|
| Status |
Public on Sep 19, 2009 |
| Title |
IPA220_day1 dye swap |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Gastric cell line treated with cotrol siRNA
|
| Organism |
Homo sapiens |
| Characteristics |
Gastric cell line treated with cotrol siRNA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from each cell line using the RNeasy kit (Qiagen) including a DNase digestion step, according to the manufacturer’s instructions
|
| Label |
Cy3
|
| Label protocol |
500 ng of total RNA was reverse transcripted to cDNA using T7 Promoter Primer and MMLV-RT. Then the cDNA was converted to cRNA using T7 RNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP (Two-Color Microarray-Based Gene Expression Analysis Protocol, Agilent).
|
| |
|
| Channel 2 |
| Source name |
Gastric cell line treated with siRNA UPF-1
|
| Organism |
Homo sapiens |
| Characteristics |
Gastric cell line treated with siRNA UPF-1
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from each cell line using the RNeasy kit (Qiagen) including a DNase digestion step, according to the manufacturer’s instructions
|
| Label |
Cy5
|
| Label protocol |
500 ng of total RNA was reverse transcripted to cDNA using T7 Promoter Primer and MMLV-RT. Then the cDNA was converted to cRNA using T7 RNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP (Two-Color Microarray-Based Gene Expression Analysis Protocol, Agilent).
|
| |
|
| |
| Hybridization protocol |
825ng of Cy3 and Cy5 labeled cRNA were hybridized for 16 hrs at 65 C (hybridization oven G2545A, Agilent), according to the manufacturer's recommnded protocol (Two-Color Microarray-Based Gene Expression Analysis, Agilent).
|
| Scan protocol |
Arrays were scanned at on an Agilent DNA Microarray Scanner using the default settings for 4x44k format two-color arrays.
|
| Description |
IPA220_day1 dye swap
|
| Data processing |
Image analysis was performed using feature extraction software version 9.5 (Agilent Technologies). The Agilent GE2-v5_95 protocol was applied using default settings. All data pre-processing and analysis was performed using the R-Bioconductor package Limma20. A robust Edwards background correction was applied
|
| |
|
| Submission date |
Sep 25, 2008 |
| Last update date |
Sep 29, 2008 |
| Contact name |
Daoud Sie |
| E-mail(s) |
d.sie@vumc.nl
|
| Phone |
+31 20 4442428
|
| Organization name |
Vrije Universiteit Medical Center
|
| Department |
Pathology
|
| Lab |
Microarray Core Facility
|
| Street address |
De Boelelaan 1117
|
| City |
Amsterdam |
| ZIP/Postal code |
1081 HV |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL4133 |
| Series (1) |
| GSE12928 |
NMD inhibition fails to identify tumour suppressor genes in microsatellite stable gastric cancer cell lines |
|
