Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

467c5412-58e9-4afa-ba50-3420ab5c865a - samples

ABSTRACT: The dataset "PGDx elioÃ¢Â„Â¢ plasma resolve assay: targeted sequencing analyses of WBC DNA" includes paired end FASTQ reads of 49 white blood cell (WBC) genomic DNA samples from metastatic colorectal cancer patients. Sequencing was performed using a panel consisting of 33 genes, covering over 237,000 bp, targeting 25,000x depth across the targeted regions.

PROVIDER: EGAD00001009721 | EGA |

REPOSITORIES: EGA

ACCESS DATA

Json Xml

Similar Datasets

Tissue DNA, WBC DNA and cfDNA (deep-)sequencing of mCRC patients treated with doublet chemotherapy and anti-EGFR in the CAIRO5 study

Project description:This study assessed whether ctDNA based treatment response monitoring could be performed in a tumor tissue-independent manner by combining ultra-deep targeted sequencing analyses of cfDNA with patient-matched white blood cell (WBC) derived DNA. In total, 183 cfDNA and 49 WBC samples, along with 28 tissue samples, from 52 metastatic colorectal cancer patients participating in the prospective phase III CAIRO5 clinical trial (NCT02162563) were analyzed using the PGDx elio plasma resolve assay.

| EGAS00001006695 | EGA

16bc9973-b599-45a2-8d06-c36dfe5b69b8 - samples

Project description:The dataset "PGDx elioÃ¢Â„Â¢ plasma resolve assay: targeted sequencing analyses of plasma cfDNA" includes paired end FASTQ reads of 183 cfDNA samples from metastatic colorectal cancer patients. Sequencing was performed using a panel consisting of 33 genes, covering over 237,000 bp, targeting 25,000x depth across the targeted regions.

| EGAD00001009719 | EGA

29c5dd63-febe-4a71-9f95-91b7de1b3541 - samples

Project description:This dataset consists of 39 noncancerous donor and 62 cancer patient plasma samples (including 29 patients with CRC across a total of 13 tumor types) that were analyzed with the PGDx elio plasma resolve assay. The PGDx elio plasma resolve assay is a hybrid capture approach targeting 33 genes with sequencing performed using the Illumina NextSeq with 150bp paired-end reads. The bam files provided have been adapter masked and contain duplicate reads.

| EGAD00001009718 | EGA

ed673335-bda4-4cfb-b851-d1c2f89024fa - samples

Project description:The dataset for the study "Early ctDNA molecular response captures therapeutic response in the first stage of CCTG BR.36 ctDNA-directed, multi-center phase II study of molecular response adaptive immunotherapy in non-small cell lung cancer", includes 134 bam files from hybrid capture targeted error-correction next-generation sequencing (PGDx Elio plasma resolve) from plasma cell-free DNA and matched white blood cell DNA from 35 individuals with non-small cell lung cancer on the BR.36 trial, alongside 11 bam files from targeted next generation sequencing (PGDx Elio tissue complete) of tumor DNA from 11 individuals with non-small cell lung cancer on the BR.36 trial.

| EGAD00001011359 | EGA

Comparative proteomic analysis between Pseudomonas putida WBC-3 and Pseudomonas putida PM1-33

Project description:A mutant strain (PM1-33) with accelerated para-nitrophenol (PNP) degradation was obtained by mutagenizing WBC-3. Comparative proteomic analysis of WBC-3 and PM1-33 was performed to compare their differentially expressed proteins at 0 h, 3 h, and 7 h to investigate the reasons for the faster degradation of PNP by PM1-33 compared to WBC-3.

2024-02-20 | PXD049703 |

Non-canonical DNA structures at eukaryotic centromeres can resolve the CENP-B paradox

Project description:Epigenetic mechanisms are thought to specify the identity of centromeres, yet the degree to which DNA sequence contributes to centromere determination remains unresolved. For example, the conserved CENP-B protein binds the 17-bp âCENP-B boxâ motif found in Î±-satellite arrays at most human centromeres. Although CENP-B is required for artificial centromere function, it is non-essential and some species lack CENP-B boxes entirely. To address this âCENP-B paradox,â we determined the distribution of CENP-B boxes in primates and directly demonstrated the absence of CENP-B at Old World Monkey centromeres. We found extensive interspecific variation in Î±-satellite arrays including abundance of <10-bp dyad symmetries and of non-B-form DNA structures. We confirmed the presence of non-canonical DNA at human centromeres and neocentromeres and detected similar structures at mouse, chicken and yeast centromeres. To resolve the CENP-B paradox, we propose that CENP-B enhances non-canonical DNA formation, thus providing a general basis for centromere specification.

2018-01-28 | GSE102111 | GEO

High intensity sequencing of plasma cfDNA and WBC gDNA

Project description:We sought to define the technical feasibility of a high-intensity sequencing assay of cfDNA and matched white-blood cell (WBC) DNA covering a large genomic region (508 genes, 2Mb, 60,000x raw-depth) in a prospective study of 124 metastatic cancer patients, with contemporaneous matched metastatic tumor tissue biopsies, and age-matched 47 non-cancer controls.

| EGAS00001003755 | EGA

The Pan-Human Library: A repository of assays to quantify 10 000 proteins by SWATH-MS

Project description:The â??Pan-Human Libraryâ?? is a compendium of highly specific assays covering more than 10 000 human proteins and enabling their targeted analysis in SWATH-MS datasets acquired from research or clinical specimens.

2016-03-16 | MSV000079593 | MassIVE

68d1d1f8-a3c7-40bd-a23d-5a88dc83dbea - samples

Project description:The dataset for the study Ã¢Â€ÂœDynamics of sequence and structural cell-free DNA landscapes in small-cell lung cancerÃ¢Â€Â includes 171 bam files from targeted next-generation sequencing (TEC-Seq) from plasma cell-free DNA and matched white blood cell DNA from 33 individuals with small cell lung cancer, alongside 10 bam files from whole exome sequencing of tumor and matched normal DNA for 5 individuals with small cell lung cancer.

| EGAD00001009860 | EGA

Variability in white blood cell counts in swine: identification of putative positional and functional candidate genes by a transcriptome-based study

Project description:The counts of total white blood cells (WBCs) and WBC subsets are well-established diagnostic factors for various diseases. It has been shown that variations in WBC counts are significantly controlled by individuals’ genetics in swine. However, despite detection of quantitative trait loci (QTLs) for these phenotypes, little is known on the molecular basis underlying their variations. Our aim was to study gene profiling variations according to variations in WBC counts and to connect results with available QTL mapping. Whole blood transcriptome of animals contrasted for levels of WBC counts were compared. A pig generic microarray enriched in immunity-related genes was used. 378 probes representing 334 genes were found significantly differentially expressed between high- and low-count WBC groups. 65 genes were associated with hematological system development and function. 336 probes could be mapped on all autosomes and the X chromosome, and 59 transcripts fell within 28 QTLs reported to affect the counts of WBC and WBC subsets. By combining probe mapping results and biological functions, 6 genes (CDKN2A, TCIRG1, SIPA1, RGL2, FLT1 and CFLAR) were found as putative relevant positional candidate genes for the WBC traits. Genetic linkage experiments are warranted to validate these candidate genes, and further investigating a possible pleiotropic effect of these genes could contribute to elucidate molecular mechanisms involved in WBC development. differentially expressed genes or transccripts between high- and low-count white blood cells groups

2014-10-31 | GSE50589 | 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