Ontology highlight
ABSTRACT:
PROVIDER: PRJNA835661 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR19213060_1.fastq.gz | Fastqsanger.gz | |||
| SRR19213060_2.fastq.gz | Fastqsanger.gz | |||
| SRR21615884_1.fastq.gz | Fastqsanger.gz | |||
| SRR21615884_2.fastq.gz | Fastqsanger.gz | |||
| SRR25000439_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 6 |
Similar Datasets
Project description:Korean native cattle (Hanwoo) Genome sequencing
| PRJNA343986 | ENA
Project description:To characterize breed-specific difference among four Korean native chicken breeds and White Leghorn, we measured their transcriptomes at liver tissue using Affymetrix Chicken gene 1.0 ST array platform.
2015-12-31 | GSE63389 | GEO
Project description:We performed chloroplast ChIP-seq (cpChIP-seq) to identify the possible DNA-binding sites of mTERF5 in Arabidopsis thaliana. To this end, we generated transgenic Arabidopsis plants expressing mTERF5 carrying an HA tag under the control of the CaMV 35S promoter. Then, We used the polyclonal antibody (abcam, ab9110, lot GR304617-8 ) against HA tag which conjugated to ChIP-Grade protein A/G agarose (Thermo scientific, 26161, lot QJ223903) to perform cpChIP assay. The obtained chromatin immunoprecipitated DNA of chloroplasts were used to build DNA libaries for high-throughput sequencing. Finally, we showed that three potenssial DNA regions across the chloroplast genome compared to the control group were enriched by mTERF5.
2019-08-21 | GSE118574 | GEO
Project description:Anim Genet. 2009 Feb;40(1):115-8. Epub 2008 Oct 17. Differentially expressed transcripts in adipose tissue between Korean native pig and Yorkshire breeds. Moon JK, Kim KS, Kim JJ, Choi BH, Cho BW, Kim TH, Lee CK. Division of Biotechnology, College of Life Sciences & Biotechnology, Korea University, Seoul, South Korea. We measured and compared the transcripts of adipose tissue from Korean native pig (KNP) and Yorkshire (YS) breeds to investigate breed-specific transcription changes. We employed both the Affymetrix porcine genome array and quantitative reverse transcription-polymerase chain reaction (qRT-PCR). We found eight genes showing significant changes between the two breeds. Based on a literature review, these genes were indicative of differences in extracellular structure density and differences in the potential to metabolize xenobiotic chemicals and lipids. The differentially expressed genes indicated that KNP has a lower extracellular structure density and a lower potential to metabolize xenobiotic chemicals than YS. PMID: 18945290
2008-10-15 | GSE9333 | 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
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:In the present study, we discover the presence of m2A in chloroplast rRNA and tRNA, as well as cytosolic tRNA, in multiple plant species. We identify six m2A-modified chloroplast tRNAs and two m2A-modified cytosolic tRNAs across different plants. Furthermore, we characterize three Arabidopsis m2A methyltransferases—RLMNL1, RLMNL2, and RLMNL3—which methylate chloroplast rRNA, chloroplast tRNA, and cytosolic tRNA, respectively. Our findings demonstrate that m2A37 promotes a relaxed conformation of tRNA, enhancing translation efficiency in chloroplast and cytosol by facilitating decoding of tandem m2A-tRNA-dependent codons. This study provides insights into the molecular function and biological significance of m2A, uncovering a layer of translation regulation in plants.
2024-02-03 | GSE127146 | GEO