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TranscriptomicsEffects of Cardiac Glycosides on RNA Expression in Prostate Cancer LNCaP-abl Cells
Prostate cancer is the most common cancer in men and cardiac glycosides inhibit prostate cancer cell proliferation. In order to investigate the mechanism by which cardiac glycosides inhibit prostate cancer cells, we observed genome-wide RNA expression in prostate cancer LNCaP-abl cells, hormone res...
ORGANISM(S): Homo sapiens 
2012-04-03 | E-GEOD-35126 | biostudies-arrayexpress
TranscriptomicsmRNA expression in iPS cells generated by a synthetic self-replicative RNA
We generated iPS cells with a synthetic self-replicative RNA that expresses four independent reprogramming factors (OCT4, KLF4, SOX2 and either c-MYC or GLIS1). We performed whole genome RNA sequencing (RNA-seq) of iPS cell clones, parental BJ and HUES9 ES cell controls. All iPS cell clones analyze...
ORGANISM(S): Homo sapiens 
2014-04-25 | E-GEOD-38265 | biostudies-arrayexpress
TranscriptomicsSR Proteins Collaborate with 7SK and Promoter-Associated Nascent RNA to Release Paused Polymerase
RNAP II is frequently paused near gene promoters in mammals and its transition to productive elongation requires active recruitment of P-TEFb, a cyclin-dependent kinase for RNAP II and other key transcription elongation factors. A fraction of P-TEFb is sequestered in an inhibitory complex containing...
ORGANISM(S): Mus musculus 
2013-05-09 | E-GEOD-45517 | biostudies-arrayexpress
TranscriptomicsToxic gain of function from mutant FUS protein is crucial to trigger cell autonomous motor neuron loss
FUS is an RNA-binding protein involved in amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Cytoplasmic FUS-containing aggregates are often associated with concomitant loss of nuclear FUS. Whether loss of nuclear FUS function, gain of a cytoplasmic function, or a combination of ...
ORGANISM(S): Mus musculus 
2016-03-14 | E-GEOD-78730 | biostudies-arrayexpress
TranscriptomicsNuclear Matrix Factor hnRNP U/SAF-A Exerts a Global Control of Alternative Splicing by Regulating U2 snRNP Maturation
The nuclear matrix associated hnRNP U/SAF-A protein has been implicated in diverse pathways from transcriptional regulation to telomere length control to X inactivation, but the precise mechanism underlying each of these processes has remained elusive. Here, we report hnRNP U as a regulator of SM...
ORGANISM(S): Homo sapiens 
2012-02-16 | E-GEOD-34491 | biostudies-arrayexpress
TranscriptomicsGenome-wide Analysis Reveals SR Protein Cooperation and Competition in Regulated Splicing
SR proteins are well-characterized RNA binding proteins that promote exon inclusion by binding to exonic splicing enhancers (ESEs). However, it has been unclear whether regulatory rules deduced on model genes apply generally to activities of SR proteins in the cell. Here, we report global analyses o...
ORGANISM(S): Mus musculus 
2013-04-05 | E-GEOD-44591 | biostudies-arrayexpress
TranscriptomicsGenome-wide Expression Assay Comparison Across Frozen and Fixed Postmortem Brain Tissue Samples
Comparison between in vitro transcription- and cDNA-mediated annealing, selection and ligation (DASL)-based assays on brain-specific reference RNA, and postmortem frozen and formalin fixed brain tissue from autistic and control cases. Investigation of data preprocessing techniques for DASL-assayed ...
ORGANISM(S): Homo sapiens 
2012-04-02 | E-GEOD-28475 | biostudies-arrayexpress
TranscriptomicsThe Akt-SRPK-SR axis constitutes a major pathway in transducing EGF signaling to regulate alternative splicing in the nucleus
Pre-mRNA splicing is regulated by developmental and environmental cues, but little is known about how specific signals are transduced in mammalian cells to regulate this critical gene expression step. Here, we report massive reprogramming of alternative splicing in response to EGF signaling. By blo...
ORGANISM(S): Homo sapiens 
2012-08-17 | E-GEOD-37731 | biostudies-arrayexpress
TranscriptomicsPTB CLIP-seq
Recent transcriptome analysis indicates that >90% of human genes undergoes alternative splicing, underscoring the contribution of differential RNA processing to diverse proteomes in higher eukaryotic cells. The polypyrimidine tract binding protein PTB is a well-characterized splicing repressor, but ...
ORGANISM(S): Homo sapiens 
2009-12-24 | E-GEOD-19323 | biostudies-arrayexpress
TranscriptomicsRBFox2 regulates a broad RNA program and is required for genome-wide targeting of polycomb complex
Increasing evidence suggests that diverse RNA binding proteins interact with regulatory RNAs to regulate transcription. RBFox2 is a ubiquitous RNA binding protein with prevalent expression in stem cells, heart, and brain. Here, we report a systematic dissection of the RBFox2-regulated RNA program in...
ORGANISM(S): Mus musculus 
2015-10-22 | E-GEOD-57926 | biostudies-arrayexpress
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