Supplementary MaterialsS1 Fig: Self-Organizing map clustering overview. can be mixed into a single through arithmetic. The common is represented by This map of every 24h map subtracted from the common of every 0h map. (F) Characteristic enrichment analysis could be FASN used on each metacluster to supply a p-value for enrichment in a specific time point. Right here, metacluster 1, formulated with genes G2 and G1, is certainly enriched in 0h, and metacluster 3, formulated with gene G3, is certainly enriched in 24h.(TIF) pcbi.1006555.s001.tif (535K) GUID:?C371FB7F-641F-4D98-9F7B-3FD040074E45 S2 Fig: scRNA-seq gene UMAP. UMAP  generated using uwat  from scRNA-seq data with each accurate stage representing a genes expression in each cell. The umap is certainly sectioned off into 4 huge clusters, which gives a poor degree of quality for downstream evaluation. Factors were shaded by RNA SOM metacluster, which divides the top clusters into many sub-clusters.(TIF) pcbi.1006555.s002.tif (1.1M) GUID:?7EC3C314-3D91-4160-96E7-403BF808DEB5 S3 Fig: scATAC-seq region UMAP. UMAP  produced using uwat  from scATAC-seq data with each stage representing a genome locations ATAC-seq sign in each cell. The umap cannot be sectioned off into any significant clusters. Factors were shaded by ATAC SOM metacluster, which divides the top cluster into many sub-clusters.(TIF) pcbi.1006555.s003.tif (2.2M) GUID:?1317CCD5-7B27-4D9A-BB7E-8611FCD8CDC7 S4 Fig: UMAPs of cells found in analysis. UMAP  produced Thioridazine hydrochloride using Seurat v3  from both data types with each stage representing a cell shaded by timepoint.(TIF) pcbi.1006555.s004.tif (790K) GUID:?E83E9288-7091-407A-89EE-015D73AC270A S5 Fig: Seurat v3 co-embedding. Co-embedding from the scATAC-seq and scRNA-seq data made out of Seurat v3 . The co-embedding been successful in overlapping cells from the various technologies, but didn’t use the very clear separation of that time period factors in the scRNA-seq data to split up the co-embedding by period.(TIF) pcbi.1006555.s005.tif (1.3M) GUID:?1B16FC22-CE46-41EE-9030-AF0B923813F4 S6 Fig: SOM overview maps (total signal in every cell). (A-B) Summary maps for the (A) RNA and (B) ATAC SOMs. Each models value is generated by totaling the values in the full SOM models vector. A blue-white-red color spectrum was used. These graphs are mainly used to determine smoothness of the SOM fit and to see if more timesteps or changes to the learning rate are needed.(TIF) pcbi.1006555.s006.tif (2.3M) GUID:?B66C2347-5BF4-40FC-9CC0-67880A62B183 S7 Fig: Statistic maps for scRNA-seq SOM. (A) U-Matrix for the SOM built with the single-cell RNA-seq dataset. Each unit contains the average of the distance to all neighboring models. Metacluster divisions are overlaid. Areas of high distance correspond primarily to a metacluster division. (B) Density map for the RNA-seq SOM. The colour corresponds to the real amount of genes within each unit. Metacluster divisions are overlaid. Many metaclusters are ruled with a few high thickness products.(TIF) pcbi.1006555.s007.tif (5.6M) GUID:?8A576ED5-8198-4F43-9302-94AD07D210C3 S8 Fig: Statistic maps for scATAC-seq SOM. (A) U-Matrix for the SOM constructed with the single-cell ATAC-seq dataset. Each device contains the typical of the length to all or any neighboring products. Metacluster divisions are overlaid. Regions of high length correspond mainly to a metacluster department. (B) Thickness map for the ATAC-seq SOM. The colour corresponds to the real amount of chromatin regions within each unit. Metacluster divisions are Thioridazine hydrochloride overlaid. Many metaclusters are ruled with a few high thickness products.(TIF) pcbi.1006555.s008.tif (4.7M) GUID:?9FEA9D54-D188-4E46-9A5C-26A935E5DDD3 S9 Fig: cisTopic Analysis of Pre-B cell ATAC-seq Data. (A) Graph detailing the rating of varied topics attempted in cisTopic schooling. The very best model got 15 topics. (B) T-sne Thioridazine hydrochloride result from cisTopic after schooling. Each point is certainly a cell shaded by timepoint (Yellowish is certainly 0 hr and green is certainly 24 hr). (C) Club graph detailing the amount of locations in each known as topic. (D) Evaluation of cisTopic topics and SOM connected metaclusters. Many ATAC-seq peaks with completely different profiles finished up in various ATAC-seq SOM metaclusters as well as the same cisTopic subject.(TIF) pcbi.1006555.s009.tif (1.2M) GUID:?DA1285B5-0CE6-4E1E-8E67-45338A019678 S10 Fig:.