Highly Parallel Genome-Wide Expression Analysis of Single Mammalian Cells

We have developed a high-throughput amplification method for generating robust gene expression profiles using single cell or low RNA inputs.The method uses tagged priming and template-switching, resulting in the incorporation of universal PCR priming sites at both ends of the synthesized cDNA for global PCR amplification. Coupled with a whole-genome gene expression microarray platform, we routinely obtain expression correlation values of R(2)~0.76-0.80 between individual cells and R(2)~0.69 between 50 pg total RNA replicates. Expression profiles generated from single cells or 50 pg total RNA correlate well with that generated with higher input (1 ng total RNA) (R(2)~0.80). Also, the assay is sufficiently sensitive to detect, in a single cell, approximately 63% of the number of genes detected with 1 ng input, with approximately 97% of the genes detected in the single-cell input also detected in the higher input.In summary, our method facilitates whole-genome gene expression profiling in contexts where starting material is extremely limiting, particularly in areas such as the study of progenitor cells in early development and tumor stem cell biology

Raw signal intensity correlations between replicates of low input RNAs and whole cells.

<p>(A) 50 pg UHR and BR total RNA and (B) single HeLa and brain tumor (BT) cells; 50 cell tumorsphere (TS) and adherent cells (AC). Pair-wise scatterplots of at least two replicates for each input type are shown for all 29 K probes across the full range of raw signal intensities. Correlations are the square of Pearson's correlation coefficient.</p

Pre-amplification scheme.

<p>(1) First strand cDNA synthesis is primed with tagged oligo-dT and random 9-mer primers. The tagged oligo-dT primer contains a VN anchor followed by a T-30 stretch with a 5′ PCR tag. The tagged random 9-mer consists of a 9-mer followed by the identical 5′ PCR tag. (2) Upon reaching the 5′ terminus of the mRNAs, the reverse transcriptase, via its terminal transferase activity, adds a few nucleotides (predominantly deoxycytidine) to the 3′ end of the newly synthesized cDNAs. (3) The template-switch primer, which consists of the same 5′ PCR tag as well as a 3′ riboguanine stretch, anneals via GC complimentary base-pairing to the 3′ end of the cDNAs, thereby serving as a new template for the reverse transcriptase. (4) After cDNA synthesis, both ends of the cDNAs now contain the identical PCR tag, allowing exponential amplification of the entire cDNA population through single primer PCR (5).</p

Intensity and detected probe concordance comparisons between low and higher 1 ng inputs.

<p>Raw signal intensity correlations between (A) 50 pg (x-axis) and 1 ng (y-axis) UHR total RNA; (B) 10 pg (x-axis) and 1 ng (y-axis) UHR total RNA; (C) single HeLa cell (x-axis) and 1 ng (y-axis) HeLa total RNA. The overlapping sets of detected probes between the low and higher inputs are shown for both the RNA equivalent (D, E) and single cell (F) inputs. All probe values shown are at a threshold of p<0.01.</p

Values are averages for at least two technical replicates.

<p>Values shown for the self-reproducibility and correlation are derived from all probes.</p>a<p>Sensitivity is calculated as the number of probes detected at p-value<0.01.</p>b<p>Probe concordance is calculated as a percentage of the number of probes with matching detected calls at p-value<0.01 between the low (50 pg or single cell) and standard (1 ng) inputs divided by the total number of probes detected in the lower input.</p>c<p>24 K WG-DASL.</p>d<p>29 K WG-DASL HT.</p