An Integrated and Comparative Encyclopedia of DNA Elements in the Mouse Genome [Stanford]

By (Secondary Ownership. The experiment uses only third-party data.)

Adapted from GEO:

This experiment consists a reanalysis of (a) probable binding sites of the specified transcription factors (TFs) and (b) probable locations of the specified histone modifications in the given cell types as determined by chromatin immunoprecipitation followed by high throughput sequencing (ChIP-seq) in Stanford university. The input signal represents the control condition where immunoprecipitation with non-specific immunoglobulin was performed in the same cell type.

-Overall design-
Cells were grown according to the approved ENCODE cell culture protocols ( For details on the chromatin immunoprecipitation protocol used, see Euskirchen et. al., (2007), Rozowsky et. al. (2009) and Auerbach et. al. (2009).
histone modifications ENCODE Project polymerase ChIP-seq transcription factors
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Illumina Genome Analyzer, Illumina Genome Analyzer II

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Input Data

Sample Groups and Experimental Factors

Genome Snapshots

'Genome snapshots' are assorted genomic regions that the creators of this experiment considered of particular interest.

Myc Locus (MEL)

E2F4 Locus (CH12)

Myc Locus (MEL)

Nanog Locus (ES)

Main Experimental Results

This is a selection of main results from the data analysis in this experiment. All intermediate results and more data are available from the workflow designer.

Other data generated in this experiment:

Typical analysis workflows my generate dozens or even hundreds of outputs. To condense the amount of information into more easily digestible portions, GeneProf will, by default, only display the experiments input data (here: input data) and a selection of the most important outputs (here: main results). You can drill down into the details of the analysis via the workflow designer or you can display other intermediate outputs here.

Analysis Workflow

This is a schematic representation of the analysis workflow used in this experiment. For more details (parameters, etc.) use the fully-featured workflow designer.
Colours represent types of data (sequences, genomic regions, features, references and files.
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