Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Gene expression profiling of archival tongue carcinoma and normal tongue tissue (subset)

ABSTRACT: RNA extracted from 78 FFPE tongue samples, 62 tongue carcinomas and 16 non-malignant controls, were succesfully analysed using the whole genome DASL array to obtain gene expression profiles. Gene expression profiles were used to identify differentially expressed genes with the ultimate goal of finding out their importance for tongue cancer development and maintenance. Sample were formalin fixed paraffin embedded biopsies taken for diagnostic purposes and had been stored between 1 and 13 years. Because of the general poor quality of RNA from archival samples a special focus were put on its effect on the detected expression levels. 28 tumours and 16 controls with a CTdiff< 5 were selected for differential gene expression analysis. Raw data for only these samples were normalized again. Data for these 44 samples can be found here.

ORGANISM(S): Homo sapiens

PROVIDER: GSE34106 | GEO | 2012/05/11

SECONDARY ACCESSION(S): PRJNA156489

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Gene expression profiling of archival tongue carcinoma and normal tongue tissue (all samples)

2012-05-11 | GSE34105 | GEO

Gene expression profiling of archival tongue carcinoma and normal tongue tissue (subset)

Project description:RNA extracted from 78 FFPE tongue samples, 62 tongue carcinomas and 16 non-malignant controls, were succesfully analysed using the whole genome DASL array to obtain gene expression profiles. Gene expression profiles were used to identify differentially expressed genes with the ultimate goal of finding out their importance for tongue cancer development and maintenance. Sample were formalin fixed paraffin embedded biopsies taken for diagnostic purposes and had been stored between 1 and 13 years. Because of the general poor quality of RNA from archival samples a special focus were put on its effect on the detected expression levels. 28 tumours and 16 controls with a CTdiff< 5 were selected for differential gene expression analysis. Raw data for only these samples were normalized again. Data for these 44 samples can be found here. Total RNA from formalin fixed paraffin embedded sample was extracted using the High Pure RNA Paraffin Kit according to the manufacturer’s protocol. Quality of FFPE sample were evaluated by comparing how well a kousekeeping gene (TUBA6) could be amplified using q-PCR in each FFPE sample compared to two fresh frozen sample (Ctdiff= CTffpe-Ctff). The DASL platform (cDNA-mediated annealing, selection, extension, and ligation assay) was used together with the whole genome arrays to obtain expression data for 20 818 genes.

2012-05-10 | E-GEOD-34106 | biostudies-arrayexpress

Gene expression profiling of archival tongue carcinoma and normal tongue tissue (all samples)

Project description:RNA extracted from 78 FFPE tongue samples, 62 tongue carcinomas and 16 non-malignant controls, were succesfully analysed using the whole genome DASL array to obtain gene expression profiles. Gene expression profiles were used to identify differentially expressed genes with the ultimate goal of finding out their importance for tongue cancer development and maintenance. Sample were formalin fixed paraffin embedded biopsies taken for diagnostic purposes and had been stored between 1 and 13 years. Because of the general poor quality of RNA from archival samples a special focus were put on its effect on the detected expression levels. 28 tumours and 16 controls with a CTdiff< 5 were selected for differential gene expression analysis. Data for only these sample were normalized again and can be found in seperate data file. Total RNA from formalin fixed paraffin embedded sample was extracted using the High Pure RNA Paraffin Kit according to the manufacturer’s protocol. Quality of FFPE sample were evaluated by comparing how well a kousekeeping gene (TUBA6) could be amplified using q-PCR in each FFPE sample compared to two fresh frozen sample (Ctdiff= CTffpe-Ctff). The DASL platform (cDNA-mediated annealing, selection, extension, and ligation assay) was used together with the whole genome arrays to obtain expression data for 20 818 genes.

2012-05-10 | E-GEOD-34105 | biostudies-arrayexpress

Gene expression profiling of archival tongue carcinoma and normal tongue tissue

Project description:This SuperSeries is composed of the following subset Series: GSE34105: Gene expression profiling of archival tongue carcinoma and normal tongue tissue (all samples) GSE34106: Gene expression profiling of archival tongue carcinoma and normal tongue tissue (subset) Refer to individual Series

