Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Germline snv g.vcf for EGAS00001004572 - samples

ABSTRACT: Bulk Germline snv vcfs from haplotypecaller analysis in EGAS00001004572

PROVIDER: EGAD00001006910 | EGA |

REPOSITORIES: EGA

ACCESS DATA

Json Xml

Similar Datasets

Strelka somatic snv vcfs for EGAS00001004572 - samples

Project description:Bulk Strelka somatic snv vcfs from tumour-normal analysis in EGAS00001004572

| EGAD00001006907 | EGA

GRIDSS somatic sv vcfs for EGAS00001004572 - samples

Project description:Bulk GRIDSS somatic sv vcfs from tumour-normal analysis in EGAS00001004572

| EGAD00001006906 | EGA

WGS fastq for EGAS00001004572 - samples

Project description:Bulk WGS fastq files for germline and tumours in EGAS00001004572.

| EGAD00001006902 | EGA

Purple copy number segments for EGAS00001004572 - samples

Project description:Bulk copy number segments from Purple analysis in EGAS00001004572

| EGAD00001006908 | EGA

RNAseq fastq for EGAS00001004572 - samples

Project description:Bulk RNA-seq data of tumours in EGAS00001004572.

| EGAD00001006876 | EGA

Methylation tumour profiles for EGAS00001004572 - samples

Project description:Bulk methylation tumour profiles from infinium methylation epic bead kit in EGAS00001004572

| EGAD00001006909 | EGA

Germline sequencing

Project description:Detection of SNV/indels in the germline of pediatric cancer patients with a focus on CHEK2 germline variants. Included in this EGA upload are the parents of the children in EGA uplodad EGAD00001008763.

| EGAS00001006651 | EGA

CGH analysis of melanomas and germline samples from Braf mutant mouse model

Project description:We investigated copy number alterations in melanomas from two cohorts of Braf mutant mice (UV exposed and no UV exposure) by comparing tumour DNA to germline DNA by array CGH

2014-06-11 | GSE58265 | GEO

Single-cell transcriptomic survey of adenomatous polyposis patients with germline APC mutations

Project description:Patients with germline APC mutations are recognized by hundreds of adenoma polyps in colon, which will give rise to adenocarcinoma inevitably. Over 700 germline APC mutations have been reported to be the leading cause of adenomatous polyposis. However, the underlying mechanism of APC mutation triggered colonic cancer remains mysterious. Here, using a modified STRT-seq protocol, we analyzed over 4000 single cells from the four matching adenomatous polyposis, adenocarcinoma, adjacent normal colon tissue and one lymphatic metastasis from four adenomatous polyposis patients with APC mutations. We identified the main cell types existed in human intestine such as B cells, mast cells, T cells, macrophage cells, endothelial cells, stromal cells and epithelial cells. And the proportional changes of various cell types during the development of adenoma were showed. The transcriptomic similarities and differences between adenoma, adenocarcinoma and adjacent normal tissue were comprehensively investigated. For better understanding the tumor progression process, we also take advantage of other genomic signatures, such as SNV and CNV. We found that the gene expression signatures of adenoma and adenocarcinoma were largely similar when compared with adjacent normal tissue. But the mutation accumulation was indeed observed during the progression from adenoma to adenocarcinoma. To summarized, our work will help us accurately investigate the pathogenic mechanism and heterogeneity of APC inactive mutation triggered colonic cancer, which will also help us better understand the non-familial colorectal cancers

2019-10-25 | GSE109308 | GEO

Comparison of collection strategies for germline analysis

Project description:Comparison of collection strategies for germline analysis

| PRJNA414452 | ENA