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Sample GSM499964 Query DataSets for GSM499964
Status Public on Jan 22, 2010
Title Patient P4011_rep2
Sample type RNA
 
Channel 1
Source name LCM-captured brain tumor cells, pediatric
Organism Homo sapiens
Characteristics tissue: type IV glioblastoma
pediatric patient: yes
angiogenesis score: pos
p53 score: na
egfr score: -
ras score: +
survival: no
sex: M
primary tumor?: no
Treatment protocol All biological samples were flash-frozen in liquid nitrogen immediately after surgery. Interesting cells were isolated by Laser Capture Microdissection (LCM).
Extracted molecule total RNA
Extraction protocol After LCM, RNA was extracted with PicoPure RNA Isolation (Molecular Devices, Sunnyvale, CA). Then, 30-40 ng were amplified with the RiboAmp RNA Amplification kit (Molecular Devices, Sunnyvale, CA).
Label Cy5
Label protocol 5 µg of aRNA were reverse transcribed with Superscript II RT (Invitrogen, Carlsbad, CA). cDNA were direct-labelled with Cy3dCTP or Cy5dCTP (GE Healtcare, Baie d'Urfe, QC) and purified using the QIAquick PCR Purification kit (Qiagen, Mississauga, ON). Labelled probes were then dried to get a final volume of 3 to 6 µl.
 
Channel 2
Source name Pooled normal brain, pediatric
Organism Homo sapiens
Characteristics tissue: brain
pediatric patient: yes
angiogenesis score: na
p53 score: na
egfr score: na
ras score: na
survival: na
sex: na
primary tumor?: na
Treatment protocol All biological samples were flash-frozen in liquid nitrogen immediately after surgery. Interesting cells were isolated by Laser Capture Microdissection (LCM).
Extracted molecule total RNA
Extraction protocol After LCM, RNA was extracted with PicoPure RNA Isolation (Molecular Devices, Sunnyvale, CA). Then, 30-40 ng were amplified with the RiboAmp RNA Amplification kit (Molecular Devices, Sunnyvale, CA).
Label Cy3
Label protocol 5 µg of aRNA were reverse transcribed with Superscript II RT (Invitrogen, Carlsbad, CA). cDNA were direct-labelled with Cy3dCTP or Cy5dCTP (GE Healtcare, Baie d'Urfe, QC) and purified using the QIAquick PCR Purification kit (Qiagen, Mississauga, ON). Labelled probes were then dried to get a final volume of 3 to 6 µl.
 
 
Hybridization protocol Sample and control probes were mixed together in a final volume of 90 µl of hybridisation buffer : DIG Easy Hyb (Roche, Laval, QC) + 0.5 µg/µl salmon sperm (Invitrogen, Carlsbad, CA) + 0.5 µg/µl yeast tRNA (Invitrogen, Carlsbad, CA). Mix was heated at 95ºC for 5 min and put on the arrray. After adding a coverslip, arrays were incubated in a hybridisation chamber at 37ºC for 16h. Arrays were then washed three times in SSC0.1X, SDS 0.1%, four times in SSC 0.1X and centrifuge to dry them.
Scan protocol Slides were scanned in a ScanArray Lite (GSI Luminomics, Billerica, MA).
Description 12565004
Data processing Spot intensity was quantified using QuantArray (GSI Luminomics, Billerica, MA). The Lowess scatter-smoothing normalization was performed in the GeneSpring 7.0 software package (Agilent, Santa Clara, CA).
 
Submission date Jan 22, 2010
Last update date Jan 22, 2010
Contact name Andre Nantel
E-mail(s) andre.nantel@nrc-cnrc.gc.ca
Phone 514-496-6370
Fax 514-496-9127
Organization name National Research Council of Canada
Department Biotechnology Research Institute
Street address 6100 Royalmount
City Montreal
State/province QC
ZIP/Postal code H4P 2R2
Country Canada
 
Platform ID GPL9966
Series (1)
GSE20018 Molecular profiling identifies prognostic subgroups of pediatric glioblastoma and shows increased tumor YB-1 expression

Data table header descriptions
ID_REF
VALUE Natural Log of Lowess-normalized fluorescence ratios representing tumor/normal brain

Data table
ID_REF VALUE
AA001103 -0.48062164
AA001104 -0.5176763
AA001107 0.006607707
AA001138 -1.4060426
AA001139 0.71231323
AA001144 0.041211095
AA001145 -0.3190009
AA001216 0.5782317
AA001227 -0.35728925
AA001250 -0.094031595
AA001256 0.3393278
AA001278 -0.30205235
AA001291 -0.37765554
AA001304 -0.13250427
AA001306 0.24365798
AA001311 -0.4290194
AA001319 -0.16539647
AA001321 0.028318925
AA001324 2.8192852
AA001326 -0.00760237

Total number of rows: 15067

Table truncated, full table size 278 Kbytes.




Supplementary file Size Download File type/resource
GSM499964.txt.gz 1.5 Mb (ftp)(http) TXT
Processed data included within Sample table

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