{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Liang Zhou"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16408"],"description":["This dataset contains processed single-cell RNA sequencing (scRNA-seq) data from peripheral blood mononuclear cells (PBMCs) collected from six hepatocellular carcinoma (HCC) patients, before and after curative therapy. Samples were profiled using the 10x Genomics Chromium platform. The dataset includes gene expression matrices and associated metadata for 12 samples (6 pre-therapy, 6 post-therapy). These data support the analysis of peripheral immune cell dynamics in response to tumor removal"],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - Peripheral blood samples were collected from hepatocellular carcinoma (HCC) patients before and after curative therapy. Blood was drawn into EDTA tubes and processed within 2 hours to isolate peripheral blood mononuclear cells (PBMCs) using Ficoll-Paque density gradient centrifugation.","Sequencing - Prepared libraries were pooled and sequenced on the Illumina NovaSeq 6000 platform using paired-end sequencing. Read 1 captured 28 bp of cell barcode and UMI; Read 2 captured 90 bp of the cDNA insert. Targeted sequencing depth was ~50,000–100,000 reads per cell.","Nucleic Acid Extraction - Total RNA was not extracted separately. Single-cell suspensions of viable PBMCs were directly used for cDNA synthesis within the 10x Genomics Chromium single-cell 3′ gene expression protocol, which includes cell lysis and RNA capture inside oil droplets.","Sample Treatment - Peripheral blood samples were collected from patients both before and approximately one to three months after curative therapy (radiofrequency ablation or surgical resection). No in vitro treatment was applied to the PBMCs before sequencing.","Library Construction - Single-cell 3′ gene expression libraries were prepared using the 10x Genomics Chromium Single Cell 3′ Reagent Kits v3 according to the manufacturer’s instructions. Each library includes reverse transcription, cDNA amplification, fragmentation, end-repair, A-tailing, adapter ligation, and sample indexing.","Growth Protocol - Not applicable. PBMCs were isolated directly from peripheral blood and were not cultured prior to library preparation."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - Raw sequencing data were processed using Cell Ranger v6.1.0 (10x Genomics). Reads were aligned to the human reference genome (GRCh38, version 2020-A) using the STAR aligner integrated within the Cell Ranger pipeline. Cell barcodes and UMIs were used to generate gene expression count matrices.","Data Transformation - Gene expression matrices were normalized using Seurat v5.0.0. Each dataset was log-normalized (scale factor = 10,000), followed by identification of variable genes and scaling prior to downstream analysis."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Cell Ranger","Not applicable","10x Genomics Chromium Controller","Illumina NovaSeq 6000","Computational analysis using R (Seurat v5.0.0)"],"study_type":["RNA-seq of coding RNA from single cells"],"species":["Homo sapiens"],"pubmed_authors":["Liang Zhou"],"additional_accession":[]},"is_claimable":false,"name":"Single-cell RNA-seq of PBMCs from HCC patients pre- and post-curative therapy","description":"This dataset contains processed single-cell RNA sequencing (scRNA-seq) data from peripheral blood mononuclear cells (PBMCs) collected from six hepatocellular carcinoma (HCC) patients, before and after curative therapy. Samples were profiled using the 10x Genomics Chromium platform. The dataset includes gene expression matrices and associated metadata for 12 samples (6 pre-therapy, 6 post-therapy). These data support the analysis of peripheral immune cell dynamics in response to tumor removal","dates":{"release":"2026-01-13T00:00:00Z","modification":"2026-05-27T13:35:01.376Z","creation":"2026-01-02T14:43:58.909Z"},"accession":"E-MTAB-16408","cross_references":{"ENA":["ERP187203"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0005684","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0004184","EFO_0003969"]}}