C26a1203-ba67-4c38-a7e2-1143007e2376 - samples
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ABSTRACT:
PROVIDER: EGAD00001008117 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:<p>Diffuse Intrinsic Pontine Glioma (DIPG) is a universally fatal childhood cancer. Here, we performed a chemical screen in patient-derived DIPG cell cultures along with RNAseq expression analysis and integrated computational modeling to identify potentially effective therapeutic strategies. Panobinostat, among the more promising agents identified, demonstrated efficacy in pontine orthotopic xenograft models of both H3K27M and histone WT DIPG. These data suggest the potential utility of specific drug combinations and provides evidence of in vivo treatment efficacy of the multi-histone deacetylase inhibitor panobinostat. We are depositing to dbGaP deep sequencing whole exome data for 22 patient tumor samples and 13 matched normals, along with RNAseq data for 12 patient tumor samples and 6 normal pediatric brain tissue samples. In addition, we are depositing 22 RNAseq samples from DIPG cell lines before and after panobinostat treatment.</p>
| phs000900 | dbGaP
Project description:Both cigarette smoking and obesity have been implicated in increased risk of clear cell renal cell carcinoma (ccRCC); however, there are limited data regarding the molecular mechanisms that underlie these associations. We used a multi-stage design to identify and validate specific molecular targets that are associated with smoking or obesity-related ccRCC. The data deposited herein are comprised of two batches of samples that were processed at two different time periods (please see Supplementary Data in Eckel-Passow et al. Carcinogenesis first published online December 28, 2013; doi:10.1093/carcin/bgt485). The first batch of samples consisted of 12 obese subjects and 13 non-obese subjects; all of whom were self-reported never-smokers. Each of the 12 obese subjects had microarray data available on both the patient-matched tumor and adjacent-normal tissues. All of the 13 non-obese subjects had microarray data available on the tumor tissue; however, only 9 of these 13 also had microarray data available on the patient-matched adjacent-normal tissue. The second batch of samples consisted of 16 self-reported smokers and 19 self-reported never smokers; all of whom were non-obese. This second batch of samples also contained 7 subjects who were obese and self-reported smokers. All subjects in the second batch had microarray data available on both the patient-matched tumor and adjacent-normal tissues. Lastly, two of the 13 patients in batch 1 were replicated in batch 2; both were non-obese and a non-smoker. These two technical replicates (two tumor samples and two normal samples) were included during normalization but removed prior to analysis. The cel files are Par007U133Plus2.0.CEL Par008U133Plus2.0.CEL Par041U133Plus2.0.CEL Par042U133Plus2.0.CEL The metadata "duplicate" column can also be used to exclude these samples. This dataset is part of the TransQST collection.
2014-01-10 | E-GEOD-46699 | biostudies-arrayexpress
Project description:We report RNAseq analysis of 12 breast cancer patients treated with the ratiotracer 18F-Fluciclovine and the associated radiotracer uptake data. FFPE samples from 12 tumor and 7 benign tissue were sequenced. In addition, tissue samples from 6 normal breast reduction cases were sequenced for a total of 25 samples.
2023-12-31 | GSE174339 | GEO
Project description:We performed whole transcriptome analysis of osteosarcoma bone samples. Initially we sequenced total RNA from 36 fresh-frozen samples (18 tumoral bone samples and 18 non-tumoral paired samples) matching in pairs for each osteosarcoma patient. We also performed independent gene expression analysis of formalin-fixed paraffin-embedded (FFPE) samples to verify the RNAseq results. The use of FFPE samples allowed to analyse the effect of chemotherapy. Data were analysed with DESeq2 and Reactome packages of R. We found 6775 genes expressed differentially between the normal bone and osteosarcoma tissues with an FDR below 0.1, of which 4092 genes were up-regulated and 2683 were down-regulated. Among those genes, BTNL9, MMP14, ABCA10, ACACB, COL11A1 and PKM2 were expressed differentially with the highest significance between tumor and normal bone. Functional annotation with the Reactome identified significant changes in the pathways related to the extracellular matrix degradation and collagen biosynthesis. Analysis of independent FFPE samples largely verified our findings in fresh frozen samples, indicating that osteosarcoma is characterized by massive bone loss. We also found that chemotherapy induced the bone formation and reverses the bone loss caused by sarcoma. Taken together, our results indicate that changes in the degradation of extracellular matrix seem to be an important mechanism of osteosarcoma and efficient chemotherapy induces the genes related to bone formation.
2017-11-03 | GSE99671 | GEO
Project description:This dataset contains samples from 5 patients with wilm's tumor. 5 samples have whole exome tumor data. 4 samples have tumor RNAseq data. 2 samples have matched normal dna sequence data
| EGAD00001008283 | EGA
Project description:SNP data from 13 childhood adrenocortical tumours from Brazilian patients and 6 matched normal samples
| PRJNA153911 | ENA
Project description:This dataset contains samples from 5 patients with ewings sarcoma. 5 samples have whole exome tumor data. 1 sample has tumor RNAseq data. 4 samples have matched normal dna sequence data
| EGAD00001008282 | EGA
Project description:This dataset contains samples from 8 patients with Sclerosing epithelioid fibrosarcoma. All 8 samples have whole exome tumor data and tumor RNAseq data. 3 samples also have matched normal dna sequence data.
| EGAD00001011100 | EGA
Project description:A major challenge to the study of tumor DNA copy number (CN) in clinical specimens is the lack of appropriate fresh frozen samples and thus a dependence on Formalin-Fixed Paraffin Embedded (FFPE) banked samples, which typically have more extensive clinical follow up information. However, on most high density CN platforms, DNA from FFPE tissues generally underperforms or suffers high failure rates compared to fresh frozen samples because of DNA degradation and cross-linking. Molecular Inversion Probe (MIP) technology has been applied successfully to obtain high quality CN and genotype data from DNA isolated from cell lines and frozen tumor samples. Since the MIP probes require only a small (~40 bp) target binding site, we reasoned they may be well suited to assess FFPE samples. In this study, we successfully applied MIP technology with a panel of 50,000 markers to CN determination in FFPE samples. Using an input of 37 ng genomic DNA, we demonstrated high quality CN data with MIP technology from 93 FFPE samples from seven diverse collections. We found that the performance of FFPE DNA for CN determination was comparable to that of DNA obtained from matched frozen tumor, with only a modest loss in performance of DNA. Tumor FFPE were analyzed using matched normal FFPE as the reference. Tumor and normal pairs: 01-02, 12-13, 16-17, 08-09, 20-21, 24-25, 28-29, and 35-36. Tumor 32 has no matched normal sample.
2009-01-22 | E-GEOD-14353 | biostudies-arrayexpress
Project description:This dataset contains samples from 9 patients with embryonal rhabdomyosarcoma. 9 samples have whole exome tumor data (one has multiple). 7 samples have tumor RNAseq data. 1 sample has matched normal dna sequence data
| EGAD00001007939 | EGA