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TranscriptomicsCTCF binding polarity determines chromatin looping [4C]
CCCTC-binding factor (CTCF) is an architectural protein involved in the three-dimensional organization of chromatin. In this study, we systematically assayed the 3D genomic contact profiles of hundreds of CTCF binding sites in multiple tissues with high-resolution 4C-seq. We find both developmentall...
ORGANISM(S): Mus musculus 
2015-10-29 | E-GEOD-72539 | biostudies-arrayexpress
TranscriptomicsSmall RNA expression and strain specificity in the rat
Background Digital gene expression (DGE) profiling has become an established tool to study RNA expression. Here, we provide an in-depth analysis of small RNA DGE profiles from two different rat strains (BN-Lx and SHR) from six different rat tissues (spleen, liver, brain, testis, heart, kidney). We ...
ORGANISM(S): Rattus norvegicus 
2010-02-17 | E-GEOD-19054 | biostudies-arrayexpress
TranscriptomicsLimitations and possibilities of small RNA digital gene expression profiling: library preparation comparison (SOLiD)
Analysis of RNA samples by massive parallel sequencing holds the promise to assay gene expression in both a quantitative and qualitative fashion and therefore allows for digital gene expression (DGE) profiling. We assessed the effect of different experimental approaches by generating small RNA libra...
ORGANISM(S): Rattus norvegicus 
2009-07-28 | E-GEOD-16370 | biostudies-arrayexpress
TranscriptomicsLimitations and possibilities of small RNA digital gene expression profiling
Analysis of RNA samples by massive parallel sequencing holds the promise to assay gene expression in both a quantitative and qualitative fashion and therefore allows for digital gene expression (DGE) profiling. We assessed the effect of different experimental approaches by generating small RNA libra...
ORGANISM(S): Rattus norvegicus 
2009-07-28 | E-GEOD-16374 | biostudies-arrayexpress
TranscriptomicsLimitations and possibilities of small RNA digital gene expression profiling: library preparation comparison (454)
Analysis of RNA samples by massive parallel sequencing holds the promise to assay gene expression in both a quantitative and qualitative fashion and therefore allows for digital gene expression (DGE) profiling. We assessed the effect of different experimental approaches by generating small RNA libra...
ORGANISM(S): Rattus norvegicus 
2009-07-28 | E-GEOD-16369 | biostudies-arrayexpress
TranscriptomicsLimitations and possibilities of small RNA digital gene expression profiling: spleen and liver comparison (SOLiD)
Analysis of RNA samples by massive parallel sequencing holds the promise to assay gene expression in both a quantitative and qualitative fashion and therefore allows for digital gene expression (DGE) profiling. We assessed the effect of different experimental approaches by generating small RNA libra...
ORGANISM(S): Rattus norvegicus 
2009-07-28 | E-GEOD-16371 | biostudies-arrayexpress
TranscriptomicsLimitations and possibilities of small RNA digital gene expression profiling: synthetic miRNAs replicates (SOLiD)
Analysis of RNA samples by massive parallel sequencing holds the promise to assay gene expression in both a quantitative and qualitative fashion and therefore allows for digital gene expression (DGE) profiling. We assessed the effect of different experimental approaches by generating small RNA libra...
ORGANISM(S): Homo sapiens 
2009-07-28 | E-GEOD-16372 | biostudies-arrayexpress
TranscriptomicsLimitations and possibilities of small RNA digital gene expression profiling: synthetic miRNA replicates (Illumina)
Analysis of RNA samples by massive parallel sequencing holds the promise to assay gene expression in both a quantitative and qualitative fashion and therefore allows for digital gene expression (DGE) profiling. We assessed the effect of different experimental approaches by generating small RNA libra...
ORGANISM(S): Homo sapiens 
2009-07-28 | E-GEOD-16373 | biostudies-arrayexpress
TranscriptomicsVariegated gene expression caused by cell-specific long-range DNA interactions
Mammalian genomes contain numerous DNA elements with potential transcription regulatory function but unknown target genes. We used transgenic, gain-of-function mice with an ectopic copy of the beta-globin locus control region (LCR) to better understand how regulatory elements dynamically search the ...
ORGANISM(S): Mus musculus 
2011-06-15 | E-GEOD-24614 | biostudies-arrayexpress
TranscriptomicsGlobal chromatin domain organization of the Drosophila genome
In eukaryotes, neighboring genes can be packaged together in specific chromatin structures that ensure their coordinated expression. Examples of such multi-gene chromatin domains are well-documented, but a global view of the chromatin organization of eukaryotic genomes is lacking. To systematically ...
ORGANISM(S): Drosophila melanogaster 
2008-04-07 | E-GEOD-10219 | biostudies-arrayexpress
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