|
Status |
Public on Dec 01, 2013 |
Title |
08SE229 |
Sample type |
RNA |
|
|
Source name |
colorectal cell fraction
|
Organism |
Homo sapiens |
Characteristics |
disease state: metastatic colorectal cancer (mCRC) response to chemotherapy: NO
|
Treatment protocol |
n/a
|
Growth protocol |
n/a
|
Extracted molecule |
total RNA |
Extraction protocol |
All colorectal tissue samples were maintained at -80ºC until RNA extraction and grinded under liquid nitrogen. Homogenization was achieved using QIAshredder homogenizers and total RNA was extracted using RNeasy Mini kit (both kits from Qiagen Inc; Valencia, CA, USA).
|
Label |
biotin
|
Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
|
|
Hybridization protocol |
Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45ºC on Human Genome U133 Plus 2.0 array. GeneChips were washed and stained following manufacturer's instructions.
|
Scan protocol |
GeneChips were scanned using the GC3000 laser confocal scanner (Affymetrix)
|
Data processing |
The microarray image data were analyzed using GeneChip Operating Software (GCOS 1.4 Affymetrix). Partek Genomics Suite v7.3.1 (Partek Inc; St Louis, MO, USA) was used for statistical analysis. Affymetrix default analysis settings were used and normalization was performed using the RMA (Robust Multichip Average) method.
|
|
|
Submission date |
Nov 26, 2013 |
Last update date |
Dec 01, 2013 |
Contact name |
Purificacion Estevez-Garcia |
E-mail(s) |
puriestevez@gmail.com
|
Organization name |
Institute of Biomedicine
|
Department |
Molecular Oncology
|
Lab |
215
|
Street address |
Manuel Siurot avenue
|
City |
Seville |
State/province |
Seville |
ZIP/Postal code |
41013 |
Country |
Spain |
|
|
Platform ID |
GPL570 |
Series (2) |
GSE52735 |
Gene signature predictive of response to chemotherapy in mCRC [array] |
GSE52847 |
Gene signature predictive of response to chemotherapy in mCRC |
|