Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

DD-SITUS_INVERSUS-2017

ABSTRACT: WGS of two individuals with developmental dyslexia and situs inversus.

PROVIDER: PRJEB23468 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR2196030.fastq.gz	Fastqsanger.gz
	ERR2196030_1.fastq.gz	Fastqsanger.gz
	ERR2196030_2.fastq.gz	Fastqsanger.gz
	ERR2196029.fastq.gz	Fastqsanger.gz
	ERR2196029_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 6

Similar Datasets

FIN-DYS

Project description:Linkage analysis and exome/WGS sequencing in a pedigree with developmental dyslexia

| PRJEB12695 | ENA

WGS of a serie of Arabidopsis thaliana tetrad's products to study the role of RECQ4A, RECQ4B, FIGL1 and FANCM genes in the rate, nature and distribution of meiotic recombination products (CO and NCO)

Project description:In this study, two accessions of Arabidopsis thaliana (Columbia and Landsberg erecta) were crossed and tetrads were obtained using thanks to the the quartet mutation, which keeps the 4 haploid pollen grains from a single meiosis attached together. By fertilising a plant (of ecotype Columbia) with a single tetrad, then selecting seeds from siliques containing exactly four seeds and finally sequencing the 4 developed plants, we can access the complete history of meiotic recombination events occurring in a single male meiosis. Comparison of the genomic sequences (WGS) of the 4 plants in a tetrad makes it possible to identify meiotic COs and NCOS events in each tetrad thanks to the numerous polymorphisms specific to each of the parental genomes. The analysis of the WGS tetrads data consists of genotyping a series of SNV markers (differentiating Columbia and Landsberg) positioned on the five chromosomes for the 4 (M1, M2, M3, M4) individuals of a tetrad, representing the 4 chromatids of each chromosomes. A total of 20 tetrads, the F1 and the two parental accessions Columbia and Landsberg erecta were sequenced.

2024-12-02 | E-MTAB-14435 | biostudies-arrayexpress

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

DYX_SWE_FAM

Project description:Exome sequencing in an family from Sweden with developmental dyslexia

| PRJEB9294 | ENA

Affymetrix CytoScan 750K and HD data for developmental delay and/or physical disability phenotypes samples

Project description:Chromosomal copy number variations (CNV) have been associated with various neurological and developmental disorders and chromosomal microarray (CMA) is a method of choice to diagnose Copy Number Gain/Loss syndromes. Recently, next-generation sequencing (NGS)-based low-coverage whole genome sequencing (LC-WGS) has been applied to detect Copy Number Gain/Loss syndromes. This dataset is intended to be used as a “Golden standard data set” for development of LC-WGS analysis method. It consists of patients (n=63) who have a mental delay and/or physical disability phenotype and normal (n=20) phenotype.

2018-09-29 | GSE120624 | GEO

AmpH, a bifunctional DD-endopeptidase and DD-carboxypeptidase of Escherichia coli.

Project description:In Escherichia coli, low-molecular-mass penicillin-binding proteins (LMM PBPs) are important for correct cell morphogenesis. These enzymes display DD-carboxypeptidase and/or dd-endopeptidase activities associated with maturation and remodeling of peptidoglycan (PG). AmpH has been classified as an AmpH-type class C LMM PBP, a group closely related to AmpC ?-lactamases. AmpH has been associated with PG recycling, although its enzymatic activity remained uncharacterized until now. Construction and purification of His-tagged AmpH from E. coli permitted a detailed study of its enzymatic properties. The N-terminal export signal of AmpH is processed, but the protein remains membrane associated. The PBP nature of AmpH was demonstrated by its ability to bind the ?-lactams Bocillin FL (a fluorescent penicillin) and cefmetazole. In vitro assays with AmpH and specific muropeptides demonstrated that AmpH is a bifunctional DD-endopeptidase and DD-carboxypeptidase. Indeed, the enzyme cleaved the cross-linked dimers tetrapentapeptide (D45) and tetratetrapeptide (D44) with efficiencies (k(cat)/K(m)) of 1,200 M(-1) s(-1) and 670 M(-1) s(-1), respectively, and removed the terminal D-alanine from muropeptides with a C-terminal D-Ala-D-Ala dipeptide. Both DD-peptidase activities were inhibited by 40 ?M cefmetazole. AmpH also displayed a weak ?-lactamase activity for nitrocefin of 1.4 × 10(-3) nmol/?g protein/min, 1/1,000 the rate obtained for AmpC under the same conditions. AmpH was also active on purified sacculi, exhibiting the bifunctional character that was seen with pure muropeptides. The wide substrate spectrum of the DD-peptidase activities associated with AmpH supports a role for this protein in PG remodeling or recycling.

| S-EPMC3232839 | biostudies-literature

Whole Genome Sequencing of Tongue cancer samples and cell line

Project description:Whole genome sequencing (WGS) of tongue cancer samples and cell line was performed to identify the fusion gene translocation breakpoint. WGS raw data was aligned to human reference genome (GRCh38.p12) using BWA-MEM (v0.7.17). The BAM files generated were further analysed using SvABA (v1.1.3) tool to identify translocation breakpoints. The translocation breakpoints were annotated using custom scripts, using the reference GENCODE GTF (v30). The fusion breakpoints identified in the SvABA analysis were additionally confirmed using MANTA tool (v1.6.0).

2024-02-17 | E-MTAB-12534 | biostudies-arrayexpress

undefined

Project description:WGS from sub-esophageal mass (SUB) and gills of two different Octopus bimaculoides individuals

| PRJEB51312 | ENA

Capture Hi-C (HiCap) experiments performed on LUHMES cell line differentiated in three (D3) and six days (D6). We fragmented the genome using DpnII. HiCap experiments at each time point (D1, D3 and D6) are performed in two replicates

Project description:LUHMES cells are non-tumorigenic model of human dopaminergic neurons. Their physiology and phenotypic changes upon differentiation can provide clues into the pathology of neurological diseases such as dyslexia, autism, schizophrenia.

2024-01-14 | E-MTAB-13665 | biostudies-arrayexpress

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

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