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Sample GSM422084 Query DataSets for GSM422084
Status Public on Dec 31, 2012
Title AICAR-3
Sample type RNA
 
Source name SK4 treated with AICAR (2mM) for 12 hrs
Organism Homo sapiens
Characteristics cell line: SK-4
tissue type: esophageal cancer
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from tissues with mirVana RNA Isolation labeling kit (Ambion Inc) according to the manufacturer's protocol. RNA quality and integrity were confirmed by ExperionTM Automated Electrophoresis System (BIO-RAD)
Label Biotin
Label protocol Biotin-labeled cRNA samples for hybridization were prepared according to Illumina's recommended sample labeling procedure: 500 ng of total RNA was used for cDNA synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA using the Illumina TotalPrep RNA Amplification kit (Ambion Inc., Austin, TX). cRNA concentrations using spectrophotometer (Nanodrop, ND-1000)
 
Hybridization protocol Labeled, amplified material (1,500 ng per array) was hybridized to the Illumina Human-6 BeadChip (48K) according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA). Array signals were developed by Amersham fluorolink streptavidin-Cy3 (GE Healthcare Bio-Sciences, Little Chalfont, UK) following the BeadChip manual.
Scan protocol Arrays were scanned with an Illumina Bead array Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc., San Diego, CA) according to the Manufacturer's instructions
Description To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software. The whole 48804 probes on the Human-6 beadChip.
Data processing Array data processing were performed on Illumina BeadStudio software. To export to a data matrix, Sample Gene Profile option of this software was used.
 
Submission date Jun 25, 2009
Last update date Dec 31, 2012
Contact name Sangbae Kim
E-mail(s) sangbkim22@gmail.com
Organization name Baylor Colleage of Medicine
Department HGSC
Street address 1 Baylor plaza
City Houston
State/province TX
ZIP/Postal code 77030
Country USA
 
Platform ID GPL6790
Series (1)
GSE16816 Combinatorial targeting of glycolysis and oxidative phosphorylation suppresses tumor growth and metastases.

Data table header descriptions
ID_REF Illumina_ID
VALUE Probes were pre-filtered by probe filtration option in Bead studio (p<0.05). Data was quantile normalized and log base 2 transformed.

Data table
ID_REF VALUE
ILMN_10001 13.17196465
ILMN_10004 9.801142693
ILMN_10005 10.73805809
ILMN_10026 9.68692112
ILMN_10033 10.51806259
ILMN_10040 8.677940369
ILMN_100436 10.00544167
ILMN_1005 8.968868256
ILMN_10054 9.814470291
ILMN_10057 11.37693977
ILMN_10062 9.458222389
ILMN_10063 9.614304543
ILMN_10073 10.57167721
ILMN_10077 11.04159069
ILMN_10078 10.24763107
ILMN_10085 8.383832932
ILMN_1009 10.54782963
ILMN_10091 10.16042614
ILMN_10095 10.79854488
ILMN_10104 13.38021755

Total number of rows: 16383

Table truncated, full table size 363 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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