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

PRJNA510946: Single cell RNA-sequencing of 75-day old human H1 and H9 embryonic stem cell-derived cerebral organoids

来源: NCBI / GSE124174
提交时间: Dec 20 2018
释放时间: Feb 28 2019
最后更新时间: May 30 2019

概要: The scRNA-seq analysis of 75 day old human cerebral organoids grown at the air-liquid interface (ALI-COs) reveals six well-defined major clusters. Cell-type and maturity markers define a (1) distinct population of deep layer subcortical projection neurons, (2) upper layer intracortical (callosal) projection neurons and intermediate progenitors, (3) ventricular and subventricular zone radial glial cells, (4) more mature upper and deep layer neurons, (5) interneurons and (6) actively dividing cells with intermediate progenitor and radial glia markers. In addition, the gene expression profile of these clusters corresponds with their expected functional characteristics appropriate to their maturity. Altogether, our data reflect a full repertoire of cortical neuronal and progenitor identities corresponding with the stages of cortical development in age-matched fetal brains.

项目整体设计: Single cell RNA-sequencing data was generated using the 10X Genomics Chromium Single Cell 3' Chip and workflow.

GEN 数据集:
GEND000120
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方案
生长方案: H1 and H9 human embryonic stem cell-derived cerebral organoids were generated and grown as slice cultures as described in Giandomenico et al., 2018. Organoids were supplemented with serum-free slice culture medium (SFSCM): Neurobasal (Invitrogen, cat. #21103049), 1:50 (v/v) B27+A (Invitrogen, cat. #17504044), 0.5% (w/v) glucose, 1X (v/v) Glutamax supplemented with Antibiotic-Antimycotic (ThermoFisher, cat. #15240062). The cultures were maintained in SFSCM at 37 ℃ and 5% CO2 with daily media changes.
处理方案: -
提取方案: The cell suspension (34μl with a total of 7000 cells) was loaded onto a 10X Genomics Chromium Single Cell 3' Chip with the appropriate amount of Mastermix. RNA extraction was performed following the same 10X Genomics Chromium workflow.
建库方案: The reverse transcriptase reaction and subsequent amplification was carried out in a C1000 Touch Thermal Cycler (Biorad), with the cDNA being amplified for 12 cycles. Before sequencing, libraries were quality tested using the 2100 Bioanalyzer Instrument (Agilent) and their concentration was measured by qPCR.
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 4000
链特异性: Specific
样本
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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
Cerebral organoids at the air-liquid interface generate diverse nerve tracts with functional output.
Nature neuroscience . 2019-03-18 [PMID: 30886407]