GEO DataSets

(Submitter supplied) 1,25-Dihydroxyvitamin D3 (1,25(OH)2D3) plays an integral role in calcium homeostasis in higher organisms through its actions in the intestine, kidney and skeleton. Interestingly, while several intestinal genes are known to play a contributory role in calcium homeostasis, the entire caste of key components remains to be identified. To examine the vitamin D receptor (VDR) cistrome in this issue, we conducted a ChIP-seq analysis of binding sites for the VDR across the proximal intestine in vitamin D-sufficient normal mice treated with vehicle or 1,25(OH)2D3. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

7 Samples

Download data: BED, BEDGRAPH

(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

31 Samples

Download data: BED, BEDGRAPH, TXT

(Submitter supplied) 1,25-Dihydroxyvitamin D3 (1,25(OH)2D3) plays an integral role in calcium homeostasis in higher organisms through its actions in the intestine, kidney and skeleton. Interestingly, while several intestinal genes are known to play a contributory role in calcium homeostasis, the entire caste of key components remains to be identified. To examine this issue, Cyp27b1 null mice on either a normal or a high calcium/phosphate-containing rescue diet were treated with either vehicle or 1,25(OH)2D3 and evaluated 6h later. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

24 Samples

Download data: TXT

(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) ChIP-seq was performed in triplicate on isolated tissues (kidney, thyroparathyroid (TPTG), peripheral blood monocytes) from hormone treated (vehicle, 1,25(OH)2D3, FGF23, or PTH) mice from wildtype (WT), M1-IKO, M21-IKO, VDR-KO, or Cyp27b1-KO mice as indicated in the sample listings. The pBMC samples were isolated from untreated mice and subsequently treated ex vivo in cell culture with the indicated concentrations of 1,25(OH)2D3 or forskolin. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

111 Samples

Download data: BEDGRAPH

(Submitter supplied) Human kidney was obtained from the University of Wisconsin Madison Organ Procurement Program from a deceased 69 year old female patient and the cortex was dissected from 3 different cortex locations. Associated publication abstract: Targeted genomic deletions identify diverse enhancer functions and generate a kidney-specific, endocrine-deficient Cyp27b1 pseudo-null mouse Vitamin D3 is terminally bioactivated in the kidney to 1α,25-dihydroxyvitamin D3 (1,25(OH)2D3) via cytochrome P450 family 27 subfamily B member 1 (CYP27B1), whose gene is regulated by parathyroid hormone (PTH), fibroblast growth factor 23 (FGF23), and 1,25(OH)2D3. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

13 Samples

Download data: BED, BEDGRAPH, BROADPEAK, NARROWPEAK

(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) 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 high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9115

35 Samples

Download data: TDF

(Submitter supplied) Assessment of regions of open chromatin by FAIRE-seq in THP-1 cells treated with 1,25(OH)2D3 for 0-48 h

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9115

14 Samples

Download data: TDF

(Submitter supplied) gene expression profiling by RNA-seq in THP-1 cells treated with 1,25(OH)2D3 for 2.5-24 h

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9115

18 Samples

Download data: DIFF, TDF

(Submitter supplied) The biologically active form of vitamin D, 1,25-dihydroxyvitamin D3 (1,25(OH)2D3), is a direct regulator of gene transcription, since it is the only high affinity natural ligand of the transcription factor vitamin D receptor (VDR). Transcriptome-wide analysis of THP-1 human monocyte-like cells had indicated more than 600 genes to be significantly (p < 0.05) regulated after a 4 h stimulation with 1,25(OH)2D3. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6102

6 Samples

Download data: TXT

(Submitter supplied) In vivo ChIP-seq in mouse kidney: we examine the genomic recruitment of VDR, RXR, pCREB, CBP, CRTC2 (TORC2), SRC1, SRC3, BRD4, RNApolII, H3K9ac, H3K27ac, and H3K36me3 after intraperitoneal injection of 10 mg/kg body weight (bw) 1,25(OH)2D3 (in propylene glycol), 230 mg/kg bw PTH (1–84) (in phosphate buffered saline (PBS)), 50 mg/kg bw FGF23 (in PBS + 0.1% BSA), 30 mg/kg YKL-05-099 (PBS + 25mM HCl), 40 mg/kg SK-124 (15% HPBCD (hydroxypropyl β-cyclodextrin)), or vehicle (EtOH, PBS, or HPBCD). more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

223 Samples

Download data: BIGWIG