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Transcriptome of Ameloblastoma using Laser capture microdissection

ABSTRACT: The goal of the study was to characterize the whole genome transcriptome profiles of pure sample population of human ameloblastoma epithelial cells for examination of molecular pathways.

ORGANISM(S): Homo sapiens

PROVIDER: GSE68531 | GEO | 2016/09/01

SECONDARY ACCESSION(S): PRJNA282997

REPOSITORIES: GEO

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Transcriptome of Ameloblastoma using Laser capture microdissection

Project description:The goal of the study was to characterize the whole genome transcriptome profiles of pure sample population of human ameloblastoma epithelial cells for examination of molecular pathways. Seventeen human ameloblastoma samples were obtained. Both fresh frozen and FFPE samples were used and placed in solution for 1-4 weeks to allow decalcification by EDTA. The tissue was sectioned at -35C at a thickness of 7 microns. These sections were used for laser capture microdissection (LCM) to isolate the neoplastic epithelial portion of the tumors, using static image settings. Total RNA was extracted from each sample and examined using the whole genome microarray against the Stratagene universal human reference RNA.

2016-09-01 | E-GEOD-68531 | biostudies-arrayexpress

Transcriptome of Keratocystic odontogenic tumor (KCOT) using Laser capture microdissection

Project description:The goal of the study was to characterize the whole genome transcriptome profiles of pure sample population of KCOT epithelial cells for examination of molecular pathways.

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Project description:We have employed whole genome microarray expression profiling as a discovery platform to identify genes that are associated with pathogenesis of ameloblastoma using ameloblastoma tumor and corresponding normal counterpart from patients.

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Ameloblastoma RNA profiling uncovers a distinct non-coding RNA signature

Project description:Ameloblastoma of the jaws remains the top difficult to treat odontogenic tumour and has a high recurrence rate. New evidence suggests that non-coding RNAs (ncRNAs) play a critical role in tumour genesis and prognosis of cancer. However, ameloblastoma ncRNA expression data is lacking. Here we present the first report of ameloblastoma ncRNA signatures. A total of 95 ameloblastoma cases and a global array transcriptome technology covering > 285.000 full-length transcripts were used in this two-step analysis. The analysis first identified in a test cohort 31 upregulated ameloblastoma-associated ncRNAs accompanied by signalling pathways of cancer, spliceosome, mRNA surveillance and Wnt. Further validation in an independent cohort points out the long non-coding (lncRNAs) and small nucleolar RNA (snoRNAs): LINC340, LINC342, SNORD116-25, SNORA11, SNORA21, SNORA47 and SNORA65 as a distinct ncRNA signature of ameloblastoma. Importantly, the presence of these ncRNAs was independent of BRAF-V600E and SMO-L412F mutations, histology type or tumour location, but was positively correlated with the tumour size. Taken together, this study shows a systematic investigation of ncRNA expression of ameloblastoma, and illuminates new diagnostic and therapeutic targets for this invasive odontogenic tumour.

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North American Brain Expression Consortium: Laser capture microdissection of Cerebellar Purkinje Cells

Project description:Previous studies in bulk tissue suggest that there are abundant expression quantitative trait loci (eQTLs) in human brain. This sample series is of cerebellar Purkinje cells isolated using laser capture microdissection from human cases without neurological disease but of known genotypes. These data may be helpful in confirming eQTLs in bulk tissue or in mapping other gene expression traits in an enriched neuronal population. Authorized Access data: Mapping of GEO sample accessions to dbGaP subject/sample IDs is available through dbGaP Authorized Access, see http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000249

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Landscape of N6-methyladenosine modification patterns in human ameloblastoma

Project description:N6-methyladenosine (m6A) is one of the most popular RNA modifications, which is widely found in messenger RNAs (mRNAs) and non-coding RNA like long no-coding RNA (lncRNAs) and circular RNA (circRNAs).In our study,we provide m6A landscape of human ameloblastoma, which expands the understanding of m6A modifications and uncovers regulation of lncRNAs and circRNAs through m6A modification in ameloblastoma.

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