C1 CAGE detection of transcription start sites and enhancer activity at single-cell resolution

C1 CAGE is a method to quantify single-cell gene expression by transcriptome sequencing on the Illumina platform. This method generates random-primed cDNAs, which allows detection of 5'-end transcripts to map transcription start sites (TSS) at single-nucleotide resolution. This method is performed in the microfluidics chips of the Fluidigm C1 system. The single cell expression data is derived from human A549 adenocarcinomic human alveolar basal epithelial cells stimulated with TGF-beta for 0, 6 and 24 h. We used the "Rev B" version of C1 CAGE, where ERCC spikes are diluted 20,000 times. The stimulations were ran in triplicates, which were multiplexed to control for chip bias using a color-coding strategy: cells stimulated at 0, 6 and 24 hrs were stained with different calcein dyes and pooled prior to loading into the C1 system. Metadata including time points, calcein dyes are indicated in the sample titles corresponding to each capture chamber. Raw images of the capture chambers before cell lysis are also available at the external links provided in this record. To validate the C1 CAGE protocol, we also performed C1 CAGE protocol with the mixture of human dermal fibroblast and mouse embryonic fibroblast cell lines, and with mouse ES cells.