Project description:CEH-60 binding profile by comparison of DNA methylation of a C. elegans strain expression ceh-60::dam to a control strain expressing gfp::dam. Sequencing libraries prepared using NEBNext Singleplex oligos for Illumina®. Data analysis performed with GeneDamIDseq (Sharma, Ritler, and Meister 2016).
Project description:62 individual Brassica napus plants of the same accession grown in the same field were expression-profiled in autumn 2016 and phenotyped extensively until harvest in spring 2017. Machine learning models were used to link gene expression to the phenotypes of individual plants, with the purpose of assessing how much phenotype information in encoded in ‘noisy’ gene expression variation among individual plants of the same background grown under the same uncontrolled field conditions. Rosette leaf 8 blades of 62 individual Brassica napus plants of the same winter-type accession (BnASSYST-120, Darmor) grown in the same field (50°58'24.9\\"N 3°46'49.1\\"E, Merelbeke, Belgium) were RNA-seq profiled. No treatments or stresses were applied, all plants were profiled individually under uncontrolled field conditions. Sown at 2016-09-08, rosette leaf 8 sampled for RNA-seq at 2016-11-28, plants harvested at 2017-06-13.
Project description:SORT-seq is a plate-based method of single-cell RNA sequencing (Muraro et al. 2016) is a partially robotized version of the CEL-seq2 protocol (Hashimshony et al. 2016). Synovial membranes from Rheumatoid arthritis' patients yield a relatively robust number of DCs using scRNAseq, we sought to validate this initial finding at protein level. We employed a rigorous gating strategy to sort specific ST DC subsets, developed based on CITEseq analysis, which was then confirmed by index cell plate sort sequencing (SORT-seq).
