{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Klas Hatje"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15144"],"description":["We used transgenic mice challenged subcutaneously with Panc02-H7-Fluc tumors to compare the efficacy of tobemstomig with nivolumab and relatlimab-like monotherapies, as well as their combination, and further investigated their mechanism of action. We used a murinized version of tobemstomig, nivolumab and relatlimab-like anti-LAG-3 to prevent the formation of anti-drug antibodies and to prolong the treatment to 3 weeks. We performed single cell RNA sequencing on the tumor samples collected at day 28. We found both qualitative and quantitative differences between vehicle, mu-tobemstomig, mu-nivolumab monotherapy and in combination with mu-relatlimab-like anti-LAG-3."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - After thawing a batch of samples, the cells were stained with a mix of FACS and oligo-labelled antibodies and sorted for CD3+T cells before performing scRNA-seq. Prior to sorting, the cells were washed with PBS, and cell number and viability were evaluated. Approximately 1 million cells per sample were resuspended in PBS and incubated with a Fc blocking reagent. The mix of FACS and oligo-labelled antibodies was added, and after incubation and washing, the cells were resuspended for sorting. The cell number and viability of the sorted cells were determined, and a total of 10,000 viable cells per sample were loaded into the 10x Genomics Chromium Connect Instrument.","Sample Collection - Mice were sacrificed, and tumor tissue was isolated. The tumor tissue was disrupted and then digested in an enzyme mix containing RPMI with 10 mg/ml DNAse and 0.25 mg/ml Liberase for 30 minutes at 37°C. The resulting tissue mix was filtered to obtain a single-cell suspension. Lymphocytes were mechanically isolated from draining lymph nodes, filtered, and resuspended to a single-cell suspension. The resulting single-cell suspensions from tumors and lymph nodes were stored in liquid nitrogen in pZerve freezing medium.","Sequencing - The resulting libraries were sequenced in an Illumina NovaSeq6000 sequencer according to 10x Genomics recommendations. The sequencing parameters were R1 = 26, i7 = 10, i5 = 10, and R2 = 90. The targeted sequencing depth was approximately 20,000 reads per cell for the GEX library and 5,000 reads per cell for both the TCR and feature barcoding libraries.","Library Construction - cDNA and library preparation was performed according to the manufacturer’s indications using the 10x Genomics Chromium Next GEM Automated Single Cell 5’ Reagent Kits v2 with TCR and feature barcoding."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Normalization was performed using count depth scaling to 10,000 total counts per cell, resulting in the cp10k (counts per 10,000) unit. Count values were then log-transformed using the natural logarithm: ln(cp10k + 1)."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA from single cells"],"species":["Mus musculus"],"pubmed_authors":["Klas Hatje"],"additional_accession":[]},"is_claimable":false,"name":"Single cell RNA-seq of Panc02-H7-Fluc model with vehicle tobemstomig, nivolumab and relatlimab-like treatment","description":"We used transgenic mice challenged subcutaneously with Panc02-H7-Fluc tumors to compare the efficacy of tobemstomig with nivolumab and relatlimab-like monotherapies, as well as their combination, and further investigated their mechanism of action. We used a murinized version of tobemstomig, nivolumab and relatlimab-like anti-LAG-3 to prevent the formation of anti-drug antibodies and to prolong the treatment to 3 weeks. We performed single cell RNA sequencing on the tumor samples collected at day 28. We found both qualitative and quantitative differences between vehicle, mu-tobemstomig, mu-nivolumab monotherapy and in combination with mu-relatlimab-like anti-LAG-3.","dates":{"release":"2025-11-27T00:00:00Z","modification":"2025-11-27T16:10:40.581Z","creation":"2025-05-19T09:52:55.98Z"},"accession":"E-MTAB-15144","cross_references":{"ENA":["ERP172709"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005684","EFO_0005518","EFO_0003816","EFO_0004184"]}}