2012-05-10 | E-GEOD-34115 | biostudies-arrayexpress

Expression profiling of archival tissues for long-term health studies

Project description:Over 20 million archival tissue samples are stored annually in the United States as formalin-fixed, paraffin-embedded (FFPE) tissue blocks, but only recently has whole-genome expression profiling from these samples become technically feasible. Here, we introduce novel general methods for assessing, summarizing, and visualizing expression data quality from archival samples. We validated these methods in technical study of 144 clinical breast cancer and autopsy samples and in an overview of all current publicly available FFPE whole-genome expression data. We additionally performed a case study incorporating over 1,000 colorectal cancer (CRC) samples collected from patients across the United States over a period of more than 25 years, integrating clinicopathological information, tumor molecular data, and archival tissue gene expression on an unparalleled scale. Both large-scale clinical studies presented a much greater range of data quality than previous smaller studies, emphasizing the need for rigorous quality control in translational applications of archival tissue gene expression profiling. This series includes 1,003 FFPE-preserved CRC tumors, assayed by Illumina HumanRef-v3 WG-DASL microarray.

2012-10-02 | E-GEOD-32651 | biostudies-arrayexpress

Tongue tissue gene profile in 4NQO induced tongue carcinogenesis before and after IL-1Ra interference

Project description:Nine groups of rat tongue tissue RNA samples, including three from normal control, three from 4NQO induced tongue tissue, and three from 4NQO induced and IL-1Ra interference tongue tissue (3 rats per group) were collected for gene microarray hybridization.

2017-02-11 | GSE42855 | GEO

Expression profiling of archival tissues for long-term health studies

2012-10-02 | GSE32651 | GEO

RNA expression in tongue squamous cell carcinoma, tumour free tongue tissue and control tongue

Project description:Tongue squamous cell carcinoma is a tumour type with rather low five year survival, around 60%. The poor survival rate has been ascribed to late detection, a high frequency of locoregional recurrence, the occurrence of secondary primary tumours and death due to comorbidity. One reason for development of recurrence is thought to be the existence of transformed cells in areas adjacent to the primary tumour, cancerization field effect. The aim of this study was to map the changes in the tumour free tongue tissue adjacent to tongue tumours compared with healthy control tongue tissue to better understand the cancerization field effect. Tissue biopsies were collected from tumour (T) and tumour free tissue adjacent to the tumour (TF) from patients with tongue squamous cell carcinoma. Control tissue was collected from latter border of the tongue of tumour free healthy volunteers (C). All samples were homogenized and RNA was extracted. The RNA was biotin labelled and run on Illumina HT-12 bead chip array.

2016-12-21 | E-MTAB-4678 | biostudies-arrayexpress

Integrated proteomics and phosphoproteomics revealed druggable kinases in neoadjuvant chemotherapy resistant tongue cancer

Project description:Tongue squamous cell carcinoma is characterised by poor prognosis and high metastatic events. Patients with unresectable tumors are benefiting from neoadjuvant chemotherapy (NACT) which surgical resection, and controls distant metastasis, and locoregional recurrence. However, resistance to NACT limit the success of the treatment regimen. In this study, we investigated the altered proteome and phosphoproteome of NACT resistant and sensitive cohort using Mass spectrometry-based proteomics. We carried out proteomic as well as phosphoproteomic analysis of treatment naïve tongue cancer patients whose response to NACT is recorded. Proteomic analysis revealed distinct protein expression between the responders and non-responders. The Phosphoproteomic analysis revealed kinases and the pathways associated with NACT resistance in tongue cancer.

2023-03-11 | PXD037356 | Pride

Gene Expression Profiling of Formalin Fixed Paraffin Embedded Familial Breast Tumours Using the Whole Genome-DASL Assay

Project description:Tissue sample acquisition is a limiting step in many studies. There are many thousands of formalin fixed paraffin embedded archival blocks collected around the world, but in contrast relatively few fresh frozen samples in tumor banks. Once samples are fixed in formalin the RNA is degraded and traditional methods for gene expression profiling are not suitable. In this study we have evaluated the whole genome DASL assay from Illumina to perform transcriptomic analysis from archived breast tumor tissue fixed in formalin paraffin embedded blocks. We profiled 76 familial breast tumors from cases carrying a BRCA1, BRCA2 or ATM mutation, or from non-BRCA1/2 families. We found that replicate samples correlated well with each other (r2=0.9-0.98). In 12/15 cases, the matched formalin-fixed and frozen samples predicted the same tumor molecular subtypes with confidence. These results demonstrate that the whole genome DASL assay is a valuable tool to profile degraded RNA from archival FFPE material. This assay will enable transcriptomic analysis of a large number of archival samples that are stored in pathology archives around the globe and consequently will have the potential to improve our understanding and characterisation of many diseases.

2010-06-09 | GSE21921 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data