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Sample GSM870540 Query DataSets for GSM870540
Status Public on Jul 05, 2012
Title MYCN 5
Sample type RNA
 
Channel 1
Source name MYCN+/- tumor cells
Organism Mus musculus
Characteristics tissue: neuroblastoma tumor
genotype: MYCN+/- transgenic
genetic background: 129X1/SvJ
Extracted molecule total RNA
Extraction protocol RNA was extracted from tumours using the miRNeasy Mini kit (Qiagen) according to the manufacturer's instructions.
Label Cy3
Label protocol Samples were labeled and processed using the Agilent Low Input Quick Amp two colour Cy3 (sample) and Cy5 (mouse reference) RNA labeling kit (Stratagene) according to the manufacturer's instructions.
 
Channel 2
Source name Universal Mouse Reference RNA
Organism Mus musculus
Characteristics sample type: Stratagene Universal Mouse Reference (RNA from 11 murine cell lines)
Extracted molecule total RNA
Extraction protocol RNA was extracted from tumours using the miRNeasy Mini kit (Qiagen) according to the manufacturer's instructions.
Label Cy5
Label protocol Samples were labeled and processed using the Agilent Low Input Quick Amp two colour Cy3 (sample) and Cy5 (mouse reference) RNA labeling kit (Stratagene) according to the manufacturer's instructions.
 
 
Hybridization protocol standard Agilent protocol
Scan protocol Slides were scanned on an Agilent C Scanner at 3um using the 20bit setting.
Description Biological replicate 5 of 5. Untreated tumour from MYCN-expressing mice.
Data processing Resulting data were feature extracted using Agilent Feature extraction v10.7.3. Raw data were first normalized by Agilent GeneSpring 11.5.1 software using the default normalization setting and relative expression value compared to the reference control calculated for each probe (threshold raw signals to 1, percentile shift to 75, baseline to the median of all samples). The genes with flags present in at least 100% of the values in any one out of the two groups (ALK^F1174L/MYCN and MYCN) were filtered.
 
Submission date Feb 06, 2012
Last update date Jul 05, 2012
Contact name Teeara Berry
Organization name The Institute of Cancer Research
Department Paediatric Oncology
Lab Neuroblastoma Drug Development Lab
Street address 15 Cotswold Road
City Sutton
State/province Surrey
ZIP/Postal code SM2 5NG
Country United Kingdom
 
Platform ID GPL10787
Series (1)
GSE35560 Transcriptional profiles of transgenic ALK^F1174L/MYCN vs. MYCN tumors

Data table header descriptions
ID_REF
VALUE Agilent GeneSpring 11.5.1 software default normalization log test/reference

Data table
ID_REF VALUE
(+)E1A_r60_1 -0.688
(+)E1A_r60_3 -2.150
(+)E1A_r60_a104 -2.103
(+)E1A_r60_a107 0.953
(+)E1A_r60_a135 0.854
(+)E1A_r60_a20 -0.024
(+)E1A_r60_a22 -3.576
(+)E1A_r60_a97 -2.216
(+)E1A_r60_n11 0.930
(+)E1A_r60_n9 2.496
3xSLv1 -0.051
A_30_P01017425 0.190
A_30_P01017426 -1.498
A_30_P01017427 0.229
A_30_P01017428 1.032
A_30_P01017429 0.041
A_30_P01017430 2.065
A_30_P01017431 -0.092
A_30_P01017432 0.684
A_30_P01017433 1.100

Total number of rows: 55821

Table truncated, full table size 1123 Kbytes.




Supplementary file Size Download File type/resource
GSM870540_252800511679_2_1.txt.gz 20.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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