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Status |
Public on Feb 27, 2009 |
Title |
Nuclear scaffold and matrix attachment of HeLa chromatin |
Organism |
Homo sapiens |
Experiment type |
Genome variation profiling by genome tiling array Expression profiling by array
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Summary |
The nuclear scaffold/matrix provides an anchor for higher order genome structure that has both structural and functional implications. Different extraction protocols, i.e., utilizing either 25 mM LIS or 2 M NaCl, isolate somewhat different protein constituents of either the nuclear scaffold or nuclear matrix respectively. We have mapped, by array CGH, the locations of attachment to each of these residual protein bodies relative to non-attached DNA along the entire length of human chromosomes 14, 15, 16, 17 and 18 in HeLa cells.
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Overall design |
LIS or 2 M NaCl solutions followed by restriction digestion with EcoR1 facilitates the separation from scaffold/matrix bound DNA from non bound DNA. Genomic CGH arrays were used to map the relative differences between attached (scaffold/matrix) and non-attached (loop) portions of HeLa DNA. The expression profile of the HeLa cells used for aCGH analysis was also determined.
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Contributor(s) |
Linnemann AK, Platts AE, Krawetz SA |
Citation(s) |
19017725 |
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Submission date |
Dec 01, 2008 |
Last update date |
Jan 18, 2013 |
Contact name |
Stephen A Krawetz |
E-mail(s) |
steve@compbio.med.wayne.edu
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Organization name |
Wayne State University
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Street address |
275 East Hancock, CS Mott Center
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City |
Detroit |
State/province |
MI |
ZIP/Postal code |
48207 |
Country |
USA |
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Platforms (2) |
GPL5820 |
NimbleGen Homo sapiens HG18 Whole Genome CGH Tiling Set (7 of 8) |
GPL6104 |
Illumina humanRef-8 v2.0 expression beadchip |
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Samples (6)
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GSM346693 |
Nuclear scaffold and matrix attachment of HeLa chromatin (NaCl_1) |
GSM346696 |
Nuclear scaffold and matrix attachment of HeLa chromatin (NaCl_2) |
GSM346699 |
Nuclear scaffold and matrix attachment of HeLa chromatin (LIS_1) |
GSM346701 |
Nuclear scaffold and matrix attachment of HeLa chromatin (LIS_2) |
GSM444700 |
Global expression profile of HeLa S3 cells, replicate #1 |
GSM444701 |
Global expression profile of HeLa S3 cells, replicate #2 |
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Relations |
BioProject |
PRJNA110783 |