Supplemental Tables for "Comparative Analysis of Isoproterenol and Lipopolysaccharide Mediated Cytoprotective Responses in the Heart"
Description
Excel file containing Tables S1–S3, each provided in a separate tab. Tables S1 and S2 present differential gene expression analyses from bulk RNA sequencing of mouse hearts treated with isoproterenol (ISO) or lipopolysaccharide (LPS). Related RNA-seq data are available in GEO accession GSE307900. Table S3 presents differential chromatin accessibility analyses from bulk ATAC sequencing of bone marrow–derived hematopoietic stem and progenitor cells (HSPCs) from mice treated with ISO or LPS, focusing on loci associated with genes implicated in clonal hematopoiesis. Related ATAC-seq data are available in GEO accession GSE305274.
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For Tables S1 and S2: Hearts were harvested from mice treated at baseline and on days 1 and 7 following isoproterenol (300 mg/kg) or lipopolysaccharide (2.5 mg/kg) administration. Total RNA was extracted using the RNeasy Fibrous Tissue Mini Kit (Qiagen) and submitted to the Genome Technology Access Center at the McDonnell Genome Institute (Washington University in St. Louis) for library preparation and bulk RNA sequencing. Libraries were indexed, pooled, and sequenced on an Illumina NovaSeq 6000. Basecalling and demultiplexing were performed with bcl2fastq2, and reads were aligned and quantitated to the Ensembl release 101 primary assembly using the Illumina DRAGEN Bio-IT platform (v3.9.3-8). Gene counts were imported into EdgeR (PMID: 19910308) for TMM normalization to adjust for library size, excluding ribosomal and low-expression genes. Normalized counts were processed in Limma (PMID: 25605792) and transformed to moderated log2 counts-per-million using voomWithQualityWeights (PMID: 25925576). Differential expression analyses were performed relative to baseline to generate Tables S1 and S2. For Table S3: Mice were treated with 300 mg/kg isoproterenol, 2.5 mg/kg lipopolysaccharide, or saline and euthanized 7 days later. Bone marrow-derived hematopoietic stem and progenitor cells (HSPCs) were isolated from femurs and sequenced at the Genome Engineering & Stem Cell Center and Genome Technology Access Center (McDonnell Genome Institute). Data processing followed previously described methods (PMID: 40924855). After peak identification, read count quantification, and normalization, differential accessibility analysis was performed using DESeq2 (v1.46.0). Peaks with adjusted p < 0.05 and |log2 fold change| > 2 were annotated with HOMER to the nearest transcription start site (mm10 reference). Chromatin accessibility at loci of murine orthologs of clonal hematopoiesis–associated genes (Tet2, Dnmt3a, Asxl1, Jak2, Trp53, Ppm1d, Sf3b1, Srsf2, U2af1, Idh1, Idh2, Cbl, Runx1, Gnb1, Zrsr2, Bcor, Setbp, Foxo3) was examined to assess transcriptionally permissive chromatin states indicative of potential gene activation.
Institutions
- Washington University in St. Louis
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Funders
- Wilkinson Foundation
Additional Metadata for Digital Commons Data@Becker
| Keywords | isoproterenol, lipopolysaccharides, myocytes, cardiac, interferons |