{"database":"GEO","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Other":["ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE336nnn/GSE336056/"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"omics_type":["Transcriptomics"],"species":["Homo sapiens"],"gds_type":[" Other","Expression profiling by high throughput sequencing"],"full_dataset_link":["https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE336056"],"repository":["GEO"],"entry_type":["GSE"],"additional_accession":[]},"is_claimable":false,"name":"A single chromosome 3p break initiates clear cell renal cell carcinoma evolution","description":"We used single-cell RNA sequencing (10x Genomics) coupled with CITE-seq cell hashing (HTO) to profile and compare the transcriptomes of renal proximal tubule epithelial cells (RPTECs) after different CRISPR-Cas9 ribonucleoprotein (RNP) perturbations. Cells were treated with a non-targeting control sgRNA (sgNTC), an sgRNA targeting chromosome 3p (sg3p), or an sgRNA targeting chromosome Yq (sgYq), and harvested at Day 5 and Day 10. Hashtag-labeled samples were pooled into three 10x Chip G lanes, and gene-expression and HTO libraries were sequenced on an Illumina NovaSeq X Plus. Copy-number alterations were inferred (inferCNV) to identify cells with chromosome 3p loss, and differential gene expression was compared between 3p-loss and no-loss populations over time.","dates":{"publication":"2026/09/21"},"accession":"GSE336056","cross_references":{"GSM":["GSM9826218","GSM9826217","GSM9826214","GSM9826213","GSM9826216","GSM9826215"],"GPL":["34284"],"GSE":["336056"],"taxon":["Homo sapiens"],"PMID":["[42465403]"]}}