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Items: 1 to 20 of 128

1.

3D genomics across the tree of life reveals condensin II as a determinant of architecture type

(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
Platforms:
GPL24676 GPL16791
29 Samples
Download data: BW
Series
Accession:
GSE163641
ID:
200163641
2.

3D genomics across the tree of life reveals condensin II as a determinant of architecture type [RNA-Seq]

(Submitter supplied) We investigated genome folding across the eukaryotic tree of life. We find two types of three-dimensional (3D) genome architectures at the chromosome scale. Each type appears and disappears repeatedly during eukaryotic evolution. The type of genome architecture that an organism exhibits correlates with the absence of condensin II subunits. Moreover, condensin II depletion converts the architecture of the human genome to a state resembling that seen in organisms such as fungi or mosquitoes. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL16791
9 Samples
Download data: BW
Series
Accession:
GSE163640
ID:
200163640
3.

3D genomics across the tree of life reveals condensin II as a determinant of architecture type [DamID-seq]

(Submitter supplied) We investigated genome folding across the eukaryotic tree of life. We find two types of three-dimensional (3D) genome architectures at the chromosome scale. Each type appears and disappears repeatedly during eukaryotic evolution. The type of genome architecture that an organism exhibits correlates with the absence of condensin II subunits. Moreover, condensin II depletion converts the architecture of the human genome to a state resembling that seen in organisms such as fungi or mosquitoes. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL16791
18 Samples
Download data: BW
Series
Accession:
GSE163626
ID:
200163626
4.

3D genomics across the tree of life reveals condensin II as a determinant of architecture type [Hi-C]

(Submitter supplied) We investigated genome folding across the eukaryotic tree of life. We find two types of three-dimensional (3D) genome architectures at the chromosome scale. Each type appears and disappears repeatedly during eukaryotic evolution. The type of genome architecture that an organism exhibits correlates with the absence of condensin II subunits. Moreover, condensin II depletion converts the architecture of the human genome to a state resembling that seen in organisms such as fungi or mosquitoes. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL24676
2 Samples
Download data: HIC, TXT
Series
Accession:
GSE163625
ID:
200163625
5.

3D genomics across the tree of life reveals condensin II as a determinant of architecture type

(Submitter supplied) We investigated genome folding across the eukaryotic tree of life. We find four general manifestations of genome organization at chromosome-scale that each emerge and disappear repeatedly over the course of evolution. The submission represents chromosome-length Hi-C contact maps, architecture type and homolog separation analyses for 26 species across the tree of life, representing all subphyla of chordates, all 7 extant vertebrate classes, and 7 out of 9 major animal phyla, as well as plants and fungi.
Organism:
Strongylocentrotus purpuratus; Ciona intestinalis; Pleurobrachia bachei; Acropora millepora; Python bivittatus; Arachis hypogaea; Agaricus bisporus; Branchiostoma lanceolatum; Xenopus laevis; Notamacropus eugenii; Pygocentrus nattereri; Cristatella mucedo; Clonorchis sinensis; Chiloscyllium punctatum; Triticum aestivum; Caenorhabditis elegans; Aplysia californica; Aedes aegypti; Culex quinquefasciatus; Homo sapiens; Muntiacus reevesi; Muntiacus muntjak; Saccharomyces cerevisiae; Drosophila melanogaster; Gallus gallus; Hypsibius dujardini; Lethenteron camtschaticum
Type:
Other
30 related Platforms
32 Samples
Download data: BEDPE, FASTA, HIC, VCF, WIG
Series
Accession:
GSE169088
ID:
200169088
6.

Genome-wide maps of nucleolus interactions in human cells using 4xAP3 DamID

(Submitter supplied) We used DamID to map nucleolus interactions in human cells using a 4x tandem repeat of the nucleolar targeting sequence of AP3D1 (Scott, 2010) ("4xAP3"). These interactions are mapped in various human cell lines, including human K562 cells
Organism:
Homo sapiens
Type:
Other
Platform:
GPL16791
8 Samples
Download data: BW
Series
Accession:
GSE148609
ID:
200148609
7.

