Ontology highlight
ABSTRACT:
PROVIDER: PRJNA648948 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Morus alba L. Raw protein sequence reads and sequence
2024-02-08 | PXD049451 |
Project description:Purpose: The goal of this study is to evaluate transcriptional regulation of the accumulation of phenols and anthocyanins in young leaves of subtropical forest tree species by using NGS-derived RNA-seq. Methods: Leaf mRNA profiles of subtropical tree Schima superba and Cryptocarya concinna grown under contasting light were generated by deep sequencing, in triplicate, using Illumina. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. FPKM produced by RSEM are provided. Results: Assemblies of the sequence data yielded 61,618 and 64,413 unigenes for Schima superba and Cryptocarya concinna,respectively. Overall,75.14% and 66.46% of the unigenes were annotated in the protein database Nonredundant protein (Nr), Nonredundant nucleotide (Nt), Swiss-Prot、Kyoto Encyclopedia of Genes and Genomes (KEGG), Cluster of Orthologous Groups of proteins (COG) and Gene Ontology (GO) for S. superba and C concinna,respectively.A total of 3896, 3488 and 266 genes were differentially expressed in full light-exposed young leaf (FLY), low light-exposed young leaf (LYL) and low light-exposed mature leaf (LML) relative to low light-exposed mature leaf (FML) of S. superba, respectively, and 2097, 2047 and 211 genes were differentially expressed in the corresponding leaves of C. concinna. Conclusions: Our study represents the first detailed analysis of transcriptomes in young and mature leaves of dorminant trees from a subtropical forest in China, with biologic replicates, generated by RNA-seq technology. Photosynthesis-related genes and phenol pathways-related genes were extensively down- and up-regulated in young versus mature leaves of the two species.
2018-10-01 | GSE104004 | GEO
Project description:Cereal genomes have undergone repeated polyploidization and transposable element (TE) proliferation, collectively generating complex regulatory landscapes. The evolutionary trajectories and functional implications of these landscapes, however, remain largely unexplored. By employing chromatin-bound RNA sequencing across seven cereal species, we systematically mapped 45,952 regulatory element transcripts (RETs), including 32,867 distal RETs corresponding to enhancer RNAs (eRNAs). Our analysis reveals that 56% of lineage-specific eRNAs originate from TE expansions, suggesting TEs as significant reservoirs of species-specific regulatory innovation in cereals. Notably, we uncovered a remarkable similarity in defense-related function, root-specific expression, and TE-derived origin of eRNAs across ancient and recent evolutionary layers of Triticeae, suggesting recurrent recruitment of TE-derived root-associated regulatory elements during Triticeae evolution. Furthermore, we found that young eRNA pairs in hexaploid wheat with high sequence similarity, many originating from RLG_famc8.3 and DTC_famc4.3, exhibit pronounced root specificity and coordinated expression, suggesting a targeted amplification and refinement of the successful ancestral regulatory strategy established after Triticeae divergence. To facilitate community access, we developed Cereal-eRNAdb (http://bioinfo.cemps.ac.cn/Cereal-eRNAdb/), a comprehensive database integrating 69,426 eRNAs with functional annotations across 296 samples. Our work indicates that TE-mediated innovation of root-specific eRNAs as a candidate mechanism that may contribute to Triticeae adaptation and provides a foundational resource for exploiting regulatory variation in cereal crop breeding.
2026-06-22 | GSE284460 | GEO
Project description:Cereal genomes have undergone repeated polyploidization and transposable element (TE) proliferation, collectively generating complex regulatory landscapes. The evolutionary trajectories and functional implications of these landscapes, however, remain largely unexplored. By employing chromatin-bound RNA sequencing across seven cereal species, we systematically mapped 45,952 regulatory element transcripts (RETs), including 32,867 distal RETs corresponding to enhancer RNAs (eRNAs). Our analysis reveals that 56% of lineage-specific eRNAs originate from TE expansions, suggesting TEs as significant reservoirs of species-specific regulatory innovation in cereals. Notably, we uncovered a remarkable similarity in defense-related function, root-specific expression, and TE-derived origin of eRNAs across ancient and recent evolutionary layers of Triticeae, suggesting recurrent recruitment of TE-derived root-associated regulatory elements during Triticeae evolution. Furthermore, we found that young eRNA pairs in hexaploid wheat with high sequence similarity, many originating from RLG_famc8.3 and DTC_famc4.3, exhibit pronounced root specificity and coordinated expression, suggesting a targeted amplification and refinement of the successful ancestral regulatory strategy established after Triticeae divergence. To facilitate community access, we developed Cereal-eRNAdb (http://bioinfo.cemps.ac.cn/Cereal-eRNAdb/), a comprehensive database integrating 69,426 eRNAs with functional annotations across 296 samples. Our work indicates that TE-mediated innovation of root-specific eRNAs as a candidate mechanism that may contribute to Triticeae adaptation and provides a foundational resource for exploiting regulatory variation in cereal crop breeding.
