Deng Y, Bartosovic M, Kukanja P, Zhang D, Liu Y, Su G, Enninful A, Bai Z, Castelo-Branco G, Fan R.
We present spatial-CUT&Tag for spatially resolved genome-wide profiling of histone modifications by combining in situ CUT&Tag chemistry, microfluidic deterministic barcoding, and next-generation sequencing.
Börner K, Teichmann SA, Quardokus EM, Gee JC, Browne K, Osumi-Sutherland D, Herr BW 2nd, Bueckle A, Paul H, Haniffa M, Jardine L, Bernard A, Ding SL, Miller JA, Lin S, Halushka MK, Boppana A, Longacre TA, Hickey J, Lin Y, Valerius MT, He Y, Pryhuber G, Sun X, Jorgensen M, Radtke AJ, Wasserfall C, Ginty F, Ho J, Sunshine J, Beuschel RT, Brusko M, Lee S, Malhotra R, Jain S, Weber G.
Tideman LEM, Migas LG, Djambazova KV, Patterson NH, Caprioli RM, Spraggins JM, Van de Plas R.
Biomarker candidate discovery in imaging mass spectrometry data can be considered a computational feature ranking problem, which we resolve by means of Shapley additive explanations (SHAP), an interpretability method that enables automated estimation of biomarker candidate potential.
We make recommendations for accurately assigning cell-type labels to CODEX multiplexed imaging after comparing five different normalization techniques crossed with four unsupervised clustering algorithms.
Black S, Phillips D, Hickey JW, Kennedy-Darling J, Venkataraaman VG, Samusik N, Goltsev Y, Schürch CM, Nolan GP.
We provide optimized protocols for conjugating purified antibodies to DNA oligonucleotides, validating the conjugation by CODEX staining and executing the CODEX multicycle imaging procedure for both formalin-fixed, paraffin-embedded (FFPE) and fresh-frozen tissues.
Kennedy-Darling J, Bhate SS, Hickey JW, Black S, Barlow GL, Vazquez G, Venkataraaman VG, Samusik N, Goltsev Y, Schürch CM, Nolan GP.
We established a sequential oligonucleotide exchange technique (called CODEX) that enables a facile imaging of tissues that leverages pre-existing imaging infrastructure to decrease the barriers to broad use of multiplexed imaging.