ABSTRACT: The tar archive contains a) the txt file with the genotypes, b) illumina annotation file with info on SNPs, c) sample info file unfiltered illumina data, autosomes only data from Pugach et al MBE 2016 The Complex Admixture History and Recent Southern Origins of Siberian Populations
Project description:Limited access to large samples and independent replication cohorts precludes genome-wide association (GWA) studies of rare but complex traits. To localize candidate genes in an on-going study utilizing family-based GWA, a novel exploratory analysis was first tested on 1,774 major histocompatibility complex single nucleotide polymorphisms (SNPs) in 240 DNA samples from 80 children with primary liver transplantation (LTx), and their biological parents. Genotyping was performed using the Illumina HumHap550k SNP BeadArray; the genotype calls for the 1813 SNPs in the MHC region are provided in the genotype_data.zip supplementary file linked to this series (see README file in the zip archive for more information). The Affymetrix Human Exon 1.0 ST array was used to measure differential splicing patterns in archived RNA isolated from 26 of 80 children for genes found near associated SNPs. This SuperSeries is composed of the SubSeries listed below.
Project description:The history of click-speaking Khoe-San, and African populations in general, remains poorly understood. We genotyped ~2.3 million SNPs in 220 southern Africans and found that the Khoe-San diverged from other populations at least 100,000 years ago, but structure within the Khoe-San dated back to about 35,000 years ago. Genetic variation in various sub-Saharan populations did not localize the origin of modern humans to a single geographic region within Africa, instead, it indicated a history of admixture and stratification. We found evidence of adaptation targeting muscle function and immune response, potential adaptive introgression of UV-light protection, and selection predating modern human diversification involving skeletal and neurological development. These new findings illustrate the importance of African genomic diversity in understanding human evolutionary history .220 samples were analysed with the Illumina HumanOmni2.5-Quad BeadChip and are described herein.
Project description:Germ cell tumors (GCT) originate from germ cells at different developmental stages (GCT type I – V) They are thought to inherit their methylation profile from (early embryonic) germ cells which undergo a characteristic epigenetic “reset” during maturation. This study aims to provide insight into the developmental timing and underlying biology of the various subtypes of GCTs and their (embryonic) cells of origin by identifying specific and global methylation differences between GCT subtypes. In total, 91 type I-IV GCTs and four cell lines were profiled using the Illumina HumanMethylation450 BeadChip (450K) platform. The data were pre-processed using a validated pipeline and analyzed using an in-house generated extension of the annotation manifest. Marked methylation differences were identified between GCT subtypes both on the global and local level (i.e. differentially methylated regions, imprinting control regions, promoters, etc). GCT subtypes indeed show major similarities to specific stages of (early) developing embryonic germ cells with regard to their methylation profile. The extended annotation manifest for the Illumina 450K platform and methylation datasets are readily available on GEO (GEO accession: GSE58538, GPL18809), providing an integrated hypothesis generating data source for future research. File S1. Differentially methylated regions between tumors classes as discussed in Table 1 of the associated publication. All figures. Please investigate using the genomic position as search term. File S2. Differentially methylated regions between GCT cell lines. DMRforPairs output. Significant results only. Please start from the html file.
Project description:Datasets used in the article "The admixture histories of Cabo Verde", by Romain Laurent et al. 2022 - doi pending
File name "eGAdeposit_233CaboVerde_SampleInfo_FINAL_01062022.txt"
Column 1 corresponds to individual alphanumeric codes as in the "eGAdeposit_233CaboVerde_GenotypeFile_FINAL_01062022.vcf" genotype file
Column 2 corresponds to individual's biological sex as per genetic inference
Column 3 corresponds to individual's self-reported age in years
Column 4 corresponds to individual's self-reported cumulated number of years spent in academic or professional education
Project description:Project represents an effort to modify chromatographic conditions for improved compound identification in untargeted metabolomics. Two different modes of chromatograph (HILIC and RPLC) and multiple run conditions (sample loading, gradient duration, iterative acquisition) were evaluated. All relevant data from different conditions are contained within the raw data archive file attached to this submission. Metadata associated with this Metabolomics Workbench submission reflects only the manually reviewed identifications obtained using modified HILIC conditions. See protocol file Mod_vs_Con_Chrom_IDs_Protocol.pdf for details.
Project description:The microarray gene expression pattern was studied using 798 different cancer cell lines. The cancer cell lines are obtained from different centers. Annotation information were provided in the supplementary file.
Project description:Responses of human adult articular chondrocytes under conditions of lack or excess of bone morphogenetic protein-7 also called osteogenic protein 1. Original processed data file is in E-MTAB-571.additional.zip archive.
Project description:Analysis of global transcription profile of wild type MC58 and hfq deletion mutant strains grown in GC until mid log phase. Original file with experiment results is in the archive E-TABM-1111.additional.zip.
Project description:We aimed to clarify the influence of IRX5 overexpression on the transcripts of human bone marrow-derived mesenchymal stem cells (hMSCs). We overexpressed IRX5 in hMSCs by Lentivirus. RNA of CTRL and IRX5-overexpressing hMSCs were generated by deep sequencing, in triplicate, using Illumina NovaSeq 6000. The Sample read counts were summarized by StringTie2 with the GENCODE V32 annotation file. Differential expression analysis was determined based on read counts by using DESeq2. As a results, we found that adipogenesis-associated genes were up-regulated in the Plvx/IRX5 group; whereas glycolysis-associated genes were down-regulated compared to control hMSCs.
