PMID- 36149794 OWN - NLM STAT- MEDLINE VI - 3 IP - 4 TI - Multiplex immunofluorescence-guided laser capture microdissection for spatial transcriptomics of metastatic melanoma tissues. PG - 101698 CI - Copyright © 2022 The Author(s). Published by Elsevier Inc. All rights reserved. LA - eng PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PL - United States TA - Star Protoc JT - STAR protocols JID - 101769501 IS - 2666-1667 (Electronic) LID - S2666-1667(22)00578-0 [pii] LID - 10.1016/j.xpro.2022.101698 [doi] FAU - Martinek, Jan AU - Martinek J AD - The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA. Electronic address: jan.martinek@jax.org. FAU - Wu, Te-Chia AU - Wu TC AD - The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA. FAU - Sun, Lili AU - Sun L AD - The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA. FAU - Lin, Jianan AU - Lin J AD - The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA. FAU - Kim, Kyung In AU - Kim KI AD - The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA. FAU - Marches, Florentina AU - Marches F AD - The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA. FAU - Robson, Paul AU - Robson P AD - The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA; Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, USA. FAU - George, Joshy AU - George J AD - The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA. FAU - Palucka, Karolina AU - Palucka K AD - The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA; Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, USA. Electronic address: karolina.palucka@jax.org. IS - 2666-1667 (Linking) SB - IM MH - Animals MH - Humans MH - Mice MH - Fluorescent Antibody Technique MH - Gene Expression Profiling/methods MH - *Laser Capture Microdissection/methods MH - *Melanoma/genetics/surgery MH - Transcriptome/genetics OTO - NOTNLM OT - Cancer OT - Cell isolation OT - Immunology OT - Microscopy OT - RNAseq OT - Single cell PMC - PMC9519630 DCOM- 20221222 LR - 20230125 DP - 20221216 DEP - 20220922 AB - We describe a pipeline for optimized and streamlined multiplexed immunofluorescence-guided laser capture microdissection allowing the harvest of individual cells based on their phenotype and tissue localization for transcriptomic analysis with next-generation RNA sequencing. Here, we analyze transcriptomes of CD3+ T cells, CD14+ monocytes/macrophages, and melanoma cells in non-dissociated metastatic melanoma tissue. While this protocol is described for melanoma tissues, we successfully applied it to human tonsil, skin, and breast cancer tissues as well as mouse lung tissues. For complete details on the use and execution of this protocol, please refer to Martinek et al. (2022).