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16 results for “tRNA abundance”
Data for: Engineering tRNA abundances for synthetic cellular systems
<p>Data for publication:<strong> Engineering tRNA abundances for synthetic cellular systems</strong></p> <p><strong>Abstract</strong></p> <p>Routinizing the engineering of synthetic cells requires specifying determining beforehand how many of each molecule are needed. First-principles tools for specifying molecular abundances enabling whole-cell synthetic biology are missing. We use a colloidal dynamics simulator to make predictions for how tRNA abundances impact protein synthesis rates. We use rational design and direct RNA synthesis to make 21 synthetic tRNA surrogates from scratch. We use evolutionary algorithms within a computer aided design framework to design engineer translation systems predicted to work faster or slower depending on tRNA abundance differences. We build and test the so-specified synthetic systems and find that qualitative agreement between expected and observed systems performance matchqualitatively match. First-principles modeling combined with bottom-up experiments can help molecular-to-cellular scale synthetic biology realize “design, build, work” frameworks that transcend tinker-and-test.</p> <p><strong>Data description</strong></p> <p>The data here consists of (1) All Colloidal Smoldyn & CD-CAD simulation input parameter and output files & (2) experimental data used for the associated publication. Simulation data was produced using Colloidal Dynamics modeling and Colloidal Dyamics-CAD (CD-CAD) as described in the associated manuscript. Data folders should be used directly with modeling and analysis code provided on Github: https://github.com/EndyLab/tRNACAD.</p>
Dynamic changes in tRNA modifications and abundance during T-cell activation [RNA/Ribo-seq]
GEO Series GSE165536. Mus musculus. 16 samples. Type: Expression profiling by high throughput sequencing; Other.
Small tRNA-derived RNAs are increased and more abundant than microRNAs in chronic hepatitis B and C
GEO Series GSE57381. Homo sapiens. 28 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Dynamic changes in tRNA modifications and abundance during T-cell activation [tRNA-seq]
GEO Series GSE165537. Mus musculus. 30 samples. Type: Non-coding RNA profiling by high throughput sequencing.
tRNA abundance, modification and fragmentation as biomarkers for COVID-19 severity
GEO Series GSE208612. Homo sapiens. 66 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Quantitative real-time PCR analysis of tRNA abundance in the developing mouse neocortex
GEO Series GSE169621. Mus musculus. 10 samples. Type: Expression profiling by RT-PCR.
Dynamic changes in tRNA modifications and abundance during T-cell activation [MARS-seq]
GEO Series GSE165535. Mus musculus. 18 samples. Type: Expression profiling by high throughput sequencing.
Impact of tRNA-Glu(UUC) and tRNA-Arg(CCG) on mRNA abundance
GEO Series GSE77285. Homo sapiens. 6 samples. Type: Expression profiling by array.
High-resolution quantitative profiling of tRNA abundance and modification status in eukaryotes by mim-tRNAseq
GEO Series GSE152621. Homo sapiens; Saccharomyces cerevisiae; Schizosaccharomyces pombe; Drosophila melanogaster. 29 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Dynamic changes in tRNA modifications and abundance during T-cell activation
GEO Series GSE165622. Mus musculus. 64 samples. Type: Expression profiling by high throughput sequencing; Other; Non-coding RNA profiling by high throughput sequencing.
Differential expression of human tRNA genes drives the abundance of tRNA-derived fragments
GEO Series GSE114904. Homo sapiens. 8 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Comparison of tRNA abundance profiling in primary M395 melanoma cultures SENS or RES to 1µM Vemurafenib
GEO Series GSE236645. Homo sapiens. 6 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Relative tRNA abundance in Lactococcus lactis as a function of growth rate and overexpression stress
GEO Series GSE55336. Lactococcus lactis. 14 samples. Type: Non-coding RNA profiling by array.
Abundance of tRNA fragments in Tau-RNA complexes from Tau-mutant PS19 (human P301S Tau transgenic) mice hippocampus
GEO Series GSE297027. Mus musculus. 6 samples. Type: Non-coding RNA profiling by array.
Dynamic changes in tRNA modifications and abundance during T-cell activation [ncRNA-seq]
GEO Series GSE163053. Mus musculus. 18 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Comparison of mitochondrial tRNA abundance profiling in wild type and mutant mitochondrial RNA polymerase overexpression flies.
GEO Series GSE164324. Drosophila melanogaster. 6 samples. Type: Expression profiling by high throughput sequencing.
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