Extended Data Fig. 3: Quality metrics of bulk RNA-seq and scRNA-seq III.
From: The changing mouse embryo transcriptome at whole tissue and single-cell resolution
a, Cell-type-specific TSS choice for Mef2c in the developing limb identified by short-read RNA-seq. UCSC genome browser tracks display Fluidigm C1 data from muscle3 (dark red) and chondrocyte (cyan) cells at Mef2c with Gencode VM20 gene and transcript models. Splice-crossing reads document exon1/2, 2/4 (red) and 3/4 junctions. Aggregate signal tracks for mus3 and chon show that the TSS at exon 1 is used in mus3, whereas chondrocytes select the TSS at exon 3. Median expressed level for MEF2c in muscle3 cells 53.4 FPKM; in chondrocytes 40.3. b, Alternative splice choices in different single mesenchymal cells of the developing limb result in alternate forms of Tcf3 (E12 and E47 bHLH TFs) with different DNA binding specificities. Individual splice-crossing reads are displayed beneath the read tracks for each of 3 separate exemplar cells. c, Comparisons of whole tissue and single-cell transcriptome gene content with external whole tissue and single-cell resources10,11. For all datasets, comparisons were restricted to only protein-coding genes that were detected.
