|
| Status |
Public on May 02, 2019 |
| Title |
LA-NPC_NM1 |
| Sample type |
RNA |
| |
|
| Source name |
368583-LA-NPC-Non-Metastasis
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Nasopharyngeal carcinoma
metastasis status: no
|
| Growth protocol |
Nasopharyngeal carcinoma biopsy samples obtained through nasopharyngoscope before treatment.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from formalin-fixed paraffin-embedded (FFPE) samples using the QIAGEN FFPE RNeasy kit (QIAGEN GmbH, Germany).
|
| Label |
biotin
|
| Label protocol |
Total RNA were amplified with the Ovation FFPE WTA System (NuGEN), the Encore Biotin Module (NuGEN) was used for fragmentation and labeling.
|
| |
|
| Hybridization protocol |
Total RNA was hybridized to Affymetrix Human Gene 2.0 ST GeneChips (Affymetrix, Santa Clara, CA, USA) using GeneChip® Hybridization, Wash and Stain Kit (Affymetrix) in Hybridization Oven 645 (Affymetrix) and Fluidics Station 450 (Affymetrix) according to the manufacturer’s instructions.
|
| Scan protocol |
Slides were scanned by GeneChip® Scanner 3000 (Affymetrix) and Command Console Software 3.1 (Affymetrix) with default settings.
|
| Description |
Gene expression data from LA-NPC which did not develop distant metastasis after treatment
|
| Data processing |
Raw data were normalized using 'oligo package' in R language with Robust Multi-array Analysis (RMA). We used Bayes statistics implemented by eBayes in 'limma package' to compute significant differentially expressed probes between metastatic and non-metastatic groups. Since RNA from FFPE samples are highly and randomly fragmented, here we impose Fisher's exact test to verify if a transcript is indeed significant differentially expressed. Differential expressed transcripts were characterized according to the criterion of empirical Fold change >1.5 and empirical Bayes test P-value <0.05. Transcript-level processed data with Fisher's test are available on the series record in the file transcriptionlevel_fisher_lima_nordata_limma.xlsx. Probe-set level data are available in the sample table and in the file nor_data_rma_probelevel.csv which includes statistics.
|
| |
|
| Submission date |
Sep 07, 2017 |
| Last update date |
May 02, 2019 |
| Contact name |
Jun Ma |
| E-mail(s) |
[email protected]
|
| Organization name |
Sun Yat-sen University Cancer Center
|
| Street address |
651 Dongfeng Road East
|
| City |
Guangzhou |
| ZIP/Postal code |
510060 |
| Country |
China |
| |
|
| Platform ID |
GPL19251 |
| Series (1) |
| GSE103611 |
Gene expression-profiling to predict distant metastasis in locoregionally advanced nasopharyngeal carcinoma |
|
