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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jan 01, 2012 |
| Title |
Gene expression analysis of hemizygous or heterozygous KIT exon 11 deletions NIH3T3 infected cells |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by array
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| Summary |
Codelink® Whole Mouse Genome Bioarrays (GE/Amersham) of one sample of WT, D6, D54, WT/D6, WT/D54 and MIGR NIH3T3 cells, cultivated in the four different conditions (SCF+, SCF- and imatinib 1 or 5 µM), were used for the analysis of differential gene expression. Our aim was to choose the best candidate genes for low density array analysis. We first selected genes differentially expressed between WT and hemizygous samples grown in the SCF+ condition, whose fold change was superior or equal to 2 and whose expression for at least one of the sample was greater than 1.3 (commonly admitted threshold for low density arrays). We selected then 83 and 126 genes more that were differentially expressed between D6 and D54 cell lines (fold change ≥ 2; gene amplification > 1.3) in SCF+ or SCF- condition, respectively. Finally we obtained a list of 235 genes in which 94 were available for Taqman® low density array (Applied®).
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| Overall design |
We have 6 samples per group: NIH3T3 MIGR (empty vector), NIH3T3 KIT wild-type (WT), NIH3T3 KIT del557-558 (D6), NIH3T3 KIT del564-581 (D54), NIH3T3 KIT WT/ KIT D6 and NIH3T3 KIT WT/KIT D54. All these samples were included in each of the 4 groups: culture medium without Stem Cell Factor (SCF-), culture medium with SCF (SCF+), culture medium with SCF and imatinib 1µM (STI 1µM), and culture medium with SCF and imatinib 5µM (STI 5µM). We analyzed each sample in one array.
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| Contributor(s) |
Tabone-Eglinger S, Bachet J, Dessaux S, Besse A, Brahimi S, Subra F, Emile J, Blay J, Alberti L |
| Citation(s) |
23593401 |
| Submission date |
Nov 28, 2011 |
| Last update date |
Apr 22, 2013 |
| Contact name |
Séverine TABONE-EGLINGER |
| E-mail(s) |
severine.eglinger@orange.fr
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| Organization name |
Centre Médical Universitaire
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| Street address |
1 rue Michel Servet
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| City |
GENEVE |
| ZIP/Postal code |
1211 |
| Country |
Switzerland |
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| Platforms (1) |
| GPL2897 |
GE Healthcare/Amersham Biosciences CodeLink™ Mouse Whole Genome Bioarray |
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| Samples (24)
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| GSM839756 |
NIH3T3 KIT D54_SCF100ng/ml |
| GSM839757 |
NIH3T3 KIT WT/D6_SCF100ng/ml |
| GSM839758 |
NIH3T3 KIT WT/D54_SCF100ng/ml |
| GSM839759 |
NIH3T3 MIGR_SCF100ng/ml_imatinib mesilate 5µM |
| GSM839760 |
NIH3T3 KIT WT_SCF100ng/ml_imatinib mesilate 5µM |
| GSM839761 |
NIH3T3 KIT D6_SCF100ng/ml_imatinib mesilate 5µM |
| GSM839762 |
NIH3T3 KIT D54_SCF100ng/ml_imatinib mesilate 5µM |
| GSM839763 |
NIH3T3 KIT WT/D6_SCF100ng/ml_imatinib mesilate 5µM |
| GSM839764 |
NIH3T3 KIT WT/D54_SCF100ng/ml_imatinib mesilate 5µM |
| GSM839765 |
NIH3T3 MIGR_without SCF or imatinib |
| GSM839766 |
NIH3T3 KIT WT_without SCF or imatinib |
| GSM839767 |
NIH3T3 KIT D6_without SCF or imatinib |
| GSM839768 |
NIH3T3 KIT D54_without SCF or imatinib |
| GSM839769 |
NIH3T3 KIT WT/D6_without SCF or imatinib |
| GSM839770 |
NIH3T3 KIT WT/D54_without SCF or imatinib |
| GSM839771 |
NIH3T3 MIGR_SCF100ng/ml_imatinib mesilate 1µM |
| GSM839772 |
NIH3T3 KIT WT_SCF100ng/ml_imatinib mesilate 1µM |
| GSM839773 |
NIH3T3 KIT D6_SCF100ng/ml_imatinib mesilate 1µM |
| GSM839774 |
NIH3T3 KIT D54_SCF100ng/ml_imatinib mesilate 1µM |
| GSM839775 |
NIH3T3 KIT WT/D6_SCF100ng/ml_imatinib mesilate 1µM |
| GSM839776 |
NIH3T3 KIT WT/D54_SCF100ng/ml_imatinib mesilate 1µM |
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| Relations |
| BioProject |
PRJNA150521 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE33968_RAW.tar |
8.0 Mb |
(http)(custom) |
TAR (of TXT) |
| Processed data included within Sample table |
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