GEO DataSets

(Submitter supplied) Members of the Chromodomain-Helicase-DNA binding (CHD) protein family are chromatin remodelers critically implicated in human pathologies. CHD6 is the least studied member of this family, and we were motivated to dissect its in-cell roles by discovering a mutated CHD6 allele in a patient suffering from the rare Hallermann-Streiff premature aging syndrome (HSS). We generated isogenic iPSC lines carrying (or not) this single point mutation in the CHD6 SANT/SLIDE domain, which allow studying HSS-relevant cell identities. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20301

19 Samples

Download data: BED, TDF

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

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20301

55 Samples

Download data: BED, BW, TDF, TXT

(Submitter supplied) Members of the chromodomain-helicase-DNA binding (CHD) protein family are chromatin remodelers critically implicated in human pathologies, with CHD6 being one of its least studied members. Here, we discovered a de novo CHD6 missense mutation in a patient clinically presenting the rare Hallermann-Streiff syndrome (HSS). We used genome editing to generate isogenic iPSC lines and model HSS in relevant cell types. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL20301

4 Samples

Download data: BW

(Submitter supplied) Members of the Chromodomain-Helicase-DNA binding (CHD) protein family are chromatin remodelers critically implicated in human pathologies. CHD6 is the least studied member of this family, and we were motivated to dissect its in-cell roles by discovering a mutated CHD6 allele in a patient suffering from the rare Hallermann-Streiff premature aging syndrome (HSS). We generated isogenic iPSC lines carrying (or not) this single point mutation in the CHD6 SANT/SLIDE domain, which allow studying HSS-relevant cell identities. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

32 Samples

Download data: BW, TXT

(Submitter supplied) Purpose: Study of the role of CHD6 linking nucleosome ejection in castration-resistant prostate cancer(CRPC) Method: The expression of CHD6 or E2F1 was silenced by 2 shRNAs (3 replicates) targeted at CHD6 or E2F1 in C4-2 cells, scramble RNA as control. mRNA profiles and genome-wide chromatin-state maps were generated by deep sequencing. CHD6 and IgG ChIP was conducted in C4-2 cells. MNase before and after CHD6-silenced was conducted in C4-2 cells. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL11154

36 Samples

Download data: BW, TXT

(Submitter supplied) We analyzed the global change in transcription upon CHD3-KO and SENP1-KO compared to control HAP1 cells.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

9 Samples

Download data: TXT

(Submitter supplied) We analysed the global effect of CHD3-KO and SENP1-KO HAP1 cell lines compared to control cell line, on chromatin accessibility using ATAC-seq.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

12 Samples

Download data: BW

(Submitter supplied) We utilized RNA-seq to profile expression levels in wild type AX2 cells and three mutants for the CHD family of ATP-dependent chromatin remodellers in Dictyostelium discoideum. Total RNA was polyA enriched and sequenced at two stages of development: in the growth stage (0H) and in 5H cAMP pulsed cells (5H). All mutants analysed were also in the AX2 background.

Organism:

Dictyostelium discoideum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15643

8 Samples

Download data: TXT

(Submitter supplied) Colorectal cancer is one of the most common cancers. Cancer cells are highly dependent on dysregulated gene expression to support their uncontrolled growth and high energy needs. The expression of gene encoding chromodomain helicase DNA binding protein 6 (CHD6) is frequently altered in tumor tissues of colorectal cancer patients.We performed transcriptomic analysis to identify the differentially expressed genes between control and CHD6 KD HCT116.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

4 Samples

Download data: CEL

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

Organism:

Homo sapiens

Type:

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

Platform:

GPL11154

61 Samples

Download data: BIGWIG, TXT

(Submitter supplied) Proper chromatin organization is essential for defining transcription units and maintaining genomic integrity in eukaryotes. Mutations affecting the chromatin structure can lead to increased cryptic transcription and genomic instability. In this study we found that deletion of the Schizosaccharomyces pombe Chd1-type chromatin remodelers, hrp1 and hrp3, causes strong, genome-wide accumulation of antisense transcripts, while the amount of coding mRNA transcripts is mostly unaffected. more...

Organism:

Schizosaccharomyces pombe

Type:

Expression profiling by array; Genome binding/occupancy profiling by array

Platforms:

GPL16060 GPL16058 GPL16059

29 Samples

Download data: TXT

(Submitter supplied) SETX (senataxin) is an RNA/DNA helicase that has been implicated in transcriptional regulation and the DNA damage response through resolution of R-loop structures. Mutations in SETX result in either of two distinct neurodegenerative disorders. SETX dominant mutations result in a juvenile form of amyotrophic lateral sclerosis (ALS) called ALS4, whereas recessive mutations are responsible for ataxia called ataxia with oculomotor apraxia type 2 (AOA2). more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL16791

4 Samples

Download data: BW

(Submitter supplied) Paramutations represent directed and meiotically-heritable changes in gene regulation leading to apparent violations of Mendelian inheritance. Although the mechanism and evolutionary importance of paramutation behaviors remain largely unknown, genetic screens in maize (Zea mays) identify five components affecting 24 nucleotide RNA biogenesis as required to maintain repression of a paramutant purple plant1 (pl1) allele. more...

Organism:

Zea mays

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL24163

5 Samples

Download data: CSV

(Submitter supplied) Cockayne syndrome (CS) is an inherited neurodevelopmental disorder with progeroid features. Although the genes responsible for CS have been implicated in a variety of DNA repair- and transcription-related pathways, the nature of the molecular defect in CS remains mysterious. We sought to define this defect by expression analysis of cells lacking functional CSB, a SWI/SNF-like ATPase that is responsible for most CS cases. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Datasets:

GDS2175 GDS2176

Platforms:

GPL96 GPL97

16 Samples

Download data: CEL

Analysis of Cockayne syndrome group B (CSB) protein-null fibroblasts rescued by expression of CSB cDNA. CS, a neurodegenerative disorder, arises mostly from CSB defects. Results provide insight into how CSB defects cause CS.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 3 protocol sets

Platform:

GPL97

Series:

GSE3407

8 Samples

Download data: CEL

Analysis of Cockayne syndrome group B (CSB) protein-null fibroblasts rescued by expression of CSB cDNA. CS, a neurodegenerative disorder, arises mostly from CSB defects. Results provide insight into how CSB defects cause CS.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 3 protocol sets

Platform:

GPL96

Series:

GSE3407

8 Samples

Download data: CEL