Ena-DATASET-RUNMC-13-11-2012-14:45:36:445-11 - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001000277 | 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:Thymi from WT and Cd226 strain knockout mice were digested to obtain single-cell suspensions and then loaded onto microfluidic devices for scRNA-seq. The scRNA-seq libraries were constructed and sequencing outputs were demultiplexed using the bcl2fastq to convert Binary Base Call files into FASTQ format.
2022-01-27 | GSE194270 | GEO
Project description:Exome sequences were aligned to the GRCH38 reference genome. Aligned sequence was analyzed with GATK/MuTect, to generate somatic variant calls. Somatic variant calls are in VCF format. Details for the mutect call can be found in the vcf header.
| EGAD00001005917 | EGA
Project description:Exome sequences were aligned to the GRCH38 reference genome. Aligned sequence was analyzed with GATK Haplotype Caller to generate germline variant calls. Variant calls are in VCF format. Details for the call can be found in the VCF header
| EGAD00001005916 | EGA
Project description:Exome sequences were aligned to the GRCH38 reference genome. Aligned sequence was analyzed with GATK/SomaticSniper, to generate somatic variant calls. Somatic variant calls are in VCF format. Details for the mutect call can be found in the vcf header.
| EGAD00001005918 | EGA
Project description:The accurate quantification of antimicrobial use (AMU) in production animals is critical for monitoring trends in exposure to antimicrobial drugs (AMD) over time and examining potential associations with antimicrobial resistance in bacteria. In this study, a census sample of cattle was used to quantify individually-dosed and in-feed AMU as both numbers of animal daily doses (nADD) and total grams of AMD (gAMD) used in cattle placed in 36 western Canadian feedlots between 1-November, 2008 and 31-October, 2012; representing about 21.5% of fed cattle in Canada during that time period. Of the ~2.6 million cattle placed during the 48-month period, 45% were calves, 63% were male, 62% arrived in the fall or winter, and 39% were assessed as high risk for developing bovine respiratory disease (BRD). The proportion of cattle categorized as high risk (HR) for developing BRD was consistent over the 4 years of placement cohorts. Both medically important AMU and ionophore use were summarized but presented separately. A decrease in AMU was observed over the study period, both as nADD and total gAMD, which was primarily driven by a decline in the in-feed administration of tetracyclines. Most in-feed AMU was directed toward prevention and control of liver abscesses. The majority of individually dosed AMU was administered as metaphylaxis to address BRD risks, with category III AMD (medium importance to human medicine as categorized by Health Canada Veterinary Drugs Directorate) used most frequently. Not surprisingly, risk level for developing BRD influenced parenteral AMD exposures, with 95% of cattle categorized as being HR for developing BRD receiving individually dosed AMD compared to 59% of cattle categorized as being low risk (LR) for developing BRD. Cattle categorized as HR for developing BRD were more likely to receive macrolides for BRD metaphylaxis compared to cattle categorized as LR for developing BRD, and cattle categorized as LR for developing BRD were more likely to receive tetracycline for the same purpose. In summary, these data provide an unprecedented representation of AMU in fed cattle in western Canada and direction for future monitoring of AMU in fed cattle.
| S-EPMC6811515 | biostudies-literature
Project description: Not available
| S-IHECRE00000016.1 | biostudies-other
Project description: Not available
| S-IHECRE00000030.1 | biostudies-other
Project description: Not available
| S-IHECRE00000094.1 | biostudies-other