|
| Status |
Public on Jan 06, 2016 |
| Title |
Adenocarcinoma 009 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Primary lung tumor
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Primary lung tumor
histology: adenocarcinoma
|
| Treatment protocol |
All tumor specimens were embedded in OCT compound and stored at −80°C.
|
| Growth protocol |
Tumors of 76 lung adenocarcinoma patients which successfully underwent potential curative resection at Aichi Cancer Center, Nagoya, Japan, were investigated. All tumors were histologically categorized according to the IASLC/ATS/ERS classification. Approval of the institutional review boards of Nagoya University Graduate School of Medicine and Aichi Cancer Center and written informed consent from the patients were obtained.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy kit (Qiagen, Valencia, CA), followed by treatment with DNase I. Double-stranded cDNA was synthesized from 100 ng of total RNA using MMLV-RT and poly dT primer incorporating the T7 promoter.
|
| Label |
Cy5
|
| Label protocol |
Cy5-sample cRNA and Cy3-sample cRNA were generated and hybridized to a SurePrint G3 Human GE 8x60K Microarray kit (Agilent Technologies) with 60k distinct probes.
|
| |
|
| Channel 2 |
| Source name |
20CL
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: mixture of 20 cell lines
|
| Treatment protocol |
All tumor specimens were embedded in OCT compound and stored at −80°C.
|
| Growth protocol |
Tumors of 76 lung adenocarcinoma patients which successfully underwent potential curative resection at Aichi Cancer Center, Nagoya, Japan, were investigated. All tumors were histologically categorized according to the IASLC/ATS/ERS classification. Approval of the institutional review boards of Nagoya University Graduate School of Medicine and Aichi Cancer Center and written informed consent from the patients were obtained.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy kit (Qiagen, Valencia, CA), followed by treatment with DNase I. Double-stranded cDNA was synthesized from 100 ng of total RNA using MMLV-RT and poly dT primer incorporating the T7 promoter.
|
| Label |
Cy3
|
| Label protocol |
Cy5-sample cRNA and Cy3-sample cRNA were generated and hybridized to a SurePrint G3 Human GE 8x60K Microarray kit (Agilent Technologies) with 60k distinct probes.
|
| |
|
| |
| Hybridization protocol |
300 ng of Cy5-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) and Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) were fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent GE hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K Microarrays (G4851A) for 17 hours at 65 °C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37 °C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
|
| Scan protocol |
SurePrint G3 Human GE 8x60K Microarray with 60k distinct probes was scanned using an Agilent DNA microarray scanner (G2539A, Agilent Technologies). Images were quantified using Agilent Scan Control Software (version A.8.5.1).
|
| Data processing |
LOWESS normalized, background subtracted VALUE data obtained from ratio of processed Red signal/processed Green signal using Agilent Scan Control Software (version A.8.5.1).
|
| |
|
| Submission date |
Mar 10, 2015 |
| Last update date |
Jan 06, 2016 |
| Contact name |
Takashi Takahashi |
| Organization name |
Aichi Cancer Center
|
| Street address |
1-1 Kanokoden, Chikusa-ku
|
| City |
Nagoya |
| State/province |
Aichi |
| ZIP/Postal code |
464-8681 |
| Country |
Japan |
| |
|
| Platform ID |
GPL14550 |
| Series (2) |
| GSE66759 |
Identification of mir-342-3p functionally associated with transcriptional activity of MYC in lung cancer [patients] |
| GSE66760 |
Identification of mir-342-3p functionally associated with transcriptional activity of MYC in lung cancer |
|
