|
| Status |
Public on Dec 13, 2011 |
| Title |
PLT5 |
| Sample type |
RNA |
| |
|
| Source name |
Tumor cells and platelet co-culture
|
| Organism |
Mus musculus |
| Characteristics |
background strain: C57BL/6
cell line: Ep5 (EpRas) cells
platelet description: Wild-type C57BL/6 platelets isolated by centrifugation
treatment protocol: roughly 1000:1 Platelet-Ep5 ratio cultured together for 24 hours
|
| Growth protocol |
Ep5 cells cultured in DMEM 10% FCS, 1% Penicillin/Streptomycin and 2 mM L-Glutamine
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Qiagen RNAeasy
|
| Label |
biotin
|
| Label protocol |
Affymetrix GeneChip® WT Sense Target Labeling
|
| |
|
| Hybridization protocol |
Performed according to manufacturer's instructions (Affymetrix) for Affymetrix Mouse Exon 1.0 ST arrays.
|
| Scan protocol |
Affymetrix Gene ChIP Scanner 3000 7G; GeneChip® Command Console.
|
| Data processing |
Data processing was done using Partek Genomics Suite 6.4 software. RMA was used to summarize and normalize the probe data into probe set expression values. The list of utilized probe sets was defined by custom .ps and .mps files. The RMA procedure used included the options adjust for GC content, probe sequence, RMA background correction, Quantile Normalization and median polish probe set summarization. Expression values for probesets were summarized to a single value per gene based on the custom file MoEx-1_0-st-v1._core+miRNA+RfSq+UCSC_.SH.2916.mps. The outlier excluded mean method was used. This procedure excludes probe set values that are more than 3 standard deviations above the mean or more and 2 standard deviations below the mean.
probe group file: MoEx-1_0-st-v1.r2.pgf
probeSet list file: MoEx-1_0-st-v1._core+miRNA+RfSq+UCSC_.SH.2916.ps
meta-probeset file: MoEx-1_0-st-v1._core+miRNA+RfSq+UCSC_.SH.2916.mps
|
| |
|
| Submission date |
Feb 23, 2011 |
| Last update date |
Dec 13, 2011 |
| Contact name |
Charles Arthur Whittaker |
| E-mail(s) |
[email protected]
|
| Organization name |
Koch Institute
|
| Street address |
77 Mass Ave 76-189
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02152 |
| Country |
USA |
| |
|
| Platform ID |
GPL6096 |
| Series (1) |
| GSE27456 |
Direct Signaling Between Platelets and Cancer Cells Induces an Epithelial-Mesenchymal-Like Transition and Promotes Metastasis |
|
