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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 01, 2008 |
| Title |
Ludwig Institute/UCSD ENCODE project August 2007 Release |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by genome tiling array
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| Summary |
The readout of genome information is controlled by transcriptional regulatory elements, but a comprehensive view of the combinatorial control by these DNA sequences, which bind regulatory protein and/or the modified histones in regulating gene transcription, is clearly preliminary. We have developed an experimental strategy for comprehensive determination of such functional elements in human DNA. This strategy involves the application of genome-wide location analysis, also known as ChIP-chip, to a panel of well-characterized regulatory proteins and histones with specific modifications, known to generally associate with transcriptional regulatory elements in vivo. Identification of their genomic binding sites will allow us to determine the sequence features in the human genome that carry out transcriptional regulatory function. We have designed and produced DNA microarrays to represent all the non-repetitive sequences in the 30 million basepair ENCODE regions of the human genome to map various types of transcriptional regulatory elements in three model cell types. We have identified promoters by mapping the genomic sequences associated with RNA polymerase II and the general transcription factor TFIID in cells, enhancer elements by mapping the genomic sequences associated with transcriptional co-activators and enhancer-specific chromatin modifications, and insulators by mapping the genomic sequences associated with the insulator binding protein CTCF. The raw microarray results are released periodically prior to publication.
Keywords: ChIP-chip ENCODE
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| Overall design |
ChIP-chip analyses were performed for various transcription factors and chromatin modifications in various cell types. Details to be described in publications.
Ren B, Glass CK, Rosenfeld MG, Webster N, Ching KA, Harp L, Ye Z, Stuart RK, Calcar SV, Kim TH, Hawkins RD, Hon G, Barrera LO, Luna R, Wang K
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| Web link |
http://www.ncbi.nlm.nih.gov/projects/geo/info/ENCODE.html
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| Contributor(s) |
Ren B, Glass CK, Rosenfeld MG, Webster N, Ching KA, Harp L, Ye Z, Stuart RK, Calcar SV, Kim TH, Hawkins RD, Barrera LO, Luna R, Wang K |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Aug 27, 2007 |
| Last update date |
Mar 17, 2012 |
| Contact name |
Bing Ren |
| E-mail(s) |
biren@ucsd.edu
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| Organization name |
Ludwig Institute for Cancer Research
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| Department |
Department of Cellular and Molecular Medicine
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| Lab |
Laboratory of Gene Regulation
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| Street address |
9500 Gilman Drive
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| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093-0653 |
| Country |
USA |
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| Platforms (1) |
| GPL1454 |
RenLab ENCODE PCR tiling array |
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| Samples (15)
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| GSM225134 |
p300(C-20) HeLa Chromatin RenLab ENCODE PCR tiling array replicate 1 ENC1708_p300_HeLa_1.gpr |
| GSM225135 |
p300(C-20) HeLa Chromatin RenLab ENCODE PCR tiling array replicate 2 ENC1725_p300_HeLa_7_repeat2.gpr |
| GSM225136 |
p300(C-20) HeLa Chromatin RenLab ENCODE PCR tiling array replicate 3 ENC2044_p300_HeLa_1_repeat2.gpr |
| GSM225137 |
YY1 HeLa Chromatin RenLab ENCODE PCR tiling array replicate 1 ENC832_hela_yy1_121704_680_600.gpr |
| GSM225138 |
YY1 HeLa Chromatin RenLab ENCODE PCR tiling array replicate 2 ENC839_hela_yy1_121904_660_600.gpr |
| GSM225139 |
YY1 HeLa Chromatin RenLab ENCODE PCR tiling array replicate 3 ENC840_hela_yy1_121904_660_600.gpr |
| GSM225140 |
YY1 HeLa Chromatin RenLab ENCODE PCR tiling array replicate 4 ENC842_hela_yy1_122204_660_600.gpr |
| GSM225141 |
YY1 HeLa Chromatin RenLab ENCODE PCR tiling array replicate 5 ENC843_hela_yy1_122204_670_600.gpr |
| GSM225146 |
H4Ac K562 Chromatin RenLab ENCODE PCR tiling array replicate 1 ENC2031_H4Ac_K562_C.gpr |
| GSM225147 |
H4Ac K562 Chromatin RenLab ENCODE PCR tiling array replicate 2 ENC2062_H4Ac_K562_B.gpr |
| GSM225148 |
H4Ac K562 Chromatin RenLab ENCODE PCR tiling array replicate 3 ENC2085_H4Ac_K562_A.gpr |
| GSM225149 |
CTCF IMR90 Chromatin RenLab ENCODE PCR tiling array replicate 1 2007-07-20_LK_ENC1357751_CTCF_IMR90_Cy3-710_Cy5-750.gpr |
| GSM225150 |
CTCF IMR90 Chromatin RenLab ENCODE PCR tiling array replicate 2 2007-08-08_LK_ENC13577673_CTCF_IMR90_Cy3-700_Cy5-800.gpr |
| GSM225151 |
CTCF IMR90 Chromatin RenLab ENCODE PCR tiling array replicate 3 2007-08-08_LK_ENC13577886_CTCF_IMR90_Cy3-750_Cy5-800.gpr |
| GSM225152 |
CTCF IMR90 Chromatin RenLab ENCODE PCR tiling array replicate 4 2007-08-08_LK_ENC13577909_CTCF_IMR90_Cy3-750_Cy5-800.gpr |
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| Relations |
| BioProject |
PRJNA102267 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE8887_RAW.tar |
34.8 Mb |
(http)(custom) |
TAR (of GPR) |
| Processed data included within Sample table |
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