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Sample GSM2151180 Query DataSets for GSM2151180
Status Public on May 13, 2016
Title Control1
Sample type RNA
 
Source name removed tumor, vehicle alone
Organism Homo sapiens
Characteristics cell line: pancreatic cancer cell line BxPC-3
treatment: Control
tissue: removed tumor
Treatment protocol Pancreatic cancer cells (BxPC-3) in culture were harvested and viable cells (5 × 106 cells) were injected subcutaneously into the backs of the mice. When tumor volumes reached 150 mm3, treatment began. The treatment group of mice received Deferasirox suspended in saline, which was administered by oral gavage every second day, with three treatments per week, over 21 days at concentrations of 200 mg/kg. The control mice were treated with the vehicle alone. At the end of the experiment, the mice were sacrificed and the tumors were excised and processed for genetic analyses.
Extracted molecule total RNA
Extraction protocol The total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.
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 8x60K v2; 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 9.5.1.1 (Agilent Technologies).
Description Gene expression after administration of Vehicle alone
Data processing The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (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 all samples were normalized by the quantile algorithm with the Bioconductor.
 
Submission date May 12, 2016
Last update date Apr 23, 2018
Contact name Hirofumi Harima
E-mail(s) harima@yamaguchi-u.ac.jp
Organization name Yamaguchi University Graduate School of Medicine
Department Department of Gastroenterology and Hepatology
Street address Minami Kogushi 1-1-1
City Ube
State/province Yamaguchi
ZIP/Postal code 755-8505
Country Japan
 
Platform ID GPL17077
Series (1)
GSE81363 Investigation of gene expression alterations of pancreatic cancer caused by Deferasirox administration
Relations
Reanalyzed by GSE113533

Data table header descriptions
ID_REF
VALUE quantile normalized signal, non-log scaled
ABS_CALL

Data table
ID_REF VALUE ABS_CALL
A_19_P00315452 690.8508833 P
A_19_P00315459 122.8557833 P
A_19_P00315482 8.53854 A
A_19_P00315492 5.081477258 A
A_19_P00315493 198.4936 P
A_19_P00315502 1475.553667 P
A_19_P00315506 269.8354 P
A_19_P00315518 71.59016833 P
A_19_P00315519 4.133850167 A
A_19_P00315524 23.66659167 P
A_19_P00315528 3.987330667 A
A_19_P00315529 4.277285167 A
A_19_P00315538 24.9478767 P
A_19_P00315541 11.16481983 A
A_19_P00315543 4.3289285 A
A_19_P00315550 218.2766833 P
A_19_P00315551 163.5711667 P
A_19_P00315554 4.141365388 A
A_19_P00315581 8722.237 P
A_19_P00315583 35.19383833 P

Total number of rows: 50599

Table truncated, full table size 1322 Kbytes.




Supplementary file Size Download File type/resource
GSM2151180_US11030397_253949435465_S01_GE1_107_Sep09_1_2.txt.gz 12.4 Mb (ftp)(http) TXT
Processed data included within Sample table

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