{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Nicole Joller"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-14959"],"description":["The experimental setup is aimed at understanding the function of the co-inhibitory receptor TIGIT in T cells. We compared sorted T cells (CD8+ T cells, CD4+Foxp3- T cells, CD4+Foxp3+ Tregs) from WT and TIGIT KO mice at steady state (naive mice) and following LCMV infection (day 10, LCMV clone 13). Cell were collected form spleen or lung."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Treatment - mice were either left naive or infected with 10`6 ffc LCMV clone 13 and organs were harvested on day 10 of infection","Sample Collection - Spleen and lung single cell suspensions were obtained from naïve and LCMV Clone 13 infected (10^6 ffu, day) 10 wild-type (C57BL6) and TIGIT KO (B6.129(Cg)-Foxp3tm4(YFP/icre)Ayr/J x Tigitfl/fl) mice. CD3+ T cells were MACS purified using the CD3 cell isolation kit (negative selection, BioLegend) and then FACS sorted using a BD FACSAria III 5L (BD Bioscience).","Library Construction - Library construction was performed following the 10x 5' (v2) Dual Index protocol: Cells were lysed for reverse transcription and complementary DNA (cDNA) amplification in the Chromium Controller (10X Genomics). The poly-adenylated mRNAs were then reverse-transcribed inside each Gel Bead. Full-length cDNA along with cell barcode identifiers were PCR-amplified and sequencing libraries were prepared . The following kits were used:  Chromium Next GEM Single Cell 5' Kit v2 Library Construction Kit Chromium 5' Feature Barcode Kit Chromium Single Cell Mouse TCR Amplification Kit Chromium Next GEM Chip K Single Cell Kit","Nucleic Acid Extraction - Sorted CD3+CD4+Foxp3+ and CD3+Foxp3- cells were mixed at a ratio of approximately 1:3 and labelled for each mouse with anti-mouse Hashtag reagents (TotalSeq™-C301, 302, 303, 304, 305 anti-mouse Hashtag 1, 2, 3, 4, 5 antibodies, respectively, BioLegend) before pooling .  Cells were loaded onto a Chromium Next GEM chip G (10X Genomics) and were lysed for reverse transcription and complementary DNA (cDNA) amplification in the Chromium Controller (10X Genomics) following the 10x 5' (v2) Dual Index protocol (https://cdn.10xgenomics.com/image/upload/v1722286086/support-documents/CG000330_Chromium_Next_GEM_Single_Cell_5_v2_Cell_Surface_Protein_UserGuide_RevG.pdf)","Sequencing - The constructed library was sequenced Illumina NovaSeq 6000"],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Gene counts were calculated using cellranger (v7.0.0) under default setting"],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA from single cells"],"species":["Mus musculus"],"pubmed_title":["seurat object of integrated data","The co-inhibitory receptor TIGIT promotes tissue protective functions in T cells"],"pubmed_authors":["Nikolaos Patikas, Martin Hemberg","Camilla Panetti, Rahel Dätwyler, Anja Moncsek, Nikolaos Patikas, Andreas Agrafiotis, Adelynn Tang, Francesco Andreata, Valeria Fumagalli, Jean De Lima, Carolyn G. King, Ajithkumar Vasanthakumar, Matteo Iannacone, Axel Kallies, Alexander Yermanos, Martin Hemberg, Nicole Joller","Nicole Joller"],"additional_accession":[]},"is_claimable":false,"name":"scRNA- and TCR-Seq of mouse T cells from WT and TIGIT KO mice at steady state and upon LCMV infection","description":"The experimental setup is aimed at understanding the function of the co-inhibitory receptor TIGIT in T cells. We compared sorted T cells (CD8+ T cells, CD4+Foxp3- T cells, CD4+Foxp3+ Tregs) from WT and TIGIT KO mice at steady state (naive mice) and following LCMV infection (day 10, LCMV clone 13). Cell were collected form spleen or lung.","dates":{"release":"2025-09-14T00:00:00Z","modification":"2025-09-14T01:02:35.552Z","creation":"2025-03-26T16:06:21.024Z"},"accession":"E-MTAB-14959","cross_references":{"ENA":["ERP170809"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005684","EFO_0005518","EFO_0003816","EFO_0004184","EFO_0003969"],"doi":["10.5281/zenodo.14041419"]}}