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Sample GSM1076200 Query DataSets for GSM1076200
Status Public on Jul 09, 2013
Title B1-19
Sample type RNA
 
Source name Medulloblastoma, Ptch+/- model
Organism Mus musculus
Characteristics strain: CBA/J
genotype: Ptch+/-;T2Onc+/-
age(weeks): 28
organ: Brain, Cerebellum
disease state: Tumour
insert in network gene: n/a
insert in nfia: n/a
Extracted molecule total RNA
Extraction protocol RNA was extracted using the Qiagen RNeasy Lipid Tissue mini kit (Qiagen, Hilden, Germany) according to manufacturer's instructions.Quality control was performed using an Agilent 2100 Bioanalyser.
Label biotin
Label protocol Approximately 200ng of each RNA was amplified and Biotinylated using the Illumina TotalPrep RNA amplification kit (Applied Biosystems, Foster City, CA. USA), with the size distribution of cRNA being assessed using the Agilent Bioanalyser.
 
Hybridization protocol Approximately 750ng of each cRNA was hybridised using the standard Illumina hybridization protocol
Scan protocol Standard Illumina scanning protocol
Description Control Group 2 - Tumour which developed in Ptch+/- predisposition background with no transposition
Data processing Standard Illumina processing followed by RMA quantile normalisation.
 
Submission date Feb 01, 2013
Last update date Jul 09, 2013
Contact name Michael Stewart Jackson
E-mail(s) m.s.jackson@ncl.ac.uk
Phone +44 191 241 8677
Organization name Newcastle University
Department Institute of Genetic Medicine
Street address Central Parkway
City Newcastle upon Tyne
ZIP/Postal code NE1 3BZ
Country United Kingdom
 
Platform ID GPL6885
Series (1)
GSE43994 Identification of genes involved in SHH subgroup medulloblastoma using murine whole-body Sleeping Beauty insertional mutagenesis

Data table header descriptions
ID_REF
VALUE log2 quantile normalized
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_2896528 10.26565594 0
ILMN_2721178 8.46979558 0
ILMN_3033922 8.110953467 0
ILMN_3092673 10.11599181 0
ILMN_2816356 6.925266324 0
ILMN_2808939 8.287506935 0
ILMN_2634564 7.958473318 0
ILMN_2737647 6.687729813 0.1716792
ILMN_2734484 7.433130332 0
ILMN_2952292 6.89837125 0
ILMN_2699078 6.681956114 0.2067669
ILMN_1213681 7.353969812 0
ILMN_2735413 6.619181747 0.7117795
ILMN_2735415 6.669417216 0.3182957
ILMN_2891688 8.141898019 0
ILMN_2637698 8.945516776 0
ILMN_2674228 7.696989766 0
ILMN_2601546 6.63558734 0.5952381
ILMN_1230831 6.652442266 0.4611529
ILMN_2848071 6.793867673 0

Total number of rows: 25697

Table truncated, full table size 788 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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