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| Status |
Public on Dec 08, 2010 |
| Title |
Bubble-chip analysis of human origin distributions demonstrates on a genomic scale significant clustering into zones and significant association with transcription |
| Organism |
Homo sapiens |
| Experiment type |
Other
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| Summary |
We have constructed and validated human origin libraries to near homogeneity from early-S- and log-phase HeLa cells, as well as from log-phase GM06990, a karyotypically-normal lymphoblastoid cell line. Hybridization to Affymetrix ENCODE tiling arrays suggests that the three origin libraries correspond to 15.3, 16.4, and 21.8% of the human genome, respectively. Approximately half the origin fragments cluster into zones, and their signals are generally higher than those of isolated fragments. Interestingly, initiation events are distributed about equally between genic and intergenic template sequences. Furthermore, while only 13.2% and 14.0% of genes within the ENCODE regions are transcribed in HeLa and GM06990 cells, 54.5% and 25.6% of zonal origin fragments overlap transcribed genes, most with activating chromatin marks in their promoters. Comparison between early-S- and log-phase HeLa origin maps shows that cell synchronization activates a significant number of inchoate origins. In addition, HeLa and GM06990 cells activate remarkably different origin populations.
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| Overall design |
5 samples, 5 controls; no replicates or reference samples included
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| Contributor(s) |
Mesner LD, Valsakumar V, Karnani N, Dutta A, Hamlin JL, Bekiranov S |
| Citation(s) |
21173031 |
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| Submission date |
Mar 29, 2010 |
| Last update date |
Mar 22, 2012 |
| Contact name |
Stefan Bekiranov |
| E-mail(s) |
sb3de@virginia.ed
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| Organization name |
University of Virginia
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| Department |
Biochemistry & Molecular Genetics
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| Lab |
Bekiranov
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| Street address |
1340 Jefferson Park Avenue
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| City |
Charlottesville |
| State/province |
VA |
| ZIP/Postal code |
22908 |
| Country |
USA |
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| Platforms (1) |
| GPL3725 |
Affymetrix ENCODE Tiling Array - SENSE - NCBI build 35 |
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| Samples (7)
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| Relations |
| BioProject |
PRJNA126683 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE21110_ENCODE_libNCBIv35.bpmap.gz |
12.5 Mb |
(ftp)(http) |
BPMAP |
| GSE21110_ENCODE_libNCBIv35.bpmap.txt.gz |
13.6 Mb |
(ftp)(http) |
TXT |
| GSE21110_RAW.tar |
187.3 Mb |
(http)(custom) |
TAR (of BAR, CEL, SGR) |
| Processed data provided as supplementary file |
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