Project description:As a test of trypanosome transcriptome responsiveness, we analysed the effects of over-expression of the early endosome small GTPase Rab5A in procyclic form T.brucei, which results in significant augmentation of fluid phase and receptor-mediated endocytic activity (Pal et al. 2002).<br><br>part 1: 2 PCFWT and 2 PCF5AWT-OE (PCF cell lines over-expressing a wildtype version of RAB5A) biological replicates, as well as dye swaps were used.<br><br>part 2: 2 PCFWT and 2 PCF5AQL-OE (PCF cell lines over-expressing a mutant version of RAB5A locked in the GTP-bound state) biological replicates, as well as dye swaps were used.<br><br>part 3: 2 PCFWT and 2 PCF5BQL-OE (PCF cell lines over-expressing a mutant version of RAB5B locked in the GTP-bound state) biological replicates, as well as dye swaps were used.
Project description:Proteomic analysis of integrin activation-state-dependent adhesion complexes. Adhesion complexes were isolated from K562 cells using activation-state-specific monoclonal antibodies coupled to magnetic beads.Tandem mass spectra were extracted using extract_msn (Thermo Fisher Scientific) executed in Mascot Daemon (version 2.2.2; Matrix Science). Peak list files were searched against the IPI Human database (version 3.70) modified to contain ten additional contaminants and reagent sequences of non-human origin. Searches were submitted to an in-house Mascot server (version 2.2.03; Matrix Science). Carbamidomethylation of cysteine was set as a fixed modification, and oxidation of methionine was allowed as a variable modification. Only tryptic peptides were considered, with up to one missed cleavage permitted. Monoisotopic precursor mass values were used, and only doubly and triply charged precursor ions were considered. Mass tolerances for precursor and fragment ions were 0.4 Da and 0.5 Da, respectively.
Project description:BAM outputs from STAR (https://github.com/alexdobin/STAR) analysis of RNASeq sequencing on HiSeq platform of 56 tumour samples from 46 melanoma cases.
Gene model = Ensembl version 70
Project description:We generated a high-resolution single-cell RNA atlas of E. coli growth transitions, which revealed that a distinct persister state. We then used ultra-dense CRISPR-interference to determine how every E. coli gene contributes to persister formation across genetic models. ***Download data version 2 whenever present***