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

PRJNA422059: RNA sequencing of human bronchial epithelial cell transcriptomes after repopulation and differentiation on bronchial scaffolds from COPD patients and healthy donors

来源: NCBI / GSE107971
提交时间: Dec 12 2017
释放时间: Feb 20 2018
最后更新时间: May 15 2019

概要: Chronic obstructive pulmonary disease (COPD) is a serious global health problem characterized by chronic airway inflammation, progressive airflow limitation and destruction of lung parenchyma. Remodeling of the bronchial airways in COPD includes changes in both the bronchial epithelium and the subepithelial extracellular matrix (ECM). To explore the impact of an aberrant ECM on epithelial cell phenotype in COPD we developed a new ex vivo model, in which normal human bronchial epithelial (NHBE) cells repopulate and differentiate on decellularized human bronchial scaffolds derived from COPD patients and healthy individuals. By using transcriptomics, we show that bronchial ECM from COPD patients induces differential gene expression in primary NHBE cells when compared to normal bronchial ECM. The gene expression profile indicated altered activity of upstream mediators associated with COPD pathophysiology, including hepatocyte growth factor, transforming growth factor beta 1 and platelet-derived growth factor B, which suggests that COPD-related changes in the bronchial ECM contribute to the defective regenerative ability in the airways of COPD patients.

项目整体设计: Normal bronchial epithelial (NHBE) cells were seeded on decellularized bronchial scaffolds from 3 COPD patients and 3 healthy donors. Differentiation was induced 4 days later and repopulated scaffolds were collected after 0, 7, 14, 21, 28 and 35 days of differentiation.

GEN 数据集:
GEND000009
测序方法:
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发育阶段:
方案
生长方案: Primary normal human bronchial epithelial (NHBE) cells were purchased from Lonza and cultured in bronchial epithelial growth medium (BEGM) (Lonza) to passage 3. The cells were harvested and seeded on decellularized bronchial scaffolds where they were allowed to attach and grow for 4 days in BEGM. Differentiation was induced after 4 days by exchanging the BEGM with a differentiation medium (50 % BEGM, 50% Dulbecco's Modified Eagle's Medium and 0.05 µM retinoic acid) and differentiation proceeded during 35 days.
处理方案: Normal bronchial epithelial (NHBE) cells were seeded on decellularized bronchial scaffolds from 3 healthy donors. Differentiation was induced 4 days later and repopulated scaffolds were collected after 0 days of differentiation.; Normal bronchial epithelial (NHBE) cells were seeded on decellularized bronchial scaffolds from 3 healthy donors. Differentiation was induced 4 days later and repopulated scaffolds were collected after 7 days of differentiation.; Normal bronchial epithelial (NHBE) cells were seeded on decellularized bronchial scaffolds from 3 healthy donors. Differentiation was induced 4 days later and repopulated scaffolds were collected after 14 days of differentiation.; Normal bronchial epithelial (NHBE) cells were seeded on decellularized bronchial scaffolds from 3 healthy donors. Differentiation was induced 4 days later and repopulated scaffolds were collected after 21 days of differentiation.; Normal bronchial epithelial (NHBE) cells were seeded on decellularized bronchial scaffolds from 3 healthy donors. Differentiation was induced 4 days later and repopulated scaffolds were collected after 28 days of differentiation.; Normal bronchial epithelial (NHBE) cells were seeded on decellularized bronchial scaffolds from 3 healthy donors. Differentiation was induced 4 days later and repopulated scaffolds were collected after 35 days of differentiation.; Normal bronchial epithelial (NHBE) cells were seeded on decellularized bronchial scaffolds from 3 COPD patients. Differentiation was induced 4 days later and repopulated scaffolds were collected after 0 days of differentiation.; Normal bronchial epithelial (NHBE) cells were seeded on decellularized bronchial scaffolds from 3 COPD patients. Differentiation was induced 4 days later and repopulated scaffolds were collected after 7 days of differentiation.; Normal bronchial epithelial (NHBE) cells were seeded on decellularized bronchial scaffolds from 3 COPD patients. Differentiation was induced 4 days later and repopulated scaffolds were collected after 14 days of differentiation.; Normal bronchial epithelial (NHBE) cells were seeded on decellularized bronchial scaffolds from 3 COPD patients. Differentiation was induced 4 days later and repopulated scaffolds were collected after 21 days of differentiation.; Normal bronchial epithelial (NHBE) cells were seeded on decellularized bronchial scaffolds from 3 COPD patients. Differentiation was induced 4 days later and repopulated scaffolds were collected after 28 days of differentiation.; Normal bronchial epithelial (NHBE) cells were seeded on decellularized bronchial scaffolds from 3 COPD patients. Differentiation was induced 4 days later and repopulated scaffolds were collected after 35 days of differentiation.
提取方案: Total RNA was extracted using the RNeasy Mini kit (Qiagen).
建库方案: 560 ng total RNA/sample was used as input to create cDNA libraries using the TruSeq Stranded mRNA kit (Illumina) with dual indexing following standard instructions.
测序信息
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 NextSeq 500
链特异性: Specific
样本
基本信息:
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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
Bronchial extracellular matrix from COPD patients induces altered gene expression in repopulated primary human bronchial epithelial cells.
Scientific reports . 2018-02-22 [PMID: 29472603]