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C6a3480a-34b1-4b1d-bfff-0c323a97217d - samples

ABSTRACT: TPM matrices of counts from RNA sequencing (RNAseq) from longitudinal CD138+ enriched BM fractions.

PROVIDER: EGAD00001011144 | EGA |

REPOSITORIES: EGA

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Integrated spatial transcriptomics (Stereo-seq) and bulk RNA-seq of cardiac sonogenetics in rodent heart tissue across time points [Stereo-seq]

Project description:This GEO Series contains two complementary transcriptomic datasets generated to study cardiac sonogenetics in rodent heart tissue. First, spatial transcriptomics was performed using Stereo-seq (SAW v8.1.3) to generate spatially resolved gene-expression maps from heart sections, providing GEF outputs, tissue images, and associated QC files. Second, bulk RNA-seq was performed on matched heart tissue samples from wild-type (WT) and sonogenetic (MscL-G22S) groups across multiple time points to quantify gene-level expression changes at the whole-tissue level. Raw sequencing files (FASTQ) and processed expression matrices (counts/TPM tables) are provided for both assays. Together, these datasets enable cross-validation of spatially localized transcriptional patterns with bulk gene-expression measurements.

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Integrated spatial transcriptomics (Stereo-seq) and bulk RNA-seq of cardiac sonogenetics in rodent heart tissue across time points [RNA-Seq]

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Interferon activation in bone marrow long-lived plasma cells in systemic lupus erythematosus

Project description:While durable antibody responses from long-lived plasma cell (LLPC) populations are important for protection against pathogens, LLPC may be harmful if they produce antibodies against self-proteins or self-nuclear antigens as occurs in autoimmune diseases such as systemic lupus erythematosus (SLE). Thus, the elimination of autoreactive LLPC may improve the treatment of antibody-driven autoimmune diseases. However, LLPC remain a challenging therapeutic target. Here, we compare the matched bone marrow and blood plasma cell compartments of SLE and healthy donors (HD). We show a similar distribution of CD138- and CD138+ plasma cells (PC), including putative LLPC (CD19- CD138+ CD38+), between SLE and HD bone marrow (BM). For both SLE and HD, CD138+ PC are at a higher frequency in BM than peripheral blood (PBL). Expression of Ki-67 associates with the PBL compartment where it is found on all PC subsets regardless of CD19 or CD138 expression. Transcriptomic analysis identifies an interferon gene signature in transitional B cells in the SLE BM, but surprisingly also in the BM PC derived from SLE. PC phosphorylate STAT1 in response to type I IFN stimulation in vitro. Circulating PC bind type I IFN receptor-blocking antibody anifrolumab, though to a lesser degree than circulating B cells. Anti-nuclear autoantibodies are found in the BM supernatant and PBL serum of SLE patients. SLE BM-derived PC have increased survival compared to their PBL counterparts when treated with selinexor. In summary, these findings show evidence of IFN activation in BM PC from SLE.

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