Ena-DATASET-dkfz_b062-18-08-2017-15:54:03:183-161 - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001003573 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:Low-coverage whole genome sequencing data for 30 PDOX models (28 early passages, 4 late passages (2 overlaps)), 3 cell lines, and 21 matching human tumors
| EGAD00001003545 | EGA
Project description:Whole exome sequencing data to 30 PDOX models (28 early passages, 3 late passages (1 overlap)), 3 cell lines, and 20 matching human tumors
| EGAD00001003544 | EGA
Project description:Single-cell RNA-sequencing was performed on the tumor microenvironment of the glioblastomas isolated from PDOX models (Golebiewska et al., Acta Neuropathologica, 2020; Oudin et al., STAR Protocols 2021). Sample names correspond to PDOX models. Normal mouse brain was used as a contol. One PDOX model was treated with temolozomide (P3TMZ).
2023-03-07 | GSE226468 | GEO
Project description:Idiopathic achalasia is a relatively infrequent esophageal motor disorder for which major histocompatibility complex (MHC) genes are well-identified risk factors. However, no information about HLA-achalasia susceptibility in Mexicans has previously been reported. We studied a group of 91 patients diagnosed with achalasia and 234 healthy controls with Mexican admixed ancestry. HLA alleles and conserved extended haplotypes were analyzed using high-resolution HLA typing based on Sanger and next-generation sequencing technologies. Admixture estimates were determined using HLA-B and short tandem repeats. Results were analyzed by non-parametric statistical analysis and Bonferroni correction. P-values < 0.05 were considered significant. Patients with achalasia had 56.7% Native American genes, 24.7% European genes, 16.5% African genes and 2.0% Asian genes, which was comparable with the estimates in the controls. Significant increases in the frequencies of alleles DRB1*14:54 and DQB1*05:03 and the extended haplotypes DRB1*14:54-DQB1*05:03 and DRB1*11:01-DQB1*03:01, even after Bonferroni correction (pC<0.05), were found in the achalasia group compared to those in the controls. Concluding, the HLA class II alleles HLA-DRB1*14:54:01 and DQB1*05:03:01 and the extended haplotype are risk factors for achalasia in mixed-ancestry Mexican individuals. These results also suggest that the HLA-DRB1*14:54-DQB1*05:03 haplotype was introduced by admixture with European and/or Asian populations.
| S-EPMC6084941 | biostudies-literature
Project description:We establish that subtelomeric regions together with some other functional elements like transposons are consistently under-replicated in metaphase.
2018-07-18 | GSE117265 | GEO
Project description:BackgroundCurrently available infant body composition measurement methods are impractical for routine clinical use. The study developed anthropometric equations (AEs) to estimate fat mass (FM, kg) during the first year using air displacement plethysmography (PEA POD® Infant Body Composition System) and Infant quantitative magnetic resonance (Infant-QMR) as criterion methods.MethodsMulti-ethnic full-term infants (n = 191) were measured at 3 days, 15 and 54 weeks. Sex, race/ethnicity, gestational age, age (days), weight-kg (W), length-cm (L), head circumferences-cm (HC), skinfold thicknesses mm [triceps (TRI), thigh (THI), subscapular (SCP), and iliac (IL)], and FM by PEA POD® and Infant-QMR were collected. Stepwise linear regression determined the model that best predicted FM.ResultsWeight, length, head circumference, and skinfolds of triceps, thigh, and subscapular, but not iliac, significantly predicted FM throughout infancy in both the Infant-QMR and PEA POD models. Sex had an interaction effect at 3 days and 15 weeks for both the models. The coefficient of determination [R2 ] and root mean square error were 0.87 (66 g) at 3 days, 0.92 (153 g) at 15 weeks, and 0.82 (278 g) at 54 weeks for the Infant-QMR models; 0.77 (80 g) at 3 days and 0.82 (195 g) at 15 weeks for the PEA POD models respectively.ConclusionsBoth PEA POD and Infant-QMR derived models predict FM using skinfolds, weight, head circumference, and length with acceptable R2 and residual patterns.
