Supplementary Materials

Comprehensive single-cell transcriptional profiling of a multicellular organism

Junyue Cao, Jonathan S. Packer, Vijay Ramani, Darren A. Cusanovich, Chau Huynh, Riza Daza, Xiaojie Qiu, Choli Lee, Scott N. Furlan, Frank J. Steemers, Andrew Adey, Robert H. Waterston,‡ Cole Trapnell, Jay Shendure

Materials/Methods, Supplementary Text, Tables, Figures, and/or References

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  • Materials and Methods
  • Figs. S1 to S24
  • Captions for Tables S1 to S14
  • References
Tables S1-14
Table S1. Summary of experiments Table S2: Summary statistics for cell type consensus expression profiles constructed in this study. Table S3: Tissue-level consensus expression profiles. Values listed are transcripts per million. Table S4: Cell type consensus expression profiles. Values listed are transcripts per million. Table S5: Neuron cluster consensus expression profiles. Values listed are transcripts per million. Table S6: Differential expression test results for the identification of tissue-enriched genes. See Methods. There is a row for each gene that is expressed in at least 10 cells in the analysis dataset. “Max tissue� is the tissue that the gene is expressed highest in. “Tissue 2� is the tissue the gene is expressed second highest in. “q-val� is the false detection rate at which the differential expression between the highest and second-highest expressing tissues can be called as non-zero. Table S7: Differential expression test results for the identification of cell type enriched genes. See Methods. There is a row for each gene that is expressed in at least 10 cells in the analysis dataset. “Max cell type� is the cell type that the gene is expressed highest in. “Cell type 2� is the cell type the gene is expressed second highest in. “q-val� is the false detection rate at which the differential expression between the highest and second-highest expressing cell types can be called as non-zero. Table S8: Differential expression test results for the identification of neuron cluster enriched genes. See Methods and Fig. 4. There is a row for each gene that is highly enriched (>5-fold) in rons relative to other tissues (as reported in Table S6). “Max cluster� is the neuron cluster that the gene is expressed highest in. “Cluster 2� is the neuron cluster the gene is expressed second highest in. “q-val� is the false detection rate at which the differential expression between the highest and second-highest expressing neuron clusters can be called as non-zero. Table S9: Differential expression test results for anterior vs. posterior body wall muscle. “moderated log2(anterior / posterior)� is equal to log2(anterior TPM+1) - log2(posterior TPM+1). Table S10: Differential expression test results for posterior vs. other intestine. “moderated log2� is defined as in Table S9. Table S11: Differential expression test results for amphid 1 vs. phasmid sheath cells. “moderated log2� is defined as in Table S9. Table S12: Differential expression test results for the ASEL vs. ASER neuron. “moderated log2� is defined as in Table S9. Table S13: Differential expression test results for AWA vs. ASG neurons. “moderated log2� is defined as in Table S9. Table S14: List of genes used in heatmaps in Fig. 3F and Fig. 4C.