GEO DataSets

(Submitter supplied) Genome-wide expression analysis of hapmap lymphoblastoid and ENCODE project cell lines stimulated with calcitriol

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6244

54 Samples

Download data: CEL

(Submitter supplied) We used ChIP-Seq to identify the genomic locations bound by the vitamin D receptor (VDR) in two lymphoblastoid cell lines (LCLs) (CEPH individuals GM10855 and GM10861 from the International HapMap Project) before and after calcitriol treatment for 36 hours. Immunoprecipitated DNA was sequenced using the Illumina Genome Analyzer II. Sequence reads (35 bases; 10-19 million quality-filtered reads/sample) were aligned to the human genome (NCBI Build 36.3) using ELAND software. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9115

10 Samples

Download data: BED, TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6244

78 Samples

Download data: CEL

(Submitter supplied) Genome-wide expression analysis of hapmap lymphoblastoid and ENCODE project cell lines stimulated with calcitriol and/or estrogen

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6244

24 Samples

Download data: CEL

(Submitter supplied) Large numbers of statistically significant associations between sentinel SNPs and case-control status have been replicated by genome-wide association studies (GWAS). Nevertheless, currently few underlying molecular mechanisms of complex disease are known. Our approach has been to investigate whether variation in binding of a transcription factor, the vitamin D receptor (VDR) whose activating ligand vitamin D has often been proposed as a modifiable factor in multiple disorders, could explain any of these associations. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

30 Samples

Download data: BED

(Submitter supplied) Open chromatin regions have been shown to associate with the location of transcriptiotal enhancers, i.e., the binding locations of DNA-binding transcription factors. To investigate the effects of short-term treatment by the nuclear hormone 1α,25-dihydroxyvitamin D3 (VD), a specific ligand of the transcription factor vitamin D receptor, on chromatin accessibility, FAIRE-seq was utilized on the chromatin samples from THP-1 monocytic leukemia cells that were treated with 100 nM 1α,25-dihydroxyvitamin D3 for 20, 40, 60, 80, 100 and 120 min, or with vehicle (0.1% (v/v) ethanol) for 20 and 100 min.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9115

9 Samples

Download data: BED

(Submitter supplied) The genome-wide analysis of the binding sites of the transcription factor vitamin D receptor (VDR) is essential for a global appreciation the physiological impact of the nuclear hormone 1α,25-dihydroxyvitamin D3 (1,25(OH)2D3). Genome-wide analysis of lipopolysaccharide (LPS)-polarized THP-1 human monocytic leukemia cells via chromatin immunoprecipitation (ChIP) coupled with massive parallel sequencing (ChIP-seq) resulted in 1,318 high-confidence VDR binding sites, of which 789 and 364 occurred uniquely with and without 1,25(OH)2D3 stimulation, while only 165 were common. more...

Organism:

Homo sapiens

Type:

Third-party reanalysis; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9115

2 Samples

Download data: TXT

(Submitter supplied) ChIP-seq for the insulator protein CTCF in THP-1 cells after stimulation with the the natural VDR ligand 1,25-dihydroxyvitamin D3 (1,25(OH)2D3)

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9115

9 Samples

Download data: TDF

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL6102 GPL9115

9 Samples

Download data: BED

(Submitter supplied) Analysis of acute effects of ligand-treatment on vitamin D receptor binding genome-wide using ChIP-seq. THP-1 monocytic leucemia cells were treated with 1?,25(OH)2D3 (1,25D) or left unstimulated to investigate the acute effects of VDR chromatin occupancy. We identified in total 2340 VDR binding sites with and without the ligand. Without the ligand, there is a considerable presence of VDR already on the chromatin. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9115

3 Samples

Download data: BED, TXT

(Submitter supplied) Identification of primary target genes of vitamin D receptor (VDR) in an immune-related cellular model (THP-1 cells) to study, in conjunction with VDR binding data from ChIP-seq, the genome-wide mechanisms of transcriptional regulation by VDR.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6102

6 Samples

Download data: TXT

(Submitter supplied) The vitamin D receptor (VDR) has been knocked out in monocytic THP-1 cells after stimulation of ko and control cells with the the natural VDR ligand 1,25-dihydroxyvitamin D3 (1,25(OH)2D3), quadruplicate mRNA-seq has been performed

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

32 Samples

Download data: XLSX

(Submitter supplied) ChIP-seq for ETS1 in THP-1 cells after stimulation with the the natural VDR ligand 1,25-dihydroxyvitamin D3 (1,25(OH)2D3)

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

4 Samples

Download data: TDF

(Submitter supplied) Three independent repeats of ChIP-seq or ChIPmentation with THP-1 cells after treatment with either 1,25(OH)2D3 (VD) or control (EtOH) using antibody against CEBPA (3 time points).

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

18 Samples

Download data: TDF, 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

43 Samples

Download data: BED, TDF, TXT

(Submitter supplied) Three independent repeats of ChIP-seq from THP-1 after 2h and 8h treatment with 1,25D or EtOH (control), using antibody against histone marker H3K4me3.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

13 Samples

Download data: BED, TDF

(Submitter supplied) Three independent repeats of siRNA knockdown of CEBPA, followed by 24h vitamin D treatment, RNA extraction and RNA-seq.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

12 Samples

Download data: CSV

(Submitter supplied) Three independent repeats of ChIP-seq from THP-1 after 24h treatment with 1,25D or EtOH (control), using antibodies against histone markers H3K27ac and H3K4me3

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

13 Samples

Download data: TDF

(Submitter supplied) ChIP-seq for VDR in THP-1 cells after stimulation with the the natural VDR ligand 1,25-dihydroxyvitamin D3 (1,25(OH)2D3)

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

12 Samples

Download data: TDF

(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:

GPL9115

35 Samples

Download data: TDF