|
| Status |
Public on Aug 01, 2012 |
| Title |
Peripheral T cell lymphoma 7 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Human lymph node from a peripheral T cell lymphoma patient
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: lymph node
disease status: peripheral T cell lymphoma (PTCL)
|
| Growth protocol |
Lymph nodes were frozen to preserve the RNA properties.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol, precipitated with isopropanol and purified with the RNeasy Mini Kit (Qiagen, Valencia, CA) following the manufacturer's instructions.
|
| Label |
Cy5
|
| Label protocol |
500 ng of total RNA were primed with the T7 promoter primer at 65°C for 10 min, then reversed transcribed at 40°C for 2 h in the presence of MMLV RT. Then, the resulting cDNA was transcribed and labeled into cRNA using T7 RNA polymerase, NTPs and a fraction of Cy3-CTP (for the RNA reference) and Cy5-CTP (for the samples) for 2 h at 40ºC (all reagents were obtained from Agilent Technologies, Inc.).
|
| |
|
| Channel 2 |
| Source name |
Universal Human Reference RNA
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: 10 human tumor cell lines
sample type: reference
|
| Biomaterial provider |
Stratagene, La Jolla, CA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol, precipitated with isopropanol and purified with the RNeasy Mini Kit (Qiagen, Valencia, CA) following the manufacturer's instructions.
|
| Label |
Cy3
|
| Label protocol |
500 ng of total RNA were primed with the T7 promoter primer at 65°C for 10 min, then reversed transcribed at 40°C for 2 h in the presence of MMLV RT. Then, the resulting cDNA was transcribed and labeled into cRNA using T7 RNA polymerase, NTPs and a fraction of Cy3-CTP (for the RNA reference) and Cy5-CTP (for the samples) for 2 h at 40ºC (all reagents were obtained from Agilent Technologies, Inc.).
|
| |
|
| |
| Hybridization protocol |
Oligoarray control targets and hybridization buffer (Agilent Technologies, Inc.) were added, and samples were applied to microarrays enclosed in Agilent hybridization chambers. After hybridization, slides were sequentially washed.
|
| Scan protocol |
Microarray slides were scanned on an Agilent G2505C scanner.
Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).
|
| Description |
PTCL 7
Biological replicate 7 of 38. Lymph node from a PTCL patient.
Universal Human Reference RNA (Stratagene, La Jolla, CA): a commercial RNA pooled from human tumor cell lines.
|
| Data processing |
Bioconductor's limma package was employed for preprocessing and normalization. Thus, background was corrected using the normexp method and data were normalized using the loess and quantiles method for within-array and inter-array normalization, respectively.
|
| |
|
| Submission date |
Feb 29, 2012 |
| Last update date |
Aug 01, 2012 |
| Contact name |
Esperanza Martín-Sánchez |
| Organization name |
Spanish National Cancer Research Centre (CNIO)
|
| Street address |
Melchor Fernandez Almagro 3
|
| City |
Madrid |
| ZIP/Postal code |
28029 |
| Country |
Spain |
| |
|
| Platform ID |
GPL6480 |
| Series (1) |
| GSE36172 |
Gene expression profiling of human peripheral T cell lymphoma cases vs. reactive lymph nodes |
|
