1. 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

2. c ef a d b Misclassification Error Value of Threshold 0.8 0.2 0.4 0.6 1112 4 Number of Genes 24681012 6886 1 Supplemental Figure 2 Value of Threshold Misclassification Error Number of Genes 24 68 10 12 0.8 0.2 0.4 0.6 6886 1112 4 1 TEL-AML1 E2A-PBX MLL Number of lincRNAs Misclassification Error 0.8 0.2 0.4 0.6 2 4 6 Value of Threshold 27 618 4 4345 TEL-AML1 E2A-PBX MLL Value of Threshold Misclassification Error 246 27 4 Number of lincRNAs 0.8 0.2 0.4 0.6 618 4345 gh

3. ab cd e f g Supplemental Figure 3 Time (days) Cumulative Survival 0 100 300 500 1.0 0.6 0.2 0 0.8 0.4 High BALR-6 Low BALR-6 Time (days) Cumulative Survival 0 100 300 500 1.0 0.6 0.2 0 0.8 0.4 High BALR-1 Low BALR-1 Time (days) Cumulative Survival 0 100 300 500 1.0 0.6 0.2 0 0.8 0.4 High LINC00958 Low LINC00958 BALR-2 Frequency 40 10 0 30 20 0 0.2 0.4 0.6 0.8 LINC00958 Frequency 30 10 0 20 0 1.0 10.0 100.0 BALR-1 Frequency 50 10 0 40 30 0 1.0 10.0 20 BALR-6 Frequency 15 10 0 0 1.0 10.0 100.0 1000.0 5

4. RASSF10 LINC00958 11q15.2 mRNA: NR_038904 Probe set on microarray qPCR primers TEAD1 RACE product LOC100506305 BALR-6 3p24.3 mRNA: NM_001257177 Probe set on microarray qPCR primers LOC339862 SATB1TBC1D5 RACE product 14q32.2 C14orf132 mRNA: NM_001252507 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

5. Supplemental Figure 5 fg h abc de

6. Supplemental Figure 6 ab c d efg hij klm

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