Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Phil-DIAMOND Project 3 WGS of Probiotic Strains

PROVIDER: PRJNA1003231 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other
	SRR25565016_1.fastq.gz	Fastqsanger.gz
	SRR25565016_2.fastq.gz	Fastqsanger.gz
	SRR25565017_1.fastq.gz	Fastqsanger.gz
	SRR25565017_2.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 5

Similar Datasets

Lactiplantibacillus plantarum

Project description:WGS of Probiotic Strains

| PRJNA1225732 | ENA

DNA-seq of the QSi5 and 129T2/SvEms mouse strains

Project description:For this project, we explored the genetic determinants of the heart development condition termed patent foramen ovale (PFO) using quantitative trait loci (QTL) mapping and genomics/transcriptomics analyses. Two mice strains were chosen that exhibit highly divergent phenotypes associated with PFO, 129T2/SvEms and QSi5. In this experiment, we performed whole genome sequencing (WGS) on genomic DNA extracted from liver specimens of 129T2/SvEms or QSi5 mice in order to identify genomic variants that may contribute to the phenotypes associated with PFO.

2023-03-31 | E-MTAB-11161 | biostudies-arrayexpress

Project description:WGS of human originated probiotic bacterial strains

| PRJNA1250561 | ENA

Evaluation of copy number variation detection between high-resolution array CGH and low-coverage short-insert and mate-pair whole-genome sequencing

Project description:In principle, whole-genome sequencing (WGS) of the human genome even at low coverage offers higher resolution for genomic copy number variation (CNV) detection compared to array-based technologies, which is currently the first-tier approach in clinical cytogenetics. There are, however, obstacles in replacing array-based CNV detection with that of low-coverage WGS such as cost, turnaround time, and lack of systematic performance comparisons. With technological advances in WGS in terms of library preparation, instrument platforms, and data analysis algorithms, obstacles imposed by cost and turnaround time are fading. However, a systematic performance comparison between array and low-coverage WGS-based CNV detection has yet to be performed. Here, we compared the CNV detection capabilities between WGS (short-insert, 3kb-, and 5kb-mate-pair libraries) at 1X, 3X, and 5X coverages and standardly used high-resolution arrays in the genome of 1000-Genomes-Project CEU genome NA12878. CNV detection was performed using standard analysis methods, and the results were then compared to a list of Gold Standard NA12878 CNVs distilled from the 1000-Genomes Project. Overall, low-coverage WGS is able to detect drastically more (approximately 5 fold more on average) Gold Standard CNVs compared to arrays and is accompanied with fewer CNV calls without secondary validation. Furthermore, we also show that WGS (at ≥1X coverage) is able to detect all seven validated deletions larger than 100 kb in the NA12878 genome whereas only one of such deletions is detected in most arrays. Finally, we show that the much larger 15 Mbp Cri-du-chat deletion can be clearly seen at even 1X coverage from short-insert WGS.

2018-06-26 | GSE105092 | GEO

Transcriptome sequencing of the halictid, Lasioglossum albipes

Project description:Deep sequencing of mRNA from the halictid Part of the Lasioglossum albipes WGS project (BioProject ID: PRJNA174755)

2012-10-02 | GSE41247 | GEO

Transcriptome sequencing of the halictid, Lasioglossum albipes

Project description:Deep sequencing of mRNA from the halictid Part of the Lasioglossum albipes WGS project (BioProject ID: PRJNA174755) Analysis of ploy(A)+ RNA of different specimens:whole body from the halictid (Lasioglossum albipes)

2012-10-02 | E-GEOD-41247 | biostudies-arrayexpress

Project description:LAB novel probiotic WGS

| PRJNA515210 | ENA

Probiotic strains diversity

Project description:Probiotic strains diversity

| PRJEB39469 | ENA

sWGS on paired cfDNA and tissue DNA from pediatric cancer patients

Project description:We performed shallow whole genome sequencing (WGS) on circulating free (cf)DNA extracted from plasma or cerebrospinal fluid (CSF), and shallow WGS on the tissue DNA extracted from the biopsy in order to evaluate the correlation between the two biomaterials. After library construction and sequencing (Hiseq3000 or Ion Proton), copy number variations were called with WisecondorX.

2021-11-17 | E-MTAB-10548 | biostudies-arrayexpress

Pseudopodoces humilis Transcriptome data used for gene annotation

Project description:To optimize the genome annotation, two tissue RNA libraries (i.e. liver and muscle) were constructed using the Illumina mRNA-Seq Prep Kit This study is a part of the Pseudopodoces humilis WGS project (BioProject ID: PRJNA179234) and was used for gene annotation improvement. We sequenced two tissues using illumina Hiseq 2000 platform.

2013-11-29 | E-GEOD-44779 | biostudies-arrayexpress

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