Active Mycobacterium tuberculosis regulatory networks from in vitro infection of mouse macrophages uncovered by Path-seq

Transcriptional profiling of Mycobacterium tuberculosis mRNA enriched from host-pathogen samples from in vitro bone marrow derived macrophages (Mus musculus). Mouse bone marrow derived macrophages (BMDMs) were infected with MTB H37Rv strain (MOI 10), followed by washing 3x with RPMI at 2 h post infection. At 2 h, 8 h, and 24 h MTB infected BMDMs were lysed with TRIzol (Invitrogen) and total RNA was isolated from mixed host-pathogen sample. MTB from bacterial culture in 7H9 media and uninfected BMDMs were also collected at the same time points. Samples were either processed by Path-seq, RNA-seq or and profiled by Illumina sequencing, in triplicate. The sequence reads that passed quality filters were aligned to a combined M. tuberculosis and M. musuclus genome with Bowtie2 and processed using the R package DuffyNGS.

本数据集为从体外培养的小鼠（Mus musculus）骨髓源巨噬细胞的宿主-病原体混合样本中富集的结核分枝杆菌（Mycobacterium tuberculosis，简称MTB）mRNA的转录组分析。将小鼠骨髓源巨噬细胞（bone marrow derived macrophages，简称BMDMs）以感染复数（multiplicity of infection，简称MOI）10的比例感染MTB H37Rv菌株，于感染后2小时用RPMI培养基洗涤细胞3次。分别于感染后2小时、8小时和24小时，使用TRIzol（Invitrogen）裂解感染MTB的BMDMs，从宿主-病原体混合样本中提取总RNA。同时收集7H9培养基中培养的MTB菌体以及未感染的BMDMs样本。所有样本均设置三次生物学重复，分别采用Path-seq、RNA-seq或Illumina测序进行转录组分析。将通过质量过滤的测序读段与结核分枝杆菌和小鼠（M. musculus）的组合基因组进行Bowtie2比对，并使用R包DuffyNGS进行后续数据处理。