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Laser Capture Microdissection-Reduced Representation Bisulfite Sequencing (LCM-RRBS) maps changes in DNA methylation associated with gonadectomy-induced adrenocortical neoplasia in the mouse

ABSTRACT: Laser Capture Microdissection-Reduced Representation Bisulfite Sequencing (LCM-RRBS) maps changes in DNA methylation associated with gonadectomy-induced adrenocortical neoplasia in the mouse

PROVIDER: PRJNA193557 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR788599.fastq.gz	Fastqsanger.gz
	SRR788600.fastq.gz	Fastqsanger.gz
	SRR788601.fastq.gz	Fastqsanger.gz
	SRR788602.fastq.gz	Fastqsanger.gz
	SRR788603.fastq.gz	Fastqsanger.gz

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Laser Capture Microdissection-Reduced Representation Bisulfite Sequencing (LCM-RRBS) maps changes in DNA methylation associated with gonadectomy-induced adrenocortical neoplasia in the mouse

Project description: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. LCM-RRBS accurately and reproducibly profiles genome-wide methylation of DNA extracted from microdissected fresh frozen or formalin-fixed paraffin-embedded tissue samples. To demonstrate the utility of LCM-RRBS, we characterized changes in DNA methylation associated with gonadectomy-induced adrenocortical neoplasia in the mouse. Compared to adjacent normal tissue, the adrenocortical tumors showed reproducible gains and losses of DNA methylation at genes involved in cell differentiation and organ development. LCM-RRBS is a rapid, cost-effective, and sensitive technique for analyzing DNA methylation in heterogeneous tissues and will facilitate the investigation of DNA methylation in cancer and organ development.

2013-03-21 | GSE45361 | GEO

Laser Capture Microdissection-Reduced Representation Bisulfite Sequencing (LCM-RRBS) maps changes in DNA methylation associated with gonadectomy-induced adrenocortical neoplasia in the mouse

2013-03-21 | E-GEOD-45361 | biostudies-arrayexpress

Laser capture microdissection-reduced representation bisulfite sequencing (LCM-RRBS) maps changes in DNA methylation associated with gonadectomy-induced adrenocortical neoplasia in the mouse.

Project description: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 owing 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 cytosine-guanine dinucleotide islands and promoters. LCM-RRBS accurately and reproducibly profiles genome-wide methylation of DNA extracted from microdissected fresh frozen or formalin-fixed paraffin-embedded tissue samples. To demonstrate the utility of LCM-RRBS, we characterized changes in DNA methylation associated with gonadectomy-induced adrenocortical neoplasia in the mouse. Compared with adjacent normal tissue, the adrenocortical tumors showed reproducible gains and losses of DNA methylation at genes involved in cell differentiation and organ development. LCM-RRBS is a rapid, cost-effective, and sensitive technique for analyzing DNA methylation in heterogeneous tissues and will facilitate the investigation of DNA methylation in cancer and organ development.

| S-EPMC3675465 | biostudies-literature

Novel markers of gonadectomy-induced adrenocortical neoplasia in the mouse and ferret

Project description: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. Two genes with hypomethylated promoters, Igfbp6 and Foxs1, were upregulated in post-GDX adrenocortical neoplasms. The neoplastic cells also exhibited hypomethylation of the fetal adrenal enhancer of Sf1, an epigenetic signature that typifies descendants of fetal adrenal rather than gonadal cells. Expression profiling demonstrated upregulation of gonadal-like genes, including Spinlw1, Insl3, and Foxl2, in GDX-induced adrenocortical tumors of the mouse. One of these markers, FOXL2, was detected in adrenocortical tumor specimens from gonadectomized ferrets. These new markers may prove useful for studies of steroidogenic cell development and for diagnostic testing.

2014-07-31 | GSE54393 | GEO

Novel markers of gonadectomy-induced adrenocortical neoplasia in the mouse and ferret

2014-07-31 | E-GEOD-54393 | biostudies-arrayexpress

Laser Capture Microdissection (LCM) analysis of mycorrhizal rice roots

Project description:Laser Capture Microdissection (LCM) analysis of mycorrhizal rice roots

| PRJNA492135 | ENA

Laser Capture Microdissection (LCM) analysis of mycorrhizal rice roots

Project description:Analysis of cell specific gene expression in mycorrhizal rice roots. Described in Roth, Chiapello et al. 2019 We used LCM to harvest arbusculated and adjacent systemic cells from mycorrhizal rice roots, along with cortical cells from mock inoculated plants

2018-09-20 | GSE120215 | GEO

Laser Capture Microdissection-based RNAseq for Profiling Mouse and Human Sebaceous Gland Transcriptomes

Project description:We describe the use of laser capture microdissection (LCM) to isolate human and murine sebaceous glands (SGs) for transcriptomic analysis and publish this SG transcriptomic data for reference. We show that compared to whole skin RNA sequencing, LCM RNA sequencing allows for high resolution in identifying and describing SG genes at homeostasis. Lastly, we compare this LCM of sebaceous glands to published SG clusters from single cell RNA sequencing of skin, and show that we achieve greater resolution and depth with the LCM approach.

2024-01-26 | GSE230682 | GEO

Laser Capture Microdissection of Hyperlipidemic Mouse Aorta Atherosclerosis

Project description:Atherosclerosis is a transmural chronic inflammatory condition of small and large arteries that is associated with adaptive immune responses at all disease stages. However, impacts of adaptive immune reactions on clinically apparent atherosclerosis such as intima lesion (plaque) rupture, thrombosis, myocardial infarction, and aneurysm largely remain to be identified. It is increasingly recognized that leukocyte infiltrates in plaque, media, and adventitia are distinct but their specific roles have not been defined. To map these infiltrates, we employed laser capture microdissection (LCM) to isolate the three arterial wall laminae using apoE-/- mouse aorta as a model. RNA from LCM-separated tissues was extracted and large scale whole genome expression microarrays were prepared. We observed that the quality of the resulting gene expression maps was compromised by tissue RNA carried over from adjacent laminae during LCM. To account for these flaws, we established quality controls and algorithms to improve the predictive power of LCM-derived microarray data. Our approach creates robust transcriptome atlases of normal and atherosclerotic aorta. Assessing LCM transcriptomes for immunity-related mRNAs indicated markedly distinctive gene expression patterns in the three laminae of the atherosclerotic aorta. These mouse mRNA expression data banks can now be mined to address a wide range of questions in cardiovascular biology.

2011-11-03 | GSE21419 | GEO

Laser Capture Microdissection (LCM) followed by RNA-seq of apical and basal domains of follicle cells from stage 9-10B Drosophila egg chambers

Project description:Laser Capture Microdissection (LCM) followed by RNA-seq of apical and basal domains of follicle cells from stage 9-10B Drosophila egg chambers. The experiment is composed of 5 Apical and 5 Basal biological replicates. Each biological replicate consists of a pool of 10 LCM fragments. Each fragment consists of 5-10 adjacent cell domains microdissected from either the apical half or the basal half of the follicular epithelium.

2022-09-02 | E-MTAB-9127 | biostudies-arrayexpress

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