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| Status |
Public on Nov 24, 2021 |
| Title |
RNA-Seq analysis of wild-type and ttpA-C240ins mutant D. discoideum amebae during short-term nutrient deprivation |
| Organism |
Dictyostelium discoideum |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
In many eukaryotes, mRNAs containing specific AU-rich motifs are regulated by proteins of the tristetraprolin (TTP) family, which bind to these motifs through a tandem zinc finger (TZF) domain. This binding leads to promotion of subsequent deadenylation and decay, partly through a conserved carboxyl-terminal CNOT1 binding domain. We explored the physiological role of the single TTP family member (TtpA) expressed in Dictyostelium discoideum. This study shows the effect of an insertional mutation in the TZF domain (ttpA-C240ins), which disrupted the TZF RNA binding domain, evaluated in amebae in axenic conditions in growth medium during surface culture, and during short term (2 and 6 hours) nutrient deprivation. RNA-Seq analysis was performed on WT and mutant cells in parallel during this short time course.
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| Overall design |
Dictyostelium discoideum amebae (strain AX3) were grown in normal growth medium under axenic conditions on plastic surfaces until they were approximately 80% confluent. Three cultures of wild-type cells and 8-9 cultures of mutant cells were then frozen and used for RNA extraction and RNA-Seq analysis. Other cultures of the same type were changed to nutrient-deficient medium, and harvested after 2 and 6 hours.
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| Contributor(s) |
Bai W, Wells ML, Burkholder AB, Perera L, Kimmel AR, Blackshear PJ |
| Citation(s) |
34718768 |
| |
| Submission date |
Aug 24, 2020 |
| Last update date |
Nov 24, 2021 |
| Contact name |
Melissa Wells |
| E-mail(s) |
wellsme@niehs.nih.gov
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| Phone |
919-541-7867
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| Organization name |
NIEHS
|
| Department |
LST
|
| Street address |
111 TW Alexander Drive
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| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27103 |
| Country |
USA |
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| Platforms (1) |
| GPL26000 |
Illumina HiSeq 4000 (Dictyostelium discoideum) |
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| Samples (35)
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| This SubSeries is part of SuperSeries: |
| GSE156813 |
RNA-Seq analysis of wild-type and mutant D. discoideum amebae |
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| Relations |
| BioProject |
PRJNA659065 |
| SRA |
SRP278685 |
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