Project description:Genome-wide patterns of DNA methylation were quantified using the Illumina Infinium EPIC array (“EPIC array”) in DNA samples isolated from buccal swabs collected at ages 5, 10 and 18 and whole blood samples collected at age 18 from 118 Monozygotic twin pairs from the Environmental Risk (E-Risk) Longitudinal Twin Study. Comparison of DNA methylation profiles of 233 age 18 blood samples with data on EPIC and Illumina 450K methylation arrays.
Project description:Primary objectives: The primary objective is to investigate circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
Primary endpoints: circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
Project description:Multiomics of faecal samples collected from individuals in families with multiple cases of type 1 diabetes mellitus (T1DM) over 3 or 4 months. Metagenomic and metatranscriptomic sequencing and metaproteomics were carried out, as well as whole human genome sequencing. Phenotypic data is available.
2016-08-22 | PXD003791 | Pride
Project description:Whole Genome Sequencing of Bacterial Isolates Collected from Avian Fecal Samples
Project description:Multiomics of faecal samples collected from individuals in families with multiple cases of type 1 diabetes mellitus (T1DM) over 3 or 4 months. Metagenomic and metatranscriptomic sequencing and metaproteomics were carried out, as well as whole human genome sequencing. Phenotypic data is available.
Project description:High throughput sequencing is performed on mRNA isolated from whole blood of adult Covid-19 patients, bacterial coinfection with Covid-19 and healthy controls in a South Indian cohort. Samples were collected from individuals at the time of hospitalization or visit to clinic. The Covid-19 samples are categorized by severeity.
2022-02-22 | GSE196822 | GEO
Project description:Whole Genome Sequencing of Bacterial Isolates Collected from Migratory Avian Fecal Samples
Project description:Purpose: This study aims to compare and analyze the differences in bacterial community composition in fecal samples from mice treated with Control(DW), Vancomycin (VAN), Ampicillin (AMP), Neomycin (NEO), Metronidazole (MET), and a combination of all antibiotics (ALL, VANM) using 16S rRNA sequencing. Methods: Each antibiotics treated mice's fecal samples were collected and stored -80'c until analyzation. DNA was extracted using the NucleoSpin DNA Stool Kit (MACHEREY-NAGEL) following the manufacturer’s protocol. Metagenomic sequencing was performed on an Illumina MiSeq platform (Illumina), targeting the V3 and V4 regions of the 16S rRNA gene according to the manufacturer's instructions. PCR products were purified using AMPure XP beads, and sequencing adapters were added using the Nextera XT Index Kit (Illumina). The library was further purified with AMPure XP beads and quantified using automated electrophoresis with the TapeStation System (Agilent). Sequencing was performed using the MiSeq v3 reagent kit (Illumina), following the manufacturer’s protocol. Results: QIIME2 (v2023.02) was used to process and analyze 16S rRNA gene amplicon sequencing data, from sequence preprocessing to taxonomic classification. Paired-end sequences were merged and quality-filtered using Deblur. The resulting amplicon sequence variants (ASVs) were used for downstream analyses. Conclusions: Our study presents a comparative analysis of bacterial community composition in fecal samples from antibiotic-treated mice. We observed that microbiota composition varied distinctly depending on the type of antibiotic administered.
Project description:Genome wide of 5-hydroxymethylcytosine profiling of normal and abnormal, and globozoospermia sperm genomes.Two semen samples were collected from a healthy man and a globozoospermia patient who had consulted a physician at ShengJing Hospital of China Medical University. Other semen samples obtained from two volunteers who were good health generally. 5-hmC enriched genomic DNA libraries were generated following the Illumina protocol for “Preparing Samples for CHIP sequencing of DNA”. 100bp single end sequencing on Illumina Hiseq2000 to get 5-hmC-enriched DNA fragment sequence was performed.
