biostudies-arrayexpressSyed Murtuza BakerMus musculushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16521The dura mater hosts a rich population of B cell progenitors, yet its capacity to sustain B cell development during systemic lymphopenia remains unclear. Using Trypanosoma brucei infection, which induces peripheral B cell depletion, we demonstrate that the murine dura mater maintains intact B cell lymphopoiesis independently of bone marrow and spleen. We performed a comparative single cell transcriptomic profiling of the calvaria bone marrow, femur bone marrow, and dura mater from naive and Trypanosoma brucei-infected female mice. The sequencing rendered high quality data from the calvaria bone marrow and the dura mater, but the femur bone marrow failed to generated reliable data and was thus excluded from downstream analyses. This data is single-cell RNA sequencing using Parse Biosciences Evercode Whole Transcriptome combinatorial barcodingbiostudies-arrayexpressLibrary Construction - Libraries were prepared using a split-pool combinatorial barcoding strategy using the Evercode whole transcriptome v2 (Parse Bioscience). The final libraries (~300-500 bp in length) were eluted from SPRI beads using molecular grade water and analysed on a TapeStation.Sequencing - The libraries were sequenced on a Novaseq X plus Illumina platform using a 450 million read, 150bp paired-end sequencing strategy at a depth of around 30,000 reads per cell.Nucleic Acid Extraction - Once single cell suspensions were obtained from the whole dura mater, calvaria bone marrow, and femur bone marrow, cells were counted using a hemocytometer, fixed using the EvercodeTM Cell Fixation kit v2 (Parse Bioscience). Cells were pelleted for 10 minutes at 600g and 4oC in 15 ml Falcon tubes pre-coated with 1% BSA to minimise cell adherence and losses. Cell pellets were resuspended in 750 μl of Cell Prefixation buffer, followed by passage through a 40 μm cell strainer to remove cell clumps and addition of 250 μl of Fixation solution. The cells were then incubated for 10 minutes on ice, resuspended in 150 μl of Cell buffer and diluted at a final density of ~500 cells/μl (dura mater) or 10,000 cells/μl (calvaria and femur bone marrow).Sample Collection - Whole dura mater was enzymatically digested with Collagenase VIII (1 mg/ml) and DNAse I (1 mg/ml; Sigma) in 1X PBS (HSBB) (Invitrogen) for ~30 minutes at 37 °C and with agitation at 200 r.p.m. Femur samples were cleared from muscle and skin prior to bone marrow isolation. Calvaria were cut into ~1mm pieces. These tissues were then placed on a 0.5 mL Eppendorf tube with a narrow opening at the bottom. This tube was then placed inside a 1.5mL Eppendorf and centrifuge at 800g for 10 minutes to harvest either femur or skull bone marrow. Red blood cells were further lysed from these single cell preparations using ACK lysis buffer (Thermo Fisher, cat. No. A1049201) for 10 minutes on ice, which was then diluted ten times with 1X PBS and cells peletted by centrifugation at 800g for 10 minutes at 4oCOrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - We used split-pipe (Parse Bioscience Evercode) software tool for pre-processingMetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000RNA-seq of coding RNA from single cellsMus musculusSyed Murtuza BakerJuan QuintanafalseThe dura mater acts as an autonomous B cell niche supporting immune responses during chronic Trypanosoma brucei infectionThe dura mater hosts a rich population of B cell progenitors, yet its capacity to sustain B cell development during systemic lymphopenia remains unclear. Using Trypanosoma brucei infection, which induces peripheral B cell depletion, we demonstrate that the murine dura mater maintains intact B cell lymphopoiesis independently of bone marrow and spleen. We performed a comparative single cell transcriptomic profiling of the calvaria bone marrow, femur bone marrow, and dura mater from naive and Trypanosoma brucei-infected female mice. The sequencing rendered high quality data from the calvaria bone marrow and the dura mater, but the femur bone marrow failed to generated reliable data and was thus excluded from downstream analyses. This data is single-cell RNA sequencing using Parse Biosciences Evercode Whole Transcriptome combinatorial barcoding2026-02-04T00:00:00Z2026-05-27T13:58:43.589Z2026-01-13T23:01:53.395ZE-MTAB-16521ERP187556EFO_0002944EFO_0004170EFO_0005684EFO_0005518EFO_0003816EFO_0004184