Shading daughter plant
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1117039 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR29195621_1.fastq.gz | Fastqsanger.gz | |||
| SRR29195621_2.fastq.gz | Fastqsanger.gz | |||
| SRR29195622_1.fastq.gz | Fastqsanger.gz | |||
| SRR29195622_2.fastq.gz | Fastqsanger.gz | |||
| SRR29195623_1.fastq.gz | Fastqsanger.gz |
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Project description:shading mother plant Raw sequence reads
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Project description:Purpose: S100A10 uesed to located in the cell membrane or cytoplasm. However nuclear-located S100A10 was observed in the polyploid tumor giant cells(PGCCs) with daughter cells induced by cobalt chloride(CoCl2). To study the function of nuclear-located S100A10, we performed ChIP-Seq. Methods:LoVo and Hct116 cells were incubated in T25 flasks in RPMI-1640 medium until they reached 80-90% confluence. The cells were treated with 450 μM CoCl2 (Sigma-Aldrich, St. Louis, MO, USA) for 48-72h based on their resistance to hypoxia. After the treatment with CoCl2 was repeated for 3-4 times, there were 20-30% of PGCCs and 70-80% of small-sized daughter cells that originated from PGCCs among the total cells.ChIP assays were performed according to the instructions of the Pierce Magnetic ChIP Kit (Thermo Fisher Scientific, #26157) For data analysis of ChIP DNA, sequencing and library preparation were performed using Novogene Technology Co., Ltd. (Tianjin, China). Raw data (raw reads) of FASTQ format were first processed through in-house PERL scripts, and then reference genome and gene model annotation files were downloaded directly from the genome website. For a specific ChIP-seq binding site, individual reads were mapped to the plus or minus strand and presented significant enrichment. After mapping the reads to the reference genome, the MACS2 version 2.1.0 (model-based analysis of ChIP-seq) peak finding algorithm was used to identify regions of specific IP enrichment over background. A p-value threshold of enrichment of 0.05 was used for all data sets. The interaction between transcription factor or chromatin histone modification and DNA was not random, but they showed some specific sequence preference. MEME 52 and DREME 53 were used to detect the sequence motif, which was used to detect long and short consensus sequences. The position of peak summit around the transcript start sites of genes can predict the interaction sites of proteins and genes. Genes associated with different peaks were identified, and GO and KEGG enrichment analyses were performed. Results:The results showed that 4148 significant ChIP-seq peaked in Hct116-derived PGCCs with daughter cells, and 1380 peaked in LoVo-derived PGCCs with daughter cells. Genes with overlapping peaks were then enriched by Gene Ontology [GO], which revealed that these genes participated in various processes including stimulus, cell migration, and cell motility.Moreover, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed the potential targets involved in metabolic pathways, axon guidance TGF-β signaling pathway, and so on. Conclusions: S100A10 can be modified by SUMOylation in PGCCs and their daughter cells induced by either CoCl2 or chemotherapeutic drugs. SUMO1-modified S100A10 can translocate to the nucleus and regulate the expression of ARHGEF18, PTPRN2, and DEFA3 to promote the proliferation, migration, and invasion of PGCCs and their daughter cells, which may contribute to the poor prognosis in patients with cancer. The discovery of detailed mechanisms of the S100A10 SUMOylation, such as the specific lysine sites involved in SUMOylation and which SUMO E3 ligase regulates the SUMOylation of S100A10 requires further study.
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Project description:Rhizosphere microbial communities under full sun and shading conditions Raw sequence reads
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Project description:An increasing amount of evidence attest that the tea made by albino tea cultivars processes characteristic aroma and taste, which has been considered as a new potential product in the market. Therefore, flavor formation mechanism of albino tea cultivars have drawn exceeding attention from researchers. In this study, transcriptome, metabolomics, and whole-genome bisulfite sequencing (WGBS) were employed to investigate shading effects on leaf color conversion and biosynthesis of three major secondary metabolites in the Albino tea cultivar ‘Yujinxiang’. The increase of leaf chlorophyll level is the major cause of shaded leaf greening from young pale or yellow leaf. Transcriptome analysis showed differentially expressed genes (DEGs) mainly participated in biosynthesis of amino acids, phenylalanine metabolism, phenylalanine, tyrosine and tryptophan biosynthesis, sulfur metabolism, purine metabolism, and pentose and glucuronate interconversions in shading period compared with control group. The result of metabolomics indicated the total catechins level of shading group was significantly decreased than the control; however, the abundance of caffeine was markedly increased, and theanine level was nearly not influenced. Whole-genome DNA methylation analysis revealed that the global genomic DNA methylation patterns of shading period were remarkably altered compared with the control. Furthermore, differentially methylated regions (DMRs) and the DMR-related DEGs between shading and non-shading analysis indicated the DMR-related DEGs were the critical participants in biosynthesis of three major secondary metabolites. To sum up, these findings suggested that the altered levels of DNA methylation may be the main cause for biosynthesis changes of three major secondary metabolites in ‘Yujinxiang’.
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