|
| Status |
Public on Oct 10, 2015 |
| Title |
Matched control of TT31_X3P Array+Nugen Ovation FFPE WTA System Kit |
| Sample type |
RNA |
| |
|
| Source name |
Normal Colorectum Mucosa (FFPE)
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Normal
platform: X3P
kit: Nugen Ovation FFPE WTA System Kit
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Qiagen RNeasy FFPE kit according to the manufacturer's instructions except deparaffinization step.
|
| Label |
biotin
|
| Label protocol |
3’ IVT Kit (Affymetrix, Santa Clara, CA) and the Ovation FFPE WTA System (NuGEN San Carlos, CA, USA) were used for amplification and labelling. 100 ng of input RNA was used to generate the amplified Ribo-SPIA product (NuGEN). Amplified cDNA samples were fragmented and labelled using Encore Biotine Module (NuGEN). 500 ng total RNA was used as input for Affymretix 3' IVT kit. The samples were amplified and labeled using the Affymetrix 3'IVT labeling kit according to manufacturer's instructions.
|
| |
|
| Hybridization protocol |
Labeled products were hybridized onto two Affymetrix microarray platforms (Human Genome U133 Plus 2.0 and U133_X3P). 15 ug amplified and labeled samples with the 3’ IVT kit were hybridized to these two Affymetrix microarray platforms following manufacturers’ recommendations (Affymetrix GeneChip® Expression Wash, Stain and Scan User Guide, P/N 702731 ). 3.5 ug amplified and labeled products using Nugen Ovation FFPE WTA system and Encore Biotin Module were also hybridized to these two Affymetrix microarray platforms following Nugen specifications. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
Scanning was performed on a GeneChip Scanner 3000 7G
|
| Description |
Gene expression data from matched normal FFPE tissues
|
| Data processing |
Array images and the CEL files were generated using the Affymetrix® GeneChip® Command Console® Software v 3.0.1 Raw data were processed with the RMA procedure using Expression Console. Gene expression data was analyzed using Partek Genomic Suite 6.6 software (Partek Inc., St. Louis, MO, USA) for the three tumor samples that had matched controls.
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| |
|
| Submission date |
Oct 09, 2015 |
| Last update date |
Oct 10, 2015 |
| Contact name |
Nevin Belder |
| E-mail(s) |
nevinbelder@gmail.com
|
| Organization name |
Ankara University
|
| Department |
Biotechnology
|
| Lab |
Genomics
|
| Street address |
De gol
|
| City |
Ankara |
| State/province |
Tandogan |
| ZIP/Postal code |
06100 |
| Country |
Turkey |
| |
|
| Platform ID |
GPL1352 |
| Series (1) |
| GSE73883 |
Optimizing microarray gene expression profiling workflow for formalin-fixed paraffin-embedded tissues |
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