WGS
Ontology highlight
ABSTRACT:
PROVIDER: EGAS00001007211 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:Whole-genome sequencing of pancreatic cancer organoids and matched germline controls.
| EGAD00001010835 | EGA
Project description:<p>We generated a collection of patient-derived pancreatic normal and cancer organoids. We performed whole genome sequencing, targeted exome sequencing, and RNA sequencing on organoids as well as matched tumor and normal tissue if available. This dataset is a valuable resource for pancreas cancer researchers, and those looking to compare primary tissue to organoid culture. In our linked publication, we show that pancreatic cancer organoids recapitulate the mutational spectrum of pancreatic cancer. Furthermore, RNA sequencing of organoids demonstrates the presence of both transcriptional subtypes of pancreas cancer.</p>
| phs001611 | dbGaP
Project description:The fallopian tube (FT) has been proposed as a potential site of origin for high-grade serous ovarian cancer (HGSOC), supporting investigation of genomic alterations across matched tissues. This dataset includes whole-genome sequencing (WGS) and DigiPico data from matched samples, including peripheral blood mononuclear cells (PBMCs), fallopian tube tissue, and tumor tissue from HGSOC patients. The data support analysis of germline and somatic variants, copy number alterations (CNAs), and neoantigen prediction across matched sample types. This submission contains the WGS data DigiPico data associated with this study.
2026-04-07 | GSE301180 | GEO
Project description:Whole genome sequencing of 10 HCLc tumor and matched-germline T cells. Genomic DNA from highly purified HCLc tumor and T cell populations were utilized for library preparation using NEBNext Ultra DNA library prep kit. Sequencing was performed as 150 bp paired end sequencing using four lanes of an Illumina HiSeq4000 to an average depth of 12X. Reads from each library were aligned to the human reference genome GRCh37 using BWA-MEM (v0.7.12). The analysis of somatic genetic alterations in WGS data from tumor-germline pair HCLc samples was divided based on the nature of the mutation, as follow: single-nucleotide variants (SNVs), indels, CNAs and SVs. Moreover, COSMIC mutational signatures and subclonal architecture was inferred for each tumor.
2023-01-01 | E-MTAB-12046 | biostudies-arrayexpress
Project description:We report bulk RNA sequencing, low pass whole genome sequencing, and targeted exome sequencing data of six uterine cancer organoids and show how specific molecular defects in these organoids make them sensitive to cell cycle targeting therapies.
2021-05-08 | GSE171515 | GEO
Project description:We performed single nuclei RNA-sequencing (snRNA-seq) with matched T cell receptor sequencing (TCR-seq), and pool matched low pass whole genome sequencing (WGS) of eight specimens from six patients, encompassing four undifferentiated polymorphic sarcomas (UPS) and four intimal sarcomas (INS), and paired specimens from two patients (one UPS and INS each) treated with immune checkpoint blockade (ICB).
2024-06-21 | GSE243377 | GEO
Project description:Primary objectives: The primary objective is to investigate circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
Primary endpoints: circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
| 2533916 | ecrin-mdr-crc
Project description:Whole genome sequencing by Complete Genomics was performed on two leiomyosarcoma samples and their matched germline
2018-07-02 | E-MTAB-5764 | biostudies-arrayexpress
Project description:Atopic dermatitis (AD), the start of the atopic march, is one of the most common skin disorders in children. Immunologically, AD involves skin barrier defects and CD4+ T cells that localize to the skin, producing inflammatory cytokines and amplifying epidermal dysfunction. To understand the gene regulatory activity differences in peripheral blood T cells in AD, we measured chromatin accessibility (ATAC-seq), NFKB1 binding (ChIP-seq), and gene expression (RNA-seq) in stimulated CD4+ T cells from subjects with active moderate-to-severe AD and age-matched healthy, non-allergic controls. Chromatin accessibility in stimulated CD4+ T cells were highly enriched for AD genetic risk variants. The vast majority of ATAC-seq peaks were shared, consistent with those sections of chromatin being equally available between matched pairs; however, NFKB DNA binding motifs were enriched in chromatin accessible in an AD-dependent manner. NFKB1 ChIP-seq identified peaks that were stronger in AD cases, enriched in controls, or shared between cases and controls. The ChIP-seq peaks that were statistically stronger in AD were more strongly enriched for NFKB DNA binding motifs. Chromatin that was more strongly accessibe and bound by NFKB1 in AD were enriched for genetic variants that increase risk for AD. Using whole genome sequencing data, we identified wide-spread genotype-dependent chromatin accessibility and allelic NFKB1 binding at AD and allergic disease genetic risk loci.
2022-04-26 | GSE189143 | GEO
Project description:The phi X 174 bacteriophage was first sequenced in 1977, and has since become the most widely used standard in molecular biology and next-generation sequencing. However, with the advent of affordable DNA synthesis and de novo gene design, we considered whether we could engineer a synthetic genome, termed SynX, specifically tailored for use as a universal molecular standard. The SynX genome encodes 21 synthetic genes that can be in vitro transcribed to generate matched mRNA controls, and in vitro translated to generate matched protein controls. This enables the use of SynX as a matched control to compare across genomic, transcriptomic and proteomic experiments. The synthetic genes provide qualitative controls that measure sequencing accuracy across k-mers, GC-rich and repeat sequences, as well as act as quantitative controls that measure sensitivity and quantitative accuracy. We show how the SynX genome can measure DNA sequencing, evaluate gene expression in RNA sequencing experiments, or quantify proteins in mass spectrometry. Unlike previous spike-in controls, the SynX DNA, RNA and protein controls can be independently and sustainably prepared by recipient laboratories using common molecular biology techniques, and widely shared as a universal molecular standard.
2024-03-22 | PXD035035 | Pride