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Sample GSM773090 Query DataSets for GSM773090
Status Public on Nov 01, 2011
Title MPNST biological rep3
Sample type RNA
 
Source name Malignant peripheral nerve sheath tumor
Organism Danio rerio
Characteristics tissue: tumor
genotype/variation: p53M214K/M214K
Treatment protocol Fish were grown under standard conditions and monitored for tumor development. Fish developing tumors were euthanized and the tumor tissue removed for histology and RNA preparation.
Growth protocol Wild-type or p53(M214K) homozygous zebrafish embryos were injected at the one cell stage with a transposon in which the Heat Shock Protein 70 (HSP70) promoter drove expression of a human EWS-FLI1 fusion oncoprotein [Tg(HSP:EWS-FLI1)].
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from tumors using Trizol reagent according to the manufacturer's instructions.
Label biotin
Label protocol Total RNA (2.5ug) from tumors was reverse-transcribed using a T7-Oligo(dT) Promoter Primer, followed by RNAseH-mediated second-strand cDNA synthesis. Biotinylated cRNA probe was prepared with MessageAmp II (Ambion).
 
Hybridization protocol Hybridization was carried out according to Affymetrix protocol 701027 rev 5, using Affymetrix Fluidics Station 450.
Scan protocol Arrays were scanned with the Affymetrix GeneChip Scanner 3000 using default parameters
Description Malignant peripheral nerve sheath tumor arising in p53M214K/M214K zebrafish
Data processing The probe-level data were background adjusted, normalized and summarized by a Robust Multi-array Average (RMA) algorithm implemented in the software package affy of the Bioconductor project release 1.7, running in the R statistical environment version 2.2.0 using default parameters.
 
Submission date Aug 03, 2011
Last update date Nov 01, 2011
Contact name James F Amatruda
E-mail(s) james.amatruda@utsouthwestern.edu
Phone 214-648-3896
Organization name University of Texas Southwestern Medical Center
Department Pediatrics and Molecular Biology
Street address 5323 Harry Hines Boulevard
City Dallas
State/province TX
ZIP/Postal code 75390-8534
Country USA
 
Platform ID GPL1319
Series (2)
GSE31186 The human Ewing's Sarcoma oncoprotein EWS-FLI1 causes Ewing's-type tumors in zebrafish
GSE31217 A zebrafish transgenic model of Ewing's Sarcoma reveals conserved mediators of EWS-FLI1 tumorigenesis

Data table header descriptions
ID_REF
VALUE Log2 RMA signal intensities
ABS_CALL

Data table
ID_REF VALUE ABS_CALL
AFFX-BioB-3_at 5.93 P
AFFX-BioB-5_at 6.41 P
AFFX-BioB-M_at 6.86 P
AFFX-BioC-3_at 7.6 P
AFFX-BioC-5_at 7.29 P
AFFX-BioDn-3_at 9.86 P
AFFX-BioDn-5_at 8.58 P
AFFX-CreX-3_at 11.89 P
AFFX-CreX-5_at 10.74 P
AFFX-DapX-3_at 2.64 A
AFFX-DapX-5_at 3.08 A
AFFX-DapX-M_at 2.93 A
AFFX-Dr-AB076373-1_at 4.19 A
AFFX-Dr-AF292559-1_at 3.24 A
AFFX-Dr-AF292559-2_s_at 2.31 A
AFFX-Dr-AF292559-3_s_at 2.43 A
AFFX-Dr-AF292559-4_s_at 3.29 A
AFFX-Dr-AF292560-1_s_at 3.08 A
AFFX-Dr-AF298789-1_at 3.67 A
AFFX-Dr-AF323980-1_at 2.78 A

Total number of rows: 15617

Table truncated, full table size 361 Kbytes.




Supplementary file Size Download File type/resource
GSM773090.CEL.gz 3.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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