RNASeq of RNA from blasted CD4+ T cells from individuals with TCF3 mutations and healthy controls. RNASeq of RNA from blasted CD4+ T cells from individuals with TCF3 mutations and healthy controls

RNA-seq was performed using RNA extracted from blasted CD4+ T cells from individuals with TCF3 (haploinsufficiency [HI], null, or dominant negative [DN] mutations and healthy controls for the following study groups: healthy controls (HC, n=4) and patients with TCF3 mutations (HI=4, null=1, DN=1 ). Libraries were prepared using the AmpliSeq for Illumina Transcriptome Human Gene Expression panel. RNA-seq was performed on the Illumina HiSeq 2500 (Illumina; AmpliSeq for Illumina/HiSeq 2500). Demultiplexed reads were mapped to the hg19 genome using the splice-aware aligner Tophat (Trapnell et al., 2009). Gene-level counts data were generated using the Rsubread feature counts a read summarization program that counts mapped reads for genomic features such as genes (Liao et al., 2019). Differential expression analysis was performed using R (v.3.5.3) and DESeq2 (v.1.22.2)(Love et al., 2014). Overall design: RNA sequencing was performed using the AmpliSeq for Illumina Transcriptome Human Gene Expression panel anf the Illumina HiSeq 2500 analyzer. We analyzed RNA samples extracted from enriched T cell blasts from healthy controls and patients with TCF3 mutations. Submitter states that raw data files were lost due to server issues