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Analysis of the Role of NuMA (TDIF) in DNA repair Through Next Generation Sequencing Techniques

ABSTRACT: Analysis of the Role of NuMA (TDIF) in DNA repair Through Next Generation Sequencing Techniques

PROVIDER: PRJNA612787 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11310331_1.fastq.gz	Fastqsanger.gz
	SRR11310331_2.fastq.gz	Fastqsanger.gz
	SRR11310332_1.fastq.gz	Fastqsanger.gz
	SRR11310332_2.fastq.gz	Fastqsanger.gz
	SRR11310333_1.fastq.gz	Fastqsanger.gz

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Analysis of the Role of NuMA (TDIF) in DNA repair Through Next Generation Sequencing Techniques [ChIP-Seq]

Project description:Purpose: To assess the role of NuMA (TDIF) in DNA repair, NuMA (TDIF) ChIP-seq, 4sU-seq in hydrogen peroxide treated and untreated WT and NuMA (TDIF) KD cells, and OGAP-seq in hydrogen peroxide treated and untreated WT and NuMA (TDIF) KD cells Methods: 4sU-seq was carried out in WT and NuMA (TDIF) KD (using a doxycyclin inducible system) untreated and peroxide treated duplicate RPE cells. The data was mapped using STAR, the bams coverted into bigwigs and differential expression between the conditions carried out using DE-seq2. NuMA (TDIF) ChIP-seq and OGAP-seq data was mapped using BWA. Both sets of mapped data were subsequently used to generate bigwigs showing fold-change relative to inputs using MACS2 and to generate metagene profiles using the CGAT suite of bioinformatics tools. Both sets of data were also run through FeatureCounts to count reads overlapping promoter regions. Results: Through our 4sU-seq data we identified a set of genes whose expression upon exposure to oxidative stress is dependent upon the presence of NuMA (TDIF). NuMA (TDIF) ChIP revealed increased occupancy of NuMA (TDIF) at promoters, which was increased for NuMA (TDIF)-regulated genes, paused genes and early response genes. OGAP-seq in the presence and absence of NuMA (TDIF) demonstrated that in the absence of NuMA (TDIF) there is increased damage across gene bodies and particularly promoters. Conclusions: Our study indicates that NuMA (TDIF) plays a role in the protection from and response to oxidative damage. This protective effect appears to be particularly strong at promoters regions, and may differ between distinct subsets of gene categories.

2022-07-15 | GSE147014 | GEO

Analysis of the Role of NuMA (TDIF) in DNA repair Through Next Generation Sequencing Techniques [OGAP-seq]

2022-07-15 | GSE147013 | GEO

Analysis of the Role of NuMA (TDIF) in DNA repair Through Next Generation Sequencing Techniques [RNA-Seq]

2022-07-15 | GSE147012 | GEO

Analysis of the Role of NuMA (TDIF) in DNA repair Through Next Generation Sequencing Techniques [NuMA (TDIF) CUT&RUN SH-SY5Y]

Project description:Purpose: To assess the role of NuMA (TDIF) in DNA repair Methods: CUT&RUN was carried out in untreated and hydrogen peroxide treated SH-SY5Y cells in triplicate. The data was mapped using bwa mem and subsequently used to generate bigwigs showing fold-change relative to inputs using MACS2 and various meta-feature profiles using the CGAT suite of bioinformatics tools Results: The data revealed increased occupancy of NuMA (TDIF) at promoters and enhancers, which increases upon hydrogen peroxide treatment Conclusions: Our study indicates that NuMA (TDIF) plays a role in the protection from and response to oxidative damage. This protective effect appears to be particularly strong at promoter and enhancer regions, and may differ between distinct subsets of gene categories.

