Comment[ArrayExpressAccession] E-GEOD-22466 Public Release Date 2011-09-30 Investigation Title A gene-expression oligo microarray for two serial passages of Ichthyophthirius multifiliis Comment[Submitted Name] A gene-expression oligo microarray for two serial passages of Ichthyophthirius multifiliis Experiment Description The protozoan Ichthyophthirius multifiliis (Ich) is a eukaryotic ciliate parasite of freshwater fish. Ich causes ichthyophthiriosis or ‘white spot disease’ characterized by white cysts covering the host skin and gills. The parasite is responsible for high mortalities and severe economic losses to farmed species as well as to ornamental species of fish. Despite the global importance of Ich, little is known about the genetic processes underlying its infectivity. Ich has three main life-stages, an infective theront, a parasitic trophont, and a reproductive tomont. Further, Ich has been demonstrated previously to display a loss of infectivity as the number of lab-passages on a fish increase, presumably relating to senescence of the organism. To compare gene expression among two of the three Ich life-stages (the tomont and trophont life-stages) at different passages, oligonucleotide microarrays were utilized. Gene expression was analyzed in samples taken from two of the three Ich life-stages (the tomont and trophont life-stages) at the first serial passage on channel catfish in the lab (P1), and at serial passage 100 (P100). The results of this study will add in the understanding of protozoan global gene regulation and biology and should aid in the development of strategies aimed at the control of this important fish parasite. Submitted is a 12 chip oligo array design using 385 K Nimblegen arrays. A total of 12 microarrays were used for the experiment: three replicates from two of the three Ich life-stages (tomont and trophont life-stages) at serial passage #1 (P1) and serial passage #100 (P100). Probes were designed using 9,129 unique Ich ESTs (clustered contigs and singletons) as well as 26,273 Tetrahymena thermophila and 5,184 Plasmodium falciparum coding sequences. The probe design strategy was to create 12 60-mer oligonucleotide probes per I. multifiliis sequence, and 10 60-mer oligonucleotide probes for both T. thermophila and P. falciparum sequences. Total RNA was isolated in triplicate from the three life-stages of I. multifiliis and submitted to Nimblegen for labeling, hybridization, and scaning. This microarray study is based on the GPL9449 platform built for the developmental stages of the parasite. Date of Experiment Term Source Name EFO Term Source Version Term Source File http://www.ebi.ac.uk/efo/efo.owl Person Last Name Peatman Abernathy Xu Peatman Kucuktas Klesius Liu Person First Name Eric Jason De-Hai Eric Huseyin Phillip Zhanjiang Person Mid Initials W Person Email peatmer@auburn.edu Person Affiliation Auburn University Person Phone Person Fax Person Address Fisheries and Allied Aquacultures, Auburn University, 203 Swingle Hall, Auburn, AL, USA Person Roles submitter Person Roles Term Source REF Person Roles Term Accession Number Normalization Type Normalization Term Accession Number Normalization Term Source REF Replicate Type Replicate Term Accession Number Replicate Term Source REF Experimental Design Experimental Design Term Accession Number Experimental Design Term Source REF Quality Control Type Quality Control Term Accession Number Quality Control Term Source REF Protocol Name P-GSE22466-1 P-GSE22466-5 P-GSE22466-4 P-GSE22466-2 P-GSE22466-3 P-GSE22466-6 P-GSE22466-7 Protocol Description ID_REF =
VALUE = RMA signal Scanning was perfomed by Nimblegen Systems, Inc., Madison, WI, USA using their standard labelling protocol. See www.nimblegen.com for further details. Hybridization was perfomed by Nimblegen Systems, Inc., Madison, WI, USA using their standard labelling protocol. See www.nimblegen.com for further details. Total RNA was isolated using the TRIzol reagent from Invitrogen, Carlsbad, CA, USA. RNA quantity and quality was assessed using a spectrophotometer and denaturing agarose gel electrophoresis containing formaldehyde. Labeling was perfomed by Nimblegen Systems, Inc., Madison, WI, USA using their standard labelling protocol. See www.nimblegen.com for further details. The raw data (.pair file) was subjected to RMA (Robust Multichip Average; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package from Nimblegen. See www.nimblegen.com for futher details. The data was quantile normalized and subjected to RMA by Nimblegen. Final differential expression was determined using the DNA-chip Analyzer (dChip) software (Li C. BMC Bioinformatics 9:231). Protocol Software Protocol Hardware Protocol Contact Protocol Type bioassay_data_transformation image_aquisition hybridization nucleic_acid_extraction labeling feature_extraction feature_extraction Protocol Term Source REF Protocol Term Accession Number Experimental Factor Name DEVELOPMENTAL STAGE LAB-PASSAGE NUMBER Experimental Factor Type developmental stage lab-passage number Experimental Factor Term Source REF Experimental Factor Term Accession Number Publication Title Publication Author List PubMed ID Publication DOI Publication Status Publication Status Term Source REF Publication Status Term Accession Number Comment[SecondaryAccession] GSE22466 Comment[GEOLastUpdateDate] 2011-09-30 Comment[AEExperimentType] transcription profiling by array Comment[GEOReleaseDate] 2011-09-29 Comment[ArrayExpressSubmissionDate] 2010-06-20 SDRF File E-GEOD-22466.sdrf.txt