NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1067234 Query DataSets for GSM1067234
Status Public on May 21, 2015
Title KM_059T
Sample type RNA
 
Source name HCC tumor
Organism Homo sapiens
Characteristics disease state: hepatocellular carcinoma (HCC)
tissue: HCC tumor
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from tissues with the mirVana RNA Isolation labeling kit (Ambion, Inc.) according to the manufacturer's protocol. RNA quality and integrity were confirmed by the 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 were determined using a spectrophotometer (Nanodrop, ND-1000).
 
Hybridization protocol Labeled, amplified material (750 ng per array) was hybridized to the Illumina HumanHT-12 V4.0 expression BeadChip according to the manufacturer's instructions (Illumina, Inc., San Diego, CA).
Scan protocol Arrays were scanned with an Illumina BeadArray Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc., San Diego, CA) according to the manufacturer's instructions.
Data processing Array data processing was performed on Illumina BeadStudio software. We normalized gene expression data using quantile normalization and log2 transformation. To export to a data matrix, the Sample Gene Profile option of this software was used.
 
Submission date Jan 18, 2013
Last update date May 21, 2015
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 GPL10558
Series (1)
GSE43619 Activation of beta-catenin in hepatocellular carcinoma (HCC patients)

Data table header descriptions
ID_REF
VALUE Log2-transformed quantile-normalized signal intensity

Data table
ID_REF VALUE
ILMN_1762337 6.76
ILMN_2055271 6.8
ILMN_1736007 6.69
ILMN_2383229 10.59
ILMN_1806310 11.68
ILMN_1779670 6.88
ILMN_1653355 6.83
ILMN_1717783 6.59
ILMN_1705025 6.78
ILMN_1814316 6.65
ILMN_2359168 6.47
ILMN_1731507 6.45
ILMN_1787689 6.38
ILMN_3241953 7.82
ILMN_1745607 12.4
ILMN_2136495 6.55
ILMN_1668111 6.75
ILMN_2295559 6.65
ILMN_1735045 7.14
ILMN_1680754 7.1

Total number of rows: 47231

Table truncated, full table size 826 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap