Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

MIAmS

ABSTRACT: MIAmS: microsatellite instability detection on NGS amplicons data

PROVIDER: PRJEB31725 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR3224180_1.fastq.gz	Fastqsanger.gz
	ERR3224180_2.fastq.gz	Fastqsanger.gz
	ERR3224190_1.fastq.gz	Fastqsanger.gz
	ERR3224190_2.fastq.gz	Fastqsanger.gz
	ERR3224200_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 572

Similar Datasets

Exon level expression profiling of colorectal cancer tissue samples (validation sample series).

Project description:Colorectal cancer is a heterogeneous disease molecularly characterized by inherent genomic instabilities, chromosome instability and microsatellite instability. In the present study we propose transcriptome instability as an analogue to genomic instability on the transcriptome level. Exon microarray data from two independent series of altoghether 160 colorectal cancer tissue samples was used for global alternative splicing detection using the FIRMA algorithm (aroma.affymetrix). The sample-wise amounts of these alternative splicing scores exceeding a defined threshold (deviating exon usage amounts) were summarized to provide the basis for description of transcriptome instability. This characteristic was shown to be associated with splicing factor expression levels and patient survival in both independent sample series.

2011-05-19 | GSE24550 | GEO

Exon level expression profiling of colorectal cancer tissue samples (test sample series).

2011-05-19 | GSE24549 | GEO

Exon level expression profiling of colorectal cancer tissue samples (validation sample series).

2011-05-19 | E-GEOD-24550 | biostudies-arrayexpress

Exon level expression profiling of colorectal cancer tissue samples (test sample series).

2011-05-19 | E-GEOD-24549 | biostudies-arrayexpress

Homo sapiens

Project description:Microsatellite instability prostate cancer

| PRJNA1010485 | ENA

Improved Detection and Identification of Microsatellite Instability Features in Colorectal Cancer

Project description:Improved Detection and Identification of Microsatellite Instability Features in Colorectal Cancer

| PRJNA575921 | ENA

Improved Detection and Identification of Microsatellite Instability Features in Colorectal Cancer

Project description:Improved Detection and Identification of Microsatellite Instability Features in Colorectal Cancer

| PRJNA575920 | ENA

Proteome-wide identification of SAPs in an industrial yeast strain

Project description:Most proteogenomic approaches for mapping single amino acid polymorphisms (SAPs) require construction of a sample-specific database containing protein variants predicted from the next-generation sequencing (NGS) data. We present a new strategy for direct SAP detection without relying on NGS data. Among the 348 putative SAP peptides identified in an industrial yeast strain, 85.6% of SAP sites were validated by genomic sequencing.

2018-04-18 | PXD003101 | Pride

Identification of HLA class I-presented peptides in MSI CRC model cell line HCT-116

Project description:HCT-116 cells were treated either with 5 µM of the NMD inhibitor 5-azacytidine (PMID: 25319547) or DMSO (negative solvent control) for 24 h to examine differences in HLA class I-mediated peptide presentation. Moreover, data were used for the identification of tumor-specific neoepitopes originating from insertion/deletion mutations due to microsatellite instability.

2021-04-14 | PXD021755 | Pride

Gastric cancers of Western European and African patients

Project description:Gastric cancer is the second most common cause of cancer death worldwide, but incidence and mortality rates show large variations across different countries. Variation in risk factors between different populations, including environmental and host factors influencing gastric cancer risk, have been reported but little is known about the biological differences between gastric cancers from different geographic locations. We set out to study genomic instability patterns of gastric cancers obtained from patients from United Kingdom (UK) and South Africa (SA). DNA was isolated from 67 gastric adenocarcinomas, 33 UK patients, 9 Caucasian SA patients and 25 native SA patients. Microsatellite instability and chromosomal instability were analyzed by PCR and microarray comparative genomic hybridization, respectively. Data was analyzed by supervised univariate and multivariate analyses as well as unsupervised hierarchical cluster analysis. Tumors from Caucasian and native SA patients showed significantly more microsatellite instable tumors (p<0.05). For the microsatellite stable tumors, geographical origin of the patients correlated with cluster membership, derived from unsupervised hierarchical cluster analysis (p=0.001). Several chromosomal alterations showed significantly different frequencies in tumors from UK patients and native SA patients, but not between UK patients and Caucasian SA patients and between native and Caucasian SA patients. In conclusion, gastric cancers from South African and UK patients show differences in genetic instability patterns, indicating possible different biological mechanisms underlying the disease.

2011-06-28 | GSE22789 | 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