Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

55 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Gene expression profiling of solitary fibrous tumors

ABSTRACT: Sixteen pre-treatment samples of pathologically confirmed solitary fibrous tumors (SFT) were available for RNA profiling. They were collected from 16 patients who underwent initial surgery and/or diagnostic biopsy. Samples were macrodissected by pathologists, and frozen within 30 min of removal in liquid nitrogen in our biobank (Biobank authorization number 2008/70, APHM). All profiled specimens contained more than 70% tumor cells. Each patient gave written informed consent for molecular analysis, and the study was approved by our institutional ethics committee. Total RNA was extracted from frozen samples by using the All-In-One Norgen Biotek kit (Thorold, Canada) and integrity was controlled by Agilent analysis (Bioanalyzer, Palo Alto, CA). Gene expression profiling was done with Affymetrix U133 Plus 2.0 human oligonucleotide microarrays with labeling kit and protocol from manufacturer.

ORGANISM(S): Homo sapiens

SUBMITTER: Pascal FINETTI

PROVIDER: E-MTAB-1361 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Solitary Fibrous Tumours gene profiling study

Project description:Using whole-genome DNA microarrays, we defined the gene expression profiles of 16 Solitary Fibrous Tumours (SFT) and haemangiopericytomas (HPC) (9 HPC and 7 SFT). Expression profiles were compared to publicly available expression profiles of additional SFT or HPC, meningiomas and synovial sarcomas.

2023-02-08 | E-MTAB-11447 | biostudies-arrayexpress

Genomic Sequencing of Solitary Fibrous Tumors

Project description:<p>Solitary fibrous tumors (SFTs) are rare mesenchymal tumors that can be benign or malignant. In this study, we sequenced and analyzed the exomes of 17 SFT matched tumor and normal pairs. This study appertains to a large endeavor to characterize cancers as part of the Slim Initiative for Genomic Medicine in the Americas (SIGMA) project.</p>

| phs000568.v1.p1 | EGA

Genomic Sequencing of Solitary Fibrous Tumors

| phs000568 | dbGaP

A Comparison of HEEBO Microarray and 3'-end Sequencing for Expression Quantification (3SEQ) (Archival Tumor Samples)

Project description:Gene expression microarrays are the most widely used technique for genome-wide expression profiling. However, microarrays do not perform well on formalin fixed paraffin embedded tissue (FFPET). Consequently, microarrays cannot be effectively utilized to perform gene expression profiling on the vast majority of archival tumor samples. To address this limitation of gene expression microarrays, we designed a novel procedure (3'-end sequencing for expression quantification (3SEQ)) for gene expression profiling from FFPET using next-generation sequencing. We performed gene expression profiling by 3SEQ and microarray on both frozen tissue and FFPET from two soft tissue tumors (desmoid type fibromatosis (DTF) and solitary fibrous tumor (SFT)) (total n = 23). Analysis of 3SEQ data revealed many genes differentially expressed between the tumor types (FDR < 0.01) on both the frozen tissue (~9.6K genes) and FFPET (~8.1K genes). Analysis of microarray data from frozen tissue revealed fewer differentially expressed genes (~4.64K), and analysis of microarray data on FFPET revealed very few (69) differentially expressed genes. Functional gene set analysis of 3SEQ data from both frozen tissue and FFPET identified biological pathways known to be important in DTF and SFT pathogenesis and suggested several additional candidate oncogenic pathways in these tumors. These findings demonstrate that 3SEQ is an effective technique for gene expression profiling from archival tumor samples and may facilitate significant advances in translational cancer research. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Preservation: either frozen (FROZEN) or formalin fixed paraffin embedded tissue (FFPET) Disease State: Tumor type: desmoid type fibromatosis (DTF) or solitary fibrous tumor (SFT) Keywords: Logical Set

2010-03-26 | GSE18209 | GEO

A Comparison of HEEBO Microarray and 3'-end Sequencing for Expression Quantification (3SEQ) (Archival Tumor Samples)

2010-03-25 | E-GEOD-18209 | biostudies-arrayexpress

microRNA and snoRNA expression profile in the solitary colorectal cancer

Project description:We evaluated the profile of miRNA and snoRNA expression in 7 solitary CRC and matched normal colorectal tissues using the Affymetrix GeneChip miRNA 1.0 array. We found that global dysregulated miRNAs and snoRNAs between cancer tissue and normal mucosa in solitary CRC. Our findings firstly implicates that dysregulation of snoRNAs and miRNA may play important role in the cancinogenesis and present therapeutic targets for solitary CRC.

2015-08-01 | GSE68377 | GEO

Loss of non-CpG methylation in inhibitory neurons impairs neural function through a mechanism that partially overlaps with Rett syndrome

Project description:Whole striatum were dissected from wild-type, as well as in mice where Dnmt3a or MeCP2 was conditional deleted in inhibitory neurons. Inhibitory neuronal nuclei were also conditionally tagged with GFP in all mice. Tissues were snap-frozen in liquid nitrogen until further analysis. Inhibitory neurons were sorted from whole striatum using anti-GFP-488 and anti-NeuN-647 signals and snap frozen until further analysis. Total nuclear RNA was purified from each sample using the Single Cell RNA Purification Kit from Norgen Biotek according to manufactures instructions and stored at -80C until library preparation at the Genomic and RNA Profiling Core at Baylor College of Medicine. NuGEN Ovation RNA-Seq v2 & Rubicon ThruPlex DNA-Seq kits were utilized for library preparation. A paired-end 100 cycle run was used to sequence the flowcell on a HiSeq 2500 Sequencing System.

2020-03-16 | GSE123941 | GEO

microRNA and snoRNA expression profile in the solitary colorectal cancer

2015-08-01 | E-GEOD-68377 | biostudies-arrayexpress

NAB2-STAT6 drives an EGR1-dependent neuroendocrine program in Solitary Fibrous Tumors (RNA-Seq)

Project description:The pathogenesis of many rare tumor types is poorly understood, preventing the design of effective treatments. Solitary Fibrous Tumors (SFTs) are neoplasms of mesenchymal origin that affect 1/1,000,000 individuals every year and are clinically assimilated to sarcomas. SFTs are commonly found throughout the body and can be surgically removed upon diagnosis. However, 30-40% of tumors become aggressive and can locally relapse or metastasize. There are no effective treatments for malignant SFTs to date. The molecular hallmark of SFTs is a gene fusion between the NAB2 and STAT6 loci on chromosome 12, resulting in a chimeric protein of poorly characterized function called NAB2-STAT6. We use primary samples and an inducible cell model to discover that NAB2-STAT6 operates as a transcriptional coactivator for a specific set of enhancers and promoters that are normally targeted by the EGR1 transcription factor. In physiological conditions, NAB2 is primarily localized to the cytoplasm and only a small nuclear fraction is available to operate as a co-activator of EGR1 targets. NAB2-STAT6 redirects NAB1, NAB2, and additional EGR1 to the nucleus and bolster the expression of neuronal EGR1 targets. The STAT6 moiety of the fusion protein is a major driver of its nuclear localization and further contributes to NAB2’s co-activating abilities. In primary tumors, NAB2-STAT6 activates a neuroendocrine gene signature that sets it apart from most sarcomas. These discoveries provide new insight into the pathogenesis of SFTs and reveal new targets with therapeutic potential.

2024-05-01 | GSE249702 | GEO

NAB2-STAT6 drives an EGR1-dependent neuroendocrine program in Solitary Fibrous Tumors (ChIP-Seq)

2024-05-01 | GSE249701 | GEO