2026-06-22 | GSE284459 | GEO
Project description:This study investigated the gene expression profiles of Erigeron breviscapus seedlings under five gradient light intensity levels with three biological replicates per group. Total RNA from leaf samples was subjected to mRNA sequencing (RNA-seq) to identify light-responsive genes and regulatory pathways. Raw sequencing reads have been deposited in the National Genomics Data Center (NGDC) Genome Sequence Archive (GSA) under accession number CRA036241. This submission includes processed gene expression count matrix and FPKM matrix.
2026-09-13 | GSE347132 | GEO
Project description:Despite their importance, there remains to be few large scale expression-based studies of tissue-specific expression information in the species belonging to the Triticeae. We used the 55K Affymetrix GeneChip® Wheat Genome Array to generate a gene expression atlas of triticale tissues. The global transcriptional profiles of seed tissues (embryo, endosperm, crease, pericarp and epiderm) and vegetative tissues (root, coleoptile, stem and leaf) were analyzed and co-regulated as well as preferentially expressed genes were identified. Data analysis revealed both novel and conserved regulatory factors underlying Triticeae tissue development and function.
2014-12-24 | GSE43127 | GEO
Project description:Rhizophora mucronata Lam., a prevalent mangrove variety of Indo-Pacific region is reported to defy saline stress up to 40 ppt, but the genome or transcriptome behind this tolerance is yet to be investigated. As an initiative to create a reference sequence database, we have forged a set of 46,366,348 paired end RNA-Seq raw reads of Rhizophora mucronata Lam. leaf tissues from Illumina HiSeq 2500 platform (SRA study accession SRP093200 ; Bioproject accession PRJNA345155). All possible gene transcripts were then reconstructed from the RNA raw seq data and 93960 Trinity assembled, annotated transcripts that are being actively expressed at a given time is proposed (TSA accession GGEC00000000). To estimate gene transcript expression, we used Bowtie 2 programme and successfully aligned back up to 95.14% of the filtered reads to the assembled transcriptome. We allowed up to 1-mismatches in the seed region (length =31bp) and all multiple mapped position were reported. Of all filtered reads about 95.14% of reads from each sample were properly aligned back to the assembled transcriptome. Overall we found 52,153 unique transcripts which have expression >=1 FPKM.
2018-03-22 | GSE112162 | GEO
Project description:Cereal genomes have undergone repeated polyploidization and transposable element (TE) proliferation, collectively generating complex regulatory landscapes. The evolutionary trajectories and functional implications of these landscapes, however, remain largely unexplored. By employing chromatin-bound RNA sequencing across seven cereal species, we systematically mapped 45,952 regulatory element transcripts (RETs), including 32,867 distal RETs corresponding to enhancer RNAs (eRNAs). Our analysis reveals that 56% of lineage-specific eRNAs originate from TE expansions, suggesting TEs as significant reservoirs of species-specific regulatory innovation in cereals. Notably, we uncovered a remarkable similarity in defense-related function, root-specific expression, and TE-derived origin of eRNAs across ancient and recent evolutionary layers of Triticeae, suggesting recurrent recruitment of TE-derived root-associated regulatory elements during Triticeae evolution. Furthermore, we found that young eRNA pairs in hexaploid wheat with high sequence similarity, many originating from RLG_famc8.3 and DTC_famc4.3, exhibit pronounced root specificity and coordinated expression, suggesting a targeted amplification and refinement of the successful ancestral regulatory strategy established after Triticeae divergence. To facilitate community access, we developed Cereal-eRNAdb (http://bioinfo.cemps.ac.cn/Cereal-eRNAdb/), a comprehensive database integrating 69,426 eRNAs with functional annotations across 296 samples. Our work indicates that TE-mediated innovation of root-specific eRNAs as a candidate mechanism that may contribute to Triticeae adaptation and provides a foundational resource for exploiting regulatory variation in cereal crop breeding.
2026-06-22 | GSE284462 | GEO