Similar studies for GEO DataSets (Select 200205885) - GEO DataSets

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Items: 20

Select item 2002058851.

Epigenomic and transcriptomic profiles a of prostate cancer cell line with and without androgen stimulation

(Submitter supplied) We performed H3K27ac ChIP-seq, ATAC-seq, and RNA-seq in LNCaP with and without androgen stimulation

Organism:: Homo sapiens

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

Platforms:: GPL24676 GPL20301
12 Samples

Download data: BW

Series

Accession:: GSE205885

ID:: 200205885

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 2001619482.

Epigenomic profiling of neuroendocrine prostate cancer and prostate adenocarcinoma xenografts

(Submitter supplied) We profiled the epigenomes of neuroendocrine prostate cancer and prostate adenocarcinoma patient-derived xenografts using ChIP-seq for transcription factors and histone modifications.

Organism:: Homo sapiens

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL11154
104 Samples

Download data: BED, BW

Series

Accession:: GSE161948

ID:: 200161948

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2001304083.

Charting the prostate epigenomic landscape from transformation to progression

(Submitter supplied) We generate transcription factor, histone modification and ATAC cistromes in nomal prostate epithelium, primary prostate tumor and metastatic prostate cancer human specimens

Organism:: Homo sapiens

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL18573
249 Samples

Download data: BW

Series

Accession:: GSE130408

ID:: 200130408

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2001415514.

Genome-wide gene expression profiles of primary prostate cancer

(Submitter supplied) Prognostic biomarkers are useful to screen patients with clinically localized prostate cancer (PCa) who are at high risk of metastatic progression. The tumor transcriptome can be used to evaluate the aggressiveness of PCa and predict adverse patient outcomes. Genomewide gene expression levels were measured in primary tumor samples of 503 patients in a population‐based cohort.

Organism:: Homo sapiens

Type:: Expression profiling by array

Platform:: GPL14951
503 Samples

Download data: IDAT, TXT

Series

Accession:: GSE141551

ID:: 200141551

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Select item 2000516215.

Comprehensive Functional Annotation of 77 Prostate Cancer Risk Loci

(Submitter supplied) Genome-wide association studies (GWAS) have revolutionized the field of cancer genetics, but the causal links between increased genetic risk and onset/progression of disease processes remain to be identified. Here we report the first step in such an endeavor for prostate cancer. We provide a comprehensive annotation of the 77 known risk loci, based upon highly correlated variants in biologically relevant chromatin annotations- we identified 727 such potentially functional SNPs. more...

Organism:: Homo sapiens

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platforms:: GPL9052 GPL10999
4 Samples

Download data: GFF

Series

Accession:: GSE51621

ID:: 200051621

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2000368686.

Simvastatin treated Lymphoblastoid Cell lines from Cholesterol and Pharmacogenomics (CAP) Trial

(Submitter supplied) Statins reduce cardiovascular disease risk by lowering plasma low density lipoprotein (LDL)-cholesterol. To identify novel pathways that modulate statin response, we assessed the influence of simvastatin exposure on expression quantitative trait locus (eQTL) associations across the genome in 480 lymphoblastoid cell lines (LCLs). Cell lines were derived blood samples collected ant entry visit from participants in the Cholesterol and Pharmacogenomics (CAP) trial, who underwent a 6 week 40mg/day simvastatin trial. more...

Organism:: Homo sapiens

Type:: Expression profiling by array

Platform:: GPL6883
960 Samples

Download data: TXT

Series

Accession:: GSE36868

ID:: 200036868

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 2000288937.

Genetic identification, replication, and functional fine-mapping of expression quantitative trait loci in primary human liver tissue [Illumina Expression Array]

(Submitter supplied) Most loci identified in genome wide association studies (GWAS) of complex traits reside in non-coding DNA and may contribute to phenotype via changes in gene regulation. The discovery of expression quantitative trait loci (?eQTLs?) can thus be used to more precisely identify modest but real disease associations and provide insights into their underlying molecular mechanisms. This is particularly true for analyses of expression in non-transformed cells from tissues relevant to the complex traits of interest. more...

Organism:: Homo sapiens

Type:: Expression profiling by array

Platform:: GPL6104
60 Samples

Download data: TXT

Series

Accession:: GSE28893

ID:: 200028893

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Select item 2000261068.

