|
| Status |
Public on Nov 21, 2013 |
| Title |
Epithelial cells MDAMB231 cocultured with fibroblast CCD1112Sk replicate-3 |
| Sample type |
RNA |
| |
|
| Source name |
Epithelial cells MDAMB231 cocultured with fibroblast CCD1112Sk replicate-3
|
| Organism |
Homo sapiens |
| Characteristics |
cell: Epithelial cells MDAMB231 cocultured with fibroblast CCD1112Sk
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the miRNeasy Mini kit (Qiagen) according to the manufacturer's protocol. The optional on-column DNA digestion was performed, using the RNase-free DNase Set (Qiagen).
|
| Label |
biotin
|
| Label protocol |
cDNA synthesis, labeling, hybridization and scanning was performed by Expression Analysis Inc. using standard Affymetrix protocols.
|
| |
|
| Hybridization protocol |
cDNA synthesis, labeling, hybridization and scanning was performed by Expression Analysis Inc. using standard Affymetrix protocols.
|
| Scan protocol |
cDNA synthesis, labeling, hybridization and scanning was performed by Expression Analysis Inc. using standard Affymetrix protocols.
|
| Description |
human cells cell cultured- tumors cell lines, human fibroblast strains
|
| Data processing |
We used R package aroma.affymetrix to analyze raw data. Chip type is HuGene-1_0-st-v1, and we used HuGene-1_0-st-v1.r3 as annotation CDF. After RMA background correction and quantile normalization we got probe-level intensity values as shown in the data matrix. We ran quality assessment to check data (not shown). In the further analysis we averaged intensity values for genes with multiple probes, then took log2 tranformed values for each gene.
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| |
|
| Submission date |
Oct 18, 2012 |
| Last update date |
Nov 21, 2013 |
| Contact name |
Jinyu Li |
| E-mail(s) |
[email protected]
|
| Organization name |
Stony Brook University
|
| Department |
Cancer Center
|
| Street address |
101 Nicolls Rd
|
| City |
Stony Brook |
| State/province |
NY |
| ZIP/Postal code |
11794 |
| Country |
USA |
| |
|
| Platform ID |
GPL6244 |
| Series (1) |
| GSE41678 |
System-Wide Analysis Reveals a Complex Network of Tumor-Fibroblast Interactions Involved in Tumorigenicity |
|
