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Sample GSM1447768 Query DataSets for GSM1447768
Status Public on Mar 01, 2015
Title healthy control S011
Sample type RNA
 
Source name Serum
Organism Homo sapiens
Characteristics disease state: healthy control
tissue: serum
gender: Male
tumor stage: uncertain
age: 62
operability: uncertain
Extracted molecule total RNA
Extraction protocol Total RNA was extracted each from 300uL serum samples using 3D-Gene® RNA extraction reagent from liquid sample kit (Toray Industries, Inc.). Total RNA was also obtained from the FFPE sections using the Arcturus® Paradise® Extraction and Isolation kit (Life Technologies) in accordance with the manufacturer's instructions.
Label Cy5
Label protocol miRNA was labeled using 3D-Gene® miRNA Labeling kit in accordance with the manufacturer's instructions.
 
Hybridization protocol Hybridized for 16 h at 32 ºC with rotary shaker (250 rpm). Hybridization buffer and washing protocol was attached in the 3D-Gene® miRNA oligo chip kit.
Scan protocol 3D-Gene® Scanner (Toray Industries, Inc.) was used for scanning. Images were quantified using Extraction version 2.0.0.6 (Toray Industries, Inc.).
Description miRNA profiling
Data processing Mean and standard deviation (SD) of the 5% trimmed signals of the negative controls were calculated. Signals of miRNAs over mean+2SD of the negative controls were subtracted with the mean of the negative controls. The undetected signal was replaced with the value that was the least signal intensity on each DNA chip minus 0.1 in log2 scale followed by quantile normalization.
 
Submission date Jul 29, 2014
Last update date Mar 01, 2015
Contact name Ichikawa Makiko
E-mail(s) makiko.ichikawa.d3@mail.toray
Organization name Toray Industries, Inc.
Lab New Frontiers Research Laboratories
Street address 6-10-1
City Kamakura
State/province Kanagawa
ZIP/Postal code 248-0036
Country Japan
 
Platform ID GPL18941
Series (1)
GSE59856 MicroRNA markers for the diagnosis of pancreatic and biliary tract cancers

Data table header descriptions
ID_REF
VALUE Quantile normalized values

Data table
ID_REF VALUE
MIMAT0004502 2.612
MIMAT0004501 2.612
MIMAT0002844 2.778
MIMAT0002843 2.612
MIMAT0002824 5.5
MIMAT0002823 2.612
MIMAT0002807 3.806
MIMAT0002806 2.612
MIMAT0001635 2.612
MIMAT0001631 11.702
MIMAT0005890 2.612
MIMAT0005889 2.612
MIMAT0005873 2.612
MIMAT0005872 2.612
MIMAT0004591 2.612
MIMAT0004590 2.612
MIMAT0000232, MIMAT0004563 2.724
MIMAT0004562 2.612
MIMAT0004518 2.612
MIMAT0004517 2.612

Total number of rows: 2555

Table truncated, full table size 47 Kbytes.




Supplementary file Size Download File type/resource
GSM1447768_S011_SH3XA26.txt.gz 62.6 Kb (ftp)(http) TXT
Processed data included within Sample table

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