|
| Status |
Public on Apr 22, 2014 |
| Title |
Lung Met, biological rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Lung metastasis derivative
|
| Organism |
Homo sapiens |
| Characteristics |
strain: balb/c
cell line: SW620
sample type: lung metastasis
|
| Growth protocol |
cells were maintained in 5% CO2 at 37oC in DMEM medium (Gibco) supplemented with 5% fetal bovine serum (FBS) (Biological Industries), Glutamine 0.29 mg/ml (Biological Industries), Penicillin 100 U/ml (Biological Industries) and Streptomycin 0.1 mg/ml (Biological Industries)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from cells using RNeasy mini kit (Qiagen)
|
| Label |
biotin
|
| Label protocol |
Labeling of the samples to HG1.0ST gene expression chip (Affymetrix) were performed by Functional Genomics Core Facility of IRB, Barcelona using standard methodology
|
| |
|
| Hybridization protocol |
Hybridization of the samples to HG1.0ST gene expression chip (Affymetrix) were performed by Functional Genomics Core Facility of IRB, Barcelona using standard methodology
|
| Scan protocol |
Gene chips were scanned using GeneChip Scanner 3000 from affymetrix
|
| Data processing |
Data analysis was performed using R (Bioconductor). Quantile normalization and RMA summarization were used to obtain probeset level expression estimates as implemented in the “oligo” package of Bioconductor. In order to prevent non-specific or miss-targeted probesets to bias the gene level expression estimates, for each gene we selected the 50% of the probesets with highest inter-quartile range across all samples and obtained a gene level expression estimate via median polish, in a fashion analogous to RMA
|
| |
|
| Submission date |
Oct 31, 2011 |
| Last update date |
Apr 23, 2014 |
| Contact name |
Xabier Garcia-Albeniz |
| E-mail(s) |
xgarciad@hsph.harvard.edu
|
| Organization name |
IRB Barcelona
|
| Lab |
Metlab
|
| Street address |
Baldiri Reixac 10
|
| City |
Barcelona |
| ZIP/Postal code |
08028 |
| Country |
Spain |
| |
|
| Platform ID |
GPL10739 |
| Series (1) |
| GSE33350 |
Comparison of metastatic derivatives of colon cancer cell line selected in vivo |
|
