{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Changqing Wang"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-17245"],"description":["This dataset provides single-nucleus RNA-sequencing (snRNA-seq) profiles of wild-type mouse spleen, generated as a matched, transcriptome-wide reference for the SpatialBench resource benchmarking high-resolution spatial transcriptomics platforms (Visium HD, Xenium and MERSCOPE). Spleens were collected from C57BL/6J mice infected intravenously with Plasmodium berghei ANKA to induce splenic germinal-center formation, then drug-cured with chloroquine and pyrimethamine, and processed into formalin-fixed paraffin-embedded (FFPE) blocks. Nuclei were isolated from FFPE scrolls by pestle dissociation (10x Genomics CG000632) and profiled with the probe-based 10x Genomics Chromium Fixed RNA Profiling (Flex) singleplexed assay (CG000691), targeting ~10,000 nuclei per sample. These nuclear profiles were used for cell-type annotation and gene-level concordance benchmarking against the matched spatial datasets."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - Five 25 µm scrolls were taken from each FFPE spleen block and dissociated into single nuclei following the 10x Genomics pestle dissociation demonstrated protocol (CG000632, Rev A). Following trituration, 1.5 million nuclei per sample were taken immediately into probe hybridization.","Library Construction - Single-nucleus libraries were prepared using the probe-based 10x Genomics Chromium Fixed RNA Profiling (Flex) assay. Nuclei were subjected to overnight probe hybridization and processed according to the NextGEM Chromium Fixed RNA Profiling Singleplexed Samples User Guide (CG000691, Rev A), targeting capture of 10,000 nuclei per sample.","Sample Collection - Spleens were collected from 8-week-old wild-type female C57BL/6J mice infected intravenously with 1×10^5 Plasmodium berghei ANKA-infected red blood cells to induce splenic germinal-center formation. After onset of clinical symptoms, infection was cleared by treatment with chloroquine and pyrimethamine. Mice were euthanised 12 days post-infection and spleens were fixed in 10% neutral buffered formalin and processed into formalin-fixed paraffin-embedded (FFPE) blocks by standard histological procedures. All animal procedures were approved by the WEHI Animal Ethics Committee.","Sequencing - Libraries were sequenced on an Illumina NextSeq 2000 following 10x Genomics sequencing guidelines."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Sequencing reads were processed with 10x Genomics Cell Ranger to demultiplex, align probe reads to the mouse reference transcriptome, and quantify per-probe/per-gene counts, producing the filtered feature-barcode matrices (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz) provided as processed data."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["NextSeq 2000"],"pubmed_abstract":["Spatial transcriptomics (ST) has rapidly expanded with the introduction of multiple high-resolution platforms, yet cross-platform benchmarking remains limited and largely focused on technical performance. Here we present  SpatialBench , a matched multi-platform resource comprising Visium HD, Xenium and MERSCOPE data together with single-cell and single-nucleus references from a malaria-challenged wild-type and B cell-specific  Tbx21 knockout mouse spleen model. In this system, loss of T-bet in B cells disrupts germinal center (GC) polarization and antibody maturation, providing a biologically grounded benchmark for technology comparison. We leveraged this system to systematically evaluate ST platform performance using technical and biological readouts. Across platforms, immune organization and  Tbx21 -associated programs were consistently recovered, indicating robustness of major biological signals. Platforms instead differed in the level of biological resolution accessible. Visium HD enabled transcriptome-scale GC characterization and, together with Xenium, resolved dark and light zone organization, whereas GC zonation was not resolved in MERSCOPE, consistent with differences in transcript detection sensitivity.  SpatialBench provides a biologically defined reference dataset for evaluation of ST technologies, method development, computational benchmarking, and studies of GC spatial organization in lymphoid tissue."],"study_type":["RNA-seq of coding RNA from single cells"],"species":["Mus musculus"],"pubmed_title":["SpatialBench: Comparative cross-platform benchmarking of high-resolution spatial transcriptomics using matched mouse lymphoid tissue"],"pubmed_authors":["Changqing Wang","Solano, Ashleigh and Yip, Raymond K. H. and Wang, Changqing and Amann-Zalcenstein, Daniela and Rajasekhar, Pradeep and Zaman, Ishrat and Motyer, Allan and Cmero, Marek and Xu, Yang and Pan, Yining and Anttila, Casey J. A. and Studniberg, Stephanie I. and Hickey, Peter F. and Wang, Layla and Sargeant, Callum J. and Ling, Ling and Chen, Yunshun and Mishi, Ruvimbo D. and Ioannidis, Lisa J. and Good-Jacobson, Kim L. and King, Hamish W. and Rogers, Kelly L. and Hansen, Diana S. and Bowden, Rory and Ritchie, Matthew E.","Matthew Ritchie"],"additional_accession":[]},"is_claimable":false,"name":"Single-nucleus RNA-seq (10x Genomics Flex) of wild-type C57BL/6J mouse spleen following Plasmodium berghei ANKA infection, generated as a transcriptome-wide reference for the SpatialBench spatial transcriptomics benchmark","description":"This dataset provides single-nucleus RNA-sequencing (snRNA-seq) profiles of wild-type mouse spleen, generated as a matched, transcriptome-wide reference for the SpatialBench resource benchmarking high-resolution spatial transcriptomics platforms (Visium HD, Xenium and MERSCOPE). Spleens were collected from C57BL/6J mice infected intravenously with Plasmodium berghei ANKA to induce splenic germinal-center formation, then drug-cured with chloroquine and pyrimethamine, and processed into formalin-fixed paraffin-embedded (FFPE) blocks. Nuclei were isolated from FFPE scrolls by pestle dissociation (10x Genomics CG000632) and profiled with the probe-based 10x Genomics Chromium Fixed RNA Profiling (Flex) singleplexed assay (CG000691), targeting ~10,000 nuclei per sample. These nuclear profiles were used for cell-type annotation and gene-level concordance benchmarking against the matched spatial datasets.","dates":{"release":"2026-07-07T00:00:00Z","modification":"2026-07-07T04:33:54.107Z","creation":"2026-06-29T13:09:04.463Z"},"accession":"E-MTAB-17245","cross_references":{"ENA":["ERP195880"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005684","EFO_0005518","EFO_0003816","EFO_0004184"],"doi":["10.64898/2026.04.29.721531"]}}