GEO DataSets

(Submitter supplied) Transcriptionally active and inactive chromatin domains tend to segregate into separate sub-nuclear compartments to maintain stable expression patterns. However, we have uncovered here an inter-chromosomal network connecting active loci enriched in circadian genes to repressed lamina-associated domains (LADs). The interactome is regulated by PARP1 and its co-factor, CTCF, which not only mediate chromatin fiber interactions, but also promote the recruitment of circadian genes to the lamina. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16791

2 Samples

Download data: BED

(Submitter supplied) Transcriptionally active and inactive chromatin domains tend to segregate into separate sub-nuclear compartments to maintain stable expression patterns. However, we have uncovered here an inter-chromosomal network connecting active loci enriched in circadian genes to repressed lamina-associated domains (LADs). The interactome is regulated by PARP1 and its co-factor, CTCF, which not only mediate chromatin fiber interactions, but also promote the recruitment of circadian genes to the lamina. more...

Organism:

Homo sapiens

Type:

Other; Expression profiling by high throughput sequencing

Platforms:

GPL15520 GPL16791 GPL9115

23 Samples

Download data: TXT

(Submitter supplied) PARP-1 binds to specific nucleosomes to regulate gene activity. While PARP-1's role in transcription inititaion is known, a surprising finding here was that PARP-1 is highly enriched at exon-intron and intron-exon boundaries, sort of demarcting exons. Thius indicating a role in alternative splicing.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16558

2 Samples

Download data: TXT, WIG

(Submitter supplied) To address the global impact of PARP-1 on DNA methylation, we treated cells with PJ34 (PARylation inhibitor) and isolated genomic DNA from vehicle and PJ34 treated cells. This DNA was bisulfite treated and hybridized to the Illumina infinium Methylation 450 Beadchip. We next used these RNA-seq data sets (control, PARP-1 KD and PARylation inhibited) to assess whether PARP plays a role in DNA methylation by assessing differential methylation patterns. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL13534

2 Samples

Download data: TXT

(Submitter supplied) Mammalian circadian rhythm is established by the negative feedback loops consisting of a set of clock genes, which lead to the circadian expression of thousands of downstream genes. As genome-wide transcription is organized under the high-order chromosome structure, it is unclear how circadian gene expression is influenced by chromosome structure. In this study, we focus on the function of chromatin structure proteins cohesin as well as CTCF (CCCTC-binding factor) in circadian rhythm. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

2 Samples

Download data: BW

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

Organism:

Mus musculus

Type:

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

Platform:

GPL13112

12 Samples

Download data: BW, TXT

(Submitter supplied) Mammalian circadian rhythm is established by the negative feedback loops consisting of a set of clock genes, which lead to the circadian expression of thousands of downstream genes. As genome-wide transcription is organized under the high-order chromosome structure, it is unclear how circadian gene expression is influenced by chromosome structure. In this study, we focus on the function of chromatin structure proteins cohesin as well as CTCF (CCCTC-binding factor) in circadian rhythm. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

4 Samples

Download data: TXT

(Submitter supplied) Mammalian circadian rhythm is established by the negative feedback loops consisting of a set of clock genes, which lead to the circadian expression of thousands of downstream genes. As genome-wide transcription is organized under the high-order chromosome structure, it is unclear how circadian gene expression is influenced by chromosome structure. In this study, we focus on the function of chromatin structure proteins cohesin as well as CTCF (CCCTC-binding factor) in circadian rhythm. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL13112

6 Samples

Download data: TXT

(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

Platform:

GPL11154

18 Samples

Download data: BED, TXT

(Submitter supplied) In our work we used high-throughput sequencing methods to get insight in the role of CTCF in ER-mediated gene regulation in luminal breast cancer cells. After assessing genome-wide binding of CTCF, ER, FOXA1 and Lamin B in MCF7 cells treated with estrogen for different time points, we could correlate the interaction to the chromatin with estrogen-induced de novo transcription (from GRO-seq data) and loop formation (from ChIA-PET, Fullwood et al., 2009). more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

15 Samples

Download data: BED

(Submitter supplied) In our work we used high-throughput sequencing methods to get insight in the role of CTCF in ER-mediated gene regulation in luminal breast cancer cells. After assessing genome-wide binding of CTCF, ER, FOXA1 and Lamin B in MCF7 cells treated with estrogen for different time points, we could correlate the interaction to the chromatin with estrogen-induced de novo transcription (from GRO-seq data) and loop formation (from ChIA-PET, Fullwood et al., 2009). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

4 Samples

Download data: TXT

(Submitter supplied) We performed Chromatin Interaction Analysis by Paired-End-Tag sequencing to elucidate CTCF-mediated long range interactions. 1,480 cis and 336 trans interacting loci were identified with high reproducibility. Associating these chromatin interaction loci with histone marks, RNA Pol II, p300 and Lamin B genome wide profiles, we uncover five distinct chromatin domains that suggest potential new models of CTCF function in chromatin organization and transcriptional control. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platform:

GPL9250

8 Samples

Download data: TXT

(Submitter supplied) Post-translational modifications, such as poly(ADP-ribosyl)ation (PARylation), regulate chromatin-modifying enzymes, ultimately affecting gene expression. This study explores the role of poly(ADP-ribose) polymerase (PARP) on global gene expression in a lymphoblastoid B cell line. We found that inhibition of PARP catalytic activity with olaparib resulted in global gene deregulation, affecting approximately 11% of genes expressed. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL10999

9 Samples

Download data: TXT

(Submitter supplied) Purpose: Many mammalian genes exhibit circadian expression patterns concordant with periodic binding of transcription factors, chromatin modifications and chromosomal interactions. We determined whether lamina-associated domains (LADs) display oscillatory circadian patterns of interaction with nuclear lamin B1 during hte circadian cycle, and identified any relationship to changes in gene expression patterns in oscillatory LADs or in their vinicity. more...

Organism:

Mus musculus

Type:

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

Platform:

GPL17021

42 Samples

Download data: BED, BEDGRAPH, FPKM_TRACKING

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

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL9250 GPL6448

7 Samples

Download data: BAR, BED, BW, CEL

(Submitter supplied) A large fraction of the mammalian genome is organized into inactive chromosomal domains associated with the nuclear lamina. Using genomic repositioning assays we show that Lamina associated domains (LADs), spanning the developmentally regulated IgH and Cyp3a loci, contain transportable DNA regions that associate chromatin with the nuclear lamina and repress gene activity in fibroblasts.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9250

5 Samples

Download data: BED, BW

(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; Other

Platform:

GPL13112

38 Samples

Download data: BW, TXT, XLSX

(Submitter supplied) In this experiment, we sought to identify how the distribution of CTCF, H3K27me3, H3K4me3, Pol II, H2AK119Ub1, EZH2

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

17 Samples

Download data: BW

(Submitter supplied) In this experiment, we sought to analyze how the spatial organization of WT, Δ5|6, and Δ5|6:7|9 cells vary during differentiation of ESCs into cervical motor neurons

Organism:

Mus musculus

Type:

Other

Platform:

GPL13112

9 Samples

Download data: TXT

(Submitter supplied) In this experiment, we sought to analyze how the transcriptome of WT, Δ5|6, and Δ5|6:7|9 cells vary during differentiation of ESCs into cervical motor neurons

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

12 Samples

Download data: XLSX