Global gene transcription analysis of Anaplasma phagocytophilum in tick and human cells using tiling microarrays

A whole genome tiling microarray based on the published sequence of the Anaplasma phagocytophilum (Ap) strain Hz genome was used to measure transcriptional activity of Ap grown to late stage in three cell lines representing the diversity of host cells naturally infected by Ap: two human cell lines, HL-60 (promyelocytic leukocyte) and HMEC-1 (microvascular endothelial), and the tick (Ixodes scapularis) cell line ISE6. Keywords: cell type comparison Total RNA was isolated from Ap (HZ strain) infected cells, used to make biotinylated cDNA fragments, and hybridized to Ap whole genome tiling arrays to measure relative abundance of mRNA transcripts. .CEL files generated by the University of Minnesota’s microarray facility were joined to Affymetrix BPMAP files specific to the tiling array using Affymetrix® Tiling Analysis Software (TAS). TAS generated a list of signal intensities and arranged them in order of genomic location and DNA strand. The intensity values were normalized via quantiles, and imported into the IgorPro data analysis program (WaveMetrics Lake Oswego OR, USA) along with the ORF and structural RNA annotations available from NCBI (http://www.ncbi.nlm.nih.gov). A script was written to index a trapezoidal integration algorithm of the intensity list with the start and end genomic positions indicated on the annotation. This script operation generated a list of 1411 “areas under the curve” (see Supplementary file at the foot of this record).