Vitamin D and Gene Expression [A690]
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE22174 | GEO | 2010/06/19
SECONDARY ACCESSION(S): PRJNA129215
REPOSITORIES: GEO
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Project description:Genome-wide expression analysis of hapmap lymphoblastoid and ENCODE project cell lines stimulated with calcitriol Genome-wide expression analysis of hapmap lymphoblastoid and ENCODE project cell lines stimulated with calcitriol for 8 or 36 hours as compared to untreated.
2010-07-08 | E-GEOD-22174 | biostudies-arrayexpress
Project description:Genome-wide expression analysis of hapmap lymphoblastoid and ENCODE project cell lines stimulated with calcitriol and/or estrogen Genome-wide expression analysis of hapmap lymphoblastoid and ENCODE project cell lines stimulated with calcitriol and/or estrogen for 36 hours as compared to untreated.
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Project description: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. The number of unique alignments ranged from 7.73 million to 14.32 million. Peaks were called in the aligned sequence data using a model-based analysis of ChIP-Seq (MACS) and compared with sequenced sonicated and amplified input DNA. In the samples not treated with calcitriol, the number of peaks ranged from 468 to 4538 (median 975, mean 1587), while in the calcitriol-treated samples the number of peaks was between 2560 and 7244 (median 4546, mean 4560). 65-75% of peaks of untreated samples were in promoters, while only 24-50% of peaks of calcitirol-treated samples were in promoters. This study provides a comprehensive map of VDR binding in lymphoblastoid cell lines. The GM10855 and GM10861 cell lines were either stimulated for 36 hours with calcitriol or unstimulated, and crosslinked with formaldehyde to generate a snapshot of all protein-DNA interactions occurring in the nucleus at that particular point in time. Antibodies were then used to immunoprecipitate the VDR protein together with the crosslinked DNA fragments. Following reversal of crosslinks and digestion of protein, adaptors were ligated to immunoprecipitated DNA, and bridge PCR was used to generate clonally amplified amplicons before sequencing by synthesis using the Illumina Solexa Genome Analyzer.
2010-06-22 | E-GEOD-22484 | biostudies-arrayexpress
Project description: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. The number of unique alignments ranged from 7.73 million to 14.32 million. Peaks were called in the aligned sequence data using a model-based analysis of ChIP-Seq (MACS) and compared with sequenced sonicated and amplified input DNA. In the samples not treated with calcitriol, the number of peaks ranged from 468 to 4538 (median 975, mean 1587), while in the calcitriol-treated samples the number of peaks was between 2560 and 7244 (median 4546, mean 4560). 65-75% of peaks of untreated samples were in promoters, while only 24-50% of peaks of calcitirol-treated samples were in promoters. This study provides a comprehensive map of VDR binding in lymphoblastoid cell lines.
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Project description:Background: Vitamin D has been observed to affect the expression of a number of genes, however its mechanism of action has not been completely elucidated. MicroRNA molecules have recently been shown to be key mediators of gene regulation. We hypothesised therefore that vitamin D might modulate gene expression by influencing the expression of microRNAs. Methodology/Principal findings: A microRNA array was used to investigate the expression of microRNAs in RNA extracted from cells exposed to calcitriol for 0, 8 or 36 hours. A diverse panel of human cell lines were analysed including Hep-G2, HL60, K562, two fibroblast cell lines (AG09309 and AG09319), and four lymphoblastoid cell lines (GM15084, GM12878, GM07348 and GM07019). When compared between 0, 8 and 36 hours of calcitriol treatment, there were several microRNAs that were differentially regulated but the significance of these was lost after correction for multiple hypothesis testing. Conclusions/Significance: No microRNA showed significantly altered expression after exposure to vitamin D. However, some nominally significant miRNA molecules may warrant further investigation for a potential vitamin D-related role in immune function.
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