Gene Expression Nebulas概要: We report the early transcriptional changes in human diabetic nephropathy by single nucleus RNA sequencing
项目整体设计: Single nucleus RNA sequencing of 3 early human diabetic kidney samples and 3 controls. Samples represent non-tumor tissue in patients undergoing nephrectomy for renal mass.
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| 生长方案: | ES cell–derived NS cells were routinely generated by re-plating d 7 adherent neural differentiation cultures (typically 2–3 × 10e6 cells into a T75 flask) on uncoated plastic in NS-A medium (Euroclone, Milan, Italy) supplemented with modified N2 and 10 ng/ml of both EGF and FGF-2 (NS expansion medium). |
| 处理方案: | - |
| 提取方案: | Nuclei were isolated with Nuclei EZ Lysis buffer (NUC-101; Sigma-Aldrich) supplemented with protease inhibitor (5892791001; Roche) and RNase inhibitor (N2615; Promega and AM2696; Life Technologies). Samples were cut into <2-mm pieces and homogenized using a Dounce homogenizer (885302-002; Kimble Chase) in 2 ml of ice-cold Nuclei EZ Lysis buffer, and they were incubated on ice for 5 minutes with an additional 2 ml of lysis buffer. The homogenate was filtered through a 40-μm cell strainer (43-0040-1; pluriSelect) and then centrifuged at 500xg for 5 minutes at 4℃. The pellet was resuspended and washed with 4 ml of the buffer, and then, it was incubated on ice for 5 minutes. After another centrifugation, the pellet was resuspended in Nuclei Suspension Buffer (1xPBS, 0.07% BSA, and 0.1% RNase inhibitor), filtered through a 20-μm cell strainer (43-0020-50; pluriSelect), and counted. |
| 建库方案: | Libraries were prepared according to Illumina's instructions and accompanying 10X Genomics Chromium Single Cell 5' Library and Gel Bead Kit |
| 分子类型: | poly(A)+ RNA |
| 库的片段类型: | PAIRED |
| 库的链类型: | Forward |
| 测序平台: | ILLUMINA |
| 测序仪型号: | Illumina NovaSeq 6000 |
| 链特异性: | 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 |
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