Sex: female laterality of tumor: left age: 62 tnm stage of tumor: T4N0M0 tumor defferentiation grade: I tissue: Normal external auditory canal tissue collected from patients during surgery
Treatment protocol
Patients did not received chemotherapy, radiotherapy or biological therapy before surgery. The normal external auditory canal tissues at a distance of more than 2 cm from tumor margin. Light microscope examination revealed that normal external auditory canal tissues were free of metaplasia, degeneration and inflammation. Selected tissues were transferred to a basket, rinsed with PBS with 0,7% NaCl, 0,04% triton-X100 and placed on ice in the Trizol solution (GibcoBRL).
Growth protocol
Patients with external auditory canal squamous cell carcinoma (EACC) were collected successively who received surgery from June 2015 to March 2016 in the Eye Ear Nose and Throat Hospital, Fudan University. One pair of samples was collected from surgical specimen of each patient, including EACC and normal external auditory canal tissues. ESCC was confirmed by pathological examination.
Extracted molecule
total RNA
Extraction protocol
RNA was extracted by Trizol (Life Technology, 15596-018) following the manufacturer's instructions
Label
biotin
Label protocol
Total RNA were amplified, labeled and purified by using WT Terminal Labeling and Controls Kit (Cat#901524, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.
Hybridization protocol
Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 640 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions
Scan protocol
Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 4.0 (Affymetrix, Santa Clara, CA, US) with default settings.
Description
Light microscope examination revealed that normal external auditory canal tissues were free of metaplasia, degeneration and inflammation
Data processing
Affymetrix GeneChip Command Console (version 4.0, Affymetrix) software was used to extract raw data. Next, Expression Console (version1.3.1, Affymetrix) software offered RMA normalization for both gene and exon level analysis. Then the gene expression analysis and alternative splice analysis proceeded by Genesrping software (version 13.0; Agilent Technologies) and Transcriptome Analysis Console (version2.0, Affymetrix) separately.
