Information on the replication time and chromatin structure of human genome were obtained from previous studies [20], [21], where DNA from S/G1 phase and open/compact chromatin were co-hybridized to a BAC clone array.
Raw data from 18 (six independent biological replicates for each parasite clone) array chips showed comparable data scales, distributions, and good RNA qualities with no apparent RNA degradation in any hybridizations (Figure S1, S2, and S3) [30].
Nuclei from unsynchronised cells were sorted into S and G1 phases, and the S and G1 DNAs were differentially labelled and simultaneously hybridized to either a genomic clone array probes (mean size 150 kb) spaced at 1 Mb intervals [7] or a chromosome 6 tile path array of BAC and PAC clones whose midpoints were spaced at 94 kb intervals on average [6].
Transcript profiling using a 3,324-cDNA 3,324-cDNAy revealed differential regulation of 133 unigenes, cloneified into 11 functionarraytegorevealed
Comparative genomic hybridization was done onto the 1 megabase (Mb) Bacterial Artificial Chromosome (BAC) clone array platform developed at the University of Pennsylvania.
Analysis was conducted with a 13 000 cDNA clone array for gene expression measurement and a Comparative Genomic Hybridisation (CGH) microarray for gene copy number measurements.
We also conducted conventional array-comparative genomic hybridization (CGH) analyses on the tissue samples to verify that no significant somatic differences in copy number existed within the same individual for sequences represented by our clone array (data not shown).
In other words, the Eif1a feature did not have one of the most significant p-values in the single clone array screen, but the Eif1a feature was derived from a feature pool which did have the most significant p-value in the 3,000 component sublibrary screen.
Each 8 × 12-cm filter contained 6,144 clones arrayed in 4 × 4 spotted pattern.
The following specific sequencing and mapping methods are discussed in detail: clone-array pooled shotgun sequencing (CAPSS); transversal shotgun pooling designs; clone-array pooled shotgun mapping (CAPS-MAP); pooled genomic indexing (PGI); short-tag pooled genomic indexing (ST-PGI); and comparative sequence assembly (the CSA™ method).