Genetic identification, replication, and functional fine-mapping of expression quantitative trait loci in primary human liver tissue

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

Organism:: Homo sapiens

Type:: Expression profiling by array; SNP genotyping by SNP array; Genome variation profiling by SNP array

Platforms:: GPL4133 GPL8887 GPL6104
748 Samples

Download data: TXT

Series

Accession:: GSE26106

ID:: 200026106

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 2000261059.

Genetic identification, replication, and functional fine-mapping of expression quantitative trait loci in primary human liver tissue [Illumina SNP array]

(Submitter supplied) Most loci identified in genome wide association studies (GWAS) of complex traits reside in non-coding DNA and may contribute to phenotype via changes in gene regulation. The discovery of expression quantitative trait loci (‘eQTLs’) can thus be used to more precisely identify modest but real disease associations and provide insights into their underlying molecular mechanisms. This is particularly true for analyses of expression in non-transformed cells from tissues relevant to the complex traits of interest. more...

Organism:: Homo sapiens

Type:: Genome variation profiling by SNP array; SNP genotyping by SNP array

Platform:: GPL8887
224 Samples

Download data: TXT

Series

Accession:: GSE26105

ID:: 200026105

PubMed Full text in PMC Similar studies

Select item 20002593510.

Genetic identification, replication, and functional fine-mapping of expression quantitative trait loci in primary human liver tissue [Agilent]

(Submitter supplied) Most loci identified in genome wide association studies (GWAS) of complex traits reside in non-coding DNA and may contribute to phenotype via changes in gene regulation. The discovery of expression quantitative trait loci (‘eQTLs’) can thus be used to more precisely identify modest but real disease associations and provide insights into their underlying molecular mechanisms. This is particularly true for analyses of expression in non-transformed cells from tissues relevant to the complex traits of interest. more...

Organism:: Homo sapiens

Type:: Expression profiling by array

Platform:: GPL4133
464 Samples

Download data: TXT

Series

Accession:: GSE25935

ID:: 200025935

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Select item 20003138811.

Variation in chromatin accessibility is a key determinant of heritable variation in gene expression

(Submitter supplied) While it is well established that variation in gene expression levels can be influenced by single nucleotide polymorphisms (SNPs), little is known about the regulatory mechanisms by which this occurs. To address this gap, we used DNaseI sequencing to measure genome-wide chromatin accessibility in 70 Yoruba lymphoblastoid cell lines (LCLs), for which genome-wide genotypes and estimates of gene expression levels based on RNA-sequencing are also available. more...

Organism:: Homo sapiens

Type:: Genome variation profiling by high throughput sequencing

Platform:: GPL9115
70 Samples

Download data: BED, PDF, TXT

Series

Accession:: GSE31388

ID:: 200031388

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20007077012.

Prostate cancer stratification using molecular profiles

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

Organism:: Homo sapiens

Type:: Expression profiling by array; Genome variation profiling by SNP array

4 related Platforms
808 Samples

Download data: CEL, IDAT

Series

Accession:: GSE70770

ID:: 200070770

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20008901313.

Identification of Breast Cancer Associated Variants That Modulate Transcription Factor Binding

(Submitter supplied) GWAS have discovered thousands of genomic loci that are associated with disease risk and quantitative traits, but most of the variants responsible for risk remain uncharacterized. The vast majority of GWAS-identified loci contain non-coding SNPs and defining molecular mechanism of risk is challenging. Many non-coding causal SNPs are hypothesized to alter Transcription Factor (TF) binding sites as the mechanism by which they affect organismal phenotypes. more...

Organism:: Homo sapiens

Type:: Other

Platform:: GPL18573
5 Samples

Download data: BED, BEDGRAPH, BIGWIG

Series

Accession:: GSE89013

ID:: 200089013

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20005335114.

Large-scale East-Asian eQTL mapping reveals novel candidate genes for LD mapping and the genomic landscape of transcriptional effects of sequence variants

(Submitter supplied) Profiles of sequence variants that influence gene transcription are very important for understanding mechanisms that affect phenotypic variation and disease susceptibility. Using genotypes at 1.4 million SNPs and a comprehensive transcriptional profile of 15,454 coding genes and 6,113 lincRNA genes obtained from peripheral blood cells of 298 Japanese individuals, we mapped expression quantitative trait loci (eQTLs). more...

