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TranscriptomicsRNAcompete: a method for rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins
Metazoan genomes encode hundreds of RNA binding proteins (RBPs) but relatively few have well-defined RNA-binding preferences. Current techniques for determining RNA targets, including those involving in vitro selection and RNA co-immunoprecipitation, require significant time and labour investment. H...
ORGANISM(S): synthetic construct 
2010-05-18 | E-GEOD-15769 | biostudies-arrayexpress
TranscriptomicsVariation in homeodomain DNA-binding revealed by high-resolution analysis of sequence preferences
Most homeodomains are unique within a genome, yet many are highly conserved across vast evolutionary distances, implying strong selection on their precise DNA-binding specificities. We determined the binding preferences of the majority (168) of mouse homeodomains to all possible 8-base sequences, re...
ORGANISM(S): Mus musculus 
2010-06-26 | E-GEOD-11239 | biostudies-arrayexpress
GenomicsAn Alternative Splicing Switch Regulates Embryonic Stem Cell Pluripotency and Reprogramming [ChIP-Seq]
Alternative splicing (AS) is a key process underlying the expansion of proteomic diversity and the regulation of gene expression. However, the contribution of AS to the control of embryonic stem cell (ESC) pluripotency is not well understood. Here, we identify an evolutionarily conserved ESC-specifi...
ORGANISM(S): Homo sapiens 
2011-09-14 | E-GEOD-31006 | biostudies-arrayexpress
TranscriptomicsAn Alternative Splicing Switch Regulates Embryonic Stem Cell Pluripotency and Reprogramming [protein binding microarray]
Alternative splicing (AS) is a key process underlying the expansion of proteomic diversity and the regulation of gene expression. However, the contribution of AS to the control of embryonic stem cell (ESC) pluripotency is not well understood. Here, we identify an evolutionarily conserved ESC-specifi...
ORGANISM(S): Homo sapiens 
2011-09-14 | E-GEOD-31007 | biostudies-arrayexpress
TranscriptomicsAn Alternative Splicing Switch Regulates Embryonic Stem Cell Pluripotency and Reprogramming [RNA-Seq]
Alternative splicing (AS) is a key process underlying the expansion of proteomic diversity and the regulation of gene expression. However, the contribution of AS to the control of embryonic stem cell (ESC) pluripotency is not well understood. Here, we identify an evolutionarily conserved ESC-specifi...
ORGANISM(S): Homo sapiens 
2011-09-14 | E-GEOD-30995 | biostudies-arrayexpress
TranscriptomicsAn Alternative Splicing Switch Regulates Embryonic Stem Cell Pluripotency and Reprogramming [AS microarray]
Alternative splicing (AS) is a key process underlying the expansion of proteomic diversity and the regulation of gene expression. However, the contribution of AS to the control of embryonic stem cell (ESC) pluripotency is not well understood. Here, we identify an evolutionarily conserved ESC-specifi...
ORGANISM(S): Homo sapiens 
2011-09-14 | E-GEOD-31948 | biostudies-arrayexpress
TranscriptomicsA library of yeast transcription factor motifs
The sequence specificity of DNA-binding proteins is the primary mechanism by which the cell recognizes genomic features. Here, we describe systematic determination of yeast transcription factor DNA-binding specificities. We obtained binding specificities for 112 DNA-binding proteins representing 19 ...
ORGANISM(S): Saccharomyces cerevisiae 
2008-12-26 | E-GEOD-12349 | biostudies-arrayexpress
TranscriptomicsDIP-chip from Cbf1, Leu3, Pho2, Pho4, Rap1, Rox1, and Swi5
DNA Immunoprecipitation was performed using purified, naked, genomic DNA and purified recombinant DNA binding domains for S. cerevisiae transcription factors (Cbf1, Leu3, Pho2, Pho4, Rap1, Rox1, and Swi5) and then competitively hybridized against input DNA on NimbleGen 385k whole-genome, 32bp, tilin...
ORGANISM(S): Saccharomyces cerevisiae 
2010-05-15 | E-GEOD-13751 | biostudies-arrayexpress
TranscriptomicsEvaluation of methods for modeling transcription factor sequence specificity
Genomic analyses often involve scanning for potential transcription-factor (TF) binding sites using models of the sequence specificity of DNA binding proteins. Many approaches have been developed to model and learn a protein’s binding specificity by representing sequence motifs, including the gaps a...
ORGANISM(S): synthetic construct 
2012-12-13 | E-GEOD-42864 | biostudies-arrayexpress
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