{"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-14594"],"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 RNA-seq data from 21 B-cell NHL patients, including both pre and on-treatment biopsies taken from lymph nodes."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - Sample library preparation was performed and quality checked by the Oxford Genomics Centre (OGC).","Sequencing - Adapter-ligated libraries were sequenced by OGC with a 150 bp paired-end read configuration, using the Illumina NovaSeq 6000. All sample sequencing was paired-end.","Nucleic Acid Extraction - Total RNA was isolated and processed using the Maxwell® RSC simplyRNA Cells and simplyRNA Tissue kits (Promega, Madison) following manufacturer’s instructions, and quantified and measured with Bioanalyser (Agilent Biosystems, Santa Clara).","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)."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Raw reads were converted to transcript-level counts and TPM (transcripts per million) using Kallisto v0.46 together with Gencode v31 human transcript reference. Counts and TPM were summarized at the gene level using tximport v1.14."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"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 multicenter RiVa trial (RNA-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 RNA-seq data from 21 B-cell NHL patients, including both pre and on-treatment biopsies taken from lymph nodes.","dates":{"release":"2025-08-09T00:00:00Z","modification":"2025-08-10T00:00:48.642Z","creation":"2024-11-06T17:27:36.427Z"},"accession":"E-MTAB-14594","cross_references":{"ENA":["ERP165983"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}