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Series GSE13774 Query DataSets for GSE13774
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
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.
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.
Contributor(s) Linnemann AK, Platts AE, Krawetz SA
Citation(s) 19017725
Submission date Dec 01, 2008
Last update date Jan 18, 2013
Contact name Stephen A Krawetz
Organization name Wayne State University
Street address 275 East Hancock, CS Mott Center
City Detroit
State/province MI
ZIP/Postal code 48207
Country USA
Platforms (2)
GPL5820 NimbleGen Homo sapiens HG18 Whole Genome CGH Tiling Set (7 of 8)
GPL6104 Illumina humanRef-8 v2.0 expression beadchip
Samples (6)
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)
BioProject PRJNA110783

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE13774_RAW.tar 76.7 Mb (http)(custom) TAR (of PAIR, TXT)
Processed data included within Sample table

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