Supplementary Materials

Spatially resolved, highly multiplexed RNA profiling in single cells

Kok Hao Chen, Alistair N. Boettiger, Jeffrey R. Moffitt, Siyuan Wang, Xiaowei Zhuang

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

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  • Figs. S1 to S9
Table S1
Two different codebooks for the 140-gene experiments. The specific code words of the 16-bit MHD4 code assigned to each RNA species studied in the two shuffles of the 140-gene experiment. The "Genes" columns contain the name of the gene. The "Codewords" columns contain the specific binary word assigned to each gene.
Table S2
GO analysis of the gene groups with co-varying expression in 140-gene measurements. The ‘Genes’ column contains the names of the genes for each identified group. "Correlation_difference" is the difference in the average correlation coefficient between the specified gene and all others in that group and the average correlation coefficient between the specified gene and all others genes not in that group. "P_value_correlation" represents the significance (p-value) of this difference in average correlation coefficient as determined by a student’s t-test. All of grouped genes have pvalues that are substantially smaller than most of p-values of the ungrouped genes. "GO_ID" lists the GO IDs associated with the enriched GO terms for each group. "GO_terms" lists the names of these GO terms. "GO_enrichment" provides the measured enrichment, defined as the ratio of the fraction of genes within each group that have this term to the fraction of all measured genes that have this term. "P_value_GO" lists the significance (p-values) of the enrichment of these terms, calculated via the hypergeometric function. Only the top 10 statistically significantly enriched GO terms are listed for each groups. "Genes_with_little_or_no_annotation" lists genes in each group with little or no prior annotation for which we can now hypothesize function based on this grouping. Non-distinct GO terms such as "protein-binding" and "DNA-binding" are not reported as top GO terms even if they are the most statistically significant in the list. In order to better predict functions for transcription factors, general terms associated with transcription factor activity have also been excluded, such as "transcription, DNAtemplated", "regulation of transcription, DNA-templated", and "sequence-specific DNA binding transcription factor activity".
Table S3
Codebook for the 1001-gene experiments. The specific code words of the 14-bit MHD2 code assigned to each RNA species studied in the 1001-gene experiments. The columns are defined as those listed in Table S1.
Table S4
GO analysis of the gene groups with co-varying expression in 1001-gene measurements. The columns are defined as those listed in Table S2. Here the p-values of the average correlation difference is greater than 0.05 for a small number of the grouped genes (marked red) suggesting that assignment to that group may not be statistically significant. The statistically most significantly enriched GO terms (maximum 10) are listed for each group. Several groups do not have statistically significant enrichment of GO terms and these groups are labeled green.
Table S5
Template sequences for the construction of all encoding probes. The "Experiment" column defines the experiment. The "Codebook" column lists the number of the codebook. The "Gene" column lists the name of the target genes. The "Index Primer 1" column lists the sequence of the first index primer. The "Common RT Primer" column lists the sequence of the common reverse transcription primer. This primer is not used in the 1001-gene experiments, and the index 1 primer is used instead as the reverse transcription primer. The "Readout 1" column lists the sequence of the first readout sequence. The "Targeting region" column lists the sequence of the region that targets cellular RNA. The "Readout 2" column lists the sequence of the second readout sequence. The "Index Primer 2" column lists the sequence of the second index primer. The sequences of the encoding probe templates are the concatenation of these sequences in order of the columns from left to right.