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standard whole mount in situ hybridization on zebrafish embryos (PDF)

preparation of pDONR and pDEST vectors (PDF)

Multisite Gateway handbook (Invitrogen; PDF)

dissociation for fluorescence activated cell sorting (FACS; PDF)

MARIS - preparation of fixed dissociated cells for FACS and subsequent RNAseq - yes, this means the cells are fixed immediately after dissociation and BEFORE FACS.  The fixed cells can also be subjected to immunostaining prior to FACS.  This protocol was originally described by Hrvatin et al. for human pancreatic islets.  We have adapted and applied the Hrvatin MARIS protocol for RNAseq on cells from transgenic zebrafish embryos (paper: URL, protocol: PDF).

Isolation of zebrafish nuclei (for ATAC-Seq; PDF).

ATAC-Seq protocol (from the Greenleaf lab; PDF).  This is the protocol we used in Quillien et al. (2017 Cell Reports.