Supplementary Information
1. Supplementary Materials and Methods
Supplementary Table 1. Sequences for primers used in RT-qPCR analyses.
target / Forward primer 5'-3' / Reverse primer 5'-3'scaRNA6 / AGG TCG ATG ATG ATT GGT AAA AGG / AGG TCT CAG ATT GAA AAC TTG AG
scaRNA9 / CTG CTT TTA GTG AAG TGG AT / CCA GAC ATA TGC CCT TAT T
SNORD24 / TGC AGA TGA TGT AAA AGA A / TGC ATC AGC GAT CTT GGT
SNORD44 / CCT GGA TGA TGA TAA GCA A / TTA GTC AGT TAG AGC TAA T
SNORD49A / TGC TCT GAT GAA ATC ACT / AAT CAG ACA GGA GTA GTC TT
SNORD55 / GTG TAT GAT GAC AAC TCG G / GCT CAG CTC TCC AAG GTT G
SNORD82 / CAG CAC AAA TGA TGA ATA AC / AGC ACA TCA GCA CAC TAC AAT
SNORD105 / CCC CTA TCT CTC ATG ATG / CCC CAT CTC TTC TTC AGA
SNORD110 / CAG TGA TGA CTT GCG AAT C / GAG ACA TGG AGA CAT CAG TGA
U6 (control)* / CTC GCT TCG GCA GCA CA / AAC GCT TCA CGA ATT TGC GT
* Primers originally described by Schmittgen et al. (2004).
2. Supplementary Figures Legends
Supplementary Figure 1. Hierarchical clustering with Euclidean metrics for the normalized snoRNA sequencing data from the individual cell line duplicate samples (s1 and s2). Samples that share the most similarity can be found in the branches nearest each other.
Supplementary Figure 2. Quantitative real-time PCR analysis of selected differentially expressed of DE snoRNAs scaRNA6, scaRNA9, SNORD24, SNORD44, SNORD49A, SNORD55, SNORD82, SNORD105, and SNORD110 in T-ALL and pre-B-ALL cell lines used in the SOLiD analysis. The pooled T-ALL template contained cDNA from CCRF-CEM and Molt-16 cell lines, and pooled pre-B-ALL template contained cDNA from KOPN-8 and MHH-CALL3 cell lines, mixed in equal amounts. The fold change of expression is shown relative to the T-ALL sample.
Supplementary Figure 3. A scatter plot of quantitative real-time PCR analysis of the expression of scaRNA6,scaRNA9, SNORD24, SNORD44, SNORD82, and SNORD105 in five pre-B-ALL and five T-ALL cell lines using cDNA from total RNA extractions. scaRNA6 and scaRNA9 showed similar expression in both small RNA and total RNA fractions, probably due to their increased stability brought about by larger size of the molecule. In the cases of SNORD24, SNORD44 and SNORD82 the expression was very low, even under the detection limit for some cell lines, making the interpretation of the results unreliable. SNORD105 shows difference in the expression opposite to the SOLiD and small RNA RT-qPCR analyses. The pre-B-ALL cell lines were Kasumi-2, KOPN-8, MHH-CALL3, Nalm-6 and REH. The T-ALL cell lines were CCRF-CEM, Jurkat, Molt-16, P12-Ichikawa and Peer. Results from two independent runs are shown. The solid horizontal line represents the median value.
3. References
Schmittgen, TD, Jiang J, Liu Q, Yang L. 2004. A high-throughput method to monitor the expression of microRNA precursors. Nucleic Acids Res32, e43.
4. Supplementary Figures
Supplementary Figure 1.
Supplementary Figure 2.
Supplementary Figure 3.