Therapeutic silencing Spp1 in cardiac macrophages suppresses atrial fibrillation
RNA-seq (gene expression) · mouse · 14 samples
- What it is
- RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
- Organism
- Mus musculus (mouse)
- Samples
- 14 samples: 4 × Vehicle vs 4 × siSpp1Groups are read from the sample names, not from the paper. Check the list below.
- Data you can get
- A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
- Paper
- Therapeutic Spp1 silencing in TREM2(+) cardiac macrophages suppresses atrial fibrillationbioRxiv : the preprint server for biology · 2024
Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.
Processed table
The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE272503_RAW.tar (it can run to tens of gigabytes).
Raw sequencing reads
The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.
What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.
Also filed as BioProject PRJNA1136982 and SRA study SRP520613. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 8 samples.
How we read this: 2 replicated groups read from 14 sample titles; they account for 8 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.
- GSM8403664 T1_ARC_142
- GSM8403665 T3_ARC_144
- GSM8403666 T8_ARC_150
- GSM8403667 C4_Saline_145
- GSM8403668 C7_Saline_149
- GSM8403669 C9_Saline_151
- GSM9340572 Vehicle_rep1 Vehicle
- GSM9340573 Vehicle_rep2 Vehicle
- GSM9340574 Vehicle_rep3 Vehicle
- GSM9340575 Vehicle_rep4 Vehicle
- GSM9340576 siSpp1_rep1 siSpp1
- GSM9340577 siSpp1_rep2 siSpp1
- GSM9340578 siSpp1_rep3 siSpp1
- GSM9340579 siSpp1_rep4 siSpp1
- GSE288504 Direct microglia replacement reveals pathologic and therapeutic contributions of brain macrophages to a monogenic neurological disease [RNA-seq] 15 samples shares therapeutic, macrophages
- GSE280003 Gpnmb and Spp1 mark a conserved macrophage injury response masking fibrosis-specific programming in the lung 81 samples shares spp1
- GSE302019 Bulk RNA sequencing to investigate transcriptional profiles of lung macrophage subpopulations isolated from wild-type C57BL/6J and Spp1-EGFP knock-in reporter mice subjected to intratracheal administration of bleomycin or PBS. 24 samples shares spp1
- GSE272755 Transcriptional effects of lysosome stress on mouse bone marrow-derived macrophages and primary microglia 263 samples shares macrophages
- GSE319684 Timecourse of FACS sorted Ly6C+ monocytes, tissue resident alveolar macrophages (trAMs), monocyte derived alveolar macrophages (bmAMs) and epithelial cells from SARS-CoV-2 (maVie16) vs. IAV (PR8) infected mouse lungs 176 samples shares macrophages
- GSE300757 Efferocytosis induces proangiogenic function and chromatin remodeling in tumor-associated macrophages 127 samples shares macrophages
- GSE319035 P21+TREM2+-Senescent Macrophages Fuel Inflammaging and Metabolic Dysfunction-Associated Steatotic Liver Disease [NAFLD_time_course] 77 samples shares macrophages
- GSE298799 Deconstructing the Intercellular Interactome in Vascular Dementia with Focal Ischemia for Therapeutic Applications 77 samples shares therapeutic
Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.