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TranscriptomicsPTBP1 - Modified iCLIP
This experiments was performed in HeLa cells according to the iCLIP protocol with the following modifications: no antiRNase was used and the concentration of RNase I was 0.5 U/ml. In iCLIP4, the dephosphorylation step was omitted from the standard protocol. The rest of the protocol was identical to...
ORGANISM(S): Homo sapiens 
2016-11-24 | E-MTAB-5026 | biostudies-arrayexpress
TranscriptomicseIFA3 - iCLIP
The exon junction complex is deposited at 24nt upstream of exon-exon junctions, but not at every junction. The core complex is comprosed of 4 proteins, eIF4A3, Magoh, Y14 and MLN51. Here we performed immunoprecipitation of Y14 with subsequent iCLIP of eIF4A3 in HeLa cells to identify the crosslink s...
ORGANISM(S): Homo sapiens 
2016-11-24 | E-MTAB-3618 | biostudies-arrayexpress
TranscriptomicsInvestigation into human Tra2 protein-dependent splicing in MDA-MB-231 cells using iCLIP and RNA-seq
Alternative splicing—the production of multiple mRNA isoforms from a single gene—is regulated in part by RNA-binding proteins (RBPs). While the RBPs Tra2? and Tra2? have both been implicated in the regulation of alternative splicing, their relative contribution to this process are not well understoo...
ORGANISM(S): Homo sapiens 
2014-07-12 | E-GEOD-59335 | biostudies-arrayexpress
TranscriptomicsiCLIP transcriptome-wide mapping of UNR (CSDE1) binding sites
Analysis of UNR (CSDE1) binding to RNA targets by iCLIP transcriptome-wide mapping.
ORGANISM(S): Homo sapiens 
2016-11-07 | E-MTAB-3818 | biostudies-arrayexpress
TranscriptomicsModified iCLIP sequencing of HEK293 cells with antibody PTBP1
For modified iCLIP experiment, 4SU was used for crosslinking as described in published protocol (citation is bellow) and the RNase conditions were optimised to ensure efficient RNase I-dependent fragmentation. In detail, HEK293T cells were grown on 10 cm 2 dishes, incubated for 8 h with 100 M 4SU an...
ORGANISM(S): Homo sapiens 
2016-11-24 | E-MTAB-5027 | biostudies-arrayexpress
TranscriptomicsAnalysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions
UV cross-linking and immunoprecipitation (CLIP) and individual-nucleotide resolution CLIP (iCLIP) are the most frequently used methods to study protein-RNA interactions in the intact cells and tissues, but their relative advantages or inherent biases have not been evaluated. To benchmark CLIP and iC...
ORGANISM(S): Mus musculus 
2012-07-20 | E-MTAB-1008 | biostudies-arrayexpress
TranscriptomicsThe RNA-binding protein Musashi1 is a central regulator of adhesion pathways in glioblastoma
The conserved RNA-binding protein Musashi1 (MSI1) has emerged as a key oncogenic factor in numerous solid tumors, including glioblastoma. However, its mechanism of action has not yet been established comprehensively. We set out to map its impact on the transcriptome in U251 cells using RNA-seq and i...
ORGANISM(S): Homo sapiens 
2015-06-29 | E-GEOD-68800 | biostudies-arrayexpress
TranscriptomicsCPSF-160 iCLIP
We performed iCLIP of CPSF-160- GFP as CPSF160 was believed to be the main RNA-binding subunit of CPSF. To this end, we used a stable HeLa cell line that expresses GFP-CPSF160 in a doxycycline (Dox)-dependent manner. After GFP-CPSF160 was induced, we irradiated the cells with UV-C (wavelength=254nm)...
ORGANISM(S): Homo sapiens 
2014-10-01 | E-MTAB-2939 | biostudies-arrayexpress
TranscriptomicsTranscriptome-wide mapping of hnRNP C and U2AF65 using iCLIP
iCLIP experiment to assess the binding of the highly abundant nuclear RNA-binding protein hnRNP C and core splicing factor U2AF65 on a genomic scale. To investigate how both proteins compete for binding at a subset of sites, U2AF65 iCLIP experiments were performed from both HNRNPC knockdown and cont...
ORGANISM(S): Homo sapiens 
2013-01-31 | E-MTAB-1371 | biostudies-arrayexpress
TranscriptomicsiCLIP mapping of coilin-RNA interactions in HeLa and P19 cells
Our ChIP resuls suggested that coilin association with U3, snRNA and histone genes might be dependent on coilin-RNA interaction. We used iCLIP of coilin-GFP expressed in HeLa and P19 cell lines at endogenous levels to identify coilin RNA targets and investigate RNA-binding specificity. P19 cells exp...
ORGANISM(S): Homo sapiens 
2014-11-06 | E-GEOD-58448 | biostudies-arrayexpress
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