RNA-seq of T-ALL patient sample: Sample C18
RNA was extracted from T-ALL patient samples using the AllPrep DNA/RNA Mini Kit (Qiagen), treated with DNAse, and DNA contamination was confirmed to be <10%.  RNA-seq library was prepared using 50-100 ng of DNAse-treated RNA using the NEBNext Ultra RNA LIbrary Prep Kit for Illumina according to the manufacturer's protocol (New England Biolabs, Ipswich, MA).  Following DNA library construction, library quantity was determined using the Qubit High Sensitivity DNA Kit (Thermo Fisher Scientific), and library size was determined using the Bioanalyzer High Sensitivity Chip Kit (Agilent). Finally, libraries were put through quantitative reverse transcriptase PCR (qRT-PCR) using the Universal Library Quantification Kit for Illumina (Kapa Biosystems, Wilmington, MA) and run on the 7900HT Fast Real-Time PCR machine (Applied Biosystems, Foster City, CA).  Libraries passing quality control were diluted to 2nM using sterile water and then sequenced on the HiSeq 2000 (Illumina, San Diego, CA) at a final concentration of 12pM on a single read flowcell with 50 sequencing cycles, following all manufacturer protocols