27 lncRNAs (predictive of subtype) 10 lncRNAs (TS & Onc.) 8 lncRNAs 4 lncRNAs (BALR-1, BALR-2, BALR-6, LINC00958) 114 lncRNAs 2 lncRNAs (BALR-2, BALR-6)

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27 lncRNAs (predictive of subtype) 10 lncRNAs (TS & Onc.) 8 lncRNAs 4 lncRNAs (BALR-1, BALR-2, BALR-6, LINC00958) 114 lncRNAs 2 lncRNAs (BALR-2, BALR-6) Microarray Nearest shrunken centroid analysis 81 lncRNAs Expression in leukemia > or < than pro-B cells 17 lncRNAs GenBank ESTs and mRNAs Available transcript models 2 lncRNAs Expression > in leukemic samples 4 lncRNAs (TS) FC > 2 adj. p < 0.01 Clinicopathological parameters 2 lncRNAs BALR-2 Prednisone response Subcellular localization Future studies Supplemental Figure 1

c ef a d b Misclassification Error Value of Threshold Number of Genes Supplemental Figure 2 Value of Threshold Misclassification Error Number of Genes TEL-AML1 E2A-PBX MLL Number of lincRNAs Misclassification Error Value of Threshold TEL-AML1 E2A-PBX MLL Value of Threshold Misclassification Error Number of lincRNAs gh

ab cd e f g Supplemental Figure 3 Time (days) Cumulative Survival High BALR-6 Low BALR-6 Time (days) Cumulative Survival High BALR-1 Low BALR-1 Time (days) Cumulative Survival High LINC00958 Low LINC00958 BALR-2 Frequency LINC00958 Frequency BALR-1 Frequency BALR-6 Frequency

RASSF10 LINC q15.2 mRNA: NR_ Probe set on microarray qPCR primers TEAD1 RACE product LOC BALR-6 3p24.3 mRNA: NM_ Probe set on microarray qPCR primers LOC SATB1TBC1D5 RACE product 14q32.2 C14orf132 mRNA: NM_ Probe set on microarray qPCR primers LINC00617BDKRB2 BALR-1 a b c Supplemental Figure 4 BALR-2 5’ RACE product 1 3’ RACE product 5’ RACE primer Un-annotated exon AAAAA 5’ RACE product 2 5’ RACE product 3 80kb Balr-2 3’ RACE product 1 3’ RACE primer 3’ RACE product 2 d e 5’ RACE3’ RACE 1000 bp 500 bp 1000 bp 500 bp 3’ RACENC

Supplemental Figure 5 fg h abc de

Supplemental Figure 6 ab c d efg hij klm

Supplemental Figure 7 PRED GR BIM BALR-2 JUN FOS Cytokines /survival genes ? Caspase-3APOPTOSIS FOS