Extended Data Fig. 8: Space-TREX enables simultaneous profiling of gene expression, clonal tracking and phenotyping of cell types in situ.
From: Clonal relations in the mouse brain revealed by single-cell and spatial transcriptomics
A total of eight 10 µm thick brain sections ‘v9-v16’ were used. Four sections ‘v9-v12’ were processed using the regular spatial transcriptomics workflow and four sections ‘v13-v16’ were used for spatial transcriptomics coupled to immunohistochemical (IHC) staining. a, b, The average number of unique molecular identifiers (UMIs) per spot (a) and the average number of genes detected per spots (b) is lower when a section undergoes IHC staining. This is most likely caused by re-folding and re-activation of RNA degrading enzymes in aqueous buffers used for IHC following methanol fixation. c, A total of 28,746 spots were sequenced from all eight sections that could be grouped into 16 distinct clusters. d, Spots belonging to sections that underwent IHC clustered together with spots from regularly processed sections indicating that IHC staining contains similar molecular information. e, f, Histograms showing the number of DAPI+ cells per spot (e) and EGFP+ cells per spot (f) as quantified from immunostained sections v13-v16. g, Workflow illustrating image processing for alignment to standardized anatomical reference atlas using WholeBrain. The resulting output contains both the coordinates of spatial transcriptomics spots within the Allen mouse brain reference atlas and each spot is displayed using the regional color code from this reference. h, Cell types in EGFP/NeuN/Olig2 triple immunostained tissue sections v13-v16 were identified image segmentation and EGFP+ barcoded cells were classified as ‘neurons’, ‘oligodendrocytes’, ‘ambivalent’ based on the overlap with NeuN, Olig2, NeuN/Olig2, respectively. Barcoded cells were classified as ‘undetermined’ in absence of overlay with a cell type marker (n = 4 sections). i, Summary of cell types amongst all EGFP+ barcoded cells. j, Targeted PCR on full length cDNA from gene expression libraries was used to achieve >4-fold enrichment of cloneIDs resulting in a total of 1,321 spots with ≥1 cloneID. k, Distribution of clone sizes for all reconstructed clones. l, m, All cloneIDs projected on reference representing non-immunostained (l) and immunostained (m) sections. n, Number of barcoded spots that contained a cell of the type ‘neuron’, ‘oligodendrocyte’, ‘undetermined’ or ‘ambivalent’.
