Leaf warblers
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA450732 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We have generated over 80 million 32 nt reads generated from RNA samples isolated from the tip and base of a developing Mo17 leaf. A comparision of these data with the maize AGP resulted in the confirmation of approximately 88% of the maize filtered gene set Keywords: Transcriptome analysis
2009-08-15 | GSE16916 | GEO
Project description:We have generated over 80 million 32 nt reads generated from RNA samples isolated from the tip and base of a developing Mo17 leaf. A comparision of these data with the maize AGP resulted in the confirmation of approximately 88% of the maize filtered gene set Keywords: Transcriptome analysis Examination of two different RNA samples from two different segments of a developing 3rd leaf
2009-08-15 | E-GEOD-16916 | biostudies-arrayexpress
Project description:This data set contains 1376 mass spectrometry reads from root, rhizosphere and leaf sample of Populus Trichocarpa, as well as associated controls. This metabolomics data set was collected as part of a larger campaign which complements the metabolomics data with metagenome sequencing, transcriptomics, and soil measurement data.
2022-12-12 | MSV000090886 | MassIVE
Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of leaf color at different development stages. The goals of this study are to compare chlorophyll metabolism and chloroplast organization transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis Methods: leaf mRNA profiles of 12 RNA sequencing libraries (S1, S2, S3_S, and S3_C) were generated by deep sequencing, in triplicate, using an Illumina HiSeq 4000 system. After removing reads of low quality, those that remained were mapped to the reference genome (ftp://ftp.ensemblgenomes.org/pub/release-38/plants/genbank/brassica_oleracea/) using the HISAT package, allowing for a maximum of two mismatches and multiple alignments per read (up to 20 by default). qRT–PCR validation was performed using SYBR Green assays Results: Using an optimized data analysis workflow, we mapped about 571.74 million sequence reads per sample to the the reference genome (ftp://ftp.ensemblgenomes.org/pub/release-38/plants/genbank/brassica_oleracea/) and identified 1028, 4323, 428, and 1033 DEGs were detected in pairwise comparison (S2 vs. S1, S3_S vs. S2, S3_S vs. S2, and S3_S vs. S3_C, respectively). The DEGs were associated with ‘photosynthesis’, ‘carbon fixation in photosynthetic organisms’, ‘porphyrin and chlorophyll metabolism’ and other pathways in the Kyoto Encyclopedia of Genes and Genomes database; DEGs related to chloroplast organization were identified in the Gene Ontology analysis. The DEGs identified by RNA sequencing were confirmed by qRT-PCR analysis, indicating that the data were reliable. These findings provide information that can be useful for investigating the molecular basis for leaf variegation in ornamental kale and other plants. Conclusions: The results presented here reveal changes in the transcriptome profile of a variegated leaf kale. DEGs related to chlorophyll metabolism and chloroplast organization were detected. These results demonstrate that leaf color at different stages of development is influenced by chloroplast and pigment metabolism, providing a foundation for investigating the molecular basis for leaf variegation in ornamental kale and other plants.
2021-03-27 | GSE112493 | GEO
Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of leaf color at different development stages. The goals of this study are to compare anthocyanin biosynthesis, chlorophyll metabolism and chloroplast organization transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis Methods: Leaf mRNA profiles of 12 RNA sequencing libraries (S1, S2, S3_S, and S3_C) were generated by deep sequencing, in triplicate, using an Illumina HiSeq 4000 system. After removing reads of low quality, those that remained were mapped to the reference genome (ftp://ftp.ensemblgenomes.org/pub/release-38/plants/genbank/brassica_oleracea/) using the HISAT package, allowing for a maximum of two mismatches and multiple alignments per read (up to 20 by default). qRT–PCR validation was performed using SYBR Green assays Results: Using an optimized data analysis workflow, we mapped about 571.74 million sequence reads per sample to the the reference genome (ftp://ftp.ensemblgenomes.org/pub/release-38/plants/genbank/brassica_oleracea/) and identified 99, 391, 74, and 543 DEGs were detected in pairwise comparison (S2 vs. S1, S3_S vs. S2, S3_C vs. S2, and S3_S vs. S3_C, respectively). The DEGs were associated with ‘photosynthesis’and other pathways in the Kyoto Encyclopedia of Genes and Genomes database; DEGs related to chloroplast organization were identified in the Gene Ontology analysis. The DEGs identified by RNA sequencing were confirmed by qRT-PCR analysis, indicating that the data were reliable. These findings provide information that can be useful for investigating the molecular basis for leaf variegation in ornamental kale and other plants. Conclusions: The results presented here reveal changes in the transcriptome profile of a bicolor leaf kale. DEGs related to anthocyanin biosynthesis, chlorophyll metabolism and chloroplast organization were detected. These results demonstrate that leaf color at different stages of development is influenced by anthocyanin biosynthesis, chloroplast and pigment metabolism, providing a foundation for investigating the molecular basis for bicolor leaf in ornamental kale and other plants.
2021-03-27 | GSE115279 | GEO