GEO DataSets

(Submitter supplied) Cockayne Syndrome (CS) is a rare neurodegenerative disease characterized by short stature, cachexia, sun-sensitivity, accelerated aging, and short lifespan. Mutations in two human genes, ERCC8/CSA and ERCC6/CSB, are causative for CS and the protein products of these genes, CSA and CSB, while structurally unrelated, play roles in DNA repair and other aspects of DNA metabolism in human cells. Many clinical and molecular features of CS remain poorly understood, and it has been suggested that CSA and CSB regulate transcription of rDNA genes and ribosome biogenesis. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

12 Samples

Download data: XLSX

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20301

25 Samples

Download data

(Submitter supplied) The rare genetic disease Cockayne syndrome (CS) results in mutations in CSA and CSB. Upon UV irradiation, RNA synthesis was arrested: RNA-seq showed 70% of down-regulated genes in common between CSA and CSB deficient cells. ATF3, the product of an immediate early gene was overexpressed and bound to its CRE/ATF site to inhibit its responsive genes. ChIP experiments showed that CSA/CUL4A/DDB1 together with CSB and MDM2, target ATF3. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20301

17 Samples

Download data: XLSX

(Submitter supplied) The rare genetic disease Cockayne syndrome (CS) results in mutations in CSA and CSB. Upon UV irradiation, RNA synthesis was arrested: RNA-seq showed 70% of down-regulated genes in common between CSA and CSB deficient cells. ATF3, the product of an immediate early gene was overexpressed and bound to its CRE/ATF site to inhibit its responsive genes. ChIP experiments showed that CSA/CUL4A/DDB1 together with CSB and MDM2, target ATF3. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

8 Samples

Download data: XLSX

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

Organism:

Homo sapiens; Caenorhabditis elegans

Type:

Expression profiling by array

Platforms:

GPL28098 GPL10094

44 Samples

Download data: TXT

(Submitter supplied) Cockayne syndrome (CS) is a rare premature aging disease, which in the majority of cases is caused by mutations of the genes encoding the CSA or CSB proteins. CS patients display cachectic dwarfism and severe neurological manifestations and die by 12 years of age on average. The CS proteins are involved in transcription and DNA repair, including a specialized form of DNA repair called transcription-coupled nucleotide excision repair (TC-NER). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL28098

12 Samples

Download data: TXT

(Submitter supplied) Cockayne syndrome (CS) is a rare premature aging disease, which in the majority of cases is caused by mutations of the genes encoding the CSA or CSB proteins. CS patients display cachectic dwarfism and severe neurological manifestations and die by 12 years of age on average. The CS proteins are involved in transcription and DNA repair, including a specialized form of DNA repair called transcription-coupled nucleotide excision repair (TC-NER). more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by array

Platform:

GPL10094

32 Samples

Download data: TXT

(Submitter supplied) Cockayne syndrome (CS) is an accelerated aging disorder, caused by mutations in the CSA or CSB genes. In CSB-deficient cells, poly (ADP ribose) polymerase (PARP) is persistently activated by unrepaired DNA damage and PARP consumes and depletes cellular nicotinamide adenine dinucleotide (NAD), which leads to mitochondrial dysfunction. Here, the distribution of poly (ADP ribose) (PAR) was determined in CSB-deficient cells using ADPr-ChAP (ADP ribose-chromatin affinity purification), and the results show striking enrichment of PAR at transcription start sites (TSS), depletion of heterochromatin, and downregulation of H3K9me3-specific methyltransferases SUV39H1 and SETDB1. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

22 Samples

Download data: BED, BIGWIG, BW, TXT

(Submitter supplied) We report how CSB affects globally the density of RNA Pol II at TSS and how this effect correlates with the gene expression alterations observed from microarray analysis. We also show globally the distribution of CSB.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL10999

12 Samples

Download data: BED

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

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL18734 GPL10999

64 Samples

Download data: BED, PAIR

(Submitter supplied) Neuroblastoma cells SH-SY5Y undergoes a morphology change upon retinoic acid (RA) treatment, the neurite outgrowth characteristic in undividing cells is accompanied by cell cycle arrest and neuronal markers expression, controlled by a precise dynamic molecular circuits. Depletion of CSB in SH-SY5Y cells leads to differentiation defects. This study examines the temporal gene expression profile during differentiation. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL18734

24 Samples

Download data: PAIR

(Submitter supplied) Fibroblasts can be directly converted into neurons in vitro by depletion of nPTB, the reprogramming process induces neuronal gene expression while inhibits fibroblast gene expression. Human fibroblasts lacking CSB can not be converted into neurons, unless CSB gene was introduced. This study characterizes the CSB-dependent gene expression alterations during reprogramming. Using Nimblegen microarray we identified differentially expressed genes in induced neurons from wild type CSB reconstituted fibroblasts, and we proved that the difference in gene expression after reprogramming was not observed in CS1AN cells.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL18734

