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TranscriptomicsSystematic dissection of regulatory motifs in 2,000 predicted human enhancers using a massively parallel reporter assay
We employ a massively parallel reporter assay (MPRA) to measure the ex vivo activities of hundreds of K562 and HepG2 enhancers with known transcription factor motif instances. For seven selected motifs that correspond to known or predicted activators and repressors in the two cell types, we make dir...
ORGANISM(S): Escherichia coli 
2013-03-15 | E-GEOD-33367 | biostudies-arrayexpress
TranscriptomicsThe Tasmanian devil transcriptome reveals Schwann cell origins of a clonally transmissible cancer (small RNA sequencing)
The Tasmanian devil, a marsupial carnivore, is endangered due to the emergence of a clonally transmissible cancer known as Devil Facial Tumor Disease (DFTD). This fatal cancer is clonally derived and is an allograft transmitted between devils by biting. We performed a large-scale genetic analysis of...
ORGANISM(S): Sarcophilus harrisii 
2010-01-01 | E-GEOD-18352 | biostudies-arrayexpress
TranscriptomicsMapping and analysis of chromatin state dynamics in nine human cell types (gene expression)
Chromatin profiling has emerged as a powerful means for annotating genomic elements and detecting regulatory activity. Here we generate and analyze a compendium of epigenomic maps for nine chromatin marks across nine cell types, in order to systematically characterize cis-regulatory elements, their ...
ORGANISM(S): Homo sapiens 
2011-03-22 | E-GEOD-26312 | biostudies-arrayexpress
GenomicsDiverse patterns of genome-wide DNA targeting by transcriptional regulators in Drosophila melanogaster
Understanding the regulatory genome remains a significant challenge. Annotation of regulatory elements and identification of the transcription factors (TFs) targeting these elements are key steps in understanding how a given cell interprets its genetic blueprint. One goal of the modENCODE (model or...
ORGANISM(S): Drosophila melanogaster 
2013-08-16 | E-GEOD-49899 | biostudies-arrayexpress
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