Presence of onco-fetal neighborhoods in hepatocellular carcinoma is associated with relapse and response to immunotherapy
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The HCC01 and HCC03 Stereo-seq data have been deposited in the China National GeneBank Sequence Archive (CNSA) under accession code CNP0004497. The M311 and M316 Stereo-seq data have been deposited in the Sequence Read Archive (SRA) under accession code PRJNA1005053. The CoxMx data have been deposited in the under accession code. The original data used to construct the HCC atlas are available with accession codes GSE156337, GSE149614, GSE151530, GSE212046 (GEO), HRA000069 (Genome Sequence Archive) and CNP0000650 (CNSA). The original data of PLANET cohort and GO30140 and IMbrave150 trials are available with accession codes EGAS00001003813 and EGAS00001005503 (European Genome-phenome Archive). The TCGA LIHC datasets were downloaded from UCSC Xena (http://xena.ucsc.edu/). All processed expression data have been uploaded to figshare, which can be visited through the following private links: HCC Atlas, https://doi.org/10.6084/m9.figshare.22332568; Onco-fetal CAF Identification, https://doi.org/ 10.6084/m9.figshare.22332655; HCC01 and HCC03 Stereo-seq Data, https://doi.org/10.6084/m9.figshare.22332223; Nanostring CosMx Data, https://doi.org/10.6084/m9.figshare.23972991; PLANET corhort Data, https://doi.org/10.6084/m9.figshare.23732370; HCC and Fetal Liver Nanostring DSP Data, https://doi.org/10.6084/m9.figshare.22332397; HCC Immunotherapy Stereo-seq Data, https://doi.org/10.6084/m9.figshare.22332352. Source data for Fig. 1-8 and Extended Data Fig. 1-10 have been provided as Source Data files. All other data supporting the findings of this study are available from the corresponding author upon reasonable request.
HCC01与HCC03时空转录组测序（Stereo-seq）数据已提交至中国国家基因库序列归档系统（China National GeneBank Sequence Archive, CNSA），登录号为CNP0004497。M311与M316时空转录组测序（Stereo-seq）数据已提交至序列读取存档（Sequence Read Archive, SRA），登录号为PRJNA1005053。CoxMx数据集已提交至某数据库，登录号未注明。用于构建肝细胞癌（Hepatocellular Carcinoma, HCC）图谱的原始数据可通过以下登录号获取：GSE156337、GSE149614、GSE151530、GSE212046（基因表达汇编（Gene Expression Omnibus, GEO））、HRA000069（基因组序列存档（Genome Sequence Archive））以及CNP0000650（中国国家基因库序列归档系统（China National GeneBank Sequence Archive, CNSA））。PLANET队列及GO30140、IMbrave150试验的原始数据可通过以下登录号获取：EGAS00001003813与EGAS00001005503（欧洲基因组-表型组存档（European Genome-phenome Archive））。TCGA LIHC数据集从UCSC Xena（http://xena.ucsc.edu/）下载获得。所有经过处理的表达数据已上传至figshare平台，可通过以下私有链接访问：HCC图谱：https://doi.org/10.6084/m9.figshare.22332568；肿瘤胎儿相关成纤维细胞鉴定：https://doi.org/10.6084/m9.figshare.22332655；HCC01与HCC03时空转录组测序数据：https://doi.org/10.6084/m9.figshare.22332223；Nanostring CosMx数据：https://doi.org/10.6084/m9.figshare.23972991；PLANET队列数据：https://doi.org/10.6084/m9.figshare.23732370；肝细胞癌与胎儿肝脏Nanostring数字空间谱型分析（Digital Spatial Profiling, DSP）数据：https://doi.org/10.6084/m9.figshare.22332397；HCC免疫治疗时空转录组测序数据：https://doi.org/10.6084/m9.figshare.22332352。图1至图8及扩展数据图1至图10的源数据已作为源数据文件提供。所有支持本研究结论的其他数据可在合理请求后向通讯作者获取。
