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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
Transcriptomicsmonitoring splicing changes in TIA1/TIAL1 double knockdown vs control HeLa cells
Not available
ORGANISM(S): Homo sapiens 
2010-10-26 | E-MTAB-526 | biostudies-arrayexpress
TranscriptomicsTranscriptome conservation of the D. discoideum and D. purpureum developmental programs revealed through RNA-sequencing
Cross species comparison of genomes and transcriptomes is a powerful tool for understanding underlying biological processes, accurate functional classification of genes, and discovery of novel elements. The shift to next-generation sequencing platforms has tremendously accelerated the analysis of ge...
ORGANISM(S): Dictyostelium purpureum 
2010-03-12 | E-GEOD-17637 | biostudies-arrayexpress
Transcriptomics3'-end targeted sequencing of 6 control and 6 TDP-43 KD samples in HEK293
HEK293 FlpIn T-Rex cells were maintained in Dulbeccos Modified Eagle Medium (DMEM) with 10% fetal bovine serum (FBS), supplemented with 3 g/ml blasticidine and 50 g/ml zeocin. For the siRNA-induced knockdown of TDP-43, 20 nM of TDP-43 stealth siRNA was mixed with 10 L of RNAiMAX following the manufa...
ORGANISM(S): Homo sapiens 
2017-05-01 | E-MTAB-4732 | 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
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
TranscriptomicsHuR- dependent regulation of mRNA splicing is essential for the B cell antibody response [RNA-Seq]
Post-transcriptional regulation of mRNA by the RNA binding protein HuR is required in B cells for the germinal centre reaction and for the production of class-switched antibodies in response to T-independent antigens. Transcriptome-wide examination of RNA isoforms, abundance and translation in HuR-d...
ORGANISM(S): Mus musculus 
2015-02-13 | E-GEOD-62129 | biostudies-arrayexpress
TranscriptomicsHuR- dependent regulation of mRNA splicing is essential for the B cell antibody response [Ribo-Seq]
Post-transcriptional regulation of mRNA by the RNA binding protein HuR is required in B cells for the germinal centre reaction and for the production of class-switched antibodies in response to T-independent antigens. Transcriptome-wide examination of RNA isoforms, abundance and translation in HuR-d...
ORGANISM(S): Mus musculus 
2015-02-13 | E-GEOD-62134 | biostudies-arrayexpress
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