Quantitative methods for genome-scale analysis of in situ hybridization and correlation with microarray data

Table 1 Gene expression platforms and data used in the cross-platform comparison

Technology	Platform	Unique probe sequences	Unique probe sequences with Entrez IDs	Mouse strain	Mouse age (weeks)	Mouse sex
Microarray	GNF [58], Affymetrix GNF1M	31,777	26,982	C57BL/6J	10-12	M and F
	Teragenomics [57], Affymetrix MG-U74Av2	12,488	11,779	C57BL/6J	8	M
ISH	ABA [3]	25,739	21,677	C57BL/6J	8	M

The table shows the technology, followed by the source of the publicly available data (platform), number of probes with unique sequences (unique probe sequences), number of probes/sequences that have Entrez IDs (unique probe sequences with Entrez IDs), and the biological samples used to generate the expression data (mouse strain, age, and sex). Replicates for GNF consist of GNF1 and GNF2 and are identified by the column names of the downloadable data file GNF1M, MGJZ030207007A and MGJZ030207007B, respectively. Teragenomics replicates (TERA1 and TERA2) are specified by GEO IDs and are listed in the Materials and methods.

ISSN: 1474-760X