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Series GSE45361 Query DataSets for GSE45361
Status Public on Mar 21, 2013
Title Laser Capture Microdissection-Reduced Representation Bisulfite Sequencing (LCM-RRBS) maps changes in DNA methylation associated with gonadectomy-induced adrenocortical neoplasia in the mouse
Organisms Homo sapiens; Mus musculus
Experiment type Methylation profiling by high throughput sequencing
Summary 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.
Overall design Laser capture microdissection-reduced representation bisulfite sequencing and reduced representation bisulfite sequencing on human blood leukocyte, human endometrial tumor, mouse liver tissue, and mouse normal and neoplastic adrenal tissue
Contributor(s) Schillebeeckx M, Mitra RD
Citation(s) 23589626, 25289806
Submission date Mar 20, 2013
Last update date Aug 16, 2019
Contact name Maximiliaan Schillebeeckx
Phone 314-362-1715
Organization name Washington University in St. Louis
Department Genetics
Lab Rob D. Mitra
Street address 4444 Forest Parkway
City St. Louis
State/province MO
ZIP/Postal code 63108
Country USA
Platforms (2)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (23)
GSM1103079 Adrenal Neoplasia Mouse 1
GSM1103080 Adrenal Neoplasia Mouse 2
GSM1103081 Adrenal Neoplasia Mouse 3
BioProject PRJNA193557
SRA SRP019884

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SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE45361_RAW.tar 3.0 Gb (http)(custom) TAR (of BED)
GSE45361_README_Methylation_Calls.txt.gz 519 b (ftp)(http) TXT
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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