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Series GSE11487 Query DataSets for GSE11487
Status Public on Aug 04, 2008
Title Global gene transcription analysis of Anaplasma phagocytophilum in tick and human cells using tiling microarrays
Platform organism Anaplasma phagocytophilum str. HZ
Sample organisms Ixodes scapularis; Homo sapiens; Anaplasma phagocytophilum str. HZ
Experiment type Expression profiling by genome tiling array
Summary 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
 
Overall design 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).
 
Contributor(s) Nelson CM, Herron MJ, Felsheim RF, Kurtti TJ, Munderloh UG
Citation(s) 18671858
Submission date May 16, 2008
Last update date Mar 19, 2012
Contact name Michael Herron
E-mail(s) herro001@umn.edu
Organization name Michael Herron
Department Entomology
Lab U. G. Munderloh
Street address 1980 Folwell Avenue, Room 219 Hodson Hall
City St. Paull
State/province MN
ZIP/Postal code 55108
Country USA
 
Platforms (1)
GPL6869 UMNENT Anaplasma phagocytophilum Hz whole genome tiling array 256K
Samples (18)
GSM289217 HzHL60_1
GSM289218 HzHL60_2
GSM289219 HzHL60_3
Relations
BioProject PRJNA106415

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE11487_Gene_lists_with_integrated_ORF.txt 258.9 Kb (ftp)(http) TXT
GSE11487_RAW.tar 73.6 Mb (http)(custom) TAR (of CEL)
Processed data included within Sample table

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