Research
Analysis of the mouse embryonic stem cell regulatory networks obtained by ChIP-chip and ChIP-PET
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* Corresponding authors: David K Gifford dkg@mit.edu - Rudolf Jaenisch jaenisch@wi.mit.edu
- † Equal contributors
1 Department of Biology, Massachusetts Institute of Technology, Ames Street, Cambridge, MA 02139, USA
2 Whitehead Institute for Biomedical Research, Cambridge Center, Cambridge, MA 02142, USA
3 Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Vassar Street, Cambridge, MA 02139, USA
Genome Biology 2008, 9:R126 doi:10.1186/gb-2008-9-8-r126
Published: 13 August 2008Additional files
Additional data file 1:
Immunoprecipitate versus whole cell extract enrichment in three biological replicate samples is shown for (a) the two-slide set promoter arrays and (b) chromosome 19 arrays.
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Additional data file 2:
Immunoprecipitate versus whole cell extract enrichment in three biological replicate samples is shown for (a) the two-slide set promoter arrays and (b) chromosome 19 arrays.
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Additional data file 3:
Plots indicate the number of ChIP-chip targets recovered (y-axis) when different percentages of ChIP-PET sequences are randomly sampled. Error bars represent the standard deviation.
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Additional data file 4:
The binding of NANOG at the REST gene promoter is identified by both ChIP-chip and ChIP-PET. However, the binding event detected in the ChIP-PET experiment is not within the region used for combining the expression profiling information (± 4 kb around the transcription start site). Consequently, the changed expression of REST after NANOG knockdown is associated with NANOG binding detected by ChIP-chip only and not ChIP-PET.
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Additional data file 5:
Protein coding gene promoter regions that were bound by OCT4 and NANOG in ChIP-chip and ChIP-PET experiments.
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Additional data file 6:
Micro-RNA gene promoter regions that were bound by OCT4 and NANOG in ChIP-chip experiments.
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Additional data file 7:
GO analyses for OCT4 and NANOG bound regions in ChIP-chip and ChIP-PET experiments.
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Additional data file 8:
Chromosome 19 regions that are bound by OCT4 and NANOG in ChIP-chip experiments.
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Additional data file 9:
OCT4 ChIP-chip and ChIP-PET recovery curve values for promoter and chromosome array experiments.
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Additional data file 10:
NANOG ChIP-chip and ChIP-PET recovery curve values for promoter and chromosome array experiments.
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Additional data file 11:
OCT4 bound genes that are differentially expressed upon Oct4 knockdown.
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Additional data file 12:
NANOG bound genes that are differentially expressed upon Nanog knockdown.
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Additional data file 13:
Gene-specific PCR binding data for OCT4 and NANOG.
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Additional data file 14:
Sequence depth analysis for OCT4 and NANOG bound regions on chromosome 19.
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Additional data file 15:
Supplementary information on additional methods and materials and results.
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Additional data file 16:
Summary of promoter array ChIP-chip binding data and corresponding ChIP-PET binding data for OCT4 and NANOG.
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Additional data file 17:
Summary of chromosome array ChIP-chip binding data and corresponding ChIP-PET binding data for OCT4 and NANOG.
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