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SRX7256497: GSM4200864: Y79-WT; Homo sapiens; RNA-Seq
1 ION_TORRENT (Ion Torrent PGM) run: 15.5M spots, 2.2G bases, 1.6Gb downloads

Submitted by: NCBI (GEO)
Study: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and CANT1 Overexpression Retinoblastoma Transcriptomes
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PURPOSE: Retinoblastoma (RB) is the most common malignant intraocular tumor of childhood. Recent studies have shown that long non-coding RNAs (lncRNAs), which are longer than 200 bp and without protein-coding ability, are key regulators of tumorigenesis. However, the role of lncRNAs in retinoblastoma remains to be elucidated. METHODS: LncRNA CASC15-New-Transcript 1 (CANT1) expression was determined by real-time PCR in RB cells. Tumor characteristics in CANT1-overexpressing RB cells were determined through CCK8 cell viability assay, soft agar assay and mouse xenograft experiment. RNA transcriptome-sequencing was performed to find downstream target genes of CANT1. CANT1's interactions with phosphoinositide 3-kinase gamma (PI3K?) were studied through chromatin oligonucleotide precipitation (ChOP) and chromatin immunoprecipitation (ChIP) assays. RESULTS: In this study, we found that the expression of lncRNA CANT1 was significantly downregulated in RB. Notably, CANT1 overexpression significantly inhibited RB growth both in vitro and in vivo. Furthermore, lncRNA CANT1, which was mainly located in the nucleus, occupied the promoter of PI3K? and blocked histone methyltransferase hSET1 from binding to the PI3K? promoter, thus abolishing hSET1-mediated histone H3K4 trimethylation of the PI3K? promoter and inhibiting PI3K? expression. Furthermore, we found that silencing PI3K? either by CANT1 overexpression or by PI3K? siRNA, reduced the activity of PI3K/Akt signaling and suppressed RB tumorigenesis. CONCLUSIONS: LncRNA CANT1 acts as a suppressor of RB progression by blocking gene-specific histone methyltransferase recruitment. These findings outline a new CANT1 modulation mechanism and provide an alternative option for RB treatment. Overall design: mRNA profiles of wild type (WT) and lncRNA CANT1 overexpressing retinoblastoma cells were generated by deep sequencing, using Ion Torrent PGM.
Sample: Y79-WT
SAMN13471158 • SRS5753979 • All experiments • All runs
Organism: Homo sapiens
Library:
Instrument: Ion Torrent PGM
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: SINGLE
Construction protocol: Total RNA from lncRNA CANT1-knockdown RB and WT RB cells was isolated and quantified. The concentration of each sample was measured by a NanoDrop 2000 (Thermo Scientific, USA). The quality was assessed by an Agilent2200 (Agilent, USA). The sequencing library of each RNA sample was prepared by using an Ion Proton Total RNA-Seq Kit v2 according to the protocol provided by manufacturer (Life Technologies, USA). RNA libraries were prepared for sequencing using standard Ion PGM protocols
Experiment attributes:
GEO Accession: GSM4200864
Links:
Runs: 1 run, 15.5M spots, 2.2G bases, 1.6Gb
Run# of Spots# of BasesSizePublished
SRR1057519715,537,0312.2G1.6Gb2020-02-05

ID:
9528561

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