Spatial-CUT&Tag: Spatially resolved chromatin modification profiling at the cellular level

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.

Additional resources

• Datasets in the GEO repository

The Blood Proteoform Atlas: A reference map of proteoforms in human hematopoietic cells

Melani RD, Gerbasi VR, Anderson LC, Sikora JW, Toby TK, Hutton JE, Butcher DS, Negrão F, Seckler HS, Srzentić K, Fornelli L, Camarillo JM, LeDuc RD, Cesnik AJ, Lundberg E, Greer JB, Fellers RT, Robey MT, DeHart CJ, Forte E, Hendrickson CL, Abbatiello SE, Thomas PM, Kokaji AI, Levitsky J, Kelleher NL.

Additional resources

• The Blood Proteoform Atlas

geneBasis: an iterative approach for unsupervised selection of targeted gene panels from scRNA-seq

Missarova A, Jain J, Butler A, Ghazanfar S, Stuart T, Brusko M, Wasserfall C, Nick H, Brusko T, Atkinson M, Satija R, Marioni JC.

Additional resources

• HBM984.GRBB.858
• HBM472.NTNN.543
• HBM556.QMSM.776
• HBM336.FWTN.636
• HBM252.HMBK.543
• HBM749.WHLC.649

Anatomical structures, cell types and biomarkers of the Human Reference Atlas

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.

Additional resources

• Supplementary materials

Automated biomarker candidate discovery in imaging mass spectrometry data through spatially localized Shapley additive explanations

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.

Additional resources

• Supplementary materials

Strategies for Accurate Cell Type Identification in CODEX Multiplexed Imaging Data

Hickey JW, Tan Y, Nolan GP, Goltsev Y.

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.

Additional resources

• Dataset: Cell type labels for all clustering and normalization combinations compared for CODEX multiplexed imaging

CODEX multiplexed tissue imaging with DNA-conjugated antibodies

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.

Additional resources

• Segmented single cell data from 7x9 tile CODEX imaging of human tonsil at 20x over all channels and cycles
• Montage image of CODEX multiplexed imaging of human tonsil (7x9 region) across best focus plane imaged with all channels and cycles

Highly multiplexed tissue imaging using repeated oligonucleotide exchange reaction

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.

Additional resources

• Lymphoid data (.csv)
• Image processing and data analysis tools