Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome assembly resources of genitourinary cancers for chromosomal aberration at the single nucleotide level

ABSTRACT: We obtained high-fidelity (HiFi) long-read sequencing data of six genitourinary tumor cell lines (PC-3, DU 145, LNCaP, Caki-1, HK-2, SNU1272) using the PacBio Revio system.

INSTRUMENT(S): -

ORGANISM(S): Homo Sapiens

SUBMITTER: Department of Convergent Bioscience and Informatics

PROVIDER: PRJEB86268 | EVA | 2025-02-26

REPOSITORIES: EVA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	CancerPanGenome.rmdup.ref.vcf.csi	Other
	CancerPanGenome.rmdup.ref.vcf.gz	Vcf
	CancerPanGenome.rmdup.ref.vcf.gz.csi	Vcf

Items per page:

1 - 3 of 3

Similar Datasets

Merging short and stranded long reads improves transcript assembly

Project description:New tools for improved long-read transcript assembly and coalescence with its short-read counterpart are required. Using our short- and long-read measurements from different cell lines with spiked-in standards, we systematically compared key parameters and biases in the read alignment and assembly of transcripts. We report a cDNA synthesis artifact in long-read datasets that impacts the identity and quantitation of assembled transcripts. We developed a computational pipeline to strand long-read cDNA libraries that markedly improves assembly of transcripts from long-reads. Incorporating stranded long-reads in a new hybrid assembly approach, we demonstrate its efficacy for improved characterization of challenging lncRNA transcripts. Our workflow can be applied to a wide range of transcriptomics datasets for superior demarcation of transcript ends and refined isoform structure, which can enable better differential gene expression analyses and molecular manipulations of transcripts.

2023-10-14 | GSE215357 | GEO

Merging short and stranded long reads improves transcript assembly

2023-10-14 | GSE215355 | GEO

Extensive OMICS resources for Sf21 and High Five cell lines

Project description:Insect derived cell-lines, from Spodoptera frugiperda (Sf21) and from Trichoplusia ni (High Five), are ones of the most widely used systems for recombinant protein expression in Baculoviral Expression Vector System (BEVS). Genomic sequences and annotations are still incomplete for Sf21 or absent for High Five. In this study we present an approach using different sequencing data types with short-read sequencing, long synthetic and Oxford Nanopore reads to build genomes at an unprecedented resolution. The Sf21 and High Five assemblies contain 4,020 scaffolds of size, 463 Mb with N50 of 364 Kb and 2,954 scaffolds of size, 332 Mb with N50 of 326 Kb, respectively. Furthermore, we build a new gene prediction workflow, which integrates transcriptome proteome information using pre-existing tools. Using this approach, we could predict 21,506 Sf21 genes and 14,159 High Five genes, which were then functionally annotated. Finally, we also generate and integrate proteomic datasets to validate predicted genes. This integrative approach could be theoretically applied to any uncharacterized genome and result in valuable new resources. With this information available, Sf21 and High Five cells will become even better tools for protein expression and could be used in a wider range of applications, from promoter identifications to genome engineering and editing.

2022-03-03 | PXD010282 | Pride

High throughput error correction using dual nucleotide dimer blocks allows direct single-cell nanopore transcriptome sequencing

Project description:Droplet-based single-cell sequencing techniques have provided unprecedented insight into cellular heterogeneities within tissues. However, these approaches only allow for the measurement of the distal parts of a transcript following short-read sequencing. Therefore, splicing and sequence diversity information is lost for the majority of the transcript. The application of long-read Nanopore sequencing to droplet-based methods is challenging because of the low base-calling accuracy currently associated with Nanopore sequencing. Although several approaches that use additional short-read sequencing to error-correct the barcode and UMI sequences have been developed, these techniques are limited by the requirement to sequence a library using both short- and long-read sequencing. Here we introduce a novel approach termed single-cell Barcode UMI Correction sequencing (scBUC-seq) to efficiently error-correct barcode and UMI oligonucleotide sequences synthesized by using blocks of dimeric nucleotides. The method can be applied to correct both short-read and long-read sequencing, thereby allowing users to recover more reads per cell that permits direct single-cell Nanopore sequencing for the first time. We illustrate our method by using species-mixing experiments to evaluate barcode assignment accuracy and multiple myeloma cell lines to evaluate differential isoform usage and Ewing’s sarcoma cells to demonstrate Ig fusion transcript analysis.

2021-01-31 | GSE162053 | GEO

Project description:Mini-vlsE system long read sequencing

| PRJNA438147 | ENA

Brassica napus

Project description:Long-read sequencing data of six Brassica napus accessions

| PRJNA1155214 | ENA

Assembly of full-length macaque gene models

Project description:We reported an atlas of de novo-defined, full-length macaque gene models on the basis of single molecule long-read transcriptome sequencing (Iso-seq).

2021-06-01 | GSE132413 | GEO

De novo assembly of macaque gene models

Project description:We reported an atlas of de novo-defined, full-length macaque gene models on the basis of single molecule long-read transcriptome sequencing (Iso-seq).

2021-04-17 | GSE158668 | GEO

Hybrid Assembly Comparisons

Project description:Study comparing hybrid assembly approaches from five long read assembly methods

| PRJEB48712 | ENA

Assembly of the Arabidopsis (Col-0) centromeres using Oxford Nanopore Technology long-read DNA sequencing.

Project description:Nanopore long-read sequencing was used to generate a complete assembly of the Arabidopsis centromeres.

2021-04-02 | E-MTAB-10272 | biostudies-arrayexpress