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Sample GSM3020876 Query DataSets for GSM3020876
Status Public on Mar 02, 2018
Title SCEC, dissected from the surgical specimens, patient 2
Sample type RNA
Source name SCEC Tumor, patient2
Organism Homo sapiens
Characteristics tissue: middle thoracic SCEC with stage III
Treatment protocol Tissue sections were cut from frozen blocks and then stained with cresyl violet for total RNA (Ambion, Austin, TX, USA). Carcinoma cells or non-malignant cells were collected from cancerous or adjacent noncancerous tissue sections using LMD (Leica Microsystems, Wetzlar, Germany) by pathologists
Growth protocol A total of 3 SCEC tissues and matched adjacent noncancerous tissues were dissected from the surgical specimens and snap-frozen in liquid nitrogen, then stored at -80°C in the tissue bank of Fudan University Shanghai Cancer Center
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using TRIZOL Reagent (Cat#15596-018,Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
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 645 (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 The gene chips were scanned using a confocal laser scanner (GeneArray Scanner 3000). The scanned image was converted into numerical values of the signal intensity by Command Console Software 3.1 (Affymetrix) with default settings.
Description gene expression data from SCEC patient2
Data processing Raw data were subjected to Robust Multiarray Average quantile normalization analysis (RMA) algorithm by GeneSpring GX 12.5 Software (Agilent technology, Santa Clara, CA, US) to generate .CEL intensity files
Submission date Feb 23, 2018
Last update date Mar 02, 2018
Contact name Juan Wang
Organization name Shanghai Jiayin Biotechnology Co., Ltd.
Street address No. 135 Guowei Road
City Shanghai
ZIP/Postal code 200438
Country China
Platform ID GPL570
Series (2)
GSE111044 Expression data from SCEC and corresponding normal samples
GSE111299 Genome-wide analysis of gene expression and DNA copy number variations in small cell esophageal carcinoma

Data table header descriptions
VALUE RMA signal intensity

Data table
AFFX-BioB-5_at 8.049162
AFFX-BioB-M_at 8.627852
AFFX-BioB-3_at 8.088302
AFFX-BioC-5_at 9.361711
AFFX-BioC-3_at 9.813063
AFFX-BioDn-5_at 10.96859
AFFX-BioDn-3_at 11.761026
AFFX-CreX-5_at 13.359216
AFFX-CreX-3_at 13.683769
AFFX-DapX-5_at 6.336691
AFFX-DapX-M_at 8.741442
AFFX-DapX-3_at 9.554435
AFFX-LysX-5_at 4.571487
AFFX-LysX-M_at 5.4936857
AFFX-LysX-3_at 6.294965
AFFX-PheX-5_at 4.90401
AFFX-PheX-M_at 5.5374336
AFFX-PheX-3_at 7.064625
AFFX-ThrX-5_at 4.0588317
AFFX-ThrX-M_at 5.366534

Total number of rows: 54675

Table truncated, full table size 1083 Kbytes.

Supplementary file Size Download File type/resource
GSM3020876_BH12632-1_E09184T_HG-U133_Plus_2_.CEL.gz 4.7 Mb (ftp)(http) CEL
Processed data included within Sample table

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