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SRX9002269: GSM4744883: ttpA-D450trx_sample_2; Dictyostelium discoideum; RNA-Seq
1 ILLUMINA (Illumina NovaSeq 6000) run: 112.8M spots, 17.1G bases, 4.6Gb downloads

Submitted by: NCBI (GEO)
Study: RNA-Seq analysis of wild-type and ttpA-D450trx 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 a carboxyl-terminal truncation (ttpA-D450trx), which removed the predicted CNOT1 binding domain, evaluated in amebae in growth medium during surface culture. The cells exhibited external and gene expression phenotypes that were very similar to those of two distinct null mutants, raising the possibility that this domain is necessary for TtpA-promoted mRNA decay in this species. 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 ttpA-D450trx cells were then frozen and used for RNA extraction and RNA-Seq analysis.
Sample: ttpA-D450trx_sample_2
SAMN15897321 • SRS7255227 • 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: GSM4744883
Runs: 1 run, 112.8M spots, 17.1G bases, 4.6Gb
Run# of Spots# of BasesSizePublished


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