| S-EPMC8821135 | biostudies-literature
Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare the epigenomes of different patient-derived models of colorectal cancer (PDO, PDX and PDOX) to the original patient tumor. Methods: The Omni-ATAC protocol was utilized for ATAC library preparations. The nulcei were extracted from samples (PT, PDO, PDX and PDOX). For each sample set, three biological replicates were included. The libraries were sequenced using Illumina HiSeq 4000 PE 150bp. Results: Using an optimized data analysis workflow, we achieved high quality ATAC-seq library. Data were mapped to hg19 with over 90% mapping rate, and relative low mitochondria fraction (<30%). We used Diffbind to assess the chromatin accessibility enrichment in each model with a strict threshold of p <0.05 and |logFC|>1. Conclusions: Our study represents the first detailed analysis of CRC PDMC epigenome. CRC cells from all three models share chromatin alterations when compared to PT cells, representing a PT-PDMC epigenetic axis. Chromatin alterations in CRC cells are more similar betweeen PDOX and PDX than between PDOX and PDO, indicating that the growth environment of the model exerts strong influence on chraomtin adaptation in tumor cells.
2024-03-01 | GSE184482 | GEO
Project description:The Library of Integrated Cellular Signatures (LINCS) is an NIH program which funds the generation of perturbational profiles across multiple cell and perturbation types, as well as read-outs, at a massive scale. The LINCS Center for Transcriptomics at the Broad Institute uses the L1000 high-throughput gene-expression assay to build a Connectivity Map which seeks to enable the discovery of functional connections between drugs, genes and diseases through analysis of patterns induced by common gene-expression changes. These files represent L1000 data generated during the LINCS Pilot Phase (2012-2015), as well as profiles generated for more specific purposes, such as assay development and validation projects or testing custom compounds or non-standard cell lines (not part of the core LINCS cell lines). Note: Related GEO projects include (a) Additional L1000 and RNA-Seq data used to validate the assay and improve the inference model, available at GSE92743 (b) The LINCS “production phase” (also termed Phase II, 2015-2020) which is generating an additional cohort of L1000 data, available at GSE70138. The Platform is GPL20573: Broad Institute Human L1000 epsilon https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL20573 For questions or assistance with this dataset, please email the CMap support team at: clue@broadinstitute.org
2017-03-03 | GSE92742 | GEO
Project description:A patient derived orthotopic xenograft (PDOX) was generated from a patient with an aggressive EMM to study in-depth genetic and epigenetic events and drug responses related to extramedullary disease. One of these studies was the evaluation of genetic imbalances by Affymetrix Cytoscan 750K array. The PDOX was derived from a fresh punch of an extramedullary cutaneous lesion that was orthotopically implanted in a NSG mouse. The PDOX mimicked histologic and phenotypic features of patient’s tumor. Cytogenetic studies revealed a hyperploid genome with multiple genetic poor-prognosis alterations. Copy number alterations were detected in all chromosomes.
2021-06-18 | E-MTAB-10630 | biostudies-arrayexpress
Project description:Binding of small molecules in the human leukocyte antigen (HLA) peptide-binding groove may result in conformational changes of bound peptide and an altered immune response, but previous studies have not considered a potential role for endogenous metabolites. We performed virtual screening of the complete Human Metabolite Database (HMDB) for docking to the multiple sclerosis (MS) susceptible DRB1*15:01 allele and compared the results to the closely related yet non-susceptible DRB1*15:03 allele; and assessed the potential impact on binding of human myelin basic peptide (MBP). We observed higher energy scores for metabolite binding to DRB1*15:01 than DRB1*15:03. Structural comparison of docked metabolites with DRB1*15:01 and DRB1*15:03 complexed with MBP revealed that PhenylalanineMBP92 allows binding of metabolites in the P4 pocket of DRB1*15:01 but ValineMBP89 abrogates metabolite binding in the P1 pocket. We observed differences in the energy scores for binding of metabolites in the P4 pockets of DRB1*15:01 vs. DRB1*15:03 suggesting stronger binding to DRB1*15:01. Our study confirmed that specific, disease-associated human metabolites bind effectively with the most polymorphic P4 pocket of DRB1*15:01, the primary MS susceptible allele in most populations. Our results suggest that endogenous human metabolites bound in specific pockets of HLA may be immunomodulatory and implicated in autoimmune disease.
| S-EPMC6054566 | biostudies-literature