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Sample GSM1321559 Query DataSets for GSM1321559
Status Public on Jun 30, 2014
Title Metastasis
Sample type RNA
Source name metastatic lesion
Organism Homo sapiens
Characteristics age: 58y
gender: male
tissue: cervical lymph node
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega)
Label Cy3
Label protocol cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).
Hybridization protocol cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8×60K ; Agilent Technologies) according to the manufacturer's instructions.
Scan protocol The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version (Agilent Technologies).
Data processing The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of two samples were log2-transformed and normalized by the quantile algorithm with the Bioconductor.
Submission date Feb 04, 2014
Last update date Jun 30, 2014
Contact name Takahiro Fujinaga
Organization name Kyushu University
Department Faculty of Dental Science
Lab Division of Maxillofacial Diagnostic and Surgical Sciences
Street address 3-1-1 Maidashi Higashi-ku
City Fukuoka
State/province Fukuoka
ZIP/Postal code 812-8582
Country Japan
Platform ID GPL17077
Series (1)
GSE54672 Analysis of biological characterization and metastasis-related genes in cell lines derived from the Primary lesion and lymph node metastasis of a squamous cell carcinoma arising in the mandibular gingiva

Data table header descriptions
VALUE quantile normalized signal, non-log scaled and ABS CALL.

Data table
A_19_P00315452 363.3343 P
A_19_P00315459 25.87102 P
A_19_P00315482 4.057922 A
A_19_P00315492 4.3544775 A
A_19_P00315493 189.61755 P
A_19_P00315502 367.2283 P
A_19_P00315506 276.6165 P
A_19_P00315518 13.25244 A
A_19_P00315519 4.1604345 A
A_19_P00315524 4.273873 A
A_19_P00315528 17.42387 A
A_19_P00315529 10.108309 A
A_19_P00315538 18.746065 A
A_19_P00315541 4.8061685 A
A_19_P00315543 4.5875855 A
A_19_P00315550 50.21246 P
A_19_P00315551 60.371425 P
A_19_P00315554 4.228826 A
A_19_P00315581 3504.677 P
A_19_P00315583 8.683103 A

Total number of rows: 50599

Table truncated, full table size 1241 Kbytes.

Supplementary file Size Download File type/resource
GSM1321559_US11030397_253949415975_S01_GE1_107_Sep09_2_3.txt.gz 12.4 Mb (ftp)(http) TXT
Processed data included within Sample table

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