Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12453946_1.fastq.gz | Fastqsanger.gz | |||
| SRR12453946_2.fastq.gz | Fastqsanger.gz | |||
| SRR12453947_1.fastq.gz | Fastqsanger.gz | |||
| SRR12453947_2.fastq.gz | Fastqsanger.gz | |||
| SRR12453948_1.fastq.gz | Fastqsanger.gz |
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Project description:The number of tRNA isodecoders has increased dramatically in mammals, but the specific molecular and physiological reasons for this expansion remain elusive. To address this fundamental question we used CRISPR editing to knockout the seven-membered phenylalanine tRNA gene family in mice, both individually and combinatorially. Using ATAC-Seq, RNA-seq and proteomics we observed distinct molecular consequences of individual tRNA deletions. We show that tRNA-Phe-1-1 is required for neuronal function and its loss is partially compensated by increased expression of other tRNAs but results in mistranslation. In contrast, the other tRNA-Phe isodecoder genes buffer the loss of each of the remaining six tRNA-Phe genes. In the tRNA-Phe gene family, the expression of at least six tRNA-Phe alleles is required for embryonic viability and tRNA-Phe-1-1 is most important for development and survival. Our results reveal that the multi-copy configuration of tRNA genes is required to buffer translation and viability in mammals.
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Project description:With the internationalization of traditional Chinese medicine, the demand for medicinal and edible Codonopsis Radix (CR) is increasing, and its medicinal resources have attracted atten- tion. CR is a famous traditional Chinese medicine with a long pharmaceutical and edible history. Guizhou has abundant CR resources, but in the absence of systematic studies on species identifi- cation and chemical compositions, it has not been fully utilized. The results of plant traits and DNA barcoding molecular identification indicated that Luodang (LD) and Weidang (WD) from Guizhou were Codonopsis tangshen, C. pilosula., respectively. Widely targeted metabolomics analysis revealed that a total of 1116 metabolites from 14 categories, including phenolic acids, lipids, flavonoids, etc., were found in LD, WD, and the three Chinese Pharmacopoeia CR. CRs shared 1054 (94.4%) me- tabolites, with extremely similar metabolite profiles. Affected by Guizhou's particular climate, LD and WD each contained 3 and 10 dominant differential metabolites, respectively, which were pri- marily flavonoids and amino acids. Amino acids, phenolic acids, and organic acids play important roles in the excellent food attributes of them. In CR, 8 dominant differential metabolites were dis- covered for the first time, including isoorientin-7-O-(6′′-feruloyl) glucoside, N-formyl-L-methionine, and cyclo (Phe-Glu), etc. Network pharmacology analyses showed that LD dominant differential metabolites were closely related to anti-tumor, cardiovascular disease improvement, nervous system protection, and metabolic disease treatment, whereas WD was closely related to nervous system protection and cardiovascular disease improvement. In conclu- sion, LD and WD can be used and promoted medicinally as CR and have potential value for new drug development. This work enriched the database of CR compounds and provided a reference for quality control, resource development, and new drug development of CR
2023-10-06 | PXD044874 | Pride
Project description:The number of tRNA isodecoders has increased dramatically in mammals, but the specific molecular and physiological reasons for this expansion remain elusive. To address this fundamental question we used CRISPR editing to knockout the seven-membered phenylalanine tRNA gene family in mice, both individually and combinatorially. Using ATAC-Seq, RNA-seq and proteomics we observed distinct molecular consequences of individual tRNA deletions. We show that tRNA-Phe-1-1 is required for neuronal function and its loss is partially compensated by increased expression of other tRNAs but results in mistranslation. In contrast, the other tRNA-Phe isodecoder genes buffer the loss of each of the remaining six tRNA-Phe genes. In the tRNA-Phe gene family, the expression of at least six tRNA-Phe alleles is required for embryonic viability and tRNA-Phe-1-1 is most important for development and survival. Our results reveal that the multi-copy configuration of tRNA genes is required to buffer translation and viability in mammals.
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Project description:ngs2021_12_endomix-phe-gradient-Identify the physiological response of poplar to the presence of 8 Phenanthrene gradient concentration.-As part of the ANR EndOMiX project, we carried out an experiment with poplars (Populus canadensis: hybrid Populus deltoides x nigra) grown in soil with a gradient of contamination in Phenanthrene (PHE), we have 8 different concentrations of PHE, and 4 biological replicates (pots with independent plants). We harvested after 4 weeks of growth, the roots and leaves of the poplars from which the RNAs were extracted for sequencing.
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