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Enhanced crosslinking and immunoprecipitation of SERBP1 in Hela cells

ABSTRACT: Enhanced crosslinking and immunoprecipitation of SERBP1 in Hela cells

PROVIDER: PRJNA656424 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12427690_1.fastq.gz	Fastqsanger.gz
	SRR12427690_2.fastq.gz	Fastqsanger.gz
	SRR12427691_1.fastq.gz	Fastqsanger.gz
	SRR12427691_2.fastq.gz	Fastqsanger.gz
	SRR12427692.fastq.gz	Fastqsanger.gz

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Enhanced crosslinking and immunoprecipitation of SERBP1 in Hela cells

Project description:Purpose:We used eCLIP experiment to analyze binding profile of SERBP1 and its relationship with G4. Result: we found 505 high-confidence SERBP1 binding sites in Hela cells, and the analysis of sequence revealed transcriptome-wide enrichment of PQS in SERBP1-binding regions

2020-10-27 | GSE156015 | GEO

Enhanced crosslinking and immunoprecipitation analysis of human fetal β-cells

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SERBP1 affects the apoptotic level by regulating the expression and alternative splicing of cellular and metabolic process genes in HeLa cells

Project description:RNA-binding proteins (RBPs) have important roles in orchestrating posttranscriptional regulation and modulating many tumorigenesis events. SERBP1 has been recognized as an important regulator in multiple cancers, while it remains unclear whether SERBP1-regulated gene expression at the transcriptome-wide level is significantly correlated with tumorigenesis.We overexpressed SERBP1 in HeLa cells and explored whether SERBP1 overexpression (SERBP1-OE) affects the proliferation and apoptosis of HeLa cells. We analyzed the transcriptome-wide gene expression changes and alternative splicing changes mediated by SERBP1-OE using transcriptome sequencing method (RNA-seq). RT-qPCR was conducted to assay SERBP1-regulated alternative splicing.SERBP1-OE induced the apoptosis of HeLa cells. The downregulated genes were strongly enriched in the cell proliferation and apoptosis pathways according to the GO analysis, including FOS, FOSB, PAK6 and RAB26. The genes undergoing at least one SERBP1-regulated alternative splicing event were enriched in transcriptional regulation, suggesting a mechanism of the regulation of gene expression, and in pyruvate and fatty acid metabolic processes critical for tumorigenesis events. The SERBP1-regulated alternative splicing of ME3, LPIN3, CROT，PDP1, SLC27A1 and ALKBH7 was validated by RT-qPCR analysis.We for the first time demonstrated the cellular function and molecular targets of SERBP1 in HeLa cells at transcriptional and post-transcriptional levels. The SERBP1-regulated gene expression and alternative splicing networks revealed by this study provide important information for exploring the functional roles and regulatory mechanisms of SERBP1 in cancer development and progression.

2022-09-02 | GSE192950 | GEO

Enhanced crosslinking and immunoprecipitation analysis of human fetal β-cells

Project description:N6-methyladenosine (m6A) is the most abundant chemical modification in mRNA, and plays important roles in human embryonic stem cell pluripotency, maintenance, and differentiation. However, the role of m6A and the precise mechanisms involved during the development of β-cells are unexplored. Here, we performed enhanced crosslinking and immunoprecipitation (eCLIP) assays to identify m6A sites regulated by METTL14 in EndoC-βh1 human fetal β-cells.

2024-06-13 | GSE236324 | GEO

Individual nucleotide resolution Crosslinking Immunoprecipitation (iCLIP)-seq

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Identifying METTL5-bound RNA by crosslinking-assisted immunoprecipitation

Project description:Identifying METTL5-bound RNA by crosslinking-assisted immunoprecipitation

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Identifying METTL5-bound RNA by crosslinking-assisted immunoprecipitation

Project description:To identify the substrates of METTL5, we used crosslinking-assisted immunoprecipitation of overexpressed, FLAG-METTL5 followed by high throughput sequencing.

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Photoactivatable-Ribonucleotide-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP) of the RNA-binding protein (RBP) RBM4 in KBM-7 derived near-haploid human cell line, HAP1.

Project description:We hypothesized that RBM4 regulates HERVs by directly binding to their transcripts. To test this possibility, we performed photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP). We performed four independent PAR-CLIP replicates of our own using HAP1 cells stably expressing a FLAG-tagged RBM4 (FLAG-RBM4) transgene under control of a doxycycline-inducible promoter. Following metabolic labeling with 4-thiouridine (4SU) and crosslinking with ultraviolet light (UV) of 312 nm wavelength, we isolated RNA covalently linked to FLAG-RBM4. The RNA recovered from four biological replicates was converted into cDNA libraries and deep sequenced.

2020-09-03 | GSE147895 | GEO

U1A iCLIP-seq (individual-nucleotide resolution UV crosslinking and immunoprecipitation coupled with RNA sequencing) analysis in HeLa cells

Project description:U1A iCLIP-seq (individual-nucleotide resolution UV crosslinking and immunoprecipitation coupled with RNA sequencing) analysis in HeLa cells

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2024-09-19 | E-MTAB-12945 | biostudies-arrayexpress

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