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Series GSE156811 Query DataSets for GSE156811
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
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.
 
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.
 
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
Phone 919-541-7867
Organization name NIEHS
Department LST
Street address 111 TW Alexander Drive
City Durham
State/province NC
ZIP/Postal code 27103
Country USA
 
Platforms (1)
GPL26000 Illumina HiSeq 4000 (Dictyostelium discoideum)
Samples (35)
GSM4744886 ttpA-C240ins_2hr_sample_1A
GSM4744887 ttpA-C240ins_2hr_sample_1B
GSM4744888 ttpA-C240ins_2hr_sample_1C
This SubSeries is part of SuperSeries:
GSE156813 RNA-Seq analysis of wild-type and mutant D. discoideum amebae
Relations
BioProject PRJNA659065
SRA SRP278685

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
GSE156811_ttpA-C240ins_0hr_6hr_normalized_counts.txt.gz 2.3 Mb (ftp)(http) TXT
GSE156811_ttpA-C240ins_0hr_6hr_raw_counts.txt.gz 883.2 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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