Additional file 1 of Dissociation protocols used for sarcoma tissues bias the transcriptome observed in single-cell and single-nucleus RNA sequencing

Additional file 1: Figure S1. Gating strategy to enrich for single-cells and single-nuclei. Figure S2. Consensus of DEGs between Sarcoma Subtypes when comparing Warm and Nuclei Protocols. Figure S3. DEGs Biases introduced by Warm and Cold Protocols. Figure S4. Differences in Sequencing Performance. Figure S5. Classifying sample type based on bias scores for ES. Figure S6. Classifying sample type based on bias scores for OS and DSRCT. Figure S7. Classifying sample type based on bias scores for Neuroblastoma. Figure S8. Biases associated gene length in gene signatures. Figure S9. Integration recovers matching cell states from different dissociation methods for ES. Figure S10. Integration recovers matching cell states from different dissociation methods for DSRCT. Table S1. Number of cells analyzed pre- and post-quality control. Table S2. Gene sets curated from literature analyzed in PDX samples. The AddModuleScore function in Seurat v3 was used to observe the averaged gene expression of the gene sets. Table S3. Differentially expressed genes between Warm and Nuclei protocols for ES. Wilcoxon test was used to compare gene expression between protocols. Table S4. Differentially expressed genes between Warm and Nuclei protocols for OS. Wilcoxon test was used to compare gene expression between protocols. Table S5. Differentially expressed genes between Warm and Nuclei protocols for DSRCT. Wilcoxon test was used to compare gene expression between protocols. Table S6. Differentially expressed genes between Warm and Cold protocols for DSRCT. Wilcoxon test was used to compare gene expression between protocols. Table S7. Differentially expressed genes between Warm and Cold protocols for ES. Wilcoxon test was used to compare gene expression between protocols. Table S8. Top 200 longest genes with the most polyA regions. The polyA stretches were defined as greater than 15 A repeats within the full-length cDNA, including intronic and exonic regions for every gene.