Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR25904113_1.fastq.gz | Fastqsanger.gz | |||
| SRR25904113_2.fastq.gz | Fastqsanger.gz | |||
| SRR25904114_1.fastq.gz | Fastqsanger.gz | |||
| SRR25904114_2.fastq.gz | Fastqsanger.gz |
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Project description:Protein phosphorylation is one of the most common post-translational modifications (PTMs), which is involved in many important physiological functions. Understanding protein phosphorylation at molecular level is critical to decipher its relevant biological processes and signaling networks. Mass spectrometry (MS) has been proved to be a powerful tool in comprehensive characterization of protein phosphorylation. Yet the low abundance and poor ionization efficiency of phosphopeptides make its MS analysis challenging; an enrichment with high efficiency and selectivity is always necessary before MS analysis. In this study, we developed a phosphorylated cotton fiber-based Ti(IV)-IMAC material (termed as: Cotton Ti-IMAC) that can serve as a novel platform for phosphopeptide enrichment. The cotton fiber can be effectively grafted with phosphate groups in a single step, where the titanium ions can then be immobilized onto to capture phosphopeptides. The material can be prepared with cost-effective reagents within only 4 hours. Benefiting from the flexibility and filterability of cotton fibers, the material can be easily packed as a spin-tip and make the enrichment process more convenient. Cotton Ti-IMAC successfully enriched phosphopeptides from protein standard digests and exhibited a high selectivity (β-casein/BSA = 1:1000) and excellent sensitivity (0.1 fmol/µL). Moreover, 2354 phosphopeptides was identified in a single LC-MS/MS injection after enriching from only 100 µg HeLa cell digests, with an enrichment specificity up to 97.51%. Taken together, we believe Cotton Ti-IMAC is ready to serve as a widely applicable and robust platform for achieving large-scale phosphopeptide enrichment and expanding our knowledge of phosphoproteomics in complex biological systems.
2023-10-23 | PXD037549 | Pride
Project description:Purpose: found out the regulated genes of nulliplex-branch and its forming molecular mechanism Methods: shoot apical mRNA and miRNA in two nulliplex branch and two normal branch cotton of three development stages were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000. Results: we found 3 825 and 353 specific stage differnent expressed genes in pre-budding stage of island cotton and upland cotton, respectively. In miRNA, we found 16 and 18 specific stage differnent expressed miRNA in pre-budding stageof island cotton and upland cotton, respectively. Conclusions: Our study represents the genes and miRNA control development of lateral branch and regulate flowering time at same times. Shoot apical mRNA and miRNA of normal branch cotton and nulliplex branch botton were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000.
2016-03-17 | E-GEOD-69025 | biostudies-arrayexpress
Project description:To examine expression of miRNAs in cotton fiber development, we employed miRNA microarrays and compared miRNA accumulation level in cotton fibers, cotton leaves and mutant fibers.
2009-12-31 | GSE16986 | GEO
Project description:Cotton fibers are seed trichomes, and their development undergoes a series of rapid and dynamic changes from fiber cell initiation, elongation to primary and secondary wall biosynthesis and fiber maturation. Previous studies showed that cotton homologues encoding putative MYB transcription factors and phytohormone responsive factors were induced during early stages of ovule and fiber development. Many of these factors are targets of microRNAs (miRNAs). miRNAs are ~21 nucleotide (nt) RNA molecules derived from non-coding endogenous genes and mediate target regulation by mRNA degradation or translational repression. Here we show that among ~4-million reads of small RNAs derived from the fiber and non-fiber tissues, the 24-nt small RNAs were most abundant and were highly enriched in ovules and fiber-bearing ovules relative to leaves. A total of 28 putative miRNAs families, including 25 conserved and 3 novel miRNAs were identified in at least one of the cotton tissues examined. Thirty-two pre-miRNA hairpins representing 19 unique families were detected in Cotton Gene Indices version 9 (CGI9) using mirCheck. Sequencing, miRNA microarray, and small RNA blot analyses showed that many of these miRNAs differentially accumulated during ovule and fiber development. The cotton miRNAs examined triggered target cleavage in the same predicted sites of the cotton targets in ovules and fibers as that of the orthologous target genes in Arabidopsis. Targets of the potential new cotton miRNAs matched the previously characterized ESTs derived from cotton ovules and fibers. The miRNA targets including those encoding auxin response factors were differentially expressed during fiber development. We suggest that both conserved and new miRNAs play an important role in the rapid and dynamic process of fiber and ovule development in cotton.
2009-11-12 | GSE16332 | GEO
Project description:Subsequently, using a combination of BSA-seq, transcriptomic sequencing (RNA-seq), and proteomic sequencing approaches, we identified the candidate gene Nitab4.5_0008674g0010 that encodes dihydroneopterin aldolase as a factor associated with tobacco leaf yellowing.
2024-06-15 | PXD053162 |
Project description:Purpose: found out the regulated genes of nulliplex-branch and its forming molecular mechanism Methods: shoot apical mRNA and miRNA in two nulliplex branch and two normal branch cotton of three development stages were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000. Results: we found 3 825 and 353 specific stage differnent expressed genes in pre-budding stage of island cotton and upland cotton, respectively. In miRNA, we found 16 and 18 specific stage differnent expressed miRNA in pre-budding stageof island cotton and upland cotton, respectively. Conclusions: Our study represents the genes and miRNA control development of lateral branch and regulate flowering time at same times.
2016-03-17 | GSE69025 | GEO