Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A5942197-b8e2-4e44-88a9-66cffddaf475 - samples

ABSTRACT: Small variants in HAE of several Canary Islanders sequenced with Illumina WES.

PROVIDER: EGAD00001009318 | EGA |

REPOSITORIES: EGA

ACCESS DATA

Json Xml

Similar Datasets

83f461c1-f510-40dc-81f0-2d7737a71415 - samples

Project description:Small variants in mtDNA of several Canary Islanders sequenced with Illumina WGS and WES and Oxford Nanopore Technologies WGS.

| EGAD00001008333 | EGA

CIRdb-CEU1

Project description:Single Nucleotide Polymorphisms in autosomes of Canary Islanders

| EGAD00010002294 | EGA

Genome-scale DNA methylation profiling of lung adenocarcinoma: validation using Ontario Tumor Bank samples

Project description:The independent population of lung adenocarcinoma and adjacent non-tumor lung used for verification of the EDRN/Canary Foundation study 28 lung adenocarcinoma and 27 adjacent non-tumor lung fresh frozen tissues were macrodissected, bisulfite treated and analyzed on the Illumina Infinium HumanMethylation27K BeadChip

2012-03-21 | E-GEOD-32866 | biostudies-arrayexpress

Genome-scale DNA methylation profiling of lung adenocarcinoma: validation using Ontario Tumor Bank samples

Project description:The independent population of lung adenocarcinoma and adjacent non-tumor lung used for verification of the EDRN/Canary Foundation study

2012-03-21 | GSE32866 | GEO

Targeted sequencing of 49 primary medulloblastoma samples using Illumina TruSight Tumor 15 assay

Project description:The mutation status of TP53 was analyzed by next generation sequencing using the Illumina TruSight Tumor (TST) 15 assay (Illumina) at the Molecular Pathology Center of the Jewish General Hospital (Montreal, QC, Canada). The CAP-compliant clinically validated TST15 assay was performed as per supplier's instruction with 10 ng DNA input. Libraries were sequenced on a MiSeq with a v3 flow cell (Illumina). Data was analyzed with a clinically validated pipeline (NextGene, SoftGenetics) and variants were annotated in Geneticist Assistant (SoftGenetics). The IARC TP53 database version R18 was consulted for the molecular interpretation of TP53 variants (www.p53.iarc.fr).

2018-03-20 | E-MTAB-6546 | biostudies-arrayexpress

Transcriptomic Genes Identified in Familial Eosinophilic Esophagitis

Project description:Background and Aims: Evidence for a genetic contribution to eosinophilic esophagitis (EoE) exists from family and genome-wide association studies. Extensive investigation into rare variants contributing to EoE has not been performed. The Aim is to evaluate families with multiple cases of EoE by genomic and transcriptomic sequencing to identify genes predisposing to EoE. Methods: We whole exome sequenced (WES) distant relative pairs (e.g., cousins) in extended EoE pedigrees and other affected relatives to identify rare, shared, potentially pathologic variants. Whole-transcriptome sequencing by RNA-Seq was performed in nuclear families with multiple EoE cases. We compared the overlap of genes from DNA and RNA sequencing for relevance to disease manifestations. Results: WES was performed in 50 familial cases in 21 EoE extended pedigrees. We observed 219 rare, candidate predisposition variants in 210 genes with complete sharing among all affected family members. Transcriptome sequencing was performed for 43 EoE cases in 18 nuclear kindreds, including 6 relatives without EoE. We observed 10,070 total differentially expressed genes compared to controls. We identified three genes (MUC16, ADGRE1, and TENM3) with evidence of rare variant sharing and differential gene expression among all affected family members. We identified 43 other genes with partial sharing of rare variants among affected family members and with differential gene expression. Several genes identified as prominent in EoE were also differentially expressed in unaffected relatives. Conclusions: Multiple genes related to immune response, barrier dysfunction, and cell adhesion were identified in familial EoE cases and unaffected family members supporting a genetic familial predisposition and a possible multi-hit background to disease pathophysiology.

2025-01-24 | GSE250595 | GEO

Whole exome sequencing of xenografts derived from human pancreatic ducal adenocarcinoma samples: CU42

Project description:We aimed to decipher APOBEC3A driven mutational differences in human PDX_PDAC tissues. 40 human PDX_PDAC tissues were grouped based on their APOBEC3A expression levels into APOBEC3A High and Low groups. Illumina whole exome sequencing (WES) was performed and downstream variant analysis was applied.

2021-09-06 | E-MTAB-10115 | biostudies-arrayexpress

Proteomic and long-read transcriptomic analysis of Amblyomma americanum salivary gland lysate

Project description:Pioneering studies (PXD014844) have identified many interesting molecules in tick saliva by LC-MS/MS proteomics, but the protein databases used to assign mass spectra were based on short Illumina reads of the Amblyomma americanum transcriptome and may not have captured the diversity and complexity of longer transcripts. Here we apply long-read Pacific Bioscience technologies to complement the previously reported short-read Illumina transcriptome-based proteome in an effort to increase spectrum assignments. Our dataset reveals a small increase in assignable spectra to supplement the previously released short-read transcriptome-based proteome.

2022-05-31 | PXD033870 | Pride

Time-resolved proteomic profile of Amblyomma americanum tick saliva during feeding Running Title: Proteins in tick saliva every 24 h during feeding

Project description:Pioneering studies (PXD014844) have identified many interesting molecules by LC-MS/MS proteomics, but the protein databases used to assign mass spectra were based on short Illumina reads of the Amblyomma americanum transcriptome and may not have captured the diversity and complexity of longer transcripts. Here we apply long-read Pacific Bioscience technologies to complement the previously reported short-read Illumina transcriptome-based proteome in an effort to increase spectrum assignments. Our dataset reveals a small increase in assignable spectra to supplement previously released short-read transcriptome-based proteome.

2020-01-23 | PXD014844 | Pride

Chickpea Small RNA Atlas - Development

Project description:In this study, we sequenced small RNA content from seven major tissues/organs employing Illumina technology. More than 154 million reads were generated using Illumina high-throughput sequencing GAII platform, which represented more than 20 million distinct small RNA sequences. After pre-processing, several conserved and novel miRNAs were identified in chickpea. Further, the putative targets of chickpea miRNAs were identified and their functional categorization was analyzed. In addition, we identified miRNAs exhibitng differential and specific expression in various tissues/organs.

2014-09-08 | GSE51300 | GEO

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