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Sample GSM741657 Query DataSets for GSM741657
Status Public on Mar 15, 2012
Title EAC4
Sample type RNA
 
Channel 1
Source name esophageal adenocarcinoma biopsy
Organism Homo sapiens
Characteristics tissue: esophagus
gender: male
tumor stage: T3N1
Stage: -
Treatment protocol none, fresh biopsy material
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from biopsy samples using miRNeasy Minikit (Qiagen) according to manufacturer protocol
Label Hy3
Label protocol Labeling was performed by Exiqon, according to manufacturer protocol; in brief 2 ug of total RNA was labeled using the miRCURY Hy3/Hy5 labeling kit according to Exiqon protocol (Vedbaek, Denmark)
 
Channel 2
Source name common reference
Organism Homo sapiens
Characteristics reference: common reference (mixture of all esophageal adenocarcinoma, Barrett's esophagus and normal squamous esophagus samples used)
Treatment protocol none, fresh biopsy material
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from biopsy samples using miRNeasy Minikit (Qiagen) according to manufacturer protocol
Label Hy5
Label protocol Labeling was performed by Exiqon, according to manufacturer protocol; in brief 2 ug of total RNA was labeled using the miRCURY Hy3/Hy5 labeling kit according to Exiqon protocol (Vedbaek, Denmark)
 
 
Hybridization protocol Hybridization was performed by Exiqon according to manufacturer protocol
Scan protocol Scanning was performed by Exiqon according to manufacturer protocol
Description EAC4_slide10.txt
Data processing Data processing was performed by Exiqon according to manufacturer protocol; in brief normalization included background subtraction and normalization with global Lowess (Locally Weighter Scatterplot Smoothing) regression algorithm. This within-slide normalization was performed to minimize differences between the colors in an intensity-dependent manner. The criterion for deciding that a miRNA had failed on a particular array was the observation that 3 or more of the 4 replicated measures of this miRNA had a signal that was below background. In addition, Hy3 and Hy5 signals lower than 1.5x of the median signal intensity of the given slide were excluded. Replicated measurements of the same miRNA from each slide were averaged to per-chip median values and then used to obtain geometric means and standard deviations for each miRNA.
 
Submission date Jun 14, 2011
Last update date Mar 15, 2012
Contact name Jantine Wilhelmina Paula Maria van Baal
E-mail(s) j.w.p.m.vanbaal-2@umcutrecht.nl
Phone +31 88 7556279
Fax +31 88 7555533
Organization name University Medical Center Utrecht
Department Gastroenterology and Hepatology
Lab Gastroenterology and Hepatology
Street address Heidelberglaan 100
City Utrecht
ZIP/Postal code 3584 CX
Country Netherlands
 
Platform ID GPL7722
Series (1)
GSE29965 microRNA expression in Barrett's esophagus and esophageal adenocarcinoma

Data table header descriptions
ID_REF
VALUE log2 normalized ratio Hy3/Hy5 ratios

Data table
ID_REF VALUE
42530 -0.554940245
17732 0.038150945
17898 -0.047425877
11015 -0.142051348
10988 -0.306101786
13177 1.164579227
42727 -0.353601254
42716 -0.18589132
29562 0.235888596
10985 0.385183222
27544 0.178460926
42641 1.168722861
10986 -0.164655978
10995 0.759361143
27559 -0.024572225
19591 1.006200934
29872 -0.129220419
42515 0.901218311
42825 -0.671681525
42487 0.187527661

Total number of rows: 866

Table truncated, full table size 10 Kbytes.




Supplementary file Size Download File type/resource
GSM741657.txt.gz 44.0 Kb (ftp)(http) TXT
Processed data included within Sample table

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