743b6e5a-2c58-45dc-a68f-c531e3e10c97 - samples
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ABSTRACT:
PROVIDER: EGAD00001010255 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:DNA was isolated from whole red blood cells from various lines and crosses of broiler chickens. DNA was genotyped using Axiom genome-wide chicken array and cel files were analyzed using Axiom Analysis Suite Software (version 3.0.1) with Gallus gallus 5.0 using the software's Best Practices for agricultural animals. The results were exported (Genotyping_Data-3-21-2018.vcf) for all genotype calls and text file of all SNPs with >= 97% call rate rate was also produced for filtering the VCF file (ALL_SNPSs_with_Call_Rate_97_Plus_3-21-2018).
2019-05-25 | GSE131764 | GEO
Project description:Genotype calls for 83 Aboriginal Australian genomes split by chromosomes. In short, genotypes were called individually with samtools. They were subsequently filtered with thresholds related to sequencing depth, location of variants, sequencing error, and strand bias. Once combined, the genotypes were filtered when not in Hardy-Weinberg equilibrium. The genomes were phased with IMPUTE using the 1000 Genomes reference panel. NB: for the Y chromosomes, only the 44 Aboriginal Australian males are included.
| EGAD00001004155 | EGA
Project description:Genome-wide association studies (GWAS) have been pivotal to increasing our understanding of intestinal disease. However, the mode by which genetic variation results in phenotypic change remains largely unknown, with many associated polymorphisms likely to modulate gene expression. Analyses of expression quantitative trait loci (eQTL) to date indicate that as many as 50% of these are tissue specific. Here we report a comprehensive eQTL scan of intestinal tissue. Subjects who had undergone ileal pouch anal anastomosis and closure of ileostomy at least one year prior to recruitment were prospectively enrolled at Mount Sinai Hospital in Toronto. Endoscopically and histologically normal tissue biopsies from the afferent limb of these individuals were obtained and preserved in RNAlater. Total RNA was extracted with the QIAGEN miRNeasy Kit and mRNA analysis was performed on Affymetrix Human Gene 1.0 ST arrays. DNA was obtained from whole-blood samples from the same individuals and genotyped using the Illumina beadchips. Cis- and trans-eQTL analyses were carried out on 173 subjects encompassing the expression levels of 19,047 unique autosomal genes listed in the NCBI database and over 580K dbSNPs (Call Rate ≥ 95%; MAF ≥ 5%; Hardy–Weinberg equilibrium (HWE) χ2 p-values ≥ 10-6). This work was done in a custom software pipeline and the Kruskal-Wallis test was used to compare expression values across different genotypes. False discovery rate correction for multiple testing was applied at an alpha level of 5%. This Series includes the Affymetrix data.
2012-12-01 | E-GEOD-40292 | biostudies-arrayexpress
Project description:Genome-wide association studies (GWAS) have been pivotal to increasing our understanding of intestinal disease. However, the mode by which genetic variation results in phenotypic change remains largely unknown, with many associated polymorphisms likely to modulate gene expression. Analyses of expression quantitative trait loci (eQTL) to date indicate that as many as 50% of these are tissue specific. Here we report a comprehensive eQTL scan of intestinal tissue. Subjects who had undergone ileal pouch anal anastomosis and closure of ileostomy at least one year prior to recruitment were prospectively enrolled at Mount Sinai Hospital in Toronto. Endoscopically and histologically normal tissue biopsies from the afferent limb of these individuals were obtained and preserved in RNAlater. Total RNA was extracted with the QIAGEN miRNeasy Kit and mRNA analysis was performed on Affymetrix Human Gene 1.0 ST arrays. DNA was obtained from whole-blood samples from the same individuals and genotyped using the Illumina beadchips. Cis- and trans-eQTL analyses were carried out on 173 subjects encompassing the expression levels of 19,047 unique autosomal genes listed in the NCBI database and over 580K dbSNPs (Call Rate ? 95%; MAF ? 5%; Hardy–Weinberg equilibrium (HWE) ?2 p-values ? 10-6). This work was done in a custom software pipeline and the Kruskal-Wallis test was used to compare expression values across different genotypes. False discovery rate correction for multiple testing was applied at an alpha level of 5%.
