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| Status |
Public on Apr 16, 2009 |
| Title |
pilocytic astrocytoma 7 |
| Sample type |
genomic |
| |
|
| Source name |
pilocytic astrocytoma
|
| Organism |
Homo sapiens |
| Characteristics |
pathology: pilocytic astrocytoma
site: cerebellum
age: 13 yrs
gender: M
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted from fresh frozen tissue using the QIAamp DNA mini kit (Qiagen, Crawley, UK).
|
| Label |
Biotin
|
| Label protocol |
As per manufacturer (Affymetrix).
|
| |
|
| Hybridization protocol |
DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.
|
| Scan protocol |
The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.
|
| Description |
Hybridized to 250K_Nsp
|
| Data processing |
CHP files generated by Affymetrix GTYPE using the DM algorithm.
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| |
|
| Submission date |
Feb 23, 2009 |
| Last update date |
Apr 15, 2009 |
| Contact name |
Tim Forshew |
| E-mail(s) |
t.forshew@qmul.ac.uk
|
| Phone |
02078822597
|
| Organization name |
Queen Mary's School of Medicine and Dentistry
|
| Department |
Centre for Neuroscience
|
| Street address |
4 Newark Street
|
| City |
London |
| ZIP/Postal code |
E1 2AT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL3718 |
| Series (1) |
| GSE14960 |
Affymetrix SNP array data for low-grade astrocytoma samples |
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| Data table header descriptions |
| ID_REF |
|
| VALUE |
Genotypes: AA, AB, BB, No Call |
| CONFIDENCE |
|
| RAS1 |
Relative allele signal for the data in the first probe group |
| RAS2 |
Relative allele signal for the data in the second probe group |
| P-VALUE AA |
|
| P-VALUE AB |
|
| P-VALUE BB |
|
| P-VALUE NO CALL |
|
| Data table |
| ID_REF |
VALUE |
CONFIDENCE |
RAS1 |
RAS2 |
P-VALUE AA |
P-VALUE AB |
P-VALUE BB |
P-VALUE NO CALL |
| AFFX-5Q-123 |
No Call |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
| AFFX-5Q-456 |
No Call |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
| AFFX-5Q-789 |
No Call |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
| AFFX-5Q-ABC |
No Call |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
| AFFX-barcodeA |
No Call |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
| AFFX-barcodeB |
No Call |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
| AFFX-barcodeC |
No Call |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
| AFFX-barcodeD |
No Call |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
| AFFX-barcodeE |
No Call |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
| AFFX-barcodeF |
No Call |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
| AFFX-barcodeG |
No Call |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
| AFFX-barcodeH |
No Call |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
| AFFX-barcodeI |
No Call |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
| AFFX-barcodeJ |
No Call |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
| AFFX-barcodeK |
No Call |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
| AFFX-barcodeL |
No Call |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
| AFFX-barcodeM |
No Call |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
| AFFX-barcodeN |
No Call |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
| AFFX-barcodeO |
No Call |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
| AFFX-barcodeP |
No Call |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
Total number of rows: 262338
Table truncated, full table size 20540 Kbytes.
| Supplementary file |
Size |
Download |
File type/resource |
| GSM373555.CEL.gz |
23.7 Mb |
(ftp)(http) |
CEL |
| GSM373555.CHP.gz |
517.8 Kb |
(ftp)(http) |
CHP |
| Processed data included within Sample table |
| Processed data provided as supplementary file |
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