Supplementary Materials

Supplementary Material for:

Tumor-derived circulating endothelial cell clusters in colorectal cancer

Igor Cima, Say Li Kong, Debarka Sengupta, Iain B. Tan, Wai Min Phyo, Daniel Lee, Min Hu, Ciprian Iliescu, Irina Alexander, Wei Lin Goh, Mehran Rahmani, Nur-Afidah Mohamed Suhaimi, Jess H. Vo, Joyce A. Tai, Joanna H. Tan, Clarinda Chua, Rachel Ten, Wan Jun Lim, Min Hoe Chew, Charlotte A.E. Hauser, Rob M. van Dam, Wei-Yen Lim, Shyam Prabhakar, Bing Lim, Poh Koon Koh, Paul Robson, Jackie Y. Ying, Axel M. Hillmer, Min-Han Tan*

*Corresponding author. Email: mhtan{at}ibn.a-star.edu.sg

Published 29 June 2016, Sci. Transl. Med. 8, 345ra89 (2016)
DOI: 10.1126/scitranslmed.aad7369

This PDF file includes:

  • Materials and Methods
  • Fig. S1. Device setup, retrieval efficiency, and sample output purity.
  • Fig. S2. scrmPCR methodology and proof of principle in cell lines.
  • Fig. S3. CD45 clusters express EMT markers, do not share common mutations with the primary tumor, and have normal chromosomal structures.
  • Fig. S4. Cytomorphology of CD45 clusters used for RNA-seq.
  • Fig. S5. Cell-type inference workflow from RNA-seq data.
  • Fig. S6. Validation of the cell-type inference algorithm.
  • Fig. S7. Comparison between endothelial clusters (this study) and CTC clusters in Aceto et al. (9).
  • Fig. S8. Circulating endothelial clusters are tumor-derived.
  • Fig. S9. tEC clusters in a mouse model of CRC.
  • Fig. S10. tEC clusters do not correlate with selected CRC tumor and patient characteristics or comorbidities.
  • Legends for tables S1 to S14
  • References (3844)

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Other Supplementary Material for this manuscript includes the following:

  • Table S1 (Microsoft Excel format). scrmPCR primers used in this study.
  • Table S2 (Microsoft Excel format). Whole genome application (WGA) false-positives are detected only at VAF < 10%.
  • Table S3 (Microsoft Excel format). Circulating CD45 clusters do not mirror matching primary tumor mutations.
  • Table S4 (Microsoft Excel format). Sporadic mutations in circulating CD45 clusters are not detected in matching primary tumor tissues.
  • Table S5 (Microsoft Excel format). Germline variants in tumor tissues and circulating CD45 cell clusters (coverage and zygosity).
  • Table S6 (Microsoft Excel format). RNA-seq data: number of uniquely mapped reads to hg19 exons.
  • Table S7 (Microsoft Excel format). RNA-seq data: processed data (FPKM) of all samples described in the study.
  • Table S8 (Microsoft Excel format). Definition of the cell types used for the inference algorithm.
  • Table S9 (Microsoft Excel format). Top 80 genes ordered from highest to lowest specificity index (S) for each cell type selected for the inference algorithm.
  • Table S10 (Microsoft Excel format). Positive published RNA-seq control samples used to validate the inference algorithm.
  • Table S11 (Microsoft Excel format). Characteristics of tEC clusters isolated in this study.
  • Table S12 (Microsoft Excel format). Circulating endothelial cell cluster count before and after surgery.
  • Table S13 (Microsoft Excel format). Baseline patients’ and healthy donors’ characteristics.
  • Table S14 (Microsoft Excel format). CD45 cluster count for each baseline sample type and number of single clusters analyzed for each technique in the corresponding samples.

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