|
| Status |
Public on Jun 30, 2016 |
| Title |
TE-1_control1_72hr |
| Sample type |
RNA |
| |
|
| Source name |
TE-1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: ESCC cell line TE-1
treatment: VTRNA1-1 ASO
genotype/variation: control
time: 72hr
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated with mirVana RNA Isolation labeling kit (Ambion Inc) according to the manufacturer protocol. RNA quality and integrity were confirmed by ExperionTM Automated Electrophoresis System (BIO-RAD)
|
| Label |
Biotin
|
| Label protocol |
Biotin-labeled cRNA samples for hybridization were prepared according to Illumina's recommended sample labeling procedure: 500 ng of total RNA was used for cDNA synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA using the Illumina. TotalPrep RNA Amplification kit (Ambion Inc., Austin, TX). cRNA concentrations using spectrophotometer (Nanodrop, ND-1000)
|
| |
|
| Hybridization protocol |
Labeled, amplified material (750 ng per array) was hybridized to the Illumina HumanHT-12 V4.0 expression beadchip according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA).
|
| Scan protocol |
Arrays were scanned with an Illumina Bead array Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc., San Diego, CA) according to the Manufacturer's instructions
|
| Description |
TE-1_con1.72hr
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software.
|
| Data processing |
Array data processing were performed on Illumina BeadStudio software. We normalized gene expression data using Quantile normalization and log2 transformatoin. To export to a data matrix, Sample Gene Profile option of this software was used.
|
| |
|
| 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 |
GPL10558 |
| Series (2) |
| GSE55854 |
Comprehensive Analysis of Recurrence-Associated Small Non-Coding RNAs in Esophageal Cancer [Illumina] |
| GSE55857 |
Comprehensive Analysis of Recurrence-Associated Small Non-Coding RNAs in Esophageal Cancer |
|
