Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Benchmarking Illumina-only and Illumina-PacBio Hybrid Assemblies with the Arabidopsis thaliana Reference Genome

PROVIDER: PRJEB5459 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR431469_1.fastq.gz	Fastqsanger.gz
	ERR431469_2.fastq.gz	Fastqsanger.gz
	ERR431470_1.fastq.gz	Fastqsanger.gz
	ERR431470_2.fastq.gz	Fastqsanger.gz
	ERR431471_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 6

Similar Datasets

Chromatin immunoprecipitation analysis of CENH3 in the Arabidopsis thaliana accessions Col-0, Ler-0, Cvi-0 and Tanz-1

Project description:Chromatin immunoprecipitation analysis of CENH3 in the Arabidopsis thaliana accessions Col-0, Ler-0, Cvi-0 and Tanz-1 was performed in order to align reads to PacBio HiFi genome assemblies which contain complete centromere repeat arrays.

2022-08-01 | E-MTAB-11974 | biostudies-arrayexpress

Homology-guided Assembly of the Genomes of the Four Diverse Accessions Ler, C24, Bur-0 and Kro-0

Project description:Here we present the first whole-genome assemblies of Arabidopsis thaliana strains since the release of the 125 Mb reference genome sequence a decade ago. We demonstrate their practical relevance in studying the expression differences of polymorphic genes and show how the analysis of sRNA sequencing data can lead to erroneous conclusions if aligned against the reference genome alone.

2011-02-11 | GSE24569 | GEO

Homology-guided Assembly of the Genomes of the Four Diverse Accessions Ler, C24, Bur-0 and Kro-0

2011-02-11 | E-GEOD-24569 | biostudies-arrayexpress

cgh_colvscvi_wg-Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions

Project description:a2e_heterosis - cgh_colvscvi_wg - Arabidopsis thaliana accessions (Col-0, C24 and Cvi) and their hybrid were used to investigate the dynamics of the epigenome after intraspecific hybridization between - Comparative genome hybridization between Arabidopsis thaliana accessions Col-0 and CVi.

2011-05-17 | GSE24835 | GEO

cgh_colvsc24_wg-Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions

Project description:a2e_heterosis - cgh_colvsc24_wg - Arabidopsis thaliana accessions (Col-0, C24 and Cvi) and their hybrid were used to investigate the dynamics of the epigenome after intraspecific hybridization between - Comparative genome hybridization between Arabidopsis thaliana accessions Col-0 and C24.

2011-05-17 | GSE24831 | GEO

cgh_colvsc24_chr4-Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions

Project description:a2e_heterosis - cgh_colvsc24_chr4 - Arabidopsis thaliana accessions (Col-0, C24 and Cvi) and their hybrid were used to investigate the dynamics of the epigenome after intraspecific hybridization between - Comparative genome hybridization between Arabidopsis thaliana accessions Col-0 and C24 Keywords: cgh,chip-chip

2011-05-17 | GSE24494 | GEO

Hi-C guided assemblies reveal conserved regulatory topologies on X and autosomes despite extensive genome shuffling [ChIP-seq]

Project description:We used an approach combining PacBio data and published Illumina reads to de novo assemble D. busckii contigs. We generated Hi-C data from D. busckii embryos to order these contigs into chromosome-length scaffolds. For D. virilis we generated Hi-C data to order and orient the published Dvir_caf1 scaffolds into chromosome-length assemblies. Furthermore, we compared Hi-C matrices from these two new assemblies with D. melanogaster with respect to synteny blocks and dosage compensation as a chromosome-wide gene-regulatory mechanism.

2019-10-14 | GSE120750 | GEO

De novo assembly and annotation of the singing mouse genome

Project description:We sequenced the genome and transcriptome of Alston’s singing mouse (Scotinomys teguina), an emerging model for social cognition and vocal communication. Using PromethION, Illumina, and PacBio sequencing, we produced an annotated genome and transcriptome, which were validated using gene expression and functional enrichment analyses. To assess the usefulness of our assemblies, we performed single nuclei sequencing on cells of the orofacial motor cortex, a brain region implicated in song coordination, identifying 12 cell types.

2023-08-03 | GSE212957 | GEO

The Arabidopsis thaliana pancentromere

Project description:Genome assemblies of 48 Arabidopsis thaliana accessions with PacBio HiFi long-reads

| PRJEB55353 | ENA

HPG1 accessions in the Atlas of telomeric repeat diversity in Arabidopsis thaliana

Project description:Genome assemblies of 3 Arabidopsis thaliana HPG1 accessions with PacBio HiFi reads

| PRJEB75768 | ENA