Cell fate transitions involve major changes to the chromatin landscape, some of which are thought to deepen the basin around a newly adopted cell state, stabilizing gene expression programs that might otherwise be transient. Transcription factors (TFs) are central to this process, binding a subset of their genome-wide...
Aidan Keith, Shruti Jain, R. Daza et al.· bioRxiv· 0 citations
Stem cells self-organize into models of early development, but even under carefully controlled conditions, the resulting organoids exhibit substantial "inter-individual" heterogeneity. To explore its origins, we generated monoclonal gastruloids, each derived from a single mouse embryonic stem cell (mESC). Molecular pro...
Samuel G. Regalado, Cheng-Xiang Qiu, Sanjay Kottapalli et al.· Cell· 1 citation
Tagmentation-based methods such as ATAC-seq and Cut&Tag have provided easy ways to profile the epigenome in low-input samples and even single cells. In this contribution, we discuss forms of bias (i.e. technical variations) in tagmentation-based data, in particular ATAC-seq, and introduce three R/bioconductor packages...
