Bulk RNA-sequencing of synovial macrophages (wild-type)
RNA-seq (gene expression) · mouse · 18 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
- 18 samples: 6 conditions, mostly in triplicateGroups 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
- Macrophages and nociceptor neurons form a sentinel unit around fenestrated capillaries to defend the synovium from circulating immune challengeNature immunology · 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 GSE247475_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 PRJNA1038751 and SRA study SRP471251. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 18 samples.
How we read this: 6 replicated groups read from 18 sample titles; they