{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Lara Buermann"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-14585"],"description":["The clinical utility of T-cell agonistic antibodies in cancer therapy, much less their ability to stimulate intratumoral T-cells in patients, has eluded us. T-cell agonistic antibodies such as anti-CD27 can induce clinically meaningful anti-tumor activity. The combination of anti-CD27 agonist varlilumab and tumor-depleting anti-CD20 rituximab was investigated in patients with relapsed/refractory B-cell non-Hodgkin lymphoma (B-NHL) (RiVa trial;NCT03307746). Our experiments detail scRNA-seq data from 6 B-cell NHL patients, including both pre and on-treatment biopsies taken from lymph nodes."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - Samples were then sequenced on an Illumina NovaSeq 6000 sequencer by the OGC with a read configuration of 91 bp paired-end.","Nucleic Acid Extraction - scRNAseq of pre- and on-treatment biopsies were performed using the 10X Genomics (Pleasanton, California) Chromium Single Cell 3’ Library & Gel Bead Kit (chemistry version 3.1) as per protocol, from thawed single-cell suspensions.","Sample Collection - Fresh cores of tumors cores collected in RPMI were minced into 1 mm3 pieces or smaller using a scalpel and added to Liberase™ DL (Roche, Basel) RPMI for 15 minutes at 37 oC on an orbital shaker at 250 rpm. The sample mixture was then passed through a 70 µm filter, washed four times, red cell lysis (Qiagen) undertaken, and washed twice more. Resultant single cell suspension was cryopreserved in 50% v/v human AB serum (Sigma, Burlington), 40% supplemented RPMI and 10% v/v DMSO (Sigma, Burlington).","Library Construction - scRNAseq of pre- and on-treatment biopsies were performed using the 10X Genomics (Pleasanton, California) Chromium Single Cell 3’ Library & Gel Bead Kit (chemistry version 3.1) as per protocol, from thawed single-cell suspensions."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Processed data are of filtered counts produced by cellranger, not from further pre-processing and filtering in standard analysis workflows."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA from single cells"],"species":["Homo sapiens"],"pubmed_authors":["Sean Lim","Lara Buermann"],"additional_accession":[]},"is_claimable":false,"name":"Anti-CD27 immunotherapy induces intratumoral immunostimulation in B-cell lymphoma: the multi centre RiVa trial (scRNA-Seq Data for RiVa)","description":"The clinical utility of T-cell agonistic antibodies in cancer therapy, much less their ability to stimulate intratumoral T-cells in patients, has eluded us. T-cell agonistic antibodies such as anti-CD27 can induce clinically meaningful anti-tumor activity. The combination of anti-CD27 agonist varlilumab and tumor-depleting anti-CD20 rituximab was investigated in patients with relapsed/refractory B-cell non-Hodgkin lymphoma (B-NHL) (RiVa trial;NCT03307746). Our experiments detail scRNA-seq data from 6 B-cell NHL patients, including both pre and on-treatment biopsies taken from lymph nodes.","dates":{"release":"2025-08-09T00:00:00Z","modification":"2025-08-10T00:01:06.453Z","creation":"2024-11-06T17:24:21.852Z"},"accession":"E-MTAB-14585","cross_references":{"ENA":["ERP165978"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005684","EFO_0005518","EFO_0003816","EFO_0004184"]}}