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Series GSE61914 Query DataSets for GSE61914
Status Public on Apr 21, 2015
Title Leaps and lulls in the developmental transcriptome of Dictyostelium discoideum
Organism Dictyostelium discoideum
Experiment type Expression profiling by high throughput sequencing
Summary Development of the soil amoeba Dictyostelium discoideum is triggered by starvation. When placed on a solid substrate, the starving solitary amoebae cease growth, communicate via extracellular cAMP, aggregate by tens of thousands and develop into fully integrated multicellular organisms. Early phases of the developmental program are often studied in cells starved in suspension while cAMP is provided exogenously. Previous studies revealed massive shifts in the transcriptome under these developmental conditions and a close relationship between gene expression and morphogenesis, but were limited by the sampling frequency and the resolution of the methods. Here, we combine the superior depth and specificity of RNA-seq with high frequency sampling during filter development and cAMP pulsing in suspension. We found that the developmental transcriptome exhibits mostly gradual changes interspersed by a few instances of large changes. Considering the whole transcriptome as a single phenotype, we treated each time point as an independent entity and were able to characterize development as groups of similar time points separated by gaps. The grouped time points represent gradual changes in mRNA abundance and the gaps represent times during which many genes are differentially expressed rapidly. Comparing development on solid substrate to development in suspension revealed that gene expression in filter developed cells lagged behind cells treated with exogenous cAMP in suspension. The high sampling frequency revealed many genes whose regulation is reproducibly more complex than indicated by previous studies. Gene Ontology enrichment analysis showed that the transition to multicellularity at the mound stage coincided with rapid accumulation of transcripts associated with mitosis and DNA replicative processes. Later development included the up-regulation of organic signaling molecules and co-factor biosynthesis. We observed multiple instances of enrichment of oxidation-reduction and reactive oxygen related terms. Our analysis also demonstrated a high level of synchrony between the developing structures throughout development. Our data describe D. discoideum development as a series of coordinated cellular and multicellular activities. Coordination occurred within fields of aggregating cells and between multicellular bodies, such as mounds or migratory slugs that experience both cell-cell contact and various soluble signaling regimes. These time courses, sampled at the highest temporal resolution to date in this system, provide a comprehensive resource for future studies of developmental gene expression.
 
Overall design Dictyosteloium discoideum gene expression (mRNA) profiles from two experimental time courses: development on filters and cAMP signaling in suspension. Filter development consists of 2 replicates of 19 time point samples, while cAMP in suspension contains 3 replicates of 10, 10 and 9 samples each.
 
Contributor(s) Rosengarten RD, Santhanam B, Fuller D, Katoh-Kurasawa M, Loomis WF, Zupan B, Shaulsky G
Citation(s) 25887420
Submission date Sep 30, 2014
Last update date May 15, 2019
Contact name Gad Shaulsky
E-mail(s) gadi@bcm.edu
Organization name Baylor College of Medicine
Street address One Baylor Plaza
City Houston
State/province TX
ZIP/Postal code 77030
Country USA
 
Platforms (1)
GPL9379 Illumina Genome Analyzer II (Dictyostelium discoideum)
Samples (67)
GSM1517221 Filter development, replicate 1, hour 00
GSM1517222 Filter development, replicate 1, hour 01
GSM1517223 Filter development, replicate 1, hour 02
Relations
BioProject PRJNA262669
SRA SRP048533

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
GSE61914_RAW.tar 9.9 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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