Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

High-throughput screening of gene expression in the patient's cholangiocarcinoma biopsy

ABSTRACT: We profiled gene expression in formalin-fixed, paraffin-embedded (FFPE) patient’s tumor biopsy sample, obtained at the time of the first CCA diagnosis. We next used bioinformatical software Oncobox to analyze gene expression data and to identify molecular pathways differentially regulated in the patient’s tumor sample.

ORGANISM(S): Homo sapiens

PROVIDER: GSE107233 | GEO | 2017/11/22

SECONDARY ACCESSION(S): PRJNA419392

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Transcriptome of tumor biopsy sample of patient with granulosa cell tumor of the ovary

Project description:We profiled gene expression in formalin-fixed, paraffin-embedded (FFPE) tumor biopsy sample of the patient with granulosa cell tumor of the ovary.

2018-04-02 | GSE112579 | GEO

Transcriptome of tumor biopsy sample of patient with non-small-cell lung adenocarcinoma, ALK rearrangement positive

Project description:We profiled gene expression in formalin-fixed, paraffin-embedded (FFPE) tumor biopsy sample of the patient with non-small-cell lung adenocarcinoma, ALK rearrangement positive.

2019-07-02 | GSE133605 | GEO

A non-hazardous deparaffinization protocol enables quantita-tive proteomics of core needle biopsy-sized formalin-fixed and paraffin embedded (FFPE) tissue specimens.

Project description:Most human tumor tissues that are obtained for pathology and diagnostic purposes are forma-lin-fixed and paraffin embedded (FFPE). To perform quantitative proteomics of FFPE samples, paraffin has to be removed and formalin-induced crosslinks have to be reversed prior to prote-olytic digestion. A central component of almost all deparaffinization protocols is xylene, a toxic and highly flammable solvent that has been reported to negatively affect protein extraction and quantitative proteome analysis. Here, we present a ‘green’ xylene-free protocol for accel-erated sample preparation of FFPE tissues based on paraffin-removal with hot water. Com-bined with tissue homogenization using disposable micropestles and a modified protein aggre-gation capture (PAC) digestion protocol, our workflow enables streamlined and reproducible quantitative proteomic profiling of FFPE tissue. Label free quantitation of FFPE cores from human ductal breast carcinoma in-situ (DCIS) xenografts with a volume of only 0.79 mm3 showed a high correlation between replicates (r2=0.992) with a median %CV of 16.9%. Im-portantly, this small volume is amenable to tissue micro array (TMA) cores and core needle bi-opsies, while our results and the easy-of-use indicate that a further downsizing is feasible. Fi-nally, our FFPE workflow does not require costly equipment and can be established in every standard clinical laboratory.

2022-05-19 | PXD031946 | Pride

microRNA profiling and clinical outcomes in human osteosarcoma (biopsy/resection pairs)

Project description:Osteosarcoma is a malignancy with variable outcomes that are not tightly aligned with chemotherapy response. Previous work has suggested a possible role for microRNAs (miRNAs) in determining the susceptibility of osteosarcomas to treatment but formal miRNA-based outcome models have not been reported. Formalin-fixed, paraffin-embedded (FFPE) specimens may be a unique approach for such studies in a rare malignancy. We used supervised principal components analysis and logistic regression to study survival and chemoresponse endpoints, and miRNA activity and gene set analysis algorithms to study miRNA regulatory networks using mRNA data. Our study also creates a paradigm for FFPE-based miRNA clinical biomarker research in rare tumors. 26 unique pairs of biopsy and surgical resection specimens were profiled. Paired samples are denoted in the Sample 'characteristics' field.

2013-01-22 | E-GEOD-39052 | biostudies-arrayexpress

mRNA profiling and clinical outcomes in human osteosarcoma (biopsy/resection pairs)

Project description:Osteosarcoma is a malignancy with variable outcomes that are not tightly aligned with chemotherapy response. Previous work has suggested a possible role for microRNAs (miRNAs) in determining the susceptibility of osteosarcomas to treatment but formal miRNA-based outcome models have not been reported. Formalin-fixed, paraffin-embedded (FFPE) specimens may be a unique approach for such studies in a rare malignancy. We used supervised principal components analysis and logistic regression to study survival and chemoresponse endpoints, and miRNA activity and gene set analysis algorithms to study miRNA regulatory networks using mRNA data. Our study also creates a paradigm for FFPE-based miRNA clinical biomarker research in rare tumors. 5 unique pairs of diagnostic biopsy and surgical resection specimens were profiled. Paired samples are denoted in the Sample 'characteristics' field.

2013-01-22 | E-GEOD-39057 | biostudies-arrayexpress

An array based analysis of miRNA expression comparing matched frozen and FFPE human tissue samples

Project description:MicroRNAs (miRNAs) are small non-coding RNAs that repress gene expression at the post transcriptional level via an antisense RNA-RNA interaction. Generally, miRNAs derived from snap frozen or fresh samples are used for array based profiling. Since tissues in most pathology departments are available only in formalin fixed and paraffin embedded state, we sought to evaluate the miRNA derived from formalin fixed and paraffin embedded (FFPE) samples for microarray analysis. In this study, miRNAs extracted from matched snap frozen and FFPE samples were profiled using the Agilent miRNA array platform. Each miRNA sample was hybridized to arrays containing probes interrogating 470 human miRNAs. A total of seven cases were compared in either duplicate or triplicate. Intrachip and interchip analyses demonstrated that the processes of miRNA extraction, labeling and hybridization from both frozen and FFPE samples are highly reproducible and add little variation to the results, as technical replicates showed high correlations (Kendall tau=0.722-0.853, Spearman rank correlation coefficient=0.891-0.954). Our results showed consistent high correlation between matched frozen and FFPE samples (Kendall tau=0.669-0.815, Spearman rank correlation coefficient=0.847-0.948), supporting the use of FFPE-derived miRNAs for profiling. Keywords: formalin-fixed and paraffin-embedded (FFPE) miRNA profiling

2008-11-01 | GSE12458 | GEO

Project description:Formalin-fixed, paraffin-embedded (FFPE) from prostate cancer patients

2016-11-30 | GSE89193 | GEO

Project description:Formalin-fixed, paraffin-embedded (FFPE) from prostate cancer patients

2016-11-30 | GSE90463 | GEO

Project description:Formalin-fixed, paraffin-embedded (FFPE) from prostate cancer patients

2016-11-30 | GSE88808 | GEO

Whole-Genome Gene Expression Profiling of Formalin-Fixed, Paraffin-Embedded Ovarian Tumor Tissue Samples: Ratios

Project description:Performance assayed with formalin-fixed, paraffin-embedded (FFPE) ovarian tumor tissues.

2010-01-13 | GSE18767 | GEO