Fig. 1: Profiling single-cell chromatin accessibility in FFPE samples with conventional scATAC-Seq. | Nature Communications

Fig. 1: Profiling single-cell chromatin accessibility in FFPE samples with conventional scATAC-Seq.

From: scFFPE-ATAC enables high-throughput single cell chromatin accessibility profiling in formalin-fixed paraffin-embedded samples

Fig. 1

a Genome-wide comparison of chromatin accessibility reads from mouse spleen FFPE samples with reverse croslinking (FFPE + RV) or without reverse crosslinking (FFPE -RV), and fresh spleen samples, prepared using conventional bulk and single-cell ATAC-Seq. b Representative genome browser tracks at the T-cell marker gene Cd3e in mouse FFPE and fresh spleen samples, prepared using conventional bulk and single-cell ATAC-Seq; dotted squares highlight peaks present in fresh samples but absent in FFPE samples. c TSS enrichment in mouse FFPE samples with reverse croslinking (FFPE + RV) or without reverse crosslinking (FFPE -RV) and fresh spleen samples, assayed by conventional single-cell ATAC-Seq. d–h Number of ATAC-Seq peaks (d) genomic annotation of ATAC-Seq peaks (e) duplication rate (f) fraction of reads in peaks (FRiP) (g) and number of unique fragments per cell h in mouse FFPE samples with reverse crosslinking (FFPE + RV) or without reverse crosslinking (FFPE -RV) and fresh spleen samples, assayed by conventional single-cell ATAC-Seq. Box boundaries in panels (f–h) represent the interquartile range (IQR), spanning from the first quartile (Q1) to the third quartile (Q3). Duplication rate (f)—Fresh (n = 5,258, max = 59.59, min = 0.19, Q1 = 18.77, median = 34.73, Q3 = 42.02); FFPE + RV (n = 2,687, max = 74.35, min = 63.00, Q1 = 67.62, median = 68.85, Q3 = 70.10); FFPE – RV (n = 1980, max = 68.96, min = 50.34, Q1 = 55.11, median = 57.41, Q3 = 60.83). FRiP per cell (g)—Fresh (n = 5258, max = 78.11, min = 2.72, Q1 = 33.38, median = 42.01, Q3 = 49.29); FFPE + RV (n = 2687, max = 79.05, min = 4.59, Q1 = 22.24, median = 28.93, Q3 = 37.15); FFPE – RV (n = 1980, max = 75.71, min = 3.07, Q1 = 21.47, median = 29.94, Q3 = 43.30). Fragments per cell (h)—Fresh (n = 5258, max = 145,645, min = 1502, Q1 = 3303, median = 6722.5, Q3 = 12,302); FFPE + RV (n = 2687, max = 11,046, min = 1501, Q1 = 1646, median = 1873, Q3 = 2354.5); FFPE – RV (n = 1980, max = 13,354, min = 1501, Q1 = 1632.5, median = 1865, Q3 = 2366). i Scatter plots show number of cells identified with same parameter cutoff (TSS enrichment score and number of unique fragments). j, k Number of clustered cells j and their proportional distribution k identified from conventional single-cell ATAC-seq in fresh and FFPE samples. l Projection of gene activity across different cell clusters or cell types under varying conditions. m Schematic illustrating that DNA breaks in FFPE samples contribute to low library complexity at the single-cell level (Right panel) compared with fresh samples (Left panel), as detected by conventional scATAC-Seq. Source data are provided as a Source Data file for Fig. 1a, c–l.

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