Metabolomic profiling of rare cell populations isolated by flow cytometry from tissues

Metabolites enriched or depleted in cells sorted using 1× phosphate buffered saline (PBS) sheath fluid vs 0.5× PBS sheath fluid (fold change >2 and false discovery rate [FDR] < 0.05). Supplementary table 1b. Metabolites enriched or depleted in cells sorted using 1× PBS sheath fluid vs 0.5× PBS sheath fluid (fold change = 1.5–2 and FDR < 0.05). Correlation analysis of metabolite levels from 1× PBS versus 0.5× PBS samples: Spearman r = 0.995, y = 1.3 × −2142387. These metabolites were not significantly enriched in any metabolic pathway by pathway enrichment analysis.

Metabolites enriched or depleted in sorted vs pipetted AML cells (fold change >2 and false discovery rate [FDR] < 0.05). Correlation analysis of sorted versus pipetted AML samples: spearman r = 0.997, y = 1.1 × +214263. Metabolites that differed between sorted and pipetted AML cells were significantly enriched in ‘cysteine and methionine metabolism’. Supplementary table 2b. Metabolites enriched or depleted in sorted versus pipetted AML cells (fold change = 1.5–2 and FDR < 0.05).

Metabolites enriched or depleted in sorted vs pipetted ALL cells (fold change >2 and false discovery rate [FDR] < 0.05). Correlation analysis: Spearman r = 0.999, y = 1.1 × –436390. The metabolites were not significantly enriched in any metabolic pathway. Supplementary table 3b. Metabolites enriched or depleted in sorted versus pipetted ALL cells (fold change = 1.5–2 and FDR < 0.05).

Metabolites that significantly differed between AML and ALL cells in both sorted and pipetted samples, sorted samples only, or pipetted samples only. Metabolites that significantly differed between AML and ALL cells in both sorted and pipetted samples were significantly enriched in ‘glycerophospholipid metabolism’. No pathways were enriched among metabolites that differed in only sorted samples or only in pipetted samples. Supplementary table 4b. Metabolites that significantly differed between sorted AML and ALL cells or pipetted AML and ALL cells and for which fold change was between 1.5 and 2 in either the sorted or pipetted samples (FDR < 0.05).

Metabolites enriched or depleted at various time points after the incubation of cell suspensions on ice. The fold change cutoff is indicated in the left column. All are false discovery rate (FDR) < 0.05. Correlation analysis: 5 min versus 15 min: Spearman r = 0.998; 5 min versus 30 min: Spearman r = 0.996; 5 min versus 60 min: Spearman r = 0.992.

Metabolites enriched or depleted in whole bone marrow (WBM) cells isolated from cells suspended in phosphate buffered saline (PBS) versus Hank's Buffered Salt Solution (HBSS) (fold change >2 and false discovery rate [FDR] > 0.05). Correlation analysis: Spearman r = 0.960, y = 0.92 × +1759331. These metabolites were not significantly enriched in any metabolic pathway. Supplementary table 6b. Metabolites enriched or depleted in WBM cells isolated from cells suspended in PBS versus HBSS (fold change = 1.5–2 and FDR < 0.05).

These files contain the raw counts for each metabolite in each sample and the statistical comparisons between samples for each metabolite.

Metabolites enriched or depleted in sorted hematopoietic stem cell (HSC)/multipotent progenitors (MPPs) as compared to whole bone marrow (WBM) cells (fold change >2 and false discovery rate [FDR] < 0.05).

Metabolites that differed between circulating melanoma cells and melanoma cells from primary subcutaneous tumors in xenografted mice (fold change >2 and p<0.05).