|
| Status |
Public on Aug 12, 2010 |
| Title |
miRNA profile in esophageal squamous cell carcinoma (ESCC) 5 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
cancerous tissue from ESCC clinical patient
|
| Organism |
Homo sapiens |
| Characteristics |
gender: Male
age: 65
tissue: cancerous esophagus
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA are harvested using TRIzol (Invitrogen) and RNeasy mini kit (QIAGEN) according to manufacturer’s instructions.
|
| Label |
Hy3
|
| Label protocol |
After having passed RNA measurement on the Nanodrop instrument, the samples are labeled using the miRCURY™ Hy3™/Hy5™ Power labeling kit according to manufacturer’s instructions.
|
| |
|
| Channel 2 |
| Source name |
normal tissue from ESCC clinical patient
|
| Organism |
Homo sapiens |
| Characteristics |
gender: Male
age: 65
tissue: normal esophagus
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA are harvested using TRIzol (Invitrogen) and RNeasy mini kit (QIAGEN) according to manufacturer’s instructions.
|
| Label |
Hy5
|
| Label protocol |
After having passed RNA measurement on the Nanodrop instrument, the samples are labeled using the miRCURY™ Hy3™/Hy5™ Power labeling kit according to manufacturer’s instructions.
|
| |
|
| |
| Hybridization protocol |
the labled RNA were hybridized on the miRCURY™ LNA Array (v.11.0)according to manufacturer’s instructions.
|
| Scan protocol |
Scanning is performed with the Axon GenePix 4000B microarray scanner. GenePix pro V6.0 is used to read the raw intensity of the image.
|
| Description |
Total RNA are harvested using TRIzol (Invitrogen) and RNeasy mini kit (QIAGEN) according to manufacturer’s instructions. After having passed RNA measurement on the Nanodrop instrument, the samples are labeled using the miRCURY™ Hy3™/Hy5™ Power labeling kit and hybridized on the miRCURY™ LNA Array (v.11.0). The samples were hybridized on a hybridization station following the scheme you outlined in the sample submission. Scanning is performed with the Axon GenePix 4000B microarray scanner. GenePix pro V6.0 is used to read the raw intensity of the image.
|
| Data processing |
The ratio of red signal to green signal (green signal to red signal for Dye Swap) was calculated after background subtraction and normalization using the global Lowess (Locally Weighted Scatter plot Smoothing) regression algorithm (MIDAS, TIGR Microarray Data Analysis System), which we have found produces the best within-slide normalization to minimize the intensity-dependent differences between the dyes. Median ratios were calculated from Lowess normalized capture probe replicates then log2 median ratios were calculated.
|
| |
|
| Submission date |
Jul 26, 2010 |
| Last update date |
Aug 11, 2010 |
| Contact name |
Enmin Li |
| E-mail(s) |
nmli@stu.edu.cn
|
| Phone |
86-754-8900847
|
| Organization name |
Shantou university, medical college
|
| Street address |
22 Xinling Road
|
| City |
shantou |
| State/province |
guangdong |
| ZIP/Postal code |
515041 |
| Country |
China |
| |
|
| Platform ID |
GPL7723 |
| Series (1) |
| GSE23142 |
miRNA profile in esophageal squamous cell carcinoma (ESCC) |
|
