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ABSTRACT:
PROVIDER: PRJNA125467 | ENA |
REPOSITORIES: ENA
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Project description:The 1q gain is related to poor survival, and to a profile of cell cycle deregulation in Ewing's Sarcoma (ES). Tumor samples with 1q gain overexpress the gene DTL. We have silenced DTL in three ES cell lines in order to compare the differential expression pattern produced with the differential expression pattern which characterizes 1q gained-tumors.
2011-08-01 | GSE20357 | GEO
Project description:The 1q gain is related to poor survival, and to a profile of cell cycle deregulation in Ewing's Sarcoma (ES). Tumor samples with 1q gain overexpress the gene DTL. We have silenced DTL in three ES cell lines in order to compare the differential expression pattern produced with the differential expression pattern which characterizes 1q gained-tumors. We silenced DTL in three ES cell lines with two different shRNA constructions by means of lentiviral transduction. pLKO.1-non-targeting control was transduced in the control samples. RNA was extracted and hybridized with Affymetrix expression microarrays.
2011-07-31 | E-GEOD-20357 | biostudies-arrayexpress
Project description:Background: Gain and/or amplification of chromosome 1q are frequently found in Multiple Myeloma (MM). The number of 1q copies correlates with a poor prognosis. The aim of this work is to study the impact on the clinical outcome and the trascriptomic changes induced by Gain1q (3 copies of 1q, 3X) and amplification 1q (Amp1q, ≥4 copies of 1q, 4X) in MM patients enrolled in the CoMMpass study (NCT145429). Methods: Fluorescence in situ hybridization (FISH) in CD138+ purified bone marrow plasma cells was centralized and performed at baseline. The cut-off level for Gain1q was 10% of nuclei with ≥3 copies of 1q (3X), while Amp1q was defined as ≥ 20% of nuclei with ≥4 copies of 1q (4X). Transcriptome data from patients were used to find differentially expressed genes (DEGs) in gain (3X) and amp1q (4X) patients.
2023-01-16 | GSE193427 | GEO
Project description:Affymetrx U95Av2 GeneChip hybridizations, RNA extracted from primary human pediatric alveolar (aRMS) and embryonal (eRMS) rhabdomyosarcoma, plus primary pediatric Ewing's sarcoma (EWS) Keywords = pediatric sarcoma Keywords = Ewing's sarcoma Keywords = rhabdomyosarcoma Keywords: other
2004-03-13 | GSE967 | GEO
Project description:Comparison of expression profiling from Ewing's sarcoma tumor specimen to Ewing's sarcoma cell lines
2008-03-26 | E-MEXP-1142 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE31185: The human Ewing's Sarcoma oncoprotein EWS-FLI1 causes developmental defects in zebrafish embryos GSE31186: The human Ewing's Sarcoma oncoprotein EWS-FLI1 causes Ewing's-type tumors in zebrafish Refer to individual Series
2011-11-01 | E-GEOD-31217 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE20355: BAC-microarrays aCGH data from 67 Ewing's Sarcoma tumor samples and 16 Ewing's Sarcoma cell lines GSE20356: Evaluation of copy number alterations in the Ewing's Sarcoma cell line SKES1 with Affymetrix 500k SNP microarray GSE20357: Expression data from DTL silenced-Ewing Sarcoma's cell lines along with their controls Refer to individual Series
2011-07-31 | E-GEOD-20368 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE37370: microRNA expression data from Ewing's sarcoma tumor samples GSE37371: Expression data from Ewing's sarcoma tumor samples Refer to individual Series
2012-06-11 | E-GEOD-37372 | biostudies-arrayexpress
Project description:Background: The high incidence of recurrence and unpredictable clinical outcome for paediatric ependymoma reflect the imprecision of current therapeutic staging and need for novel risk stratification markers. Gain of chromosome 1q has been reported as a frequent aberration and correlate of adverse outcome in ependymoma. We therefore evaluated a prognostic role for 1q25 gain across three age-defined European clinical trial cohorts of paediatric intracranial ependymoma. Methods: The frequency of 1q gain in paediatric ependymoma was assessed across 51 tumours (42 primary, 9 recurrent) using Affymetrix® 500K SNP arrays. Gain of 1q25 was evaluated by interphase FISH (iFISH) across 189 primary intracranial ependymomas from children treated on the CCLG/SIOP CNS9204 (n = 60) and BBSFOP (n = 65) adjuvant chemotherapy trials, or with primary post-operative radiotherapy (SIOP CNS9904/RT group, n = 64). Results were correlated with clinical, histological and survival data. Findings: Gain of 1q was the most frequent imbalance in primary (7/42, 17 %) and recurrent ependymomas (3/9, 33 %). Gain of 1q25 was the strongest independent predictor of tumour progression in both CNS9204 (HR 3·36, p = 0·0009) and BBSFOP (HR 4·10, p = 0·0009) trial cohorts. In contrast, 1q25 gain was not prognostic for the older CNS9904/RT only group (PFS: p = 0·37, OS: p = 0·95). Clinical variables implicated in adverse outcome amongst cohorts included incomplete tumour resection and posterior fossa location. Interpretation: This is the first study to prospectively identify then validate a prognostic genomic marker for childhood ependymoma across independent prospective trial groups. 1q25 gain predicts progression in primary chemotherapy cohorts but not those treated by post-operative radiotherapy. We propose 1q25 gain is incorporated as an adverse marker into future European chemotherapeutic clinical trial design. Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from flash frozen tumour specimens and patient-matched peripheral blood Copy number analysis of Affymetrix 500K SNP arrays was performed for DNA from 51 ependymomas and 40 constitutional DNA samples. Analysing broad genomic aberrations in 51 paediatric ependymomas, looking particularly at 1q gain.
2012-02-09 | E-GEOD-32101 | biostudies-arrayexpress
Project description:Genome wide DNA methylation profiling of Rhabdoid tumor of the kidney, Clear cell sarcoma of the kidney, Ewing's sarcoma family of tumors and non-neoplastic kidney. The Illumina Infinium HumanMethylation 27 BeadChip was used to obtain DNA methylation profiles across approximately 27000 CpGs . Samples included 3 Rhabdoid tumor of the kidney, 3 Clear cell sarcoma of the kidney, 3 Ewing's sarcoma family of tumor and 3 non-neoplastic kidney.
2015-06-12 | GSE44847 | GEO