Molecular maps of the Lamin B1-associated genomic regions in oligodendrocyte lineage cells

(Submitter supplied) This study addresses the mechanisms regulating the identity of oligodendrocyte progenitor cells (OPC) in physiological conditions and the pathological mechanisms leading to autosomal  adrenoleukodystrophy (ADLD), a disease caused by persistence of lamin B1 (LMNB1) expression in oligodendrocytes (OL).  Using mouse primary OPCs and a novel technique for the study of DNA-protein interaction, we identify the genomic regions showing dynamic interactions with LMNB1.  The transition from ESC to OPC revealed increased association of gene involved in pluripotency and neuronal function and decreased association of gene categories associated with the differentiation of OPC into OL (including genes regulating epigenetic modifiers, RNA processing and protein phosphorylation).  Since LMNB1 declines during the transition from OPC to OL, and its persistent expression has been linked to pathological conditions, such as ADLD, we further identified the molecular maps of genome-lamina reorganization in OPC differentiating into OL which continue to express LMNB1 (mOLLMNB1).  The transition from OPC to mOLLMNB1 revealed increased association to LMNB1 of genomic regions encoding for lipid metabolism and protein phosphorylation, and decreased association of genes negatively regulating differentiation. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL13112
11 Samples
Download data: BW, TXT
Series
Accession:
GSE135834
ID:
200135834
8.

Effects of transcription on genome - nuclear lamina interactions

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens; Mus musculus
Type:
Other; Expression profiling by high throughput sequencing
Platforms:
GPL24676 GPL16791 GPL17021
174 Samples
Download data: TXT
Series
Accession:
GSE133275
ID:
200133275
9.

Effects of transcription on genome - nuclear lamina interactions: Repli-seq data

(Submitter supplied) In mammalian nuclei, transcriptionally active genomic regions tend to localize to the interior of the nucleus while inactive regions are often located at at the nuclear lamina. In this study we activated specific genes in lamina-associated domains by TALE-VP64 or CRISPRa-mediated activation. We also reduced transcription of individual genes by knockout of promoter/enhancer regions, or by insertion of a transcription termination sequence. more...
Organism:
Homo sapiens
Type:
Other
Platform:
GPL24676
24 Samples
Download data: TXT
Series
Accession:
GSE133274
ID:
200133274
10.

Effects of transcription on genome - nuclear lamina interactions: RNA-seq data

(Submitter supplied) In mammalian nuclei, transcriptionally active genomic regions tend to localize to the interior of the nucleus while inactive regions are often located at at the nuclear lamina. In this study we activated specific genes in lamina-associated domains by TALE-VP64 or CRISPRa-mediated activation. We also reduced transcription of individual genes by knockout of promoter/enhancer regions, or by insertion of a transcription termination sequence. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL16791
20 Samples
Download data: TXT
Series
Accession:
GSE133273
ID:
200133273
11.

Effects of transcription on genome - nuclear lamina interactions: DamID-seq data

(Submitter supplied) In mammalian nuclei, transcriptionally active genomic regions tend to localize to the interior of the nucleus while inactive regions are often located at at the nuclear lamina. In this study we activated specific genes in lamina-associated domains by TALE-VP64 or CRISPRa-mediated activation. We also reduced transcription of individual genes by knockout of promoter/enhancer regions, or by insertion of a transcription termination sequence. more...
Organism:
Homo sapiens; Mus musculus
Type:
Other
Platforms:
GPL17021 GPL16791
130 Samples
Download data: TXT
Series
Accession:
GSE133272
ID:
200133272
12.

Systematic identification of human SNPs affecting regulatory element activity

(Submitter supplied) Most of the millions of single-nucleotide polymorphisms (SNPs) in the human genome are non-coding, and many overlap with putative regulatory elements. Genome-wide association studies have linked many of these SNPs to human traits or to gene expression levels, but rarely with sufficient resolution to identify the causal SNPs. Functional screens based on reporter assays have previously been of insufficient throughput to test the vast space of SNPs for possible effects on enhancer and promoter activity. more...
Organism:
Homo sapiens
Type:
Other
Platforms:
GPL16791 GPL20795
48 Samples
Download data: BW, TXT
13.

The large fraction of heterochromatin in Drosophila neurons is simultaneously bound by B-type lamin and HP1a

(Submitter supplied) In most mammalian cell lines, chromatin located at the nuclear periphery is represented by condensed heterochromatin as observed by both microscopy observations and DamID mapping of lamina-associated domains (LADs), enriched in dimethylated Lys9 of histone H3 (H3K9me2). In Drosophila Kc167 cell culture, where LADs were only mapped to the moment, they are neither H3K9me2-enriched, nor overlap with the domains of Heterochromatin Protein 1a (HP1a). more...
Organism:
Drosophila melanogaster
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL13304
16 Samples
Download data: BEDGRAPH
Series
Accession:
GSE109495
ID:
200109495
14.

