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Sample GSM238350 Query DataSets for GSM238350
Status Public on Dec 14, 2007
Title mammary tumor CR115-4, transplanted, unsorted
Sample type RNA
 
Source name mammary tumor isolated from a RAG2-/- recipient #4 transplanted with primary tumor from mouse CR115, unsorted
Organism Mus musculus
Characteristics Wap-Cre;Etv6-NTRK3 parous female
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA followed by cleaning up using columns from the Promega SV total RNA isolation kit.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol.
 
Hybridization protocol The fragmented cRNA was added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to MOE 430.2 chips overnight at 45°C. The chips were then transferred to a fluidics instrument that performs washes to remove cRNA that had not hybridized to its complementary oligonucleotide probe. The bound cRNA was then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors were then added using biotinylated anti-streptavidin antibody and additional SAPE.
Scan protocol Each cRNA bound at its complementary oligonucleotide was excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions were captured.
Description Gene expression data from unfractionated mammary tumor
Data processing The raw CEL files were imported into dChip and normalized with dChip.
 
Submission date Oct 17, 2007
Last update date Aug 28, 2018
Contact name Zhe Li
E-mail(s) li@bloodgroup.tch.harvard.edu
Phone 617-919-2052
Organization name Children's Hospital Boston
Department Division of Hematology/Oncology
Lab Stuart Orkin's Lab
Street address
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
Platform ID GPL1261
Series (1)
GSE9355 Microarray expression profiles of mammary tumors developed in Wap-Cre;Etv6-NTRK3 mice
Relations
Reanalyzed by GSE119085

Data table header descriptions
ID_REF
VALUE After normalization, the model-based expression values were calculated by dChip and exported.
CR115-4 call
CR115-4 SE

Data table
ID_REF VALUE CR115-4 call CR115-4 SE
AFFX-BioB-5_at 141.883 P 5.32648
AFFX-BioB-M_at 128.667 P 7.96543
AFFX-BioB-3_at 131.105 P 7.85102
AFFX-BioC-5_at 335.578 P 18.1952
AFFX-BioC-3_at 336.42 P 12.5929
AFFX-BioDn-5_at 706.951 P 18.7243
AFFX-BioDn-3_at 1767.3 P 55.8847
AFFX-CreX-5_at 5736.58 P 206.133
AFFX-CreX-3_at 5399.84 P 193.09
AFFX-DapX-5_at 19.3139 A 1.56477
AFFX-DapX-M_at 28.5622 A 3.24773
AFFX-DapX-3_at 7.86128 A 1.70314
AFFX-LysX-5_at 14.419 A 1.54569
AFFX-LysX-M_at 12.2718 A 1.86832
AFFX-LysX-3_at 18.395 P 2.13912
AFFX-PheX-5_at 5.75597 A 1.23337
AFFX-PheX-M_at 11.81 A 1.39314
AFFX-PheX-3_at 42.5166 A 2.27594
AFFX-ThrX-5_at 38.3686 A 3.12763
AFFX-ThrX-M_at 15.0553 A 2.41038

Total number of rows: 45101

Table truncated, full table size 1285 Kbytes.




Supplementary file Size Download File type/resource
GSM238350.CEL.gz 6.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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