BRG1缺失在肺癌中频发并通过转录和表观遗传重编程转化肺上皮细胞

数据集获取

源站：https://ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE307857

标准获取流程：

1. 访问源站链接，注册/登录账号；
2. 进入数据集详情页，按页面指引申请权限或直接下载；
3. 部分平台提供 SDK，例如：
   • OpenDataLab: pip install openxlab 后 openxlab.dataset.get(...)
   • ModelScope: pip install modelscope 后 modelscope download
   • 天池: 登录后页面提供直链下载
     以源站「数据下载/使用文档」页面为准。

数据说明

Background/Objectives: BRG1 loss-of-function (LOF) mutation is found in ~10% non-small cell lung cancer (NSCLC) but its role in lung tumorigenesis is unclear and investigated in this study. Methods: BRG1-knockout (KO) lines were generated from various non-malignant, pre-malignant, and malignant human lung epithelia-derived cell lines using CRISPR. Effects of BRG1-KO on cell growth, transcriptome, methylome, and epigenetic therapy were compared with wild-type (BRG1-WT) isogenic controls using standard in vitro and in vivo assays. Results: BRG1 protein was expressed in all non/pre-malignant lung epithelial cells but lost in 47% (14/30) of NSCLC cell lines. BRG1-KO and cigarette smoke (CS) exposure individually transformed human bronchial epithelial cell lines (HBECs) as evident by anchorage-independent growth. BRG1-KO and CS produced additive to synergistic effects on sensitivity to transformation that differed across HBECs. RNA-seq analysis revealed BRG1-KO significantly changed expression of over 8,500 genes on average impacting lung development, function, damage repair and cancer pathways including axonal guidance, pulmonary wound healing, and epithelial-to-mesenchymal transition (EMT). BRG1-KO also led to hypermethylation of >47,000 promoter CpGs within ~9,500 genes on average in different HBECs that included silencing of epithelial genes involved in EMT and tumor suppressor genes. BRG1-KO also moderately increased the in vitro and in vivo sensitivity of NSCLC cells to some epigenetic drugs. Conclusion: BRG1-LOF is frequent in NSCLC, can drive transformation of lung epithelial cells to acquire properties of premalignant cells indicating a potential role in lung cancer initiation, and sensitizes lung tumors to epigenetic therapy.

数据加载示例（图像类）

from PIL import Image
import glob, os

files = (glob.glob(os.path.join(path, "**", "*.png"), recursive=True)
       + glob.glob(os.path.join(path, "**", "*.jpg"), recursive=True)
       + glob.glob(os.path.join(path, "**", "*.tif"), recursive=True))
print("图像文件数:", len(files))
img = Image.open(files[0]); print("尺寸/模式:", img.size, img.mode)

# torchvision Dataset 方式:
# from torchvision import datasets
# ds = datasets.ImageFolder(path)  # 要求 子目录=类别

目录组织与标注格式以源站说明和下载后实际文件为准。