Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR9945410.fastq.gz | Fastqsanger.gz | |||
| SRR9945420.fastq.gz | Fastqsanger.gz | |||
| SRR9945401.fastq.gz | Fastqsanger.gz | |||
| SRR9945411.fastq.gz | Fastqsanger.gz | |||
| SRR9945421.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Genomic approaches to the discovery of promoters for sustained expression in cotton (Gossypium hirsutum L.) under field conditions: expression analysis in transgenic cotton and Arabidopsis of a Rubisco small subunit promoter identified using EST sequence analysis and cDNA microarrays. Keywords: Promoter Discovery
2006-06-01 | GSE4939 | GEO
Project description:In response to infection, viral genomes are processed by Dicer-like (DCL) ribonuclease proteins into viral small RNAs (vsRNAs) of discrete sizes. vsRNAs are then used as guides for silencing the viral genome. The profile of vsRNAs produced during the infection process has been extensively studied for some group of viruses. However, nothing is known for members of the economically important family Luteoviridae, a group of phloem-restricted viruses. Here, the population of vsRNAs from cotton plants infected with Cotton leafroll dwarf virus (CLRDV), a member of the genus Polerovirus, family Luteoviridae, is characterized.Deep sequencing of small RNAs (sRNAs) from CLRDV-infected cotton leaves was performed. Results showed 21-nt to 24-nt long vsRNAs matching all the viral genome, with a higher frequency of matches in the 3â region. Equivalent amounts of sense and antisense vsRNAs were found, and the 22-nt long small RNA class was the most prominent one. Looking for cotton Dcl transcripts levels during infection, we could observe that Dcl4 seems to be up-regulated, while Dcl2 seems to be down-regulated.This is the first report on the profile of sRNAs coming from a plant infected with a member of the family Luteoviridae. Our sequence data strongly suggest that virus-derived double-stranded RNA functions as one of the main precursors of vsRNAsOur results indicate that secondary structures of the viral RNAs are not the main source of the viRNAs observed, as suggested for other viruses. Judging by the profiled size classes, all cotton DCLs might be working to silence the virus. The possible causes for the unexpected high accumulation of 22-nt viRNAvsRNAs are discussed. CLRDV is the causal agent of worldwide cotton pathology named Cotton blue disease. Our results are an important contribution for understanding the molecular mechanisms involved in this and related diseases.
2012-07-16 | GSE31062 | GEO
Project description:This study introduced the use of cotton in 200µL tips, namely cotton HILIC as a convenient tool for enriching large-scale glycopeptides before MS analysis in this study. The optimal loading buffer for cotton HILIC was investigated by using mouse brain as a complex test sample. Subsequently, the performance of cotton HILIC was evaluated by comparing with other two commercial enrichment approaches, venusil HILIC and Oasis MAX in both mouse brain and seminal plasma. Moreover, capacity and recovery rate were evaluated using different milligram of cotton in 200µL tips. Thus, a simple, convenient, and cost-friendly cotton HILIC method was proposed to achieve highly selective intact glycopeptide profiling.
2023-03-04 | PXD035078 | Pride
Project description:Cotton fiber were used for the expression analysis at different developmental stages Affymetrix Cotton Genome array were used for the global profiling of gene expression of cotton fiber at different developmental stages
2012-03-20 | GSE36228 | GEO
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 ovule development, mutant vs wild type, Comparisons of DP16 0 dpa ovule Keywords: WildType vs Mutant
2005-11-03 | GSE3546 | GEO
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: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:To identify potential miRNAs involved in fiber development and elucidate their expression differences between G. barbadense and G. hirsutum, we constructed two small RNA libraries, Gb10 and Gh10, prepared from fibers of 3-79 (G. barbadense) and TM-1 (G. hirsutum) collected at 10 days post-anthesis (DPA). We identified 28 conserved miRNA families, including 24 that exactly match known plant miRNA families in miRBase. With MIREAP and newly developed software miRsearcher, 7 candidate-novel miRNAs were found. 5 candidate-novel miRNAs were expressed in both species, 2 candidate-novel miRNAs were expressed only in one species. Moreover, 4 miRNA families showed significant expression differences between sea-island cotton and upland cotton in 10 DPA fibers.
2010-12-03 | GSE25773 | GEO