|
| Status |
Public on Mar 02, 2018 |
| Title |
SCEC and corresponding normal tissue, replicate 2 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
SCEC, patient 2
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: middle thoracic SCEC with stage III
|
| Treatment protocol |
Tissue sections were cut from frozen blocks and then stained with toluidine blue for genomic DNA (gDNA). 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 |
genomic DNA |
| Extraction protocol |
Sample DNA was extracted using DNeasy Blood &Tissue Kit (Cat#69506, QIAGEN, GmBH, Germany), Use Nano Drop (Cat#ND-1000, ThermoFisher, Waltham, MA, US) and 1% agarose gel electrophoresis to check the quantity and quality of purified DNA.
|
| Label |
Cy5
|
| Label protocol |
Experimental sample and control sample were labeled with Cy5 NHS ester and Cy3 NHS ester respectively, using Agilent Genomic DNA Labeling Kit PLUS followed the manufacturer’s instructions. Labeled DNA fragments were purified using Amicon Ultra-0.5, Ultracel-30 Membrane, 30 kDa. Measured the absorbance at A260nm (DNA), A550nm(Cyanine 3), and A650nm(Cyanine 5)of purified DNA fragments to calculate the Specific Activity.
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| |
|
| Channel 2 |
| Source name |
corresponding normal tissue, patient 2
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: control
|
| Treatment protocol |
Tissue sections were cut from frozen blocks and then stained with toluidine blue for genomic DNA (gDNA). 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 |
genomic DNA |
| Extraction protocol |
Sample DNA was extracted using DNeasy Blood &Tissue Kit (Cat#69506, QIAGEN, GmBH, Germany), Use Nano Drop (Cat#ND-1000, ThermoFisher, Waltham, MA, US) and 1% agarose gel electrophoresis to check the quantity and quality of purified DNA.
|
| Label |
Cy3
|
| Label protocol |
Experimental sample and control sample were labeled with Cy5 NHS ester and Cy3 NHS ester respectively, using Agilent Genomic DNA Labeling Kit PLUS followed the manufacturer’s instructions. Labeled DNA fragments were purified using Amicon Ultra-0.5, Ultracel-30 Membrane, 30 kDa. Measured the absorbance at A260nm (DNA), A550nm(Cyanine 3), and A650nm(Cyanine 5)of purified DNA fragments to calculate the Specific Activity.
|
| |
|
| |
| Hybridization protocol |
Array hybridization was performed using Agilent Oligo aCGH Hybridization Kit in Hybridization Oven at 65℃, 20rpm for 24 hours.Array wash was performed using Agilent Oligo aCGH Wash Buffer 1 and 2 set in staining dishes follow the manufacturer's instructions.
|
| Scan protocol |
Images were quantified using Agilent Feature Extraction Software (version 10.7).
|
| Description |
Biological replicate from SCEC patient 3
252206030966_1_3
|
| Data processing |
Agilent data analysis using the agilent cytogenomics software which provides no normalized data on probe level. Therefore, the preliminary results from cytogenomics software are reported in matrix linked at the foot of the Series record.
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| |
|
| Submission date |
Mar 01, 2018 |
| Last update date |
Mar 02, 2018 |
| Contact name |
Juan Wang |
| E-mail(s) |
wangj@rainbow-genome.com
|
| Organization name |
Shanghai Jiayin Biotechnology Co., Ltd.
|
| Street address |
No. 135 Guowei Road
|
| City |
Shanghai |
| ZIP/Postal code |
200438 |
| Country |
China |
| |
|
| Platform ID |
GPL10123 |
| Series (2) |
| GSE111298 |
aCGH data from SCEC and corresponding normal samples |
| GSE111299 |
Genome-wide analysis of gene expression and DNA copy number variations in small cell esophageal carcinoma |
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