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SRX9002256: GSM4744870: WT_sample_1; Dictyostelium discoideum; RNA-Seq
1 ILLUMINA (Illumina NovaSeq 6000) run: 29.3M spots, 4.5G bases, 1.2Gb downloads

Submitted by: NCBI (GEO)
Study: RNA-Seq analysis of wild-type and ttpA-C231S, ttpA-E236fsx, and ttpA-Y242fsx mutant D. discoideum amebae
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 three distinct putative null mutations in the ttpA gene on transcript expression in amebae in growth medium during surface culture under axenic conditions. The cells exhibited similar external and gene expression phenotypes, suggesting that they are all null mutants, despite two different types of mutations (two frame shifts and one amino acid substitution). Overall design: Dictyostelium discoideum amebae (strain AX3) were grown in normal growth medium under axenic conditions in plastic flasks until they were approximately 80% confluent. Four cultures of wild-type cells and four cultures of each type of mutant cells were then frozen and used for RNA extraction and RNA-Seq analysis.
Sample: WT_sample_1
SAMN15897310 • SRS7255214 • All experiments • All runs
Instrument: Illumina NovaSeq 6000
Strategy: RNA-Seq
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: GSM4744870
Runs: 1 run, 29.3M spots, 4.5G bases, 1.2Gb
Run# of Spots# of BasesSizePublished


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