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TranscriptomicsWild type vs. Nova2 KO mouse P10 cortex RNA
To assess the requirement of Nova2 for alternative processing of RNA in mouse brain. Protein-RNA interactions play critical roles in all aspects of gene expression. Here we develop a genome-wide means of mapping protein-RNA binding sites in vivo, by high throughput sequencing of RNA isolated by cros...
ORGANISM(S): Mus musculus 
2010-06-20 | E-GEOD-12965 | biostudies-arrayexpress
TranscriptomicsWild type vs. Nova2 KO mouse E14.5 cortex RNA
To assess the requirement of Nova2 for alternative processing of RNA in the developping brain. Neuronal migration leads to a highly organized laminar structure in the mammalian brain and its mis-regulation causes lissencephaly, behavioral and cognitive defects. Reelin signaling, mediated in part by ...
ORGANISM(S): Mus musculus 
2010-07-07 | E-GEOD-22758 | biostudies-arrayexpress
Transcriptomicscdr2 siRNA knockdown during passage through mitosis: HeLa cells, Rat1 wild type and c-myc null cells
[Hela cells]: We performed cdr2 knockdown with a pool of 4 cdr2-specific siRNAs to test whether cdr2 may regulate c-myc target genes as cells passage through mitosis. [Rat1a wild type and myc null cells]: We performed cdr2 knockdown using a pool of 4 cdr2-specific siRNAs to test whether cdr2 may r...
ORGANISM(S): Rattus norvegicus 
2010-04-07 | E-GEOD-20037 | biostudies-arrayexpress
TranscriptomicsPtbp2 represses adult-specific splicing to regulate the generation of neuronal precursors in the embryonic brain [HITS-CLIP]
Two polypyrimidine tract RNA-binding proteins (PTBs), one near-ubiquitously expressed (Ptbp1) and another highly tissue-restricted (Ptbp2), regulate RNA in interrelated but incompletely understood ways. Ptbp1, a splicing regulator, is replaced in the brain and differentiated neuronal cell lines by P...
ORGANISM(S): Mus musculus 
2013-05-31 | E-GEOD-47564 | biostudies-arrayexpress
TranscriptomicsWild type vs. Ptbp2 KO mouse E18.5 cortex RNA
To assess the requirement of Ptbp2 for alternative mRNA expression in mouse brain RNA from the cortex of 4 wild type and 4 Ptbp2 KO E18.5 mice. One array per sample (biological replicate), 8 arrays total.
ORGANISM(S): Mus musculus 
2013-05-31 | E-GEOD-47565 | biostudies-arrayexpress
TranscriptomicsWild type vs. Ptbp2 KO mouse embryonic cortex RNA
To assess the requirement of Ptbp2 for alternative processing of RNA in mouse brain RNA from the cortex of 3 wild type and 3 Ptbp2 KO E18.5 mice. One array per biological replicate. Comparative analysis
ORGANISM(S): Mus musculus 
2013-05-31 | E-GEOD-47566 | biostudies-arrayexpress
TranscriptomicsFlag-RBM47 HITS-CLIP in brain metastatic derivatives of MDA-MB-231
Brain metastatic breast cancer cells were subjected to HITS-CLIP to identify the targets of the RNA binding protein RBM47 MDA231-BrM2a is characterized in PMID: 19421193; Related data published together with these data are found in GSE53779 Non-clonal brain metastatic breast cancer cells stably exp...
ORGANISM(S): Homo sapiens 
2014-06-11 | E-GEOD-58380 | biostudies-arrayexpress
TranscriptomicsIdentification of alternatively spliced transcripts in brain metastatic derivatives of MDA-MB-231 breast cancer cells in response to RBM47 expression
Changes in alternative splicing in breast cancer cells expressing control, empty vector or Flag-tagged wild type RBM47 were analyzed using paired-end, 100bp RNAseq. Related data published together with these data are found in GSE53779 Triplicate RNAseq libraries were prepared from non-clonal brain m...
ORGANISM(S): Homo sapiens 
2014-06-11 | E-GEOD-58379 | biostudies-arrayexpress
TranscriptomicsTranscriptome-wide miR-155 binding map reveals widespread non-canonical microRNA targeting [mRNA expression data]
microRNAs (miRNAs) are essential components of gene regulation, but identification of miRNA targets remains a major challenge. Most target prediction and discovery relies on perfect complementarity of the miRNA seed to the 3’ untranslated region (UTR). However, it is unclear to what extent miRNAs ...
ORGANISM(S): Mus musculus 
2012-11-09 | E-GEOD-41241 | biostudies-arrayexpress
TranscriptomicsTranscriptome-wide miR-155 binding map reveals widespread non-canonical microRNA targeting [CLIP-seq data]
microRNAs (miRNAs) are essential components of gene regulation, but identification of miRNA targets remains a major challenge. Most target prediction and discovery relies on perfect complementarity of the miRNA seed to the 3’ untranslated region (UTR). However, it is unclear to what extent miRNAs ...
ORGANISM(S): Mus musculus 
2012-11-09 | E-GEOD-41285 | biostudies-arrayexpress
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