TABLE 1.
Microarrays and samples used in this studya
| Array | Probe type (oligonucleotide) | Surface coating and specification | Intrareplicate | Reference probe (amt [%] of test probes) | Test targets/samples | Normalization method(s)b |
|---|---|---|---|---|---|---|
| Pilot array | 50-mer | 30 functional genes derived from D. vulgaris, R. palustris, and S. oneidensis | Six replicates on a slide | 10, 5, 2.5, 1, 0.5, 0.25, 0.1, and 0.05 | gDNAs of D. vulgaris, R. palustris, and S. oneidensis | I, IV |
| D. vulgaris whole-genome array | 70-mer | ORFs for the genome of D. vulgaris Hildenborough | Duplicates on a slide | 2.5 | RNAs and gDNA of wild type D. vulgaris and Δfur mutant | II, III, IV |
| GeoChip | 50-mer | 37,000 gene sequences for more than 290 gene families | No intrareplicates | 2.5 | Microbial gDNAs from environmental soil samples of oilfield | I, IV |
a
For the CORS sequence, the reference probe was 5′-CCGCACCTCGGACCGCACACAATCGTTTGAGGACGTGTAGCTGTGCTGGC-3′. The reference target was complementary to the probe with Cy3 labeled at the 5′ end.
b
I, mean signal intensity normalization; II, dye swap normalization; III, gDNA normalization; IV, CORS normalization. See Materials and Methods for additional details.