GEO DataSets

(Submitter supplied) Chromatin is composed of DNA wrapped around nucleosomes, complexes consisting of highly basic proteins called histones. Histone variants are non-canonical variants of histones that have specific functions. The Apicomplexan parasite Toxoplasma gondii possesses conserved histone variants CenH3, H3.3, H2A.Z, H2A.X, as well as the parasite-specific H2B variant, H2BV (or H2B.Z). We surveyed the genome-wide distribution of T. more...

Organism:

Toxoplasma gondii RH

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24058

23 Samples

Download data: BED, BROADPEAK, BW, NARROWPEAK

(Submitter supplied) Chromatin is composed of DNA wrapped around nucleosomes, complexes consisting of highly basic proteins called histones. Histone variants are non-canonical variants of histones that have specific functions. The Apicomplexan parasite Toxoplasma gondii possesses conserved histone variants CenH3, H3.3, H2A.Z, H2A.X, as well as the parasite-specific H2B variant, H2BV (or H2B.Z). We surveyed the genome-wide distribution of T. more...

Organism:

Toxoplasma gondii RH; Toxoplasma gondii ME49

Type:

Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL15564 GPL15563

10 Samples

Download data: GFF, PAIR, TXT

(Submitter supplied) Histone variants are key components of the epigenetic code and evolved to perform specific functions in transcriptional regulation, DNA repair, chromosome segregation and other fundamental processes. H2B.Z is a rare, apicomplexan-specific variant of histone H2B. Here we show that in Plasmodium falciparum H2B.Z localises to euchromatic intergenic regions throughout intraerythrocytic development and together with H2A.Z forms a double-variant nucleosomes subtype. more...

Organism:

Plasmodium falciparum 3D7

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL15857

6 Samples

Download data: GFF

(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 GPL11002

9 Samples

Download data: BED, BIGWIG

(Submitter supplied) The H2A variant H2AZ is essential for embryonic development and for proper execution of developmental gene expression programs in embryonic stem cells (ESCs). Divergent regions in H2AZ are likely key for its functional specialization, but we know little about how these differences contribute to chromatin regulation. Here, we show that the extended acidic patch, specifically the three divergent residues in the C-terminal docking domain, is necessary for lineage commitment during ESC differentiation and proper execution of gene expression programs during ESC differentiation. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

6 Samples

Download data: TXT

(Submitter supplied) The H2A variant H2AZ is essential for embryonic development and for proper execution of developmental gene expression programs in embryonic stem cells (ESCs). Divergent regions in H2AZ are likely key for its functional specialization, but we know little about how these differences contribute to chromatin regulation. Here, we show that the extended acidic patch, specifically the three divergent residues in the C-terminal docking domain, is necessary for lineage commitment during ESC differentiation and proper execution of gene expression programs during ESC differentiation. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11002

3 Samples

Download data: BED, BIGWIG

(Submitter supplied) Histone variant H2A.Z-containing nucleosomes are incorporated at most eukaryotic promoters. This incorporation is mediated by the conserved SWR1 complex, which replaces histone H2A in canonical nucleosomes with H2A.Z in an ATP-dependent manner. Here, we show that promoter-proximal nucleosomes are highly heterogeneous for H2A.Z in Saccharomyces cerevisiae, with substantial representation of nucleosomes containing one, two, or no H2A.Z molecules. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL11034

5 Samples

Download data: TXT

(Submitter supplied) Chromatin landscapes are disrupted during DNA replication and need to be restored faithfully to maintain appropriate gene expression, including post-translational modifications (PTMs) of newly deposited histones. Whether histones H2A-H2B are accurately recycled during DNA replication and the behaviour of their associated marks during and post replication is unknown. Here we comprehensively map key modifications on H2A-H2B including H2A.Z during DNA replication. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL19057

22 Samples

Download data: TXT

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

Organism:

Homo sapiens; Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platforms:

GPL19057 GPL30172 GPL30173

366 Samples

Download data: BW, TXT

(Submitter supplied) Chromatin landscapes are disrupted during DNA replication and must be restored faithfully to maintain genome regulation and cell identity. The H3-H4 modification landscape is restored by parental histone recycling and post-replication modification of new histone H3-H4. How DNA replication impact on histone H2A-H2B is unknown. Here, we track H2A-H2B modifications and H2A.Z during DNA replication and across the cell cycle using quantitative genomics. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL19057

134 Samples

Download data: BED, TXT

(Submitter supplied) Chromatin landscapes are disrupted during DNA replication and must be restored faithfully to maintain genome regulation and cell identity. The H3-H4 modification landscape is restored by parental histone recycling and post-replication modification of new histone H3-H4. How DNA replication impact on histone H2A-H2B is unknown. Here, we track H2A-H2B modifications and H2A.Z during DNA replication and across the cell cycle using quantitative genomics. more...

