Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Sequencing, assembly and annotation of Eimeria species

ABSTRACT: Sequencing, assembly and annotation of Eimeria species

PROVIDER: PRJEB4918 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other
	ERR019305_1.fastq.gz	Fastqsanger.gz
	ERR019305_2.fastq.gz	Fastqsanger.gz
	ERR019306_1.fastq.gz	Fastqsanger.gz
	ERR019306_2.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 25

Similar Datasets

Cryptic Eimeria species

Project description:Partial 18S rDNA and COI sequences from cryptic Eimeria species.

| PRJEB23613 | ENA

Sequencing, Assembly and Annotation of B104

Project description:Sequencing, Assembly and Annotation of B104

| PRJEB44462 | ENA

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

Eimeria acervulina

Project description:Eimeria acervulina Genome sequencing and assembly

| PRJNA1012808 | ENA

Comparative Transcriptome Analyses of Drug-sensitive and Drug-resistant Strains of Eimeria tenella by RNA-sequencing

Project description:To gain insights into the molecular mechnism governing the drug resistance of Eimeria tenella, two drug-resistant strains of E. tenella, maduramicin-resistant (MRR) strain and diclazuril-resistant (DZR) strain were induced.We carried out comparative transcriptome analyses of a drug-sensitive strain (DS) and two drug-resistant strains (MRR and DZR) of E. tenella by RNA-seqencing. A total of 1070 DEGs, 672 upregulated and 398 downregulated, were identified in MRR vs. DS; and 379 DEGs, 330 upregulated and 49 downregulated, were detected in DZR vs. DS. Functional annotation analysis identified several DEGs coding for proteins associated with catalytic activity in the DZR strain that were involved in glycolysis and the tricarboxylic acid (TCA) cycle. Other DEGs were associated with ion binding and ion transmembrane transporter activity in the MRR strain. Some DEGs coded for surface antigens that were downregulated in two drug-resistant strains involved invasion, pathogenesis, and host–parasite interactions.These results contribute to developing rapid molecular methods to detect drug resistance of Eimeria spp. in poultry.

2020-03-03 | GSE114347 | GEO

Saccharomyces species genome sequencing

Project description:Genome assembly and annotation of three Saccharomyces species

| PRJEB57075 | ENA

High resolution annotation of Zebrafish transcriptome using long-read sequencing

Project description:With the emergence of zebrafish as an important model organism, a concerted effort has been made to study its transcriptome. This effort is limited by gaps in zebrafish annotation, which is especially pronounced concerning transcripts dynamically expressed during zygotic genome activation (ZGA). To date, short read sequencing has been the principal technology for zebrafish transcriptome annotation. In part because these sequence reads are too short for assembly methods to resolve the full complexity of the transcriptome, the current annotation is rudimentary. By providing direct observation of full-length transcripts, recently refined long-read sequencing platforms can dramatically improve annotation coverage and accuracy. Here, we leveraged the SMRT platform to study the early ZGA-stage zebrafish transcriptome. Our analysis revealed additional novelty and complexity in the zebrafish transcriptome, identifying 2748 high confidence novel transcripts that originated from previously unannotated loci and 1835 new isoforms in previously annotated genes.

2018-05-24 | GSE101843 | GEO

Eimeria tenella

Project description:Eimeria tenella Genome sequencing

| PRJNA1012853 | ENA

Eimeria tenella

Project description:Eimeria tenella Genome sequencing

| PRJNA850893 | ENA

Transcriptomic analysis of Quercus mongolica leaves: de novo assembly, functional annotation and molecular markers mining

Project description:Purpose: The goal of this study is to provided a comprehensive genomic information for functional genomic studies in Q. mongolica. Methods:The Quercus mongolica leaves were generated by deep sequencing, using Illumina Hiseq 4000. The high-quality reads were obtained by removing the reads that contained adaptor contamination, low quality bases and undetermined bases.The transcriptome were de novo assembly. Results:A total of 52934562 raw reads were obtained from Illumina sequencing platform. After filtering out the low quality reads, we obtained 52076914 clean reads, which assembled into 39130 transcripts with a mean length of 742 bp and GC content of 42.12%, and 24196 unigenes with a mean length of 732 bp and GC content of 42.34%, based on Trinity assembly platform. Conclusions:RNA-Seq was applied to polyadenylate-enriched mRNAs from leaves of Q. mongolica to obtain the transcriptome. De novo assembly was then applied followed by gene annotation and functional classification. The SSRs and SNPs were also obtained using assembled transcripts as reference sequences. The results of this study lay the foundation for further research on genetic diversity of Quercus.

2019-01-29 | GSE125799 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data