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SRX9002273: GSM4744889: ttpA-C240ins_2hr_sample_2A; Dictyostelium discoideum; RNA-Seq
5 ILLUMINA (Illumina HiSeq 4000) runs: 78.6M spots, 12G bases, 4.5Gb downloads

Submitted by: NCBI (GEO)
Study: RNA-Seq analysis of wild-type and ttpA-C240ins mutant D. discoideum amebae during short-term nutrient deprivation
show Abstracthide Abstract
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.
Sample: ttpA-C240ins_2hr_sample_2A
SAMN15897315 • SRS7255231 • All experiments • All runs
Library:
Instrument: Illumina HiSeq 4000
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: PAIRED
Construction protocol: RNA was purified using the Illustra RNAspin Kit (GE Healthcare Life Sciences) following the manufacturer's protocol. Total cellular RNA was quantitated with a Qubit fluorometer, and 250 ng of each sample was transcribed to generate cDNA libraries using the Illumina TruSeq RNA Kit (Illumina Inc, San Diego, CA) following the manufacturer's Low Sample (LS) protocol, with the following modifications: 2 minutes of centrifugation were used during the bead drying steps and 12 cycles were used to enrich DNA fragments.
Experiment attributes:
GEO Accession: GSM4744889
Links:
Runs: 5 runs, 78.6M spots, 12G bases, 4.5Gb
Run# of Spots# of BasesSizePublished
SRR1251152716,022,5642.4G928.1Mb2021-11-25
SRR1251152815,830,9792.4G929.2Mb2021-11-25
SRR1251152916,240,6572.5G945.7Mb2021-11-25
SRR1251153016,618,4362.5G968.4Mb2021-11-25
SRR1251153113,920,1822.1G849.8Mb2021-11-25

ID:
11699087

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