The microarray was scanned with an InnoScan microarray scanner (Innopsys) and the data collected was normalized [ 95, 96].
The microarray data we collected are available from the Gene Expression Omnibus (accession number GSE66088), and the previously collected ChIP-Seq data [ 20] are available from the Sequence Read Archive (accession number SRX338012).
It implies that these progression-related sub-networks, especially the ones which are annotated with significant functions, can be helpful in the understanding of molecular mechanism that underlies the progression of HCV induced hepatocarcinogenesis. Microarray data was collected from Gene Expression Omnibus (GEO) database.
Briefly, raw microarray data was collected from NCBI's Gene Expression Omnibus (GEO) [25], [26], and features on the array were mapped to NCBI Entrez Gene IDs using Version 9 of the mapping provided by Dai et al. [27], yielding 16,297 gene probe sets and 64 Affymetrix control gene probe sets.
Microarray data was collected by Roche NimbleGen (Iceland) as a service using 4 × 72 k format arrays.
Microarray data was collected at Asuragen using GeneChip Affymetrix HuGene10stv1_Hs_ENTREZG_desc array, according to standardized operating procedures.
Blood used for RNA microarray analysis was collected from the present cohort via venipuncture into PAXgene tubes (QIAGEN Inc., Valencia, CA).
Microarray data was collected by confocal scanning using the Roche NimbleGen MS200 Microarray Scanner at 2 μm pixel resolution (Roche NimbleGen, Inc., Madison, WI, USA).
The microarray data was collected for different rice tissues/organs and developmental stages, including germinating seedling (GS), seedling root (R), mature leaf (ML), leaf (YL; leaf subtending the shoot apical meristem), shoot apical meristem (SAM), and various stages of panicle (P1-P6) and seed (S1-S5) development (Jain et al., 2007; GSE6893).
The data from the microarray was collected and analyzed in accordance to the MIAME guidelines.
