Organisms
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA825711 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Morus alba L. Raw protein sequence reads and sequence
2024-02-08 | PXD049451 | iProX
Project description:We introduce FACIL (http://www.cmbi.ru.nl/FACIL), a fast, reliable tool to evaluate nucleic acid sequences for non-standard codes that detects alternative genetic codes even in species distantly related to known organisms. Results are visualized in a Genetic Code Logo. To illustrate the use of our method, we analysed several contigs derived from the mitochondrial genome of the foraminifer Globobulimina pseudospinescens. These are particularly challenging data, as the genome is highly fragmented and incomplete. Approximately 10,000 single-cell Globobulimina pseudospinescens organisms were isolated by hand from Gullmar Fjord Sweden sediment. After washing, total DNA was extracted and sequenced by Illumina sequencing. The reads were assembled using Edena. To illustrate the use of our method, we analysed several contigs derived from the mitochondrial genome of the foraminifer Globobulimina pseudospinescens, an organism without any sequenced relatives in the databases. These are particularly challenging data, as the genome is highly fragmented and incomplete. DNA isolated from approximately 10,000 single-cell Globobulimina pseudospinescens organisms
2011-06-20 | E-GEOD-26664 | biostudies-arrayexpress
Project description:We introduce FACIL (http://www.cmbi.ru.nl/FACIL), a fast, reliable tool to evaluate nucleic acid sequences for non-standard codes that detects alternative genetic codes even in species distantly related to known organisms. Results are visualized in a Genetic Code Logo. To illustrate the use of our method, we analysed several contigs derived from the mitochondrial genome of the foraminifer Globobulimina pseudospinescens. These are particularly challenging data, as the genome is highly fragmented and incomplete. Approximately 10,000 single-cell Globobulimina pseudospinescens organisms were isolated by hand from Gullmar Fjord Sweden sediment. After washing, total DNA was extracted and sequenced by Illumina sequencing. The reads were assembled using Edena. To illustrate the use of our method, we analysed several contigs derived from the mitochondrial genome of the foraminifer Globobulimina pseudospinescens, an organism without any sequenced relatives in the databases. These are particularly challenging data, as the genome is highly fragmented and incomplete.
2011-06-20 | GSE26664 | GEO
Project description:Escherichia, Shigella, Salmonella, Listeria, Campylobacter, Vibrio Raw sequence reads
| PRJNA590944 | ENA
Project description:We have developed a method based on 454 sequencing of 3’ cDNA fragments from a normalized library constructed from pooled RNAs to generate, through de novo reads assembly, a large catalog of unique transcripts in organisms for which a comprehensive collection of transcripts or the complete genome sequence, is not available. This “virtual transcriptome” provides extensive coverage depth, and can be used for the set up of a comprehensive microarray based expression analysis. We evaluated the potential of this approach by monitoring gene expression during berry maturation in Vitis vinifera. The microarray designed on the berries’ transcriptome derived from half of a 454 run detected the expression of 19,609 genes, and proven to be more informative than one of the most comprehensive grape microarrays available to date, the GrapeArray 1.2 developed by the Italian-French Public Consortium for Grapevine Genome Characterization, which could detect the expression of 15,556 genes.
2009-12-01 | GSE14276 | GEO
Project description:Purpose: The goal of this study is to compare endothelial small RNA transcriptome to identify the target of OASL under basal or stimulated conditions by utilizing miRNA-seq. Methods: Endothelial miRNA profilies of siCTL or siOASL transfected HUVECs were generated by illumina sequencing method, in duplicate. After sequencing, the raw sequence reads are filtered based on quality. The adapter sequences are also trimmed off the raw sequence reads. rRNA removed reads are sequentially aligned to reference genome (GRCh38) and miRNA prediction is performed by miRDeep2. Results: We identified known miRNA in species (miRDeep2) in the HUVECs transfected with siCTL or siOASL. The expression profile of mature miRNA is used to analyze differentially expressed miRNA(DE miRNA). Conclusions: Our study represents the first analysis of endothelial miRNA profiles affected by OASL knockdown with biologic replicates.
2022-09-06 | GSE186354 | GEO
Project description:A cDNA library was constructed by Novogene (CA, USA) using a Small RNA Sample Pre Kit, and Illumina sequencing was conducted according to company workflow, using 20 million reads. Raw data were filtered for quality as determined by reads with a quality score > 5, reads containing N < 10%, no 5' primer contaminants, and reads with a 3' primer and insert tag. The 3' primer sequence was trimmed and reads with a poly A/T/G/C were removed
2021-07-21 | GSE180131 | GEO
Project description:We have developed a method based on 454 sequencing of 3â?? cDNA fragments from a normalized library constructed from pooled RNAs to generate, through de novo reads assembly, a large catalog of unique transcripts in organisms for which a comprehensive collection of transcripts or the complete genome sequence, is not available. This â??virtual transcriptomeâ?? provides extensive coverage depth, and can be used for the set up of a comprehensive microarray based expression analysis. We evaluated the potential of this approach by monitoring gene expression during berry maturation in Vitis vinifera. The microarray designed on the berriesâ?? transcriptome derived from half of a 454 run detected the expression of 19,609 genes, and proven to be more informative than one of the most comprehensive grape microarrays available to date, the GrapeArray 1.2 developed by the Italian-French Public Consortium for Grapevine Genome Characterization, which could detect the expression of 15,556 genes. Microarray oligo probes were designed based on 454 sequencing of 3'-ends of transcripts of a sample constituted by pooling RNAs from grape berries at 6 time points from veraison to whitering. The array was used to analyze the same pool and results were compared to GrapeArray 1.2 developed by the Italian-French Public Consortium for Grapevine Genome Characterization.
2010-06-25 | E-GEOD-14276 | biostudies-arrayexpress
Project description:Pine Wilt Disease organisms Raw sequence reads
| PRJNA297944 | ENA