biostudies-arrayexpressKatherine WilliamsMus musculushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16524Bulk RNA-seq data for Trex1 WT and KO mice from the heart. Used for manuscript in submission at Science Advances.biostudies-arrayexpressSample Collection - Hearts were harvested from mice and collected into cold RPMI media.Nucleic Acid Extraction - Following procedures previously described (J. Lim, R. Rodriguez, K. Williams, J. Silva, A. G. Gutierrez, P. Tyler, F. Baharom, T. Sun, E. Lin, S. Martin, B. D. Kayser, R. J. Johnston, I. Mellman, L. Delamarre, N. R. West, S. Müller, Y. Qu, K. Heger, The Exonuclease TREX1 Constitutes an Innate Immune Checkpoint Limiting cGAS/STING-Mediated Antitumor Immunity. Cancer Immunol. Res. 12, OF1–OF10 (2024).), hearts were homogenized with nuclease-free hard tissue homogenizing 2.8 mm ceramic beads (OMNI International) by using a Bead Mill Homogenizer (OMNI International, 19-628) in RLT buffer. Tissue homogenates were centrifuged at 13,000 rpm for 15 minutes at 4°C. The supernatants were collected and processed for RNA isolation with RNeasy Mini Kit (Qiagen).Sequencing - Libraries were pooled and sequenced on NovaSeq 6000 (Illumina) to generate 30 million single-end 50-base pair reads for each sample.Library Construction - Total RNA was quantified with the Qubit RNA HS Assay Kit (Thermo Fisher Scientific) and quality was assessed using RNA ScreenTape on a TapeStation 4200 (Agilent Technologies). For sequencing library generation, the TruseqStranded mRNA Kit (Illumina) was used with an input of 100 to 1,000 ng of total RNA. Libraries were quantified with Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and the average library size was determined using D1000 ScreenTape on a TapeStation 4200 (Agilent Technologies).OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - To quantify gene expression levels, the number of reads mapping unambiguously to the exons of each gene was calculated. Processed data file is raw counts.Sequence Alignment - Following procedures previously described (J. Lim, R. Rodriguez, K. Williams, J. Silva, A. G. Gutierrez, P. Tyler, F. Baharom, T. Sun, E. Lin, S. Martin, B. D. Kayser, R. J. Johnston, I. Mellman, L. Delamarre, N. R. West, S. Müller, Y. Qu, K. Heger, The Exonuclease TREX1 Constitutes an Innate Immune Checkpoint Limiting cGAS/STING-Mediated Antitumor Immunity. Cancer Immunol. Res. 12, OF1–OF10 (2024).), bulk RNA-seq data were processed using the BioConductor package HTSeqGenie (version 4.4.2, (https://bioconductor.org/packages/release/bioc/html/HTSeqGenie.html) as follows: first, reads with low nucleotide qualities (70% of bases with quality <23) or matches to rRNA and adapter sequences were removed. The remaining reads were aligned to the human reference genome (GRCm38.p5) using GSNAP (25) version “2013–11–01,” allowing maximum of two mis- matches per 75 base sequence (parameters: -M 2 -n 10 -B 2 -i 1 -N 1 -w 200000 -E 1 –pairmax-rna 1⁄4 2000000). Transcript annotation was based on the Gencode genes data base (GENCODE M15).MetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000RNA-seq of coding RNAMus musculusKatherine WilliamsfalseBulk RNA-seq from Trex1 KO in heartBulk RNA-seq data for Trex1 WT and KO mice from the heart. Used for manuscript in submission at Science Advances.2026-03-25T00:00:00Z2026-03-25T02:03:18.571Z2026-01-14T15:49:33.539ZE-MTAB-16524ERP187581EFO_0002944EFO_0004170EFO_0004917EFO_0005518EFO_0003816EFO_0003738EFO_0004184