Similar Datasets
Project description:Evaluating EURL Reference Laboratories performance in bacterial sequencing in the 2020 DTU Genomic Proficiency Test.
| PRJEB58706 | ENA
Project description:EU reference laboratory for Campylobacter - Proficiency test 28 - 2020
| PRJEB45600 | ENA
Project description:We performed RNA-Seq based gene expression analysis of Arabidopsis Col-0 plants grown in presence of SynComCol-0 (eubiotic bacterial community), SynCommfec (dysbiotic bacterial community) and Axenic conditions in GnotoPot plant gnotobiotic growth system. SynCom preparation was done by mixing equal ratio of the each strain measured based on optical density of (OD600) in 10 mM MgCl2 and adjusting to the final combined OD600 of 0.04. Plants were grow in GnotoPots as described in (Chen et al, Nature 2020). We identified genes differentially enriched in response to presence of eubiotic and dysbiotic bacterial communities. Our results suggested that in presence of dysbiotic community there is over abundance of gene expression for immunity/defense-related genes in SynCommfec compared SynComCol-0 colonized plants.
2023-07-19 | GSE218962 | GEO
Project description:We report a method for specific capture of an arbitrary subset of genomic targets for single molecule bisulfite sequencing, and for digital quantitation of DNA methylation at a single nucleotide resolution. We used targeted bisulfite sequencing to characterize the changes of DNA methylation during the de-differentiation of human fibroblasts into hybrid stem cells, and into induced pluripotent stem cells. We compared the methylation level of approximately 66,000 CpG sites within 2020 CpG islands on chromosome 12, chromosome 20, and 34 selected regions. A total of 288 differentially methylated regions were identified between fibroblasts and pluripotent cells. Methylation cluster analysis revealed distinct methylation patterns between fibroblasts and pluripotent cells. Furthermore iPS cells are globally more methylated than human embryonic stem cells, which could be due to the reprogramming process. This targeted bisulfite sequencing method is particularly useful for efficient and large-scale analysis of DNA methylation in organisms with large genomes. Experiment Overall Design: Comparison of DNA methylation on 2020 CpG islands and 34 other selected regions among eleven human ES, iPS and fibroblast lines.
2009-08-28 | E-GEOD-15007 | biostudies-arrayexpress
Project description:Test for Nudibranch Works from Okinawan Organisms 2020
2020-05-27 | MSV000085481 | GNPS
Project description:Single Molecule Footprinting (SMF) data from Sonmezer et al., 2020. SMF data is obtained by treating isolated nuclei with methyltransferases, where binding of proteins on DNA, e.g. nucleosomes and TFs, leave behind unmethylated cytosines as footprints. Data in this experiment comprises SMF data obtained from ES cells and various derivatives of ES cells, such DNMT-null, REST-knockout ES cells, neural progenitors and ES cells treated with NRF1 sirNA.
2020-12-26 | E-MTAB-9033 | biostudies-arrayexpress