Comment[ArrayExpressAccession] E-GEOD-57209 MAGE-TAB Version 1.1 Public Release Date 2014-05-01 Investigation Title Sociogenomics of self vs. non-self cooperation during development of Dictyostelium discoideum [NC105.1_RFP_vs_NC28.1] Comment[Submitted Name] Sociogenomics of self vs. non-self cooperation during development of Dictyostelium discoideum [NC105.1_RFP_vs_NC28.1] Experiment Description Dictyostelium discoideum, a microbial model for social evolution, is known to distinguish self from non-self and show genotype-dependent behavior during chimeric development. Aside from a small number of cell-cell recognition genes, however, little is known about the genetic basis of self/non-self recognition in this species. Based on the key hypothesis that there should be differential expression of genes if D. discoideum cells were interacting with non-clone mates, we performed transcriptomic profiling study in this species during clonal vs. chimeric development. Wild strains isolated from North Carolina, which have been shown to form a dominance hierarchy when co-developing in chimeras, were used. The transcriptomic profiles of D. discoideum cells in clones vs. different chimeras were compared at five different developmental stages using a customized microarray. Effects of chimerism on global transcriptional patterns associated with social interactions were observed. The chimera developmental program may also provide insights on behavioral changes associated with social conflicts in this species. two-condition chimera experiments: two conditions (chimeric: NC105.1-RFP + NC28.1 vs. control: NC105.1-RFP + NC105.1), five time points for each condition (4 h, 8 h, 12 h, 16 h, and 20 h), two biological replicates for each condition at each time point, two technical replicates for each biological replicate (Cy5 vs. Cy3) Term Source Name ArrayExpress EFO Term Source File http://www.ebi.ac.uk/arrayexpress/ http://www.ebi.ac.uk/efo/efo.owl Person Last Name Li Li Purugganan Person First Name Si Si Michael Person Mid Initials I D Person Email geo@ncbi.nlm.nih.gov Person Affiliation New York University Person Address Biology, New York University, 12 Waverly Place, New York, New York, USA Person Roles submitter Protocol Name P-GSE57209-1 P-GSE57209-5 P-GSE57209-6 P-GSE57209-2 P-GSE57209-3 P-GSE57209-4 P-GSE57209-7 Protocol Description Gene expression data was log2-transformed and normalized within array using a combined rank consistency filtering with LOWESS intensity normalization in FE. Between-array normalization was implemented using the Aquantile method in the Limma package in R (http://www.R-project.org/) to ensure the A-values (average intensities) have the same empirical distribution across arrays leaving the M-values (log2-ratios) unchanged ID_REF = VALUE = normalized log2 ratio representing sample/biological reference Samples were amplified and labeled using the Agilent Low Input Quick Amp Labeling Kit together with positive control transcripts Equal amounts of sample and common biological reference cRNA were hybridized against the same microarray at 65M-0C for 17 hours and washed afterwards Equal amounts of RFP and non-RFP amoebae were mixed and spread evenly on two developing plates (1.5% KK2 agar) at a density of 1.6M-CM-^W106 cells/cm2 as biological replicates. Developing plates were incubated in a dark and humid environment at 22M-0C for 4 h, 8 h, 12 h, 16 h, and 20 h, respectively, before harvest. Samples collected at these different time points/developmental stages were mechanically disaggregated in disassociation buffer (KK2, 20mM EDTA) and subject to fluorescence-activated cell sorting (FACS) with a FACS Aria from BD Biosciences (San Jose, CA) immediately with a nozzle size of 70 M-NM-