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Sample GSM1069840 Query DataSets for GSM1069840
Status Public on Aug 01, 2014
Title Cancer tissue from patient 120
Sample type RNA
 
Source name Cancer tissue from patient 120
Organism Homo sapiens
Characteristics tissue type: Cancer tissue
patient: patient 120
dataset: test
age: 50
gender: male
tobacco use: yes
alcohol use: yes
family history: negative
tumor location: upper
tumor grade: moderately
t stage: 1
n stage: 3
tnm stage: III
status: dead
survival_month: 17.5
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from the specimens using Trizol reagent (Invitrogen) and purified with mirVana miRNA Isolation Kit (Ambion, Austin, TX, USA). RNA purity and concentration were determined from OD260/280 readings using spectrophotometer (NanoDrop ND-1000) and RNA integrity was determined by 1% formaldehyde denaturing gel electrophoresis.
Label Cy3
Label protocol The extracted RNA were labeled according to the Agilent manufacturer's instructions. Briefly, the miRNAs were labeled using the Agilent miRNA labeling reagent. Total RNA (100 ng) was dephosphorylated and ligated with pCp-Cy3.
 
Hybridization protocol The labeled RNA was purified and hybridized to miRNA arrays according to the Agilent manufacturer's instructions.
Scan protocol Images were scanned with the Agilent microarray scanner (Agilent), gridded, and analyzed using Agilent feature extraction software version 10.10.
Description Cancer tissue from patient 120
Data processing The miRNA array data were analyzed for data summarization, normalization and quality control by using the Percentile Shift (90th percentile) with GeneSpring software V11.5 (Agilent).
 
Submission date Jan 24, 2013
Last update date Aug 01, 2014
Contact name Jiagen Li
E-mail(s) [email protected]
Organization name Cancer Institute, CAMS
Street address 17 Panjiayuannanli Chaoyang District
City Beijing
ZIP/Postal code 100021
Country China
 
Platform ID GPL16543
Series (1)
GSE43732 MiRNA Expression Profile Study Reveals a Prognostic Signature for Esophageal Squamous Cell Carcinoma

Data table header descriptions
ID_REF
VALUE Normalized miRNA probe signal intensity

Data table
ID_REF VALUE
Blank
NC1_00000197
NC1_00000215
NC2_00079215
NC2_00092197
NC2_00106057
NC2_00122731
NegativeControl
bkv-miR-B1-3p
bkv-miR-B1-5p
dmr_285 0.6971111
dmr_3 1.0110884
dmr_308
dmr_316
dmr_31a -0.5910864
dmr_6 0.82782555
ebv-miR-BART1-3p
ebv-miR-BART1-5p
ebv-miR-BART10
ebv-miR-BART10*

Total number of rows: 2029

Table truncated, full table size 35 Kbytes.




Supplementary file Size Download File type/resource
GSM1069840_US10313827_253816610011_S01_miRNA_107_Sep09_1_3.txt.gz 8.9 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record

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