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Series GSE7230 Query DataSets for GSE7230
Status Public on Mar 10, 2007
Title Genome-wide assessment of DNA aberrations in human neuroblastoma primary tumors using BAC array
Organism Homo sapiens
Experiment type Genome variation profiling by genome tiling array
Summary DNA signature patterns embed important prognostic information in diagnostic neuroblastoma samples, and can identify candidate cancer-related genes.
Keywords: aCGH
 
Overall design Measure DNA copy number alterations in a carefully annotated and representative set of 82 neuroblastoma tumors obtained at diagnosis on a customized high-resolution BAC array-based aCGH platform supplemented with additional clones at tiling path density across 1p36, 2p24, 3p21-22, 11q14-24, and 16p12-13, and integrate these data with genome-wide RNA expression data from the same tumors.
 
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Submission date Mar 09, 2007
Last update date Mar 16, 2012
Contact name Jayanti Jagannathan
E-mail(s) [email protected]
Phone 2674262286
Organization name Childrens Hospital of Philadelphia
Department Oncology
Street address 34th & Civic center blvd
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
 
Platforms (1)
GPL4894 Penn/CHOP Homo sapiens 4.5K (BAC array for studying Neuroblastoma)
Samples (82)
GSM174386 11 (4.5K BAC array)
GSM174387 1043 (4.5K BAC array)
GSM174388 1012 (4.5K BAC array)
Relations
BioProject PRJNA97941

Gains_and_Losses header descriptions
ID Matches the Title in GEO Sample records; this is the CHOP identifier.
Chr chromosome
Start Start genomic coordinate based on Build 35.
Stop Stop genomic coordinate based on Build 35.
Aberration 1=Gain, -1 = Loss

Data table
ID Chr Start Stop Aberration
11 2 1 243018229 1
11 3 1 199505740 -1
11 4 1 191411218 -1
11 7 1 158628139 1
11 10 1 135413628 -1
11 13 1 114142980 -1
11 14 1 41410883 -1
11 14 52884096 104788120 -1
11 15 1 100338915 -1
11 16 1 88827254 -1
11 17 1 78774742 1
11 18 6067013 7614693 -1
11 19 1 63811651 -1
15 3 1 199505740 -1
15 4 1 191411218 -1
15 7 1 158628139 1
15 10 1 135413628 -1
15 14 1 103175842 -1
15 17 1 78774742 1
15 19 1 63811651 -1

Total number of rows: 1014

Table truncated, full table size 24 Kbytes.




Amplifications header descriptions
ID Matches the Title in GEO Sample records; this is the CHOP identifier.
Chr chromosome
Start Start genomic coordinate based on Build 35 (Kb); + = Single-BAC amplification, coordinates of the BAC in bp.
Stop Stop genomic coordinate based on Build 35 (Kb); + = Single-BAC amplification, coordinates of the BAC in bp.
Log2 Segment Mean average Log2 ratio across the region.

Data table
ID Chr Start Stop Log2 Segment Mean
241 2 15855 16028 3.8475
260 2 15855 16028 2.3277
433 2 16028 17096 3.8374
493 2 10004 13310 1.9847
493 2 13516 14167 1.1425
493 2 14413 15580 2.3989
493 2 15855 16796 3.4511
969 2 15103 16028 4.6761
1009 2 15580 16796 4.7560
1043 2 15580 16028 4.6691
1066 2 15855 16028 3.9921
1068 2 16028 16565 1.5209
1068 2 28547 34156 1.2109
1068 2 156721 159363 1.2590
1068 2 228201 230026 1.0067
1068 2 231003 231003 1.3920
1109 2 15103 16028 4.1512
1129 2 15103 16028 4.0839
1243 2 10491 11918 2.9943
1243 2 14413 16028 3.1720

Total number of rows: 28

Table truncated, full table size <1 Kbytes.




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
GSE7230_RAW.tar 159.1 Mb (http)(custom) TAR (of GPR)

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