Transcriptomics,Genomics

Dataset Information

18

Discovery of microRNAs and other small RNAs in solid human tumors: sequencing


ABSTRACT: MicroRNAs (miRNAs) are ~22 nucleotide-long, non-coding RNAs that regulate gene silencing. It is known that many human miRNAs are deregulated in numerous types of tumors. Here we report the sequencing of small RNAs from 23 breast, bladder, colon, and lung tumor samples using high-throughput sequencing. We identified 49 novel miRNA and miRNA-like small RNAs. We further validated the expression of 10 novel small RNAs in 31 different types of blood, normal and tumor tissue samples using two independent platforms, namely microarray and RT-PCR. Some of the novel sequences show a large difference in expression between tumor and tumor-adjacent tissues, between different tumor stages, or between different tumor types. We also report the identification of novel small RNA classes in human: highly expressed small RNA derived from Y-RNA and endogenous siRNA. Finally, we identified dozens of new miRNA sequence variants that demonstrate the existence of miRNA-related SNP or post-transcriptional modifications. Our work extends the current knowledge of the tumor small RNA transcriptome and provides novel candidates for molecular biomarkers and drug targets. Overall design: 2 samples of pools of different tumor samples: pool1: breast (5 samples), bladder (5 samples); 2 replicates each pool2: colon (7 samples), lung (6 samples); 2 replicates each

INSTRUMENT(S): 454 GS FLX (Homo sapiens)

SUBMITTER: Einat Sitbon  

PROVIDER: GSE20417 | GEO | 2010-05-20

SECONDARY ACCESSION(S): PRJNA129825

REPOSITORIES: GEO

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Publications


MicroRNAs (miRNAs) are ∼22-nt long, non-coding RNAs that regulate gene silencing. It is known that many human miRNAs are deregulated in numerous types of tumors. Here we report the sequencing of small RNAs (17-25 nt) from 23 breast, bladder, colon and lung tumor samples using high throughput sequencing. We identified 49 novel miRNA and miR-sized small RNAs. We further validated the expression of 10 novel small RNAs in 31 different types of blood, normal and tumor tissue samples using two indepen  ...[more]

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