E-GEOD-45190 - The genomic landscape of small intestine neuroendocrine tumors [CGH]

Status
Released on 16 March 2013, last updated on 2 June 2014
Organism
Homo sapiens
Samples (2)
Array (1)
Protocols (7)
Description
Small intestine neuroendocrine tumors are the commonest neuroendocrine tumors of the GI tract. Next gen sequencing of the whole exome was undertaken to identify SNPs and SCNA in these tumor samples. Subsequent bioinformatic anlaysis was done where the reads ratios of tumor/normal were log2 tranformed, segments indentified with DNAcopy (R package) and regions of SCNA were identified. Amplification of chr 4, 5, 14 and 20 was observed. The validation of these SCNAs was done with arrayCGH. The results of array CGH is in concordeance with the exome sequencing data. DNA from matched tumor and normal sample of SI-NETs was done by spin column method. Libraries were constructed and exome enriched for next gen sequencing. The same gDNA was hybridized with Cy5 and Cy3 and subsequent analysis was done. This study represents the CGH portion of the study.
Experiment type
comparative genomic hybridization by array 
Contacts
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-45190.idf.txt
Sample and data relationshipE-GEOD-45190.sdrf.txt
Raw data (1)E-GEOD-45190.raw.1.zip
Processed data (1)E-GEOD-45190.processed.1.zip
Array designA-GEOD-16795.adf.txt
Links