We mapped genomic binding sites for endogenous c-Myc in murine embryonic stem (ES) cells by employing DNA derived from anti-Myc chromatin-immunoprecipitation to probe DNA microarrays (ChIP-chip) comprised of 21,632 mouse gene promoters.
Furthermore, using this protocol of cross-species hybridisation, we have compared gene expression in bovine unfertilised oocytes and blastocyst using a larger microarray (The Human Ensembl Chip) comprising 15,500 fully sequenced and annotated genes and ESTs.
Depending on the coverage of the probes on the microarray chips, the intersection with the HPRD network comprised of 5574 to 8651 nodes including 559 to 706 receptors and 505 to 617 transcription factors (Table 1).
The microarray chips used for this study were the commercially available Affymetrix GeneChip® Cotton Genome Microarray (Affymetrix Inc., Santa Clara, CA), comprising 239,777 probe sets representing 21,854 cotton transcripts from a variety of EST databases.
The reference list comprised 1050 mRNA IDs of 530 TGF- β related genes that were analyzed with HGU 133A microarray chips.
Microarray chips were scanned using a DNA Microarray Scanner (Agilent Technologies).
Microarray chips and reagents used in the experiment of a given colony were from the same Affymetrix batch.
Genome-wide studies using microarray chips to identify copy number changes in human cancer are becoming more common.
The microarray chips were scanned with GeneChip® scanner (Affymetrix).
Commercially available microarray chips for mouse genes (Agilent MouseGE 4 × 44 K, Agilent Technologies) were used.
