生长方案:	For the latency model, CD4+ T cells were purified from the buffy coat of uninfected donors by Ficoll gradient separation followed by negative selection and magnetic separation using the human CD4+ T Cell enrichment kit (Stem Cell Technologies #17952). Then the cells were resuspended at 106 cells/ml in Activation Medium (Immunocult XF T cell expansion medium (Stem Cell Technologies #10981) supplemented with 100 U/ml IL-2 (RD #202-IL) and 25 l/ml of ImmunoCult_ Human CD3/CD28 T Cell Activator (Stem Cell Technologies #10971)). Three days post-TCR activation, cells (2 mio) were transduced with 1.2x105 TU of HIVGFP/VSV-G in presence of 5 g/ml polybrene by spinoculation (3h, 1500g, 25C). Cells were then washed with RPMI-1640 supplemented with 10% heat i-ctivated fetal calf serum (RNA10) and resuspended in 4 ml Expansion Medium (Immunocult XF T cell expansion medium supplemented with 100 U/ml IL-2). After three days, cells were washed, resuspended in RPMI without phenol red and sorted by FACS based on GFP expression. Infected GFP+ cells were resuspended in 0.5 ml Activation Medium and then maintained in Expansion Medium at 106 cells/ml for ~2.5 weeks. Cells were stimulated once again in Activation Medium and maintained in Expansion Medium for further 2.5 weeks. Cells were then allowed to revert to a resting phenotype by long-term culture in Latency Medium (50% RNA10/50% H80 feeder cell supeRNAtant supplemented with 40 U/ml IL-2) for 8 weeks. In parallel, blood was collected from two HIV-infected individuals participating in the Swiss HIV Cohort Study (http://www.shcs.ch), that were on antiretroviral therapy for more than 3 years, with undetectable viremia and a CD4 cell count above 300 for more than one year. Blood (~25 ml) was directly collected in 4 CPT tubes (BD Vacutainer CPT; BD Biosciences #362753) and processed for peripheral blood mononuclear cells (PBMC) isolation according to manufacturer__ instructions. Resting CD4+ T cells were purified by negative selection and magnetic separation using the human CD4+ T Cell enrichment kit supplemented with anti-HLA-DR, anti-CD25 and anti-CD69 (Stem Cell Technologies #19052/#17962), and resuspended in RNA10 (0.45 m filtered).
处理方案:	Human primary CD4+ T-cells were infected, cultured, and maintained in a resting, latent phenotype in order to generate a primary model of HIV latency. Latently infected cells were either left untreated; Human primary CD4+ T-cells were infected, cultured, and maintained in a resting, latent phenotype in order to generate a primary model of HIV latency. Latently infected cells were exposed to SAHA stimulation; Human primary CD4+ T-cells were infected, cultured, and maintained in a resting, latent phenotype in order to generate a primary model of HIV latency. Latently infected cells were exposed to TCR stimulation
提取方案:	Cells were washed and collected for bulk or single-cell RNA-Seq. On one hand, cells (1 mio) were resuspended in 400 l lysis buffer of the ZRNADuet DNA/RNA miniprep (Zymo Research #D7001) and processed for RNA extraction according to manufacturer__ instructions, and used for bulk RNA-Seq (Illumina HiSeq Ribo-Zero TruSeq str RNA-Seq). On the other hand, cells were resuspended at 0.5-1x106 cells/ml in RNA10 (0.45 m filtered) and processed for single cell isolation and cDNA synthesis on a small 5-10 m fluidigm plate (fluidigm C1 Single Cell AutoPrep System, Clontech SMARTer Ultra Low RNA kit for Illumina sequencing), followed by single-cell RNA-Seq (Illumina Nextera XT DNA Sample Preparation).
建库方案:	-

分子类型:	poly(A)+ RNA
库的片段类型:	SINGLE
库的链类型:	-; Forward
测序平台:	ILLUMINA
测序仪型号:	Illumina HiSeq 2500
链特异性:	Unspecific; Specific

数据来源	GEN样本编号	GEN数据集编号	系列编号	项目编号	样本编号	样本名称	生物样本编号	样本访问号	实验访问号	释放时间	提交时间	最后更新时间	物种	种族	族裔	年龄	年龄单位	性别	来源名称	组织	细胞类型	细胞亚型	细胞系	疾病	疾病状态	发育阶段	突变/变异	表型	Condition Detail	生长方案	处理方案	提取方案	建库方案	分子类型	库的片段类型	链特异性	库的链类型	加标（Spike-In）	测序方法	测序平台	测序仪型号	细胞数	测序片段数	碱基数	平均测序片段长度_1	平均测序片段长度_2	唯一比对率	多重比对率	覆盖度