GEO DataSets

(Submitter supplied) DNA methylation is a mechanism for long-term transcriptional regulation and is required for normal cellular differentiation. Failure to properly establish or maintain DNA methylation patterns leads to cell dysfunction and diseases such as cancer. Identifying DNA methylation signatures in complex tissues can be challenging due to inaccurate cell enrichment methods and low DNA yields. We have developed a technique called Laser Capture Microdissection-Reduced Representation Bisulfite Sequencing (LCM-RRBS) for the multiplexed interrogation of the DNA methylation status of CpG Islands and promoters. more...

Organism:

Homo sapiens; Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL13112 GPL11154

23 Samples

Download data: BED, TXT

(Submitter supplied) Gonadectomy (GDX) induces sex steroid-producing adrenocortical tumors in certain mouse strains and in the domestic ferret. Complementary approaches, including DNA methylation mapping and microarray expression profiling, were used to identify novel genetic and epigenetic markers of GDX-induced adrenocortical neoplasia in female DBA/2J mice. Markers were validated by quantitative RT-PCR, laser capture microdissection, in situ hybridization, and immunohistochemistry. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6887

6 Samples

Download data: TXT

(Submitter supplied) Sequencing based approaches have led to new insights about DNA methylation. While many different techniques for genome-scale mapping of DNA methylation have been employed, throughput has been a key limitation for most. To further facilitate the mapping of DNA methylation, we describe a protocol for gel-free multiplexed reduced representation bisulfite sequencing (mRRBS) that reduces the workload dramatically and enables processing of 96 or more samples per week. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL11154

96 Samples

Download data: BB, TXT

(Submitter supplied) Using a pooled (n=10) zebrafish liver DNA, we generated base-resolution DNA methylation maps to document epigenetic landscape in zebrafish genome.

Organism:

Danio rerio

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL14875

1 Sample

Download data: TXT

(Submitter supplied) Using 2 male and 2 female zebrafish (pool of 6) brain samples, we generated base-resolution DNA methylation maps to document sex-specific epigenetic differences.

Organism:

Danio rerio

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL14875

4 Samples

Download data: TXT

(Submitter supplied) Reduced representation bisulfite sequencing (RRBS) has been proven a powerful method in DNA methylome profiling. Since the initial development of this method, the RRBS protocol has been modified in order to optimize it for genomic coverage, starting material, and library-construction throughput, which has resulted in new methods such as enhanced RRBS (ERRBS), double-enzyme RRBS (dRRBS), gel-free and multiplexed RRBS (mRRBS), and single-cell RRBS (scRRBS). more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL11154

2 Samples

Download data: TXT

(Submitter supplied) DNA methylation in CpG context is fundamental to the epigenetic regulation of gene expression in high eukaryotes. Disorganization of methylation status is implicated in many diseases, cellular differentiation, imprinting, and other biological processes. Techniques that enrich for biologically relevant CpG-rich genomic regions are desired since, depending on the size of an oragnism's methylome, the depth of sequencing required to cover all CpGs can be prohibitively expensive. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL16791

7 Samples

Download data: TXT

(Submitter supplied) Profiling the methylation and gene expression between vegetative (coleoptile-stage shoots) and reproductive (tassel primordium) tissues with RRBS and RNA-seq

Organism:

Zea mays

Type:

Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL15463 GPL20156

6 Samples

Download data: CGMAP, TXT

(Submitter supplied) Reduced representation bisulfite sequencing (RRBS) was conducted on dorsolateral prefrontal cortex tissue samples taken from the brains of control individuals not affected by neurological disorder

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL10999

24 Samples

Download data: TXT

(Submitter supplied) Genome wide DNA methylation profiling of normal adrenocortical tissue, adrenocortical adenomas and adrenocortical carcinomas. The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles. Samples included 6 normal adrenocortical tissue samples, 27 adenomas and 15 carcinomas.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL8490

48 Samples

Download data: TXT

(Submitter supplied) Boar taint (BT) is an offensive flavor observed in non-castrated male pigs that reduces the carcass price. Surgical castration effectively avoids the taint but is associated with animal welfare concerns. The functional annotation of farm animal genomes (FAANG) for understanding the biology of complex traits and diseases can be used in the selection of breeding animals to achieve favorable phenotypic outcomes. more...

