Project description:We used RNA-seq to investigate the effects of single transcription factor knockouts on growth of E. coli BW25113 in fed-batch cultures at multiple timepoints. Cells were grown in an ambr automated bioreactor and maintained at 30 degrees and pH 6.5 in Medium C.
Project description:High titer, rates, yields (TRY) and scalability are challenging metrics to achieve due to trade-offs between carbon use for growth and production. To achieve these metrics, we took the minimal cut set (MCS) approach that predicts metabolic reactions for elimination to couple metabolite production strongly with growth. We computed MCS solution-sets for a non-native product indigoidine, a sustainable pigment, in Pseudomonas putida KT2440, an emerging industrial microbe. From 63 computed solution-sets, our -omics guided process identified one experimentally feasible solution requiring 14 simultaneous reaction interventions. Using multiplex-CRISPRi, this is the first experimental implementation of a 14-gene MCS-based solution that shifted production from stationary to exponential phase. We achieved 25.6 g/L, 0.22 g/l/h, and ~50% maximum theoretical yield (0.33 g indigoidine/g glucose) TRY respectively. These phenotypes were maintained from batch to fed-batch mode, and across scales (100-ml shake flasks, 250-ml ambr® and 2-L bioreactors).
Project description:Single cell Methylome and Transcriptome Sequencing (scM&T-Seq) was performed on index-sorted single CD48- CD135- Lin- Sca-1+ c-Kit+ cells from Scl-tTA; H2B-GFP mouse bone marrow after 100 days of chase. Methylation data is uploaded here.
Project description:C8orf33-proficient and deficient DIvA cells were treated with 4-hydroxy tamoxifen (4OHT) to induce DNA double strand breaks (DSB) at several loci within the human genome. following 4OHT treatment cells were subject to ChIP-seq analysis for KAT8 acetyltransferase to map its enrichment at DSB sites in C8orf33 proficient deficient cells.
