Supplementary Figure 3: MARS-seq2.0: method overview.

(A) Molecular yield. Shown is a cumulative cell percentage (y-axis) vs. the total number of detected molecules per cell (x-axis). (B) Sequencing depth. Shown is a cumulative cell percentage (y-axis) vs. the total number of reads per cell (x-axis) for amplification batches of FACS sorted mouse ES (black curves) and MEF (red curves). (C) Total number of molecules detected vs. flow cytometry forward scatter values. Data was analyzed from 5500 bone marrow myeloid progenitors index sorted single cells (Lineage- c-Kit+ Sca1+) generated as previously reported⁹. (D) Average gene expression (number of detected molecules per gene divided by the total number of molecules) for two randomly selected groups of 100 mouse ES single-cells (x and y axis) is shown for 7567 genes with average expression higher than 10⁻⁶ (E) Similarly to D, showing average gene expression over groups of MEF (y-axis) vs. mouse ES (x-axis) single cells for 2350 differentially expressed genes (fold change >4 and FDR<10-5; red dots) and other genes (black dots). (F-I) Absolute molecules count for TPM1 (y-axis) vs. KLF5 (x-axis) (F), Id3 vs. Oct4 (G), Lgals1 vs. Dppa4 (H), and Actn1 vs. Dphs1 (I) in 1128 mouse ES cells (black dots) and 752 MEF cells (red dots).