8 Samples

Download data: PAIR

(Submitter supplied) As the causative gene for cockayne syndrome, CSB has a well-characerized function in transcription-coupled nucleotide excision repair. However, the complex neurological abnormalities that affect CS patients can not be simply explained by the DNA repair defects. CSB is also involved in RNAP II transcription regulation. This study characterizes the gene expression signatures affected by CSB protein. Using Nimblegen microarray we identified differentially expressed genes in human fibroblasts derived from CS patients as compared to CSB reconstituted cell lines (wild type).

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL18734

8 Samples

Download data: PAIR

(Submitter supplied) The intricate features of human brain development and function are reflected on the precise regulation of transcriptional architecture. This study characterizes the gene expression perturbations of Cockayne Syndrome brain tissue samples underlying the complex neurological abnormalities.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL18734

12 Samples

Download data: PAIR

(Submitter supplied) Cockayne syndrome (CS) is a rare genetic neurodevelopmental disorder, characterized by a deficiency in the transcription-coupled nucleotide excision repair pathway. Mutation of Cockayne syndrome B (CSB) affects basal transcription which is considered a major cause of CS neurological dysfunction. Here, we generated a rat model by mimicking a nonsense mutation in the CSB(ERCC6) gene of CS-B patients. CSB-deficient rats exhibit the well-known CS repair characteristics: inability to resume RNA synthesis from stalled RNA polymerase II (RNAP II) and persistent gamma H2AX overexpression after UV damage. In contrast to that of the Csb-/- mouse models, the cerebella of the CSB-deficient rats are more profoundly affected. Both the molecular and the granular layers of the cerebellum cortex showed significant atrophy. The white matter of the cerebellum demonstrated high GFAP staining indicative of reactive astrogliosis. RNA-seq analysis of CSB-deficient rat cerebella revealed that even in the absence of UV damage, CSB affects the expression of hundreds of genes, many of which are neuronal genes, suggesting that transcription dysregulation could contribute to the neurological features in CSB rat models.

Organism:

Rattus norvegicus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24688

11 Samples

Download data: XLSX

(Submitter supplied) Gene expression profile in CS1AN deficient and CSBwt restored cell lines after 24 hours of UV or alphe-amanitin treatment (only for restored). The comaprison of expression profile between 0 and 24 hours revealed continouse suppresion of transcription upon UV treatment in CS1AN cell line and alpha-amanitin treated CS1AN CSBwt restored cells.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6244

10 Samples

Download data: CEL

(Submitter supplied) The CSB-PGBD3 fusion protein arose over 43 million years ago when a 2.5 kb piggyBac 3 (PGBD3) transposon inserted into intron 5 of the Cockayne syndrome Group B (CSB) gene in the common ancestor of all higher primates. The CSB-PGBD3 fusion protein binds internally-deleted PGBD3 elements called MER85s in vitro, and induces a strong interferon-like innate antiviral immune response when expressed in CSB-null UVSS1KO cells. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9115

2 Samples

Download data: BED, WIG

(Submitter supplied) Cockayne syndrome is a segmental progeria most often caused by mutations in the CSB gene encoding a SWI/SNF-like ATPase required for transcription-coupled DNA repair (TCR). Over 43 Mya before marmosets diverged from humans, a piggyBac3 (PGBD3) transposable element integrated into intron 5 of the CSB gene. As a result, primate CSB genes now generate both CSB protein and a conserved CSB-PGBD3 fusion protein in which the first 5 exons of CSB are alternatively spliced to the PGBD3 transposase. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

12 Samples

Download data: CEL

(Submitter supplied) We used eXcision Repair-sequencing (XR-seq) to map UV induced damage in U2OS cells and in U2OS cells in which CSA or UVSSA genes were knocked out. Complementation of UVSSA knockout with WT or mutant proteins shows UVSSA is a core component of human transcription coupled repair.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18573 GPL16791

9 Samples

Download data: BW

(Submitter supplied) Cockayne syndrome is an inherited premature aging syndrome associated with developmental and neurological disorders. Mutations in the genomic locus encoding CSB are associated with 80% Cockayne syndrome cases. Transcription profiling assays reveal the association of mis-regulation of gene expression with Cockayne syndrome, highlighting the importance of CSB in transcription regulation. However, many questions remain unanswered as how CSB regulates transcription. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

4 Samples

Download data: BED