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

PRJNA299330: A Primate lncRNA Mediates Notch Signaling During Neuronal Development by Sequestering miRNA [single cell sequencing analysis]

来源: NCBI / GSE74207
提交时间: Oct 20 2015
释放时间: Jun 23 2016
最后更新时间: May 15 2019

概要: Long non-coding RNAs (lncRNAs) are a diverse category of transcripts with poor conservation and have expanded greatly in primates; particularly in their brain. We identified a lncRNA; which has acquired 16 microRNA response elements (MREs) for miR-143-3p in the Catarrhini branch of primates. This lncRNA termed LncND (neuro-development) gets expressed in neural progenitor cells and then declines in mature neurons. Binding and release of miR-143-3p; by LncND; can control the expression of Notch. Its expression is highest in radial glia cells in the ventricular and outer subventricular zones of human fetal brain. Down-regulation of LncND in neuroblastoma cells reduced cell proliferation and induced neuronal differentiation; an effect phenocopied by miR-143-3p over-expression and supported by RNA-seq analysis. These findings support a role for LncND in miRNA-mediated regulation of Notch signaling in the expansion of the neural progenitor pool of primates and hence contributing to the rapid growth of the cerebral cortex.

项目整体设计: Cerebral organoids were generated as in Lancaster et al. (Lancaster and Knoblich; 2014). Organoids were dissociated into single cells and captured on C1 Single-Cell Auto Prep Integrated Fluidic Circuit (IFC) (Fluidigm). The RNA extraction and amplification was performed on the chip as described by the manufacturer. We captured 68 single-cells on a C1 Single-Cell Auto Prep System (Fluidigm) and sequenced the RNA on a NextSeq500 System (Illumina) (Pollen et al.; 2014). Out of 68 cells; we obtained 60 high quality cells.

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GEND000199
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方案
生长方案: Cerebral organoids were generated as in Lancaster?et al. (Lancaster and Knoblich, 2014).?"
处理方案: Briefly, human iPS cells were isolated in single-cell solution and plated in a 96-well ultra-low attachment plate in hESC media with ROCK-inhibitor and low bFGF for 5 to 6 days to form embryoid bodies (EBs). EBs were then transferred to 24-well ultra-low attachment plates in neural induction media containing N2 supplement for 4 to 5 days to form neuroepithelium, then embedded in matrigel droplets and cultured in 60 mm dishes in organoid differentiation media containing N2 and B27 supplements. Vitamin A was added after 4 days in organoid differentiation media, and organoids were incubated until indicated time points on an orbital shaker.
提取方案: Cerebral organoids were dissociated into single cells and captured on C1 Single-Cell Auto Prep Integrated Fluidic Circuit (IFC) (Fluidigm). The RNA extraction and amplification was performed on the chip as described by the manufacturer.
建库方案: cDNA was processed to prepare libraries using Nextera XT DNA Sample Preparation kit (Illumina) to sequence them on NextSeq500 platform (Illumina).
测序信息
分子类型: poly(A)+ RNA
库的片段类型: PAIRED
库的链类型: -
测序平台: ILLUMINA
测序仪型号: Illumina NextSeq 500
链特异性: Unspecific
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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
A Primate lncRNA Mediates Notch Signaling during Neuronal Development by Sequestering miRNA.
Neuron . 2016-06-02 [PMID: 27263970]