Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

RNAi profiling by array of human HeLa cells with hnRNP C siRNA knockdown using a splice-junction microarray to detect changes in alternative splicing.

ABSTRACT: poly(A)+ RNA samples from hnRNP C siRNA knockdown and control HeLa cells were compared on a splice-junction microarray to detect changes in alternative splicing. Using the ASPIRE3 algorithm, we detected changes in splicing at 1,340 alternative exons. We observed a similar incidence of increased or decreased exon inclusion in hnRNP C knockdown cells, indicating that hnRNP C can either silence or enhance exon inclusion, respectively. We validated changes at 26 exons by RT-PCR with a 92% success rate.

ORGANISM(S): Homo sapiens

SUBMITTER: Melis Kayikci

PROVIDER: E-MTAB-367 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution.

König Julian J Zarnack Kathi K Rot Gregor G Curk Tomaz T Kayikci Melis M Zupan Blaz B Turner Daniel J DJ Luscombe Nicholas M NM Ule Jernej J

Nature structural & molecular biology 20100704 7

In the nucleus of eukaryotic cells, nascent transcripts are associated with heterogeneous nuclear ribonucleoprotein (hnRNP) particles that are nucleated by hnRNP C. Despite their abundance, however, it remained unclear whether these particles control pre-mRNA processing. Here, we developed individual-nucleotide resolution UV cross-linking and immunoprecipitation (iCLIP) to study the role of hnRNP C in splicing regulation. iCLIP data show that hnRNP C recognizes uridine tracts with a defined long ...[more]

PMID: 20601959

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Dataset Information

RNAi profiling by array of human HeLa cells with hnRNP C siRNA knockdown using a splice-junction microarray to detect changes in alternative splicing.

Publications

iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution.

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