Retinoblastoma tumors NGS data
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR550406.fastq.gz | Fastqsanger.gz | |||
| ERR550407.fastq.gz | Fastqsanger.gz | |||
| ERR550408.fastq.gz | Fastqsanger.gz |
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Project description:Retinoblastoma is a malignant tumor of the retina which most often occurs in children below 5 years of age with an incident rate of about 1 in 15,000 to 18,000 live births. Retinoblastoma is the first ever cancer that was reported to have a genetic basis. It occurs widely due to inactivating mutations in RB1 gene. Gene expression studies, copy number variation analysis, epigenetic profiling including miRNA and methylation of retinoblastoma has been carried to understand the disease mechanism and key players in the disease. Our group has earlier performed differential proteomics of retinoblastoma to identify proteins of therapeutic importance. However, there are no studies to understand the signalling mechanisms associated with retinoblastoma. Hence, global phosphoproteomics of retinoblastoma was carried out to identify signalling events associated with this cancer. Our study identified stress response proteins to be hyper phosphorylated which included H2AFX and sirtuin 1. In particular, Ser140 of H2AFX also known as gamma-H2AX was found to be hyperphosphorylated in retinoblastoma that indicated activation of DNA damage response pathways. We also observed activation of anti-apoptotic proteins in retinoblastoma compared to control. These observations showed activation of survival pathways and signalling networks activated in tumors.
2019-11-11 | PXD007228 | Pride
Project description:Transcriptome analysis of partially degraded and fragmented RNA samples from retinoblastoma primary tumors. Global gene expression profiling has shown great promise in high-throughput biomarker discovery for early disease detection in Retinoblastoma tumors. In this analysis we have used 3 retinoblastoma primary tumors in triplicates which was normalised against human healthy Retina. Here, we have used nanogram scale of retinoblastoma RNA, processed in HUMAN GENE 1.0 ST ARRAYS.
2010-10-14 | GSE24673 | GEO
Project description:Transcriptome analysis of partially degraded and fragmented RNA samples from retinoblastoma primary tumors. Global gene expression profiling has shown great promise in high-throughput biomarker discovery for early disease detection in Retinoblastoma tumors. In this analysis we have used 3 retinoblastoma primary tumors in triplicates which was normalised against human healthy Retina. Here, we have used nanogram scale of retinoblastoma RNA, processed in HUMAN GENE 1.0 ST ARRAYS. We have analysed the gene expression in 2 normal healthy adult retina collected from cadaveric eyes and 3 retinoblastoma primary tumors
2010-10-14 | E-GEOD-24673 | biostudies-arrayexpress
Project description:Retinoblastoma is the most common intraocular cancer of infancy and childhood, with an incidence of one case per 15,000 - 20,000 live births. An early event in retinoblastoma genesis is a functional loss of both alleles of the RB1 gene. However, other genes are likely to be involved in the development of this cancer. In this study we sought to build a comprehensive molecular portrait of this cancer by performing transcriptomic, methylomic, genomic profiling of primary retinoblastoma samples. Most of the patients whose tumors were studied had received no treatment prior to surgical enucleation.
2021-07-06 | GSE58781 | GEO
Project description:Retinoblastoma is the most common intraocular cancer of infancy and childhood, with an incidence of one case per 15,000 - 20,000 live births. An early event in retinoblastoma genesis is a functional loss of both alleles of the RB1 gene. However, other genes are likely to be involved in the development of this cancer. In this study we sought to build a comprehensive molecular portrait of this cancer by performing transcriptomic, methylomic, genomic profiling of primary retinoblastoma samples. Most of the patients whose tumors were studied had received no treatment prior to surgical enucleation.
2021-07-06 | GSE58783 | GEO
Project description:Retinoblastoma is the most common intraocular cancer of infancy and childhood, with an incidence of one case per 15,000 - 20,000 live births. An early event in retinoblastoma genesis is a functional loss of both alleles of the RB1 gene. However, other genes are likely to be involved in the development of this cancer. In this study we sought to build a comprehensive molecular portrait of this cancer by performing transcriptomic, methylomic, genomic profiling of primary retinoblastoma samples. Most of the patients whose tumors were studied had received no treatment prior to surgical enucleation.
2021-07-06 | GSE58780 | GEO
Project description:Genomic losses on chromosome 16q are among the most frequent alterations found in retinoblastoma. In this study, Affymetrix GeneChip analyses along with LOH analysis of microsatellie markers was used to identify candidate tumor suppressor loci in a set of retinoblastoma. We used microarrays to identify genes differentially expressed in retinoblastoma with LOH on 16q (M19484, M22590, M22641, M22860) compared to retinoblastoma without alterations in this region (M20517, M22067, M22233, M23209, M23449, M23818, M23896, M23978) Keywords: Disease progression
2007-01-29 | GSE5222 | GEO
Project description:mRNA expression profile from retinoblastoma tumors and pediatric controls
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Project description:MicroRNA expression profile from retinoblastoma tumors and pediatric controls
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Project description:Gene expression profiles in retinoblastoma by whole Human Genome DNA microarrays in comparison to the normal retina gave an insight into several genes and pathways that were regulated in the tumor. The upregulated and the downregulated genes were further validated by quantitative real time PCR and tissue microarray (TMA) on retinoblastoma tumors. Theoverall goal is to determine the global gene expression profile in retinoblastoma tumors which is first of its kind on a whole genome microarray. Two coloured microarray:retinoblastoma tumor (4 samples) vs. normal retina (4 samples).
2012-03-30 | E-GEOD-33048 | biostudies-arrayexpress