Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Fungal HiFi genome sequencing

PROVIDER: PRJNA1198377 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR31719410_subreads.fastq.gz	Fastqsanger.gz
	SRR31719411_subreads.fastq.gz	Fastqsanger.gz
	SRR31719412_subreads.fastq.gz	Fastqsanger.gz
	SRR31719413_subreads.fastq.gz	Fastqsanger.gz

Items per page:

1 - 4 of 4

Similar Datasets

Amplicon sequencing of a K562 cell line model with a patient-based t(3;8) translocation following CRISPR treatment

Project description:Genome editing was conducted on a t(3;8) K562 model to investigate the effects of deleting different modules or CTCF binding sites within the MYC super-enhancer. To check mutations after targeting with CRISPR-Cas9 we performed amplicon sequencing using the Illumina PCR-based custom amplicon sequencing method using the TruSeq Custom Amplicon index kit (Illumina). The first PCR was performed using Q5 polymerase (NEB), the second nested PCR with KAPA HiFi HotStart Ready mix (Roche). Samples were sequenced paired-end (2x 250bp) on a MiSeq (Illumina).

2021-07-26 | E-MTAB-9937 | biostudies-arrayexpress

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

Genome sequence and annotation of the fungus Periconia digitata

Project description:The Periconia genus belongs to the phylum Ascomycota, order Pleosporales, family Periconiaceae. Periconia is widespread in many habitats but little is known about its ecology. Several species produce bioactive molecules, among them, Periconia digitata extracts were shown to be deadly active against the pine wilt nematode. The strain CNCM I-4278, here identified as P. digitata was able to inhibit the plant pathogen Phytophthora parasitica. Since P. digitata has great potential as biocontrol agent and the only other genome available in the Periconiaceae family is that of Periconia macrospinosa, which is quite fragmentary, we generated long-read genomic data for P. digitata. Thanks to the PacBio Hifi sequencing technology, we obtained a high-quality genome with a total length of 38,967,494 bp, represented by 13 haploid chromosomes. The transcriptomic and proteomic data strengthen and support the genome annotation. Besides representing a new reference genome within the Periconiaceae, this work will also contribute in our understanding of the Eukaryotic tree of life. Not least, opens new possibilities to the biotechnological use of the species.

2023-08-04 | PXD038112 | Pride

Genome sequence and annotation of the fungus Periconia digitata

2023-08-04 | PXD038175 | Pride

A multicenter translational biomarker phase II trial of regorafenib in patients with non-resectable pretreated colorectal cancer.

Project description:Primary objectives: The primary objective is to investigate circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS). Primary endpoints: circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).

| 2533916 | ecrin-mdr-crc

Malus ioensis

Project description:Malus ioensis hifi genome sequencing

| PRJNA1098637 | ENA

Project description:KOLF2.1J HiFi sequencing

| PRJNA1290418 | ENA

Genome assembly of silkworm BmN4 cells

Project description:BmN4 cells are cultured cells derived from Bombyx mori ovaries and widely used to study transposon silencing by PIWI-interacting RNAs (piRNAs). A high-accurate genome sequence of BmN4 cells is required to analyze the piRNA pathway using RNA-seq. The genome sequence of BmN4 cells was assembled using Pacific Biosciences (PacBio) HiFi and Oxford Nanopore technology Ultralong (ONT-UL) reads. Microscopic observation and image analysis showed that BmN4 cells were octoploid on average, and the number of chromosomes per cell was highly variable. We concluded the haplotype-resolved assembly of such a complex genome would be difficult; therefore, we assembled a consensus genome sequence. RNA-seq analysis of Siwi knockdown cells also revealed that Siwi-piRISC may target Countdown (Cd), an LTR retrotransposon. By comparing the consensus genome sequence with the reads, we identified differences between haplotypes, particulary structural variants, suggesting that some transposons, including Countdown, increased their copy number in BmN4 cells.

2025-02-03 | GSE288600 | GEO

Lathyrus sativus LS007 HiFi genome sequencing

Project description:Lathyrus sativus LS007 HiFi genome sequencing

| PRJEB70892 | ENA

Project description:Lathyrus sativus LS007 HiFi genome sequencing

| PRJNA1019112 | ENA