Kinetics and fidelity of the repair of Cas9-induced double-strand DNA breaks

(Submitter supplied) The RNA-guided DNA endonuclease Cas9 is a powerful tool for genome editing. Little is known about the kinetics and fidelity of the double-strand break (DSB) repair process that follows a Cas9 cutting event in living cells. Here, we developed a strategy to measure the kinetics of DSB repair for single loci in human cells. Quantitative modeling of repaired DNA in time series after Cas9 activation reveals variable and often slow repair rates, with half-life times up to ~10 h. more...
Organism:
Homo sapiens
Type:
Other
Platform:
GPL15520
647 Samples
Download data: TXT
15.

TSA-Seq Mapping of Nuclear Genome Organization [seq]

(Submitter supplied) We describe TSA-Seq, a new mapping method able to estimate mean chromosomal distances from nuclear speckles genome-wide and predict several Mbp chromosome trajectories between nuclear compartments without sophisticated computational modeling. Ensemble-averaged results reveal a clear nuclear lamina to speckle axis correlated with a striking spatial gradient in genome activity. This gradient represents a convolution of multiple, spatially separated nuclear domains, including two types of transcription ?hot-zones?. more...
Organism:
Homo sapiens
Type:
Other
Platforms:
GPL11154 GPL16791 GPL20301
43 Samples
Download data: BB, BED, BW
16.

TSA-Seq Mapping of Nuclear Genome Organization

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Other; Genome binding/occupancy profiling by genome tiling array
4 related Platforms
45 Samples
Download data: PAIR
Series
Accession:
GSE66019
ID:
200066019
17.

TSA-Seq Mapping of Nuclear Genome Organization [array]

(Submitter supplied) We describe TSA-Seq, a new mapping method able to estimate mean chromosomal distances from nuclear speckles genome-wide and predict several Mbp chromosome trajectories between nuclear compartments without sophisticated computational modeling. Ensemble-averaged results reveal a clear nuclear lamina to speckle axis correlated with a striking spatial gradient in genome activity. This gradient represents a convolution of multiple, spatially separated nuclear domains, including two types of transcription "hot-zones". more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by genome tiling array
Platform:
GPL10559
2 Samples
Download data: PAIR
Series
Accession:
GSE66018
ID:
200066018
18.

CHRAC/ACF Contribute to the Repressive Ground State of Chromatin

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Drosophila melanogaster
Type:
Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform:
GPL19951
33 Samples
Download data: BEDGRAPH
Series
Accession:
GSE106733
ID:
200106733
19.

CHRAC/ACF Contribute to the Repressive Ground State of Chromatin [RNA-seq]

(Submitter supplied) The chromatin remodeling complexes CHRAC and ACF combine the ATPase ISWI with the signature subunit ACF1. These enzymes catalyze well-studied nucleosome sliding reactions in vitro, but how their actions affect physiological gene expression is unclear. Here we explored the influence of Drosophila CHRAC/ACF on transcription by complementary gain- and loss-of-function approaches. Targeting ACF1 to multiple reporter genes inserted at many different genomic locations revealed a context-dependent inactivation of poorly transcribed reporters in repressive chromatin. more...
Organism:
Drosophila melanogaster
Type:
Expression profiling by high throughput sequencing
Platform:
GPL19951
24 Samples
Download data: CSV
Series
Accession:
GSE106732
ID:
200106732
20.

CHRAC/ACF Contribute to the Repressive Ground State of Chromatin [Mnase-seq]

(Submitter supplied) The chromatin remodeling complexes CHRAC and ACF combine the ATPase ISWI with the signature subunit ACF1. These enzymes catalyze well-studied nucleosome sliding reactions in vitro, but how their actions affect physiological gene expression is unclear. Here we explored the influence of Drosophila CHRAC/ACF on transcription by complementary gain- and loss-of-function approaches. Targeting ACF1 to multiple reporter genes inserted at many different genomic locations revealed a context-dependent inactivation of poorly transcribed reporters in repressive chromatin. more...
Organism:
Drosophila melanogaster
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL19951
9 Samples
Download data: BEDGRAPH
Series
Accession:
GSE106731
ID:
200106731
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