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Links from GEO DataSets

Items: 20

1.
Full record GDS4477

Pediatric glioblastoma brain tumors: histone H3.3 mutations

Analysis of pediatric glioblastoma (GBM) tumors with mutations in H3F3A gene. Mutation of key residues in histone H3.3 are specific to GBM and highly prevalent in children and young adults. Results indicate that defects in chromatin architecture underlie pediatric GBM pathogenesis.
Organism:
Homo sapiens
Type:
Expression profiling by array, count, 4 genotype/variation sets
Platform:
GPL570
Series:
GSE34824
27 Samples
Download data: CEL
DataSet
Accession:
GDS4477
ID:
4477
2.

Frequent driver mutations in histone H3.3 and chromatin remodeling genes in paediatric glioblastoma

(Submitter supplied) Whole exome sequencing identified frequent driver mutations in a series of paediatric glioblastomas We used microarray-based profiling to investigate differences in gene expression according to mutational status of driver genes
Organism:
Homo sapiens
Type:
Expression profiling by array
Dataset:
GDS4477
Platform:
GPL570
27 Samples
Download data: CEL
Series
Accession:
GSE34824
ID:
200034824
3.

WT and ATRX KO

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL17021 GPL13112
8 Samples
Download data: WIG
Series
Accession:
GSE59271
ID:
200059271
4.

Genome-wide ChIP seq of H3.3 in WT and ATRX KO mouse ES cells

(Submitter supplied) Regions of H3.3 binding in WT and ATRX KO mouse ES cells were identified by ChIP seq
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL13112
4 Samples
Download data: WIG
Series
Accession:
GSE59270
ID:
200059270
5.

Transcriptome analysis of WT and ATRX KO Cast x 129 mouse ES cells

(Submitter supplied) Analysis of gene expression in WT and ATRX KO Cast x 129 Mouse ES cells
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17021
4 Samples
Download data: WIG
Series
Accession:
GSE59269
ID:
200059269
6.

H3.Y discriminates between HIRA and DAXX chaperone complexes and reveals unexpected insights into human DAXX-H3.3-H4 binding and deposition requirements

(Submitter supplied) Histone chaperones prevent promiscuous histone interactions before chromatin assembly. They guarantee faithful deposition of canonical histones and functionally specialized histone variants into chromatin in a spatial- and temporally-restricted manner. Here, we identify the binding partners of the primate-specific and H3.3-related histone variant H3.Y using several quantitative mass spectrometry approaches, and biochemical and cell biological assays. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL11154
13 Samples
Download data: BED, BW
Series
Accession:
GSE94034
ID:
200094034
7.

Structural and mechanistic insights into ATRX-dependent and –independent functions of the histone chaperone DAXX [RNA-seq]

(Submitter supplied) The histone variant H3.3 is incorporated in a replication-independent manner at heterochromatic regions by the ATRX-DAXX histone chaperone complex. Here, we present a high-resolution x-ray crystal structure of an interaction surface between ATRX and DAXX. We used single amino acid substitutions in DAXX that abrogate formation of the complex to explore ATRX-dependent and -independent functions of DAXX. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17021
10 Samples
Download data: TXT
Series
Accession:
GSE102688
ID:
200102688
8.

The DAXX/ATRX Complex Protects Tandem Repetitive Elements in the Absence of DNA Methylation by Promoting H3K9 Trimethylation

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL13112 GPL9185
14 Samples
Download data: BED, TXT
Series
Accession:
GSE70850
ID:
200070850
9.

The DAXX/ATRX Complex Protects Tandem Repetitive Elements in the Absence of DNA Methylation by Promoting H3K9 Trimethylation [RNA-Seq]

(Submitter supplied) In mammals, DNA methylation is essential for protecting repetitive sequences from aberrant transcription, translocation, and homologous recombination. However, DNA hypomethylation occurs during specific developmental stages (e.g. preimplantation embryos) and in certain cell types (e.g., primordial germ cells). The absence of dysregulated repetitive elements in these cells suggests the existence of alternative mechanisms that prevent genome instability triggered by DNA hypomethylation. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL13112
8 Samples
Download data: TXT
Series
Accession:
GSE70849
ID:
200070849
10.

The DAXX/ATRX Complex Protects Tandem Repetitive Elements in the Absence of DNA Methylation by Promoting H3K9 Trimethylation [ChIP-Seq]

(Submitter supplied) In mammals, DNA methylation is essential for protecting repetitive sequences from aberrant transcription, translocation, and homologous recombination. However, DNA hypomethylation occurs during specific developmental stages (e.g. preimplantation embryos) and in certain cell types (e.g., primordial germ cells). The absence of dysregulated repetitive elements in these cells suggests the existence of alternative mechanisms that prevent genome instability triggered by DNA hypomethylation. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL9185
6 Samples
Download data: BED, TXT
Series
Accession:
GSE70811
ID:
200070811
11.

