Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Genome assembly and annotation for Vaccinium bracteatum Thunb.

PROVIDER: PRJNA1110808 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other
	SRR29004620_1.fastq.gz	Fastqsanger.gz
	SRR29004620_2.fastq.gz	Fastqsanger.gz
	SRR29004621_1.fastq.gz	Fastqsanger.gz
	SRR29004621_2.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 16

Similar Datasets

Project description:Transcriptome of Vaccinium bracteatum Thunb. fruits

| PRJNA694726 | ENA

Transcriptomic analysis of plant Cd-regulated genes in the ericoid mycorrhizal symbiosis

Project description:Illumina HiSeq2000 technology was used to generate mRNA profiles from Vaccinium myrtillus mycorrhizal and non-mycorrhizal roots with or without Cadmium treatment. 150bp reads were generated and aligned to a Vaccinium myrtillus de novo assembly as reference using CLC Genomics Workbench 8.

2020-02-12 | GSE119554 | GEO

RNAseq and WGBS of Vaccinium corymbosum

Project description:We did whole-genome methylation sequencing for 21 Vaccinium samples. This project attempts to analyze the improvement breeding process of cultivated blueberry from two aspects of heredity and epigenetic inheritance.

2024-05-20 | GSE228041 | GEO

RNA-seq analysis of Selaginella kraussiana leaf, rhizophore, seedling and stem

Project description:Annotation of the draft assembly of selaginella kraussiana

2016-02-09 | GSE69388 | GEO

Cranberry

Project description:Vaccinium macrocarpon and Vaccinium oxycoccos genome sequencing and assembly

| PRJNA738865 | ENA

Proteomics Informed by Transcriptomics for Characterising Active Transposable Elements and Genome Annotation in Aedes aegypti

Project description:The incomplete genome annotation of non-model organisms hampers molecular and proteomic studies. Proteomics informed by transcriptomics (PIT) is suited to non-model organisms because peptides are identified using transcriptomic, not genomic, data. Aedes aegypti is the mosquito vector for the (re-)emerging dengue, chikungunya, yellow fever and Zika viruses. An Ae. aegypti genome sequence is available, however experimental evidence for >90% of the Ae. aegypti proteome or the activity of transposable elements (TEs) that constitute 50% of the Ae. aegypti genome is lacking. We used PIT to characterise the proteome of the Aedes aegypti derived cell line Aag2. Hotspots of incomplete genome annotation were identified which are not explained by poor sequence and assembly quality. We developed criteria for the characterisation of proteomically active TEs and demonstrate that protein expression does not correlate with a TE’s genomic abundance. Finally, we identify Phasi Charoen-like virus as an unrecognised contaminant of Aag2 cells. We therefore present the first proteomic characterisation of mobile genetic elements, and provide proof-of-principle that PIT can evaluate a genome’s annotation to guide annotation efforts.

2017-02-15 | PXD003799 | Pride

A draft genome sequence of the elusive giant squid, Architeuthis dux

Project description:We present a draft genome assembly that includes 200 Gb of Illumina reads, 4 Gb of Moleculo synthetic long-reads and 108 Gb of Chicago libraries, with a final size matching the estimated genome size of 2.7 Gb, and a scaffold N50 of 4.8 Mb. We also present an alternative assembly including 27 Gb raw reads generated using the Pacific Biosciences platform. In addition, we sequenced the proteome of the same individual and RNA from three different tissue types from three other species of squid species (Onychoteuthis banksii, Dosidicus gigas, and Sthenoteuthis oualaniensis) to assist genome annotation. We annotated 33,406 protein coding genes supported by evidence and the genome completeness estimated by BUSCO reached 92%. Repetitive regions cover 49.17% of the genome.

2019-12-16 | PXD016522 | Pride

Sequence data for annotation and scaffolding of the Lathyrus sativus LS007 Rbp1.0 genome assembly

Project description:This dataset includes RNAseq data of 7 tissues/developmental stages of Lathyrus sativus genotype LSWT11 and 2 tissues with drought- and well-watered treatments of Lathyrus sativus genotypes LS007 and Mahateora. These data were used in the functional annotation pipeline of the Rbp1.0 genome assembly of LS007. The multi-tissue transcriptome was also used to support gene candidate identification by mRNA abundance. Also included is Hi-C sequencing data used to scaffold the assembly into pseudochromosomes

2023-01-31 | GSE223956 | GEO

Chromosome-level de novo assembly and annotation of pig-tailed (macaca nemestrina) macaque genome

Project description:Macaque species share over 93% genome homology with humans and develop many disease phenotypes similar to those of humans, making them valuable animal models for the study of human diseases (e.g.,HIV and neurodegenerative diseases). However, the quality of genome assembly and annotation for several macaque species lags behind the human genome effort. To close this gap and enhance functional genomics approaches, we employed a combination of de novo linked-read assembly and scaffolding using proximity ligation assay (HiC) to assemble the pig-tailed macaque (Macaca nemestrina) genome. This combinatorial method yielded large scaffolds at chromosome-level with a scaffold N50 of 127.5 Mb; the 23 largest scaffolds covered 90% of the entire genome. This assembly revealed large-scale rearrangements between pig-tailed macaque chromosomes 7, 12, and 13 and human chromosomes 2, 14, and 15. We subsequently annotated the genome using transcriptome and proteomics data from personalized induced pluripotent stem cells (iPSCs) derived from the same animal. Reconstruction of the evolutionary tree using whole genome annotation and orthologous comparisons among three macaque species, human and mouse genomes revealed extensive homology between human and pig-tailed macaques with regards to both pluripotent stem cell genes and innate immune gene pathways. Our results confirm that rhesus and cynomolgus macaques exhibit a closer evolutionary distance to each other than either species exhibits to humans or pig-tailed macaques. These findings demonstrate that pig-tailed macaques can serve as an excellent animal model for the study of many human diseases particularly with regards to pluripotency and innate immune pathways.

2020-05-04 | PXD018943 | Pride

Project description:genome assembly of Sarcandra glabra (Thunb.) Nakai

| PRJNA1132672 | ENA