{"id":["DOI:10.17504/protocols.io.yxmvmb7dog3p/v1"],"title":["scMTR-seq"],"description":["Here, we describe a protocol for scMTR-seq (single cell multi-targets and mRNA sequencing), which is a multi-omics sequencing technology that can simultaneously profile multiple histone modifications or other chromatin-bound proteins and transcriptome in the same single cells. scMTR-seq has high sensitivity, high cell recovery and is highly scalable in terms of starting material requirement. The protocol has the following steps: i) pre-assemble antibodies specific for each target histone modification or protein with indexed proteinA-Tn5-adapters; ii) perform in situ Tn5-mediated tagmentation with indexed complexes; iii) capture nuclear mRNA with a barcoded poly-T primer followed by in situ reverse transcription; iv) label single cells using split-pool combinatorial barcoding. We have applied scMTR-seq to profile histone modifications and transcriptomes in single cells from a broad range of heterogeneous samples including pluripotent stem cell differentiation and mouse pre-implantation embryos."],"authors":{"ORCID:0000-0003-2802-5392":{"id":["ORCID:0000-0003-2802-5392"],"family_name":["Wang"],"personal_name":["Yang"],"affiliations":{"ROR:01d5qpn59":{"organization_name":["Babraham Institute"]}},"HDBItheme":["Early"]},"ORCID:0000-0002-9601-5949":{"id":["ORCID:0000-0002-9601-5949"],"family_name":["Rugg-Gunn"],"personal_name":["Peter J."],"affiliations":{"1":{}},"HDBItheme":["Early"]}}}