Similar studies for GEO DataSets (Select 200245527) - GEO DataSets

Select item 2002455271.

KRYPTONITE shapes TAD-like boundaries through the control of H3K9ac [Hi-C]

(Submitter supplied) Employing high-throughput sequencing and advanced microscopy techniques, we explored twenty-six histone modifications and Pol II distribution landscape in tomato (Solanum lycopersicum). Our findings revealed a comprehensive epigenetic landscape, uncovering distinct chromatin states associated with heterochromatin formation and gene silencing, allowing for the classification of genomic regions.

Organism:: Solanum lycopersicum

Type:: Other

Platform:: GPL21762
5 Samples

Download data: TXT

Series

Accession:: GSE245527

ID:: 200245527

PubMed Full text in PMC Similar studies

Select item 2002644302.

KRYPTONITE shapes TAD-like boundaries through the control of H3K9ac [ChIP-Seq]

(Submitter supplied) Employing high-throughput sequencing and advanced microscopy techniques, we explored twenty-six histone modifications and Pol II distribution landscape in tomato (Solanum lycopersicum). Our findings revealed a comprehensive epigenetic landscape, uncovering distinct chromatin states associated with heterochromatin formation and gene silencing, allowing for the classification of genomic regions.

Organism:: Solanum lycopersicum

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL21762
8 Samples

Download data: BIGWIG

Series

Accession:: GSE264430

ID:: 200264430

PubMed Full text in PMC Similar studies

Select item 2002644293.

KRYPTONITE shapes TAD-like boundaries through the control of H3K9ac [ATAC-Seq]

(Submitter supplied) Employing high-throughput sequencing and advanced microscopy techniques, we explored twenty-six histone modifications and Pol II distribution landscape in tomato (Solanum lycopersicum). Our findings revealed a comprehensive epigenetic landscape, uncovering distinct chromatin states associated with heterochromatin formation and gene silencing, allowing for the classification of genomic regions.

Organism:: Solanum lycopersicum

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL21762
4 Samples

Download data: BIGWIG

Series

Accession:: GSE264429

ID:: 200264429

PubMed Full text in PMC Similar studies

Select item 2002455294.

KRYPTONITE shapes TAD-like boundaries through the control of H3K9ac

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

Organism:: Solanum lycopersicum

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

Platforms:: GPL27957 GPL21762
51 Samples

Download data: BIGWIG, BROADPEAK, NARROWPEAK

Series

Accession:: GSE245529

ID:: 200245529

PubMed Full text in PMC Similar studies

Select item 2002455285.

KRYPTONITE shapes TAD-like boundaries through the control of H3K9ac [RNA-seq]

(Submitter supplied) Employing high-throughput sequencing and advanced microscopy techniques, we explored twenty-six histone modifications and Pol II distribution landscape in tomato (Solanum lycopersicum). Our findings revealed a comprehensive epigenetic landscape, uncovering distinct chromatin states associated with heterochromatin formation and gene silencing, allowing for the classification of genomic regions.

Organism:: Solanum lycopersicum

Type:: Expression profiling by high throughput sequencing

Platform:: GPL27957
6 Samples

Download data: TXT

Series

Accession:: GSE245528

ID:: 200245528

PubMed Full text in PMC Similar studies

Select item 2002455256.

KRYPTONITE shapes TAD-like boundaries through the control of H3K9ac [ChIP-seq]

(Submitter supplied) Employing high-throughput sequencing and advanced microscopy techniques, we explored twenty-six histone modifications and Pol II distribution landscape in tomato (Solanum lycopersicum). Our findings revealed a comprehensive epigenetic landscape, uncovering distinct chromatin states associated with heterochromatin formation and gene silencing, allowing for the classification of genomic regions.

Organism:: Solanum lycopersicum

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL21762
28 Samples

Download data: BIGWIG, BROADPEAK, NARROWPEAK

Series

Accession:: GSE245525

ID:: 200245525

PubMed Full text in PMC Similar studies

Select item 2001269527.

Interplay of pericentromeric genome organization and chromatin landscape regulates the expression of Drosophila melanogaster heterochromatic genes

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

Organism:: Drosophila melanogaster

Type:: Expression profiling by high throughput sequencing; Other

Platform:: GPL17275
19 Samples

Download data: TXT

Series

Accession:: GSE126952

ID:: 200126952

PubMed Full text in PMC Similar studies

Select item 2001269518.

