RNA sequencing and ChIP-sequencing in 38B9 cells expressing WT or H195Y IKZF3

The goal of this project is to determine the effect of ectopic expression of H195Y mutant IKZF3 (Aiolos) transcription factor on STAT5 binding genome-wide, using the pre-B cell line 38B9. 38B9 cells were infected with retroviral vectors encoding wild type (WT) or H195Y IKZF3 and enriched by cell sorting. RNA-sequencing was performed on 38B9 cells ectopically expressing WT or H195Y IKZF3 with or without treatment with Interleukin-7 for 4 hrs. Three biological replicates of RNA-sequencing were performed for a total of 12 biosamples. Next, chromatin-immunoprecipitation-sequencing (ChIP-seq) was performed using anti-STAT5 antibody on 38B9 cells ectopically expressing WT or H195Y IKZF3 and treated with or without interleukin-7. Biological replicates were combined before sequencing, for a total of 4 biosamples. Next, ChIP-seq was performed using anti-IKZF3 antibody on 38B9 cells ectopically expressing WT or H195Y IKZF3, for a total of 2 biosamples. Input DNA was also sequenced for 38B9 cells ectopically expressing WT or H195Y IKZF3 for an additional 2 biosamples. For each biosample, paired-end Illumina sequencing was performed, generating two separate files containing read 1 and read 2. Raw data in gzipped fastq format is provided.