PML protein organizes heterochromatin domains where it regulates histone H3.3 deposition by ATRX/DAXX

(Submitter supplied) Maintenance of chromatin homeostasis involves proper delivery of histone variants to the genome. The interplay between different chaperones regulating the supply of histone variants to distinct chromatin domains remains largely undeciphered. We report a role of promyelocytic leukemia (PML) protein in the routing of histone variant H3.3 to chromatin and in the organization of megabase-size heterochromatic PML-associated domains that we call PADs. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms:
GPL17021 GPL19057
20 Samples
Download data: BED, BW, CSV
Series
Accession:
GSE66364
ID:
200066364
12.

miRNA expression data from pediatric high grade gliomas

(Submitter supplied) miRNA expression analysis was performed on 14 cases of high grade gliomas and 4 controls obtained from age-matched epileptic patients. After this differentially miRNA analysis has been done among T53,H3F3A,normal and pediatric high grade glioma patient and try to identify the highly altered miRNA expression as well as sno expression pattern.
Organism:
synthetic construct; Homo sapiens
Type:
Non-coding RNA profiling by array
Platform:
GPL16384
18 Samples
Download data: CEL
Series
Accession:
GSE63319
ID:
200063319
13.

ATRX-mediated chromatin association of histone variant macroH2A1 regulates alpha globin gene expression

(Submitter supplied) The histone variant macroH2A generally associates with transcriptionally inert chromatin, however the factors that regulate its chromatin incorporation remain elusive. Here, we identify the SWI/SNF helicase, ATRX, as a novel macroH2A interacting protein. Unlike its role in assisting H3.3 chromatin deposition, ATRX acts as a negative regulator of macroH2A’s chromatin association. In human erythroleukemic cells deficient for ATRX, ChIP-sequencing studies reveal that macroH2A accumulates at the HBA gene cluster on the subtelomere of chromosome 16, coinciding with the loss of α globin expression. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL11154
3 Samples
Download data: BED, WIG
Series
Accession:
GSE35339
ID:
200035339
14.

Analysis of gene expression and of H3.3 distribution and abundance in a ATRX loss-of-function line

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Arabidopsis thaliana
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL9062 GPL17639
11 Samples
Download data
Series
Accession:
GSE87918
ID:
200087918
15.

Analysis of eH3.3 occupancy in a ATRX loss-of-function line [ChIP-seq]

(Submitter supplied) Analysis of H3.3 position and abundance in the presence and absence of a functionnal ATRX protein: we wanted to analyse how the absence of the Arabidopsis putative ATRX chaperone would impact the abundance and the distribution of H3.3 variant at a genome-wide level.
Organism:
Arabidopsis thaliana
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL9062
5 Samples
Download data: WIG, XLS
Series
Accession:
GSE87917
ID:
200087917
16.

Analysis of gene expression in a ATRX loss-of-function line [RNA-seq]

(Submitter supplied) Comparison between WT and atrx-1 mutant of genome expression to analyse the impact of loss of the ATRX chaperone
Organism:
Arabidopsis thaliana
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17639
6 Samples
Download data: XLSX
Series
Accession:
GSE87916
ID:
200087916
17.

RNA-Seq of osteosarcoma cell lines

(Submitter supplied) The Alternative Lengthening of Telomeres (ALT) pathway stimulates telomere elongation and prevents cellular senescence in approximately 60% of osteosarcoma. While the precise mechanisms underlying the ALT pathway are unclear, mutations in the chromatin remodeling protein ATRX, histone chaperone DAXX, and the histone variant H3.3, correlate with ALT status. ATRX and DAXX facilitate deposition of the histone variant H3.3 within heterochromatic regions including the telomere suggesting that loss of ATRX, DAXX, and/or H3.3 lead to defects in heterochromatin maintenance at telomeres, ultimately contributing to ALT activity. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18573
39 Samples
Download data: TXT
Series
Accession:
GSE118488
ID:
200118488
18.

The H3.3 G34R glioma-associated mutation alters H3K9me3 and H3K36me3 chromatin modifications

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms:
GPL21493 GPL18480
6 Samples
Download data: BW, TXT
Series
Accession:
GSE106205
ID:
200106205
19.

RNA-seq in WT and H3.3 G34R mouse ES cells

(Submitter supplied) Sequencing of paediatric gliomas has identified two common substitution mutations (K27M and G34R) in genes encoding histone H3.3. We introduced a single-copy H3.3 G34R targeted mutation in mouse ES cells and observed gains in H3K36me3 and H3K9me3 across the genome. Altered chromatin profiles correlated with enrichment of KDM4 A/B/C, a histone lysine (K9/K36) demethylase. RNA-seq of H3.3 G34R mutant showed disrupted gene expression patterns which also correlated with KDM4 enrichment. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL21493
2 Samples
Download data: BW, TXT
Series
Accession:
GSE106204
ID:
200106204
20.

H3K9me3 and H3K36me3 ChIP-seq in WT and H3.3 G34R mouse ES cells

(Submitter supplied) Sequencing of paediatric gliomas has identified two common substitution mutations (K27M and G34R) in genes encoding histone H3.3. We introduced a single-copy H3.3 G34R targeted mutation in mouse ES cells and observed gains in H3K36me3 and H3K9me3 across the genome. Altered chromatin profiles correlated with enrichment of KDM4 A/B/C, a histone lysine (K9/K36) demethylase. RNA-seq of H3.3 G34R mutant showed disrupted gene expression patterns which also correlated with KDM4 enrichment. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL18480
4 Samples
Download data: BW, TXT
Series
Accession:
GSE106203
ID:
200106203
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