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). 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

本研究针对以下两个研究分组开展RNA测序（RNA-seq）：健康对照组（HC，n=4）与携带TCF3基因突变的患者组（其中单倍剂量不足[haploinsufficiency, HI]型4例、无效突变[null]型1例、显性负效[dominant negative, DN]型1例），测序所用RNA提取自受试者的blast化CD4+ T细胞。
测序文库基于Illumina AmpliSeq转录组人类基因表达检测panel（AmpliSeq for Illumina Transcriptome Human Gene Expression panel）构建，测序在Illumina HiSeq 2500测序平台（Illumina; AmpliSeq for Illumina/HiSeq 2500）上完成。
将已去复用的读段利用支持剪接位点识别的比对工具Tophat（Tophat，Trapnell等，2009）比对至hg19参考基因组；通过Rsubread软件包中的featureCounts（一款用于统计基因等基因组特征的比对读段数的读段汇总工具，Liao等，2019）生成基因水平计数数据。
使用R软件（版本3.5.3）及DESeq2工具（版本1.22.2，Love等，2014）完成差异表达分析。本次RNA测序同样采用Illumina AmpliSeq转录组人类基因表达检测panel与Illumina HiSeq 2500测序仪开展。
本研究分析的RNA样本提取自健康对照及TCF3突变患者的富集T细胞母细胞。数据提交者说明，原始数据文件因服务器故障丢失。