Organism:: Homo sapiens

Type:: Expression profiling by array

Platform:: GPL14550
301 Samples

Download data: TXT

Series

Accession:: GSE53351

ID:: 200053351

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Select item 20015730615.

Integrative analysis of liver-specific noncoding regulatory variants associated with the risk of coronary artery disease

(Submitter supplied) We performed promoter Capture Hi-C in HepG2 to investigate interactions between gene promoters and distal elements as a transcription-regulating mechanism contributing to these phenotypes. We also performed ChIP-Seq at 2h, 8h and 23h timepoints in HepG2 for Il1B treatment.

Organism:: Homo sapiens

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platforms:: GPL20301 GPL11154
10 Samples

Download data: BIGWIG, TXT

Series

Accession:: GSE157306

ID:: 200157306

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20004607416.

Comprehensive Functional Annotation of Seventy-One Breast Cancer Risk Loci

(Submitter supplied) We report the application of FAIRE seq in Human Mammary Epithelial Cells for identifying the breast cancer risk functional SNPs in enhancer region.

Organism:: Homo sapiens

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL11154
3 Samples

Download data: BED, BEDGRAPH

Series

Accession:: GSE46074

ID:: 200046074

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20003791617.

FAIRE-seq in primary human megakaryocytes, erythroblasts and monocytes

(Submitter supplied) Maps of open chromatin in three primary human blood cell types of the myeloid lineage (megakaryocytes, erythroblasts and monocytes) using the formaldehyde-assisted isolation of regulatory elements method followed by next-generation sequencing (FAIRE-seq). We also generated FAIRE-seq data in the megakaryocytic cell line CHRF-288-11. In addition to our data sets, we retrieved FAIRE-seq data for the erythroblastoid cell line K562 (ENCODE Project Consortium 2012) and pancreatic islets (Gaulton et al. more...

Organism:: Homo sapiens

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platforms:: GPL11154 GPL10999 GPL9115
6 Samples

Download data: BED

Series

Accession:: GSE37916

ID:: 200037916

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20003582918.

Integrative functional genomics identifies an enhancer looping to the SOX9 gene disrupted by the 17q24.3 prostate cancer risk locus

(Submitter supplied) Genome-wide association studies (GWAS) are identifying genetic predisposition to various diseases. The rs1859962 single nucleotide polymorphism (SNP) part of the 17q24.3 locus is a risk factor for prostate cancer (PCa). It defines a 130kb linkage disequilibrium (LD) block that lies in a ~2Mb gene desert area. Despite a role for the proximal SOX9 gene in PCa development, the functional biology driving the risk of this 17q24.3 risk locus is unknown. more...

Organism:: Homo sapiens

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL9052
3 Samples

Download data: BED

Series

Accession:: GSE35829

ID:: 200035829

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20005523219.

Genome-wide identification of expression quantitative trait loci (eQTLs) in human heart

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

Organism:: Homo sapiens

Type:: Expression profiling by array; SNP genotyping by SNP array

Platforms:: GPL10558 GPL13135
258 Samples

Download data

Series

Accession:: GSE55232

ID:: 200055232

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20005523120.

Genome-wide identification of expression quantitative trait loci (eQTLs) in human heart: gene expression

(Submitter supplied) In recent years genome-wide association studies (GWAS) have uncovered numerous chromosomal loci associated with various electrocardiographic traits and cardiac arrhythmia predisposition. A considerable fraction of these loci lie within inter-genic regions. Trait-associated SNPs located in putative regulatory regions likely exert their effect by modulating gene expression. Hence, the key to unraveling the molecular mechanisms underlying cardiac traits is to interrogate variants for association with differential transcript abundance by expression quantitative trait locus (eQTL) analysis. more...

Organism:: Homo sapiens

Type:: Expression profiling by array

Platform:: GPL10558
129 Samples

Download data: TXT

Series

Accession:: GSE55231

ID:: 200055231

PubMed Full text in PMC Similar studies Analyze with GEO2R

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