Project description:This study consists of 24 genome-wide methylation profiles which have been generated from blood and saliva samples collected from ten volunteers in the Personal Genome Project UK. The Personal Genome Project UK aims to create publicly available genome, health and trait data, and these ten volunteers represent the pilot study (PGP-UK10) and the first three genome donation participants. These samples were bisulphite converted using the EZ DNA methylation kit (Zymo), using the alternative incubation conditions recommended for HumanMethylation450 BeadChip (Illumina). Genome-wide DNA methylation was then profiled using the HumanMethylation450 BeadChip (Illumina).
Project description:This study consists of 10 whole genome RNA-seq profiles which have been generated from blood samples collected from ten different volunteers in the Personal Genome Project UK
Project description:Urine was obtained from healthy kidney donors, from transplanted kidneys intrasurgery, at postoperative day 1 and at later timepoints. Exosomes were isolated and measured using nLC-MS/MS. For details, see the accompanying manuscript.
Project description:Size fractionated small RNA from total RNA extracts of Cicer arietinum leaves and from Nicotiana benthamiana infected by Cymbidium ringspot virus were mixed in a ratio of 1000 to 1 in amount, respectively. The RNA was ligated to adapters, purified again and reverse transcribed. After PCR amplification the sample was subjected to Illumina high throughput pyrosequencing. The kit used is TrueSeq Small RNA kit Please see www.illumina.com for details of the sequencing technology.
2015-01-30 | GSE63378 | GEO
Project description:A Personal Microbiome-dependent Glucose Response in Healthy Young Volunteers (MIGLUCOSE)
Project description:These is a collection of chromatin proteomics experiments that make up the 80 "in-house" biological conditions covered by ProteomeHD (see publication for more details). All experiments use SILAC, resulting in 80 SILAC ratios comparing the impact of various drugs (estradiol, TSA, hydroxytamoxifen, etc.), growth factors (TNFalpha) or other treatments (ionizing radiation) on chromatin composition. For a more detailed description see the Supplementary Table S2 of the publication, which can also be downloaded from here.
Project description:Long-term effects of ciprofloxacin treatment on the gastrointestinal and oropharyngeal microbiome are more pronounced after longer antibiotic courses
Project description:We surveyed the variation and dynamics of active regulatory elements genome-wide in CD4+ T cells, using Assay of Transposase Accessible Chromatin with sequencing (ATAC-seq) in longitudinal samples from healthy volunteers and during T cell activation. We created robust pipelines that enable accurate single molecule counting and allelic discrimination from clinical material. Over 4000 regulatory elements (7.2%) showed reproducible personal variation in activity. Gender was the most significant attributable source of regulome variation. ATAC-seq revealed novel elements that escape X chromosome inactivation and predicted gender-specific gene regulatory networks across autosomes, which coordinately impact genes with immune function. Noisy regulatory elements with personal variation in accessibility are significantly enriched for autoimmune disease loci. Over one third of regulome variation lacked genetic variation in cis, suggesting contributions from environmental or epigenetic factors. These results refine concepts of human individuality and provide foundational reference to compare disease-associated regulomes.