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| Status |
Public on Jun 15, 2021 |
| Title |
Transcriptional milestones in Dictyostelium development |
| Organism |
Dictyostelium discoideum |
| Experiment type |
Expression profiling by high throughput sequencing
Third-party reanalysis
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| Summary |
Dictyostelium development begins with single-cell starvation and ends with multicellular fruiting bodies. Developmental morphogenesis is accompanied by sweeping transcriptional changes, encompassing nearly half of the 13,000 genes in the genome. We performed time-series RNA-sequencing analyses of the wild type and 20 mutants to explore the relationships between transcription and morphogenesis,. These strains exhibit developmental arrest at different stages, accelerated development, or atypical morphologies. Considering eight major morphological transitions, we identified 1,371 milestone genes whose expression changes sharply between consecutive transitions. We also identified 1,099 genes as members of 21 regulons, which are groups of genes that remain coordinately regulated despite the genetic, temporal, and developmental perturbations. The gene annotations in these groups validate known transitions and reveal new developmental events. For example, DNA replication genes are tightly co-regulated with cell division genes, so they are expressed in mid-development even though chromosomal DNA is not replicated. Our dataset includes 486 transcriptional profiles that can help identify new relationships between transcription and development and improve gene annotations. We demonstrate its utility by showing that cycles of aggregation and disaggregation in allorecognition-defective mutants involve dedifferentiation. We also show sensitivity to genetic and developmental conditions in two commonly used actin genes, act6 and act15, and robustness of the coaA gene. Finally, we propose that gpdA is a better mRNA quantitation standard because it is less sensitive to external conditions than commonly used standards. The dataset is available for democratized exploration through the web application dictyExpress and the data mining environment Orange.
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| Overall design |
In this study 486 developmental samples were used, consisting of 21 strains, 5-19 time points, and 2-7 replicates. Using 486 transcriptomes, including existing GEO data (from GSE61914, GSE131209, GSE144892) transcriptional comparisons between strains, phenotype groups, and morphological stages and clustering analyses were performed.
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| Contributor(s) |
Katoh-Kurasawa M, Hrovatin K, Shaulsky G, Zupan B, Hirose S, Webb A, Ho H |
| Citation(s) |
34183452 |
| Submission date |
Jun 19, 2020 |
| Last update date |
Sep 15, 2021 |
| Contact name |
Gad Shaulsky |
| E-mail(s) |
gadi@bcm.edu
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| Organization name |
Baylor College of Medicine
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| Department |
Molecular and Human Genetics
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| Street address |
One Baylor Plaza
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| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
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| Platforms (3) |
| GPL9379 |
Illumina Genome Analyzer II (Dictyostelium discoideum) |
| GPL22784 |
Illumina HiSeq 2500 (Dictyostelium discoideum) |
| GPL26668 |
Illumina NovaSeq 6000 (Dictyostelium discoideum) |
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| Samples (486)
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| Relations |
| Reanalysis of |
GSM4300090 |
| Reanalysis of |
GSM4300091 |
| Reanalysis of |
GSM4300092 |
| Reanalysis of |
GSM4300094 |
| Reanalysis of |
GSM4300096 |
| Reanalysis of |
GSM4300097 |
| Reanalysis of |
GSM4300098 |
| Reanalysis of |
GSM4300105 |
| Reanalysis of |
GSM4300106 |
| Reanalysis of |
GSM4300107 |
| Reanalysis of |
GSM4300109 |
| Reanalysis of |
GSM4300111 |
| Reanalysis of |
GSM4300112 |
| Reanalysis of |
GSM4300113 |
| Reanalysis of |
GSM4300134 |
| Reanalysis of |
GSM4300135 |
| Reanalysis of |
GSM4300136 |
| Reanalysis of |
GSM4300137 |
| Reanalysis of |
GSM4300138 |
| Reanalysis of |
GSM4300139 |
| Reanalysis of |
GSM4300152 |
| Reanalysis of |
GSM4300153 |
| Reanalysis of |
GSM4300154 |
| Reanalysis of |
GSM4300155 |
| Reanalysis of |
GSM4300156 |
| Reanalysis of |
GSM4300157 |
| BioProject |
PRJNA640642 |
| SRA |
SRP268025 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE152851_GSE144892_re-analyzed_samples_metadata.xlsx |
21.6 Kb |
(ftp)(http) |
XLSX |
| GSE152851_RAW.tar |
76.0 Mb |
(http)(custom) |
TAR (of TAB) |
| GSE152851_buf_processed_data.tar.gz |
1.9 Mb |
(ftp)(http) |
TAR |
| GSE152851_media_processed_data.tar.gz |
2.3 Mb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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