2022-07-15 | GSE201983 | GEO

Analysis of the Role of NuMA (TDIF) in DNA repair Through Next Generation Sequencing Techniques [NuMA (TDIF) and TDP1 CUT&RUN RPE1]

Project description:Purpose: To assess the role of NuMA (TDIF) in DNA repair Methods: CUT&RUN was carried out in untreated/hydrogen peroxide treated RPE1 cells in duplicate. The data was mapped using bwa mem and subsequently used to generate bigwigs showing fold-change relative to inputs using MACS2 and various meta-feature profiles using the CGAT suite of bioinformatics tools Results: The data revealed increased occupancy of NuMA (TDIF) at promoters and enhancers, which increases upon hydrogen peroxide treatment Conclusions: Our study indicates that NuMA (TDIF) plays a role in the protection from and response to oxidative damage. This protective effect appears to be particularly strong at promoter and enhancer regions, and may differ between distinct subsets of gene categories.

2022-07-15 | GSE201984 | GEO

Analysis of the Role of NuMA (TDIF) in DNA repair Through Next Generation Sequencing Techniques [OGAP-seq SH-SY5Y]

Project description:Purpose: To assess the role of NuMA (TDIF) in DNA repair Methods: OGAP-seq was carried out in in each pairwise combination of untreated/hydrogen peroxide treated and no doxycyclin (NuMA (TDIF) WT)/doxycyclin treated (NuMA (TDIF) KD) SH-SY5Y cells in duplicate. The data was mapped using bwa mem and subsequently used to generate bigwigs showing fold-change relative to inputs using MACS2 and various meta-feature profiles using the CGAT suite of bioinformatics tools Results: The data revealed elevated OGAP-seq signal in promoter and enhancer regions upon NuMA (TDIF) KD Conclusions: Our study indicates that NuMA (TDIF) plays a role in the protection from and response to oxidative damage. This protective effect appears to be particularly strong at promoter and enhancer regions.

2022-07-15 | GSE201981 | GEO

Analysis of the Role of NuMA (TDIF) in DNA repair Through Next Generation Sequencing Techniques [PolII ChIP-seq RPE1]

Project description:Purpose: To assess NuMA (TDIF)’s role in facilitating PolII pausing Methods:Pol2 ChIP-Seq was carried out in each pairwise combination of untreated/hydrogen peroxide treated and no doxycyclin (NuMA (TDIF) WT)/doxycyclin treated (NuMA (TDIF) KD) RPE1 cells in duplicate. The data was mapped using bwa mem and subsequently used to generate bigwigs showing fold-change relative to inputs using MACS2 and various meta-feature profiles using the CGAT suite of bioinformatics tools Results: The data revealed increased occupancy of PolII at promoter regions and increased pausing ratios for genes in H2O2- cells after NuMA (TDIF) KD relative to controls, but decreased occupancy in NuMA (TDIF) KD in H2O2+ cells compared to controls. Conclusions: Our study indicates that NuMA (TDIF) plays a role in PolII pause-release.

2022-07-15 | GSE201982 | GEO

Analysis of the Role of NuMA (TDIF) in DNA repair Through Next Generation Sequencing Techniques [NuMA (TDIF) CUT&RUN SH-SY5Y]

Project description:Analysis of the Role of NuMA (TDIF) in DNA repair Through Next Generation Sequencing Techniques [NuMA (TDIF) CUT&RUN SH-SY5Y]

| PRJNA833893 | ENA

Analysis of the Role of NuMA (TDIF) in DNA repair Through Next Generation Sequencing Techniques [NuMA (TDIF) and TDP1 CUT&RUN RPE1]

Project description:Analysis of the Role of NuMA (TDIF) in DNA repair Through Next Generation Sequencing Techniques [NuMA (TDIF) and TDP1 CUT&RUN RPE1]

| PRJNA833892 | ENA

Analysis of the Role of NuMA (TDIF) in DNA repair Through Next Generation Sequencing Techniques [ChIP-Seq]

Project description:Analysis of the Role of NuMA (TDIF) in DNA repair Through Next Generation Sequencing Techniques [ChIP-Seq]

| PRJNA612794 | ENA