GEO DataSets

Analysis of xpa-1 mutants deficient in nucleotide excision repair (NER). Transcription-blocking DNA damage is believed to contribute to aging and underlie activation of oxidative stress responses (OSR). Results provide insight into the transcriptomic reprogramming response in xpa-1 mutants.

Organism:

Caenorhabditis elegans

Type:

Expression profiling by array, transformed count, 2 genotype/variation sets

Platform:

GPL200

Series:

GSE39252

10 Samples

Download data: CEL

(Submitter supplied) Background: The ability of an organism to repair DNA damage is implicated in carcinogenesis and aging. Interestingly expression profiling of Nucleotide Excision Repair (NER) deficient segmental progeroid mice revealed gene expression changes resembling these observed in aged wild type animals. Our previous transcriptional profiling of NER-deficient C. elegans xpa-1 mutant showed overrepresentation of genes involved in lifespan determination and upregulation of several oxidative stress response genes (Fensgard et al. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by array

Dataset:

GDS4564

Platform:

GPL200

10 Samples

Download data: CEL

(Submitter supplied) Background: The ability of an organism to repair damages to DNA is inextricably linked to aging and cancer. We have characterized and compared the transcriptome of C. elegans mutants deficient in DNA base excision repair, nucleotide excision repair or both to elucidate the transcriptional changes incurred by the reduction of these repair pathways. Results: The gene expression signatures from nth-1, xpa-1 and nth-1;xpa-1 are deciphered. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by array

Platform:

GPL200

9 Samples

Download data: CEL, CHP

(Submitter supplied) We compared the transcriptomic response to UVC radiation in widltype (N2), DNA repair-deficient (xpa-1), and germ cell-deficient (glp-1) young adult nematodes. We were interested in the wildtype response to this stressor, and postulated that the early (3h post-exposure) difference might be different in nucleotide excision repair-deficient (xpa-1) nematodes. We also hypothesized that the response would be different in young adults composed entirely of somatic cells (glp-1 strain at this temperature), compared to germ cell-bearing and gravid young adults (N2 and xpa-1). more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by array

Platform:

GPL200

24 Samples

Download data: CEL

(Submitter supplied) Purpose: Nucleotide excision repair (NER) in mammalian cells requires the xeroderma pigmentosum group A protein (XPA) as a core factor. Remarkably, XPA and other NER proteins have been detected by chromatin immunoprecipitation at some active promoters, and NER deficiency is reported to influence the activated transcription of selected genes. However, the global influence of XPA on transcription in human cells has not been determined. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

48 Samples

Download data: TXT

(Submitter supplied) Embryonic stem cells can self-renew and differentiate, holding great promise for regenerative medicine. They also employ multiple mechanisms to preserve the integrity of their genomes. Nucleotide excision repair, a versatile repair mechanism, removes bulky DNA adducts from the genome. However, the dynamics of the capacity of nucleotide excision repair during stem cell differentiation remain unclear. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

14 Samples

Download data: CSV

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL6885 GPL10558

28 Samples

Download data

(Submitter supplied) Mitochondrial dysfunction is a common feature in neurodegeneration and aging. We identify mitochondrial dysfunction in xeroderma pigmentosum group A (XPA), a nucleotide excision DNA repair disorder with severe neurodegeneration, in silico and in vivo. XPA deficient cells show defective mitophagy with excessive cleavage of PINK1 and increased mitochondrial membrane potential. The mitochondrial abnormalities appear to be caused by decreased activation of the NAD+-SIRT1-PGC-1α axis triggered by hyperactivation of the DNA damage sensor PARP1. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6885

12 Samples

Download data: TXT

(Submitter supplied) Mitochondrial dysfunction is a common feature in neurodegeneration and aging. We identify mitochondrial dysfunction in xeroderma pigmentosum group A (XPA), a nucleotide excision DNA repair disorder with severe neurodegeneration, in silico and in vivo. XPA deficient cells show defective mitophagy with excessive cleavage of PINK1 and increased mitochondrial membrane potential. The mitochondrial abnormalities appear to be caused by decreased activation of the NAD+-SIRT1-PGC-1α axis triggered by hyperactivation of the DNA damage sensor PARP1. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

16 Samples

Download data: TXT

(Submitter supplied) We have adapted the eXcision Repair-sequencing (XR-seq) method to generate single-nucleotide resolution dynamic repair maps of UV-induced cyclobutane pyrimidine dimers (CPD) photoproducts in the Caenorhabditis elegans (C. elegans) genome. We focus on the C. elegans ortholog of the human XPC-deficient strain (xpc-1) and its exclusive use of transcription-coupled repair. We provide evidence demonstrating the utility of xpc-1 XR-seq as a remarkable tool for detecting nascent transcription and identifying new transcripts. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL32326 GPL26672

8 Samples

Download data: BW