Genome wide transcriptome analysis (RNA-seq) of adult hippocampal neural stem cells in vitro a.k.a. HCN cells in quiescent and proliferative conditions in non-electroporated or electroporated with control empty vector or REST knock-down shRNA vector

We report the high-throughput transcriptome profiling of induced quiescent (iQNP) and proliferative (TAP) conditions in mammalian adult hippocampal stem cells in culture (HCN cells). By obtaining 145 to 78 million pair-end reads of sequence from isolated RNA from HCN cells in iQNP and TAP conditions. Thereafter, we intersected this gene expression data with REST bound ChIP-seq peaks within +/-10kb of transcription start site of genes also from HCN cells in iQNP and TAP conditions. We find that with +/-10kb of transcription start site of genes, REST efficiently binds neuronal genes and represses them in HCN cells in both iQNP and TAP conditions. Moreover, only in the iQNP REST also binds non-neuronal genes like DNA replication genes. We also report the high-throughput transcriptome profiling of iQNP and TAP condition HCN cells electroporated with a control empty vector or REST knock-down shRNA vector. By obtaining 145 to 78 million pair-end reads of sequence from isolated RNA from HCN cells in electroporated control empty vector or REST knock-down vector in iQNP and TAP conditions. In REST knockdown in iQNP and TAP conditions we found that predominantly non-neuronal genes and neuronal genes were derepressed. This study reveals that in addition to its well known function as a neuronal repressor in non-neuronal tissue, REST can also play other diverse roles in non-neuronal tissues.本研究报道了体外培养的哺乳动物成年海马干细胞（HCN cells，HCN细胞）在诱导静止态（induced quiescent, iQNP）与增殖态（proliferative, TAP）两种培养条件下的高通量转录组谱分析数据。我们从处于iQNP和TAP培养条件下的HCN细胞中分离总RNA并进行测序，获得145百万至78百万的双端测序读段（pair-end reads）。随后，我们将该基因表达数据与同样来自iQNP和TAP条件下HCN细胞的、结合REST的染色质免疫共沉淀测序（Chromatin Immunoprecipitation Sequencing, ChIP-seq）峰进行交集分析，该峰位于基因转录起始位点（transcription start site, TSS）上下游10kb范围内。研究发现，在基因转录起始位点上下游10kb范围内，REST可在两种培养条件下的HCN细胞中有效结合神经元基因并对其实施转录抑制。此外，仅在iQNP培养条件下，REST还可结合DNA复制基因等非神经元基因。本研究同时报道了经电转染对照空载体或REST敲减短发夹RNA（short hairpin RNA, shRNA）载体的、处于iQNP和TAP培养条件下的HCN细胞的高通量转录组谱分析数据：我们从经上述转染处理并处于iQNP和TAP培养条件下的HCN细胞中分离总RNA并测序，获得145百万至78百万的双端测序读段。在iQNP和TAP培养条件下进行REST敲减后，我们发现主要的非神经元基因与神经元基因均被解除转录抑制。本研究揭示，除其在非神经元组织中作为神经元基因转录抑制因子的经典功能外，REST在非神经元组织中还可发挥其他多样的生物学功能。