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Sample GSM1347487 Query DataSets for GSM1347487
Status Public on Jun 30, 2016
Title ESCC normal sample_045
Sample type RNA
 
Source name surgically resected esophagus preserved in tumor bank
Organism Homo sapiens
Characteristics sample id: 45
tissue: ESCC normal
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_045N
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

Data table header descriptions
ID_REF
VALUE Log2 transformed normalized signal intensity.

Data table
ID_REF VALUE
1367452_st 1.404886842
1367453_st 1.011558533
1367454_st 1.533748388
1367455_st 1.010019779
1367456_st 1.357534647
1367457_st 1.551581264
1367458_st 1.186787367
1367459_st 0.80637008
1367460_st 0.831752121
1367461_st 1.34648335
1367462_st 0.661596477
1367463_st 0.81476903
1367464_st 1.025484443
1367465_st 0.965022147
1367466_st 1.278615713
1367467_st 1.373429656
1367468_st 1.09576726
1367469_st 1.749154091
1367470_st 0.903781652
1367471_st 2.530525446

Total number of rows: 20706

Table truncated, full table size 578 Kbytes.




Supplementary file Size Download File type/resource
GSM1347487_NCC_LHS_045N.CEL.gz 682.6 Kb (ftp)(http) CEL
Processed data included within Sample table

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