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Sample GSM3020874 Query DataSets for GSM3020874
Status Public on Mar 02, 2018
Title SCEC, dissected from the surgical specimens, patient 1
Sample type RNA
Source name SCEC Tumor, patient1
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 patient1
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 8.194301
AFFX-BioB-M_at 8.684573
AFFX-BioB-3_at 8.184688
AFFX-BioC-5_at 9.570193
AFFX-BioC-3_at 10.0034
AFFX-BioDn-5_at 11.144365
AFFX-BioDn-3_at 11.9117565
AFFX-CreX-5_at 13.410001
AFFX-CreX-3_at 13.737501
AFFX-DapX-5_at 6.4999437
AFFX-DapX-M_at 8.575435
AFFX-DapX-3_at 9.498759
AFFX-LysX-5_at 4.5377417
AFFX-LysX-M_at 5.6025987
AFFX-LysX-3_at 6.0495353
AFFX-PheX-5_at 4.6968117
AFFX-PheX-M_at 5.4050055
AFFX-PheX-3_at 7.1415877
AFFX-ThrX-5_at 3.781248
AFFX-ThrX-M_at 5.1275806

Total number of rows: 54675

Table truncated, full table size 1084 Kbytes.

Supplementary file Size Download File type/resource
GSM3020874_BH12632-1_E09154T_HG-U133_Plus_2_.CEL.gz 4.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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