Gene Expression Nebulas
基于标准化流程分析的转录图谱综合数据库

Gene Expression Nebulas

多物种转录图谱整合数据库

PRJNA533795: Single cell RNA-sequencing of iPS cells derived multicellular human liver organoids

来源: NCBI / GSE130073
提交时间: Apr 19 2019
释放时间: Jul 31 2019
最后更新时间: Oct 30 2019

概要: By taking advantage of the foregut generation method, we initially differentiated iPSCs to foregut spheroids through definitive endoderm specification as described. The foregut spheroids were embedded in Matrigel and cultured with retinoic acid (RA). Following 4-day RA treatment, we switched into hepatocyte maturation media for the induction of the hepatocyte differentiation process to establish human liver organoids, hereafter defined as HLO, as early as day 20. To gain quantitative insights regarding the cellular composition in HLO, single-cell RNA sequencing was used to analyze their mRNA expression from 4,059 cells. t-distributed stochastic neighbor embedding analysis confirmed the five distinct major clusters among the cells in HLO, containing hepatocyte-, biliary cell-, hepatic stellate cell-, Kupffer cell-, biliary tree (or peribiliary gland) stem cell-like populations.

项目整体设计: Examination of mRNA expression profile at single cell level in multicellular human liver organoids

GEN 数据集:
GEND000126
测序方法:
物种:
组织:
健康状况:
细胞类型:
方案
生长方案: iPSCs were differentiated into definitive endoderm. At day1, medium was changed to RPMI 1640 medium containing 100 ng/mL Activin A and 50 ng/mL bone morphogenetic protein 4, 100 ng/mL Activin A and 0.2% fetal calf serum at day 2, and 100 ng/mL Activin A and 2% FCS at day 3. On Day4-6, cells were cultured in Advanced DMEM/F12 with B27 and N2 containing 500 ng/ml fibroblast growth factor and 3 μM CHIR99021. Cells were maintained at 37 ℃ in 5% CO2 with 95% air and the medium was replaced every day. At day 6, spheroids and attached cells were gently pipetted to be delaminated from dishes. They were centrifuged at 800 rpm for 3 minutes, embedded in a 100% Matrigel drop on the dishes in Advanced DMEM/F12 with B27, N2 and 2 μM retinoic acid, and cultured for 4 days. After RA treatment, the media was switched to Hepatocyte Culture Medium with 10 ng/mL hepatocyte growth factor, 0.1 碌M Dexamethasone and 20 ng/mL Oncostatin M. Cultures for HLO induction were maintained at 37 ℃ in 5% CO2 with 95% air and the medium was replaced every 3 days.
处理方案: -
提取方案: 17,500 cells were underwent the single cell RNA-seq
建库方案: Libraries were prepared by the Chromium Single Cell 3' Reagent version 2 kit and Chromium Controller (10X Genomics, CA, USA) as previously described at Zheng, G. X. Y. et al Nature communications 2017.
测序信息
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 HiSeq 2500
链特异性: Specific
样本
基本信息:
样本描述:
生物条件:
实验变量:
方案:
测序信息:
质量评估:
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
文章
Modeling Steatohepatitis in Humans with Pluripotent Stem Cell-Derived Organoids.
Cell metabolism . 2019-05-30 [PMID: 31155493]