Interplay of pericentromeric genome organization and chromatin landscape regulates the expression of Drosophila melanogaster heterochromatic genes [5C]

(Submitter supplied) Transcription of genes residing within constitutive heterochromatin is paradoxical to the tenets of epigenetic code. Regulatory mechanisms of Drosophila melanogaster heterochromatic gene transcription remain largely unknown. We investigated the contribution of pericentromeric genome organization and heterochromatic factors in orchestrating heterochromatic gene expression. Using 5C-seq, we characterized the pericentromeric TADs in Drosophila melanogaster. more...

Organism:: Drosophila melanogaster

Type:: Other

Platform:: GPL17275
10 Samples

Download data: TXT

Series

Accession:: GSE126951

ID:: 200126951

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2001269509.

Interplay of pericentromeric genome organization and chromatin landscape regulates the expression of Drosophila melanogaster heterochromatic genes [RNA-seq]

(Submitter supplied) Transcription of genes residing within constitutive heterochromatin is paradoxical to the tenets of epigenetic code. Regulatory mechanisms of Drosophila melanogaster heterochromatic gene transcription remain largely unknown. We investigated the contribution of pericentromeric genome organization and heterochromatic factors in orchestrating heterochromatic gene expression. Using 5C-seq, we characterized the pericentromeric TADs in Drosophila melanogaster. more...

Organism:: Drosophila melanogaster

Type:: Expression profiling by high throughput sequencing

Platform:: GPL17275
9 Samples

Download data: TSV, TXT

Series

Accession:: GSE126950

ID:: 200126950

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20007542610.

Local compartment changes and regulatory landscape alterations in histone H1-depleted cells

(Submitter supplied) Linker histone H1 is a core chromatin component that binds to nucleosome core particles and the linker DNA between nucleosomes. It has been implicated in chromatin compaction and gene regulation and is anticipated to play a role in higher-order genome structure. We find that depletion of histone H1 changes the epigenetic signature of thousands of potential regulatory sites across the genome. Many of them show cooperative loss or gain of multiple chromatin marks. more...

Organism:: Mus musculus

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

4 related Platforms
41 Samples

Download data: BED, TXT

Series

Accession:: GSE75426

ID:: 200075426

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20013120211.

Chromatin Loops Associated with Active Genes and Heterochromatin Shape Rice Genome Architecture for Transcriptional Regulation

(Submitter supplied) We systematically analyze the basic features of chromatin interaction mediated by RNAP2, H3K4me3 and H3K9me2. All interactions further aggregated into higher-order clusters and modular interacting domains with distinct genomic and transcriptional properties. Together, our strategy provides hierarchical and modular 3D genome architecture for transcription regulation in rice.

Organism:: Oryza sativa Indica Group

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL26667
12 Samples

Download data: BED

Series

Accession:: GSE131202

ID:: 200131202

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20007378512.

Three-dimensional disorganisation of the cancer genome occurs coincident with long range genetic and epigenetic alterations

(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; Other

Platforms:: GPL16791 GPL11154
22 Samples

Download data: BED

Series

Accession:: GSE73785

ID:: 200073785

PubMed Full text in PMC Similar studies

Select item 20007378413.

Three-dimensional disorganisation of the cancer genome occurs coincident with long range genetic and epigenetic alterations [RNA-seq]

(Submitter supplied) A three-dimensional chromatin state underpins the structural and functional basis of the genome by bringing regulatory elements and genes into close spatial proximity to ensure proper, cell-type specific gene expression profiles. Here, we perform HiC chromosome conformation, ChIP-seq and RNA-seq to investigate how the three-dimensional organization of the cancer genome is disrupted in the context of epigenetic remodelling and atypical gene expression programs.

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL16791
6 Samples

Download data: TSV

Series

Accession:: GSE73784

ID:: 200073784

PubMed Full text in PMC Similar studies Analyze with GEO2R SRA Run Selector

Select item 20007378314.

