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Sample GSM1023487 Query DataSets for GSM1023487
Status Public on Dec 28, 2012
Title HybA-T4
Sample type RNA
 
Source name mouse neurofibroma
Organism Mus musculus
Characteristics genotype/variation: T-P0CreB; Nf1 flox/flox
tissue: Mouse neurofibroma
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from frozen human tissue and cells using the RNeasy kit (Qiagen) and verified RNA integrity with an Agilent Bioanalyser 2100 (with typical 28S/18S ratios = 2 +/- 0.1). For mouse, total RNA was isolated from nerves and tumors using the Qiagen fibrous tissue protocol (Qiagen, Inc. Valencia, CA).
Label biotin
Label protocol We generated biotinylated cDNA probes from a single round of DNA displacement synthesis amplification of 20ng total RNA (Ovation Biotin RNA Amplification and Labelling System; NuGen) for hybridization to the whole-genome Affymetrix GeneChips using the Affymetrix protocol.
 
Hybridization protocol The hybridization cocktail was hybridized for 16 hr at 45 degrees C on GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450:FS450_0004.
Scan protocol GeneChips were scanned and quantified using an Affymetrix Gene Array scanner and GeneChip Operating Software V1.4 (default settings.)
Description T4
SAMPLE 30
Data processing Microarrays were analyzed with Affymetrix Microarray Suite 5.0 to generate “CEL” files that were processed using Robust Multichip Analysis (RMA) in Bioconductor/R. A custom CDF was used for each species (mouse: Brainarray, Mouse4302_Mm_REFSEQ_11.0.1; Human, Brainarray, HGU133Plus2_Hs_REFSEQ_11.0.1).
 
Submission date Oct 22, 2012
Last update date Dec 28, 2012
Contact name Nancy Ratner
E-mail(s) nancy.ratner@cchmc.org
Phone 513-636-9469
Organization name Cincinnati Children's Hospital Medical Center
Street address 3333 Burnet Ave.
City Cincinnati
State/province OH
ZIP/Postal code 45229
Country USA
 
Platform ID GPL14757
Series (1)
GSE41747 MEK inhibition exhibits efficacy in human and mouse neurofibromatosis tumors, despite transcriptional feedback onto ERK.

Data table header descriptions
ID_REF
VALUE RMA signal intensity

Data table
ID_REF VALUE
AFFX-18SRNAMur/X00686_3_at 9.704797676
AFFX-18SRNAMur/X00686_5_at 9.895665596
AFFX-18SRNAMur/X00686_M_at 13.76673398
AFFX-b-ActinMur/M12481_3_at 11.3618535
AFFX-b-ActinMur/M12481_5_at 9.932413255
AFFX-b-ActinMur/M12481_M_at 10.08331566
AFFX-BioB-3_at 10.88154195
AFFX-BioB-5_at 10.65902743
AFFX-BioB-M_at 11.26613884
AFFX-BioC-3_at 11.24848801
AFFX-BioC-5_at 11.9035255
AFFX-BioDn-3_at 13.55809386
AFFX-BioDn-5_at 12.4640626
AFFX-CreX-3_at 14.45105085
AFFX-CreX-5_at 14.16930226
AFFX-DapX-3_at 2.911741378
AFFX-DapX-5_at 2.688072741
AFFX-DapX-M_at 2.610409484
AFFX-GapdhMur/M32599_3_at 12.64146107
AFFX-GapdhMur/M32599_5_at 11.29789107

Total number of rows: 21940

Table truncated, full table size 548 Kbytes.




Supplementary file Size Download File type/resource
GSM1023487_HybA-T4_MOE430_2.CEL.gz 3.6 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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