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Sample GSM850509 Query DataSets for GSM850509
Status Public on Dec 20, 2011
Title BT474 xenograft_SHP2 miR1_3
Sample type RNA
 
Source name BT474 tumors
Organism Homo sapiens
Characteristics cell line: BT474
transfection: SHP2 miR1
Treatment protocol Doxycycline in drinking water (2 g per liter). The treatment started after tumor development and continued until the end of the experiment (day 30). The drinking water containing doxycycline was refreshed every two days.
Growth protocol BT474 cells were injected orthotopically into the fat pad of mammary gland 2/3 of imuunodeficient mice. After tumor development, we depleted SHP2 for 30 days in vivo.
Extracted molecule total RNA
Extraction protocol Tumors were dissected and total RNA was isolated with a standard TRIZOL extraction method.
Label Biotin
Label protocol 100ng total RNA was processed according to the GeneChip Whole Transcript (WT) Double-Stranded Target Assay Manual from Affymetrix (GeneChip Whole Transcription Sense Target Labeling technical manual, Rev. 2).
 
Hybridization protocol Affymetrix Human Gene 1.0 st v1 GeneChip arrays were hybridized following the GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix) with a hybridization time of 16h. The Affymetrix Fluidics protocol FS450_0007 was used for washing.
Scan protocol Scanning was performed with Affymetrix GCC Scan Control v. 3.0.0.1214 on a GeneChip® Scanner 3000 with autoloader.
Description HuGene-1_0-st-v1
Data processing CEL files were read into R (v2.10) using the R/Bioconductor (v2.4) package oligo (v1.8) and normalized probeset level expression values were calculated with the command rma and the R/Bioconductor annotation package pd.hugene.1.0.st.v1
 
Submission date Dec 19, 2011
Last update date Dec 20, 2011
Contact name Tim Roloff
E-mail(s) tim.roloff@fmi.ch
Organization name FMI
Department Functional Genomics
Street address Maulbeerstrasse 66
City Basel
ZIP/Postal code 4058
Country Switzerland
 
Platform ID GPL6244
Series (2)
GSE34523 BT474 tumors in the presence or absence of SHP2
GSE34525 BT474 tumors, primary TN tumors and MCF10A-HER2/3 cells in the presence or absence of SHP2

Data table header descriptions
ID_REF
VALUE RMA normalized probeset-level expression values

Data table
ID_REF VALUE
7896736 5.511453555
7896738 2.438774665
7896740 2.442133498
7896742 7.520957403
7896744 6.353671905
7896746 9.951088791
7896748 9.944736794
7896750 6.446376724
7896752 9.170433174
7896754 6.766105592
7896756 3.809866532
7896759 6.315863112
7896761 5.066250798
7896779 5.911741166
7896798 6.045951549
7896817 4.608619677
7896822 6.86045433
7896859 4.733514168
7896861 3.262449431
7896863 4.874466764

Total number of rows: 28869

Table truncated, full table size 560 Kbytes.




Supplementary file Size Download File type/resource
GSM850509_mb20090326hg10_07_SHP2+_2LP_Dox_295_HuGene-1_0-st-v1_.CEL.gz 3.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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