|
| Status |
Public on Jun 30, 2016 |
| Title |
ESCC tumor sample_107 |
| Sample type |
RNA |
| |
|
| Source name |
surgically resected esophagus preserved in tumor bank
|
| Organism |
Homo sapiens |
| Characteristics |
sample id: 107
tissue: ESCC tumor
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from fresh frozen tissues was extracted using TRIzol® (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's procedures. RNA quality was assessed by Agilent 2100 bioanalyser using the RNA 6000 Nano Chip (Agilent Technologies, Santa Clara, CA), and quantity was determined by ND-1000 Spectrophotometer (NanoDrop Technologies, DE, USA).
|
| Label |
Biotin
|
| Label protocol |
1 μg of total RNA was labeled using the Genisphere® FlashTag® Biotin HSR RNA Labeling Kit (Genisphere LLC, Hatfield, PA, USA) following the manufacturer’s recommendation.
|
| |
|
| Hybridization protocol |
Then labeled small non-coding RNA was hybridized to the array and incubated as described in the protocol (Affymetrix). Then, the chips were washed and stained with GeneChip® Fluidics Station 450 (Affymetrix).
|
| Scan protocol |
Arrays were scanned using GeneChip® scanner 3000 7G (Affymetrix). Feature extraction was performed using Affymetrix Command Console software.
|
| Description |
NCC_LHS_107T
Esophagus
To export to gene expression data based on unique gene, we used BRB array tools.
|
| Data processing |
We analyzed all data of microarray using the Robust Multichip Averaging method and implemented quantile normalization with log2 transformation of gene expression intensities with BRB-Array Tools version 4.3.0 (Biometric Research Branch, National Cancer Institute, Bethesda, MD, USA) and the R-script from the Bioconductor project (www.bioconductor.org).
|
| |
|
| Submission date |
Mar 13, 2014 |
| Last update date |
Jun 30, 2016 |
| Contact name |
Hyun-Sung Lee |
| E-mail(s) |
hyun-sung.lee@bcm.edu
|
| Phone |
7137988010
|
| Organization name |
BAYLOR COLLEGE OF MEDICINE
|
| Department |
Surgical Research
|
| Lab |
ABBR R651H
|
| Street address |
One Baylor Plaza
|
| City |
HOUSTON |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL14613 |
| Series (2) |
| GSE55856 |
Comprehensive Analysis of Recurrence-Associated Small Non-Coding RNAs in Esophageal Cancer [Affymetrix] |
| GSE55857 |
Comprehensive Analysis of Recurrence-Associated Small Non-Coding RNAs in Esophageal Cancer |
|