Organism:

Homo sapiens; Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL30172 GPL30173 GPL19057

156 Samples

Download data: BW

(Submitter supplied) Chromatin landscapes are disrupted during DNA replication and must be restored faithfully to maintain genome regulation and cell identity. The H3-H4 modification landscape is restored by parental histone recycling and post-replication modification of new histone H3-H4. How DNA replication impact on histone H2A-H2B is unknown. Here, we track H2A-H2B modifications and H2A.Z during DNA replication and across the cell cycle using quantitative genomics. more...

Organism:

Mus musculus; Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL30173 GPL30172 GPL19057

54 Samples

Download data: BED, BW

(Submitter supplied) Nucleosome is the basic structural unit of chromatin, and its dynamics plays critical roles in the regulation of genome functions. However, how the nucleosome structure is regulated by histone variants in vivo is still largely uncharacterized. Here, by employing Micrococcal nuclease (MNase) digestion of crosslinked chromatin followed by chromatin immunoprecipitation (ChIP) and paired-end sequencing (MNase-X-ChIP-seq), we mapped genome-wide unwrapping states of nucleosomes containing histone variant H2A.Z in mouse embryonic stem (ES) cells. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL24247 GPL13112

35 Samples

Download data: BED

(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

Platform:

GPL13112

33 Samples

Download data

(Submitter supplied) In this study, we demonstrate that the UBN1 or UBN2 subunit is mainly responsible for specific recognition and direct binding of H3.3 by the HIRA complex, while the HIRA subunit can enhance the binding affinity of UBN1 toward H3.3, but Cabin1 subunit cannot. We also demonstrate that both Ala87 and Gly90 residues of H3.3 are required and sufficient for the specific recognition and binding by UBN1. ChIP-seq studies reveal that two independent HIRA complexes (UBN1-HIRA and UBN2-HIRA) can cooperatively deposit H3.3 to cis-regulatory regions, including active promoters and active enhancers in mouse embryonic stem (mES) cells. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

25 Samples

Download data: BED

(Submitter supplied) In this study, we demonstrate that the UBN1 or UBN2 subunit is mainly responsible for specific recognition and direct binding of H3.3 by the HIRA complex, while the HIRA subunit can enhance the binding affinity of UBN1 toward H3.3, but Cabin1 subunit cannot. We also demonstrate that both Ala87 and Gly90 residues of H3.3 are required and sufficient for the specific recognition and binding by UBN1. ChIP-seq studies reveal that two independent HIRA complexes (UBN1-HIRA and UBN2-HIRA) can cooperatively deposit H3.3 to cis-regulatory regions, including active promoters and active enhancers in mouse embryonic stem (mES) cells. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

8 Samples

Download data: TXT

(Submitter supplied) This experiment highlights the extreme sequence bias generated by standard PCR amplication of sequencing libraries and decribes an adapted T7-polymerase based amplification method, which results in non-baised, representative libraries for Illumina sequencing

Organism:

Plasmodium falciparum 3D7

Type:

Other

Platform:

GPL10866

4 Samples

Download data: BED, GFF

(Submitter supplied) This experiment characterizes the localisation of H2A.Z, H3K9ac and H3K4me3 in the epigenome of the human malaria parasite, P. falciparum at 4 different stages of intraerythrocytic development.

Organism:

Plasmodium falciparum 3D7

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL10866

17 Samples

Download data: BED, GFF

(Submitter supplied) This experiment characterizes the transcriptome of the human malaria parasite, P. falciparum at 8 different stages of the intraerythrocytic cycle

Organism:

Plasmodium falciparum 3D7

Type:

Expression profiling by high throughput sequencing

Platform:

GPL10866

8 Samples

Download data: GFF, TXT

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

Organism:

Plasmodium falciparum 3D7

Type:

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

Platform:

GPL10866

29 Samples

Download data: BED, GFF, TXT