normalization data transformation protocol
Basecalls performed using CASAVA-1.8.2 Sequenced reads were aligned to the mm9 genome assembly using Bowtie v126.96.36.199 with default settings RPKM (Reads per kilo base per million) were calculated and differentially expressed genes detected using cuffdiff v2.0.2 Genome_build: mm9 Supplementary_files_format_and_content: Tab-delimited text files generated by Cuffdiff, including RPKM values for each gene and whether they are differentially expressed (fold change >1.5 and adjusted p value <0.05)
Bone marrow from C57B6 mice was lineage depleted using the EasyStep Mouse Hematopoietic Progenitor Cell Enrichment Kit (Stem Cell Tech) and retrovirally transduced with MIGR1-HA-Hoxa9-ER and MIGR1-Flag-Meis1. Cells cultured in the presence of IL3 and 4OHT (100nM). Withdrawal of 4OHT, and culture in EtOH (vehicle) leads to loss of nuclear Hoxa9-ER.
sample treatment protocol
Cells transformed by continuous culture with 100nM 4OHT were washed 3x and cultured for 72hrs in EtOH or 100nM 4OHT.
nucleic acid library construction protocol
RNA was purified using Qiagen RNeasy Kit with on-column DNase digestion. Libraries were generated from purified RNA using Illumina TruSeq RNA Sample Preparation Kit