2012-12-01 | E-GEOD-41238 | biostudies-arrayexpress
Project description: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
| EGAD00010002304 | EGA
Project description:Fusarium head blight (FHB) incited by Fusarium graminearum Schwabe is a devastating disease of barley and other cereal crops worldwide. Fusarium head blight is associated with trichothecene mycotoxins such as deoxynivalenol (DON), where contaminated grains are unfit for malting or animal feed industries. While genetically resistant cultivars offer the best economic and environmentally responsible means to mitigate disease, parent lines with adequate resistance are limited in barley. Resistancebreeding based upon quantitative genetic gains has been slow to date, due to intensive labour requirements of disease nurseries. The development of high throughput genome-wide molecular markers, allow application in genomic prediction models. A diverse genomic panel consisting of 400 two-row spring barley lines was assembled to focus on Canadian barley breeding programs. The panel was evaluated for FHB and DON content in three environments and over two years. Moreover, it was genotyped using an Illumina Infinium HTS iSelect custom beadchip array of single nucleotide polymorphic molecular markers (50K SNP), where over 23K molecular markers were polymorphic. Genomic prediction has been successfully demonstrated for reducing FHB and DON content in cereals using various statistically-based models of different underlying assumptions. Herein, we have studied an alternative method basedon machine learning and compare it with a statistical approach. Two encoding techniques were utilized (categorical or Hardy-Weinberg frequencies), followed by selecting essential genomic markers for phenotype prediction. Subsequently, we applied a transformer-based deep learning algorithm to predict FHB and DON. Apart from the transformer method, we also implemented a Residual Fully Connected Neural Network (RFCNN). Pearson correlation coefficients were calculated to compare true vs. predicted outputs. Under most model scenarios, the use of all markers vs. selected markers marginally improved prediction performance except for RFCNN method for FHB (27.6%). Hardy-Weinberg encoding generally improved correlation for FHB (6.9%) and DON (9.6%) for transformer. This study suggests the potential of the transformer based method for genomic prediction of complex traits such as FHB or DON, having performed better or equally compared with existing machine learning and statistical method. To genomic prediction in barley for Fusarium head blight and deoxynivalenol content using a custom Illumina Infinium array (BarleySNP50-JHI) (www.illumina.com). Sample types included leaves from 400 barley genotypes mostly of Canadian origin. This series includes 400 genotypes assayed on an Illumina infinium HTS platform 50K BeadChip.
2022-01-05 | GSE188791 | GEO
Project description:CRAM files and VCF for DDD_1 and their parents. Also de novo mutations file for hypermutated DDD_1 child as described in the manuscript ‘Genetic and chemotherapeutic influences of germline hypermutation’ by Kaplanis et al. which will be published in Nature shortly.
| EGAD00001008497 | EGA
Project description:This experiment was conducted to generate targeted resequencing data covering a region associated with osteosarcoma in greyhounds. 8 greyhounds diagnosed with osteosarcoma and 7 greyhounds without tumors were sequenced. DNA from the 15 dogs was used to prepare libraries and hybrid capture performed to enrich the region of interest prior to paired-end sequencing using Illumina Genome Analyzer II. The reads were aligned to the dog-genome CanFam2.0 using bwa and pre-processed using Picard and GATK. Variant discovery was performed using GATK. The resulting list of variants were used in the study to finemap the associated region and look for causal variants. We submit the preprocessed BAM-files that still have all reads although some reads are flagged. We also submit the resulting vcf-file with called and filtered variants in all individuals.
2013-11-16 | E-MTAB-1984 | biostudies-arrayexpress
Project description:MPSS mouse transcriptome analysis project. See http://www.ncbi.nlm.nih.gov/geo/info/mouse-trans.html for more details. Keywords: other
2004-10-26 | GSE1581 | GEO