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Status |
Public on Jun 30, 2016 |
Title |
ESCC normal sample_048 |
Sample type |
RNA |
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Source name |
surgically resected esophagus preserved in tumor bank
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Organism |
Homo sapiens |
Characteristics |
sample id: 48 tissue: ESCC normal
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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).
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Label |
Biotin
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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.
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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).
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Scan protocol |
Arrays were scanned using GeneChip® scanner 3000 7G (Affymetrix). Feature extraction was performed using Affymetrix Command Console software.
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Description |
NCC_LHS_048N Esophagus To export to gene expression data based on unique gene, we used BRB array tools.
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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).
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Submission date |
Mar 13, 2014 |
Last update date |
Jun 30, 2016 |
Contact name |
Hyun-Sung Lee |
E-mail(s) |
hyun-sung.lee@bcm.edu
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Phone |
7137988010
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Organization name |
BAYLOR COLLEGE OF MEDICINE
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Department |
Surgical Research
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Lab |
ABBR R651H
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Street address |
One Baylor Plaza
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City |
HOUSTON |
State/province |
TX |
ZIP/Postal code |
77030 |
Country |
USA |
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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 |
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