patient: patient 1 disease state: CCC tissue: liver_non-tumor part gender: male age: 74 histol information: moderate tubular date of birth: 1933/12/11 afp: 6 pivka-ii: 24 cea: 9.4 ca19-9: 34 tumor size: 35 x 45 hospotal id: 07-240-050
Treatment protocol
Surgically resected hepatocellular carcinoma (HCC) samples and surrounded non-tumor samples, and cholangiocarcinoma (CCC) samples and surrounded non-tumor samples
Extracted molecule
total RNA
Extraction protocol
RNA was prepared using the mirVana miRNA isolation kit (Life Technologies, CA, USA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-2000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
Label
Cy3
Label protocol
For miRNA microarray, 100 ng of RNA was labeled and hybridized using the Human microRNA Microarray Kit (Rel 14.0) (Agilent Technologies, CA, USA) according to manufacturer’s protocol for use with Agilent microRNA microarrays Version 1.0.For mRNA micaroarray, 100 ng of RNA was labeled and hybridized using the SurePrint G3 Human GE microarray kit (G4851B) (Agilent Technologies, CA, USA) according to manufacturer’s protocol for use with Agilent microarrays.
Hybridization protocol
For miRNA microarray, 100 ng of RNA was labeled and hybridized using the Human microRNA Microarray Kit (Rel 14.0) (Agilent Technologies, CA, USA) according to manufacturer’s protocol for use with Agilent microRNA microarrays Version 1.0.For mRNA micaroarray, 100 ng of RNA was labeled and hybridized using the SurePrint G3 Human GE microarray kit (G4851B) (Agilent Technologies, CA, USA) according to manufacturer’s protocol for use with Agilent microarrays.
Scan protocol
For miRNA microarray, hybridization signals were detected with Agilent DNA microarray scanner G2539B and the scanned images were analyzed using Agilent feature extraction software (v10.10.1.1). For mRNA microarray, hybridization signals were detected with Agilent DNA microarray scanner G2539A and the scanned images were analyzed using Agilent feature extraction software (v10.10.1.1).
Description
non-tumor miRNA_2
Data processing
For miRNA and mRNA microarray, gProcessedSignal was extracted and normalized so as to have zero mean and variance of 1.