Three-dimensional disorganisation of the cancer genome occurs coincident with long range genetic and epigenetic alterations [ChIP-seq]

(Submitter supplied) A three-dimensional chromatin state underpins the structural and functional basis of the genome by bringing regulatory elements and genes into close spatial proximity to ensure proper, cell-type specific gene expression profiles. Here, we perform HiC chromosome conformation, ChIP-seq and RNA-seq to investigate how the three-dimensional organization of the cancer genome is disrupted in the context of epigenetic remodelling and atypical gene expression programs.

Organism:: Homo sapiens

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL11154
3 Samples

Download data: BED

Series

Accession:: GSE73783

ID:: 200073783

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20007378215.

Three-dimensional disorganisation of the cancer genome occurs coincident with long range genetic and epigenetic alterations [Hi-C]

(Submitter supplied) A three-dimensional chromatin state underpins the structural and functional basis of the genome by bringing regulatory elements and genes into close spatial proximity to ensure proper, cell-type specific gene expression profiles. Here, we perform Hi-C chromosome conformation to investigate how the three-dimensional organization of the cancer genome is disrupted in the context of epigenetic remodelling and atypical gene expression programs.

Organism:: Homo sapiens

Type:: Other

Platform:: GPL16791
13 Samples

Download data: BED, TXT

Series

Accession:: GSE73782

ID:: 200073782

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20014762716.

Analysis of the DNA topology in T47D-MTVL cells by Hi-C data

(Submitter supplied) The topology of the genome in untreated T47D-MTVL cells expressing a Dox-inducible shRNA against multiple H1 variants was analyzed by performing a Hi-C experiment. The data allowed the obtention of Hi-C chromosome interaction maps, which were used to define TADs and A/B compartments, and to study the relationship between the 3D genome in breast cancer cells and other genomic properties as well as the histone H1 variants genome-wide distribution.

Organism:: Homo sapiens

Type:: Other

Platform:: GPL16791
1 Sample

Download data: BED, BEDGRAPH

Series

Accession:: GSE147627

ID:: 200147627

PubMed Similar studies SRA Run Selector

Select item 20005541617.

Replication timing in Suz12 knockout ESCs

(Submitter supplied) We profiled replication timing in Suz12 knockout ESCs and observed no differences relative to wild-type controls.

Organism:: Mus musculus

Type:: Genome variation profiling by genome tiling array

Platform:: GPL11620
2 Samples

Download data: PAIR

Series

Accession:: GSE55416

ID:: 200055416

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20005133418.

DNA replication-timing boundaries separate stable chromosome domains with cell-type-specific functions

(Submitter supplied) Eukaryotic chromosomes replicate in a temporal order known as the replication-timing program. In mammals, replication timing is cell type-specific with at least half the genome switching replication timing during development, primarily in units of 400-800 kilobases ('replication domains;), whose positions are preserved in different cell types, conserved between species, and appear to confine long-range effects of chromosome rearrangements. more...

Organism:: Homo sapiens; Mus musculus

Type:: Other

25 related Platforms
993 Samples

Download data: BAM, BED, BIGWIG, BROADPEAK, NARROWPEAK, PAIR, TSV, TXT

Series

Accession:: GSE51334

ID:: 200051334

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20001609619.

Dynamic histone H3 epigenome marking during the intraerythrocytic cycle of P. falciparum

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

Organism:: Plasmodium falciparum

Type:: Genome binding/occupancy profiling by genome tiling array; Expression profiling by genome tiling array

Platform:: GPL8456
18 Samples

Download data: PAIR

Series

Accession:: GSE16096

ID:: 200016096

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20001609520.

Mapping of H3, H3K4me3 and H3K9ac on Ring and Schizont stages of P. falciparum

(Submitter supplied) Epigenome profiling has led to the paradigm that promoters of active genes are decorated with H3K4me3 and H3K9ac marks. These data on synchronized parasites reveals significant developmental stage specificity of the epigenome. In rings, H3K4me3 and H3K9ac are homogenous across the genes marking active and inactive genes equally, whilst in schizonts they are enriched at the 5’end of active genes.

Organism:: Plasmodium falciparum

Type:: Genome binding/occupancy profiling by genome tiling array; Expression profiling by genome tiling array

Platform:: GPL8456
8 Samples

Download data: PAIR

Series

Accession:: GSE16095

ID:: 200016095

PubMed Full text in PMC Similar studies Analyze with GEO2R

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