E-MEXP-2759 - RNAi profiling by array of human Ewings carcinoma cells to down regulate EWS-FLI1

Status
Released on 7 July 2010, last updated on 2 May 2014
Organism
Homo sapiens
Samples (8)
Array (1)
Protocols (7)
Description
We report here the DNA-binding profiles for all human and mouse ETS factors, which we generated using two different methods: a high-throughput microwell-based transcription factor DNA-binding specificity assay, and protein binding microarrays (PBMs). Both approaches reveal that the ETS binding profiles cluster into four distinct classes, and that all ETS factors linked to cancer, ERG, ETV1, ETV4 and FLI1, fall into just one of these classes. We identify amino acid residues that are critical for the differences in specificity between all the classes, and confirm the specificities in vivo using chromatin immunoprecipitation followed by sequencing (ChIP-seq) for a member of each class. To determine whether the ChIP-seq peaks were near genes regulated by the respective ETS-factors, we used RNAi to downregulate EWS-FLI1 in SK-N-MC Ewing's sarcoma cells. The results indicate that even relatively small differences in in vitro binding specificity of a TF contribute to site selectivity in vivo.
Experiment types
transcription profiling by array, cellular modification, co-expression, in vitro
Contact
Citation
Genome-Wide Analysis of ETS Family DNA-Binding in vitro and in vivo.
MIAME
PlatformsProtocolsFactorsProcessedRaw
Files
Investigation descriptionE-MEXP-2759.idf.txt
Sample and data relationshipE-MEXP-2759.sdrf.txt
Raw data (1)E-MEXP-2759.raw.1.zip
Processed data (1)E-MEXP-2759.processed.1.zip
Array designA-AFFY-44.adf.txt
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