Organism:

Sus scrofa

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL19176

9 Samples

Download data: COV

(Submitter supplied) SF-1, a transcription factor belonging to the nuclear receptor superfamily, has a pivotal role for adrenogonadal development in humans and mice. A constant feature of childhood adrenocortical tumors (ACT) is SF-1 amplification and overexpression. Using an inducible cellular system, here we show that SF-1 overexpression increases human adrenocortical cell proliferation through opposing effects on cell cycle and apoptosis. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1476

12 Samples

Download data: GPR

(Submitter supplied) SF-1, a transcription factor belonging to the nuclear receptor superfamily, has a pivotal role for adrenogonadal development in humans and mice. A constant feature of childhood adrenocortical tumors (ACT) is SF-1 amplification and overexpression. Using an inducible cellular system, here we show that SF-1 overexpression increases human adrenocortical cell proliferation through opposing effects on cell cycle and apoptosis. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL1456

4 Samples

Download data: GPR

(Submitter supplied) Mutations of β-catenin gene (CTNNB1) are frequent in adrenocortical adenomas (AA) and carcinomas (ACC). However, the target genes of CTNNB1 have not yet been identified in adrenocortical tumors. Our objective was to identify genes de-regulated in adrenocortical tumors harbouring CTNNB1 genetic alterations.

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS3912

Platform:

GPL570

8 Samples

Download data: CEL

Analysis of adrenocortical adenomas (AA) with β-catenin missense mutations and AAs with wild-type CTNNB1. Mutations of CTNNB1 are common in AA and adrenocortical carcinomas (ACC). Results provide insight into molecular mechanisms deregulated in adrenocortical tumors with CTNNB1 genetic alterations.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 4 genotype/variation, 3 other, 2 tissue sets

Platform:

GPL570

Series:

GSE28476

8 Samples

Download data: CEL

(Submitter supplied) Transcription factor GATA6 is expressed in the fetal and adult adrenal cortex and has been implicated in steroidogenesis. To characterize the role of GATA6 in adrenocortical development and function, we generated mice in which Gata6 was conditionally deleted using Cre-LoxP recombination with Sf1-cre. The adrenal glands of adult Gata6 conditional knockout (cKO) mice were small and had a thin cortex with thickened capsule. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6887

6 Samples

Download data: TXT

(Submitter supplied) We scored adrenocortical carcinomas and adenomas for abnormal beta-catenin staining, and sequenced the beta-catenin gene in some samples. We compared adrenocortincal carcinomas with and without abnormal beta-catenin staining and found many significant expression differences and significant results from enrichment testing. A similar comparison in the adenomas gave relatively few differences, and they did not correlate to differences found for the carcinomas. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

65 Samples

Download data: CEL, XLS

(Submitter supplied) Context: Adrenocortical carcinomas (ACC) are a rare tumor type with a poor five-year survival rate and limited treatment options. Objective: Understanding of the molecular pathogenesis of this disease has been aided by genomic analyses highlighting alterations in TP53, WNT, and IGF signaling pathways. Further elucidation is needed to reveal therapeutically actionable targets in ACC. Design: In this study, global DNA methylation levels were assessed by the Infinium HumanMethylation450 BeadChip Array on 18 ACC tumors and 6 normal adrenal tissues. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL13534

24 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL887 GPL570

63 Samples

Download data: CEL, TXT

(Submitter supplied) Adrenocortical carcinoma (ACC) is an aggressive endocrine tumor with a poor 5 year survival rate of 10-20%. We used expression profiling to assess the transcriptional changes associated with ACC as compared to normal adrenal glands with the goal of identifying new targets for treatment. Fourteen ACC tumors were profiled on both Affymetrix U133 Plus 2 or Agilent 22K Human Genome arrays; an additional six tumors were profiled on one or the other array. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL887

15 Samples

Download data: TXT