based on the experimental and RNA sequence features. Importantly, m6Aboost allows prediction of genuine m6A sites in miCLIP data without filtering for DRACH motifs or the need for Mettl3 depletion. Using m6Aboost, we identify thousands of high-confidence m6A sites in different murine and human cell lines, which provide a rich resource for future analysis. Collectively, our combined experimental and computational methodology greatly improves m6A identification.

2021-06-05 | GSE163499 | GEO

Deep and accurate detection of m6A RNA modifications in human and mouse cells using miCLIP2 and m6Aboost machine learning [b]

2021-06-05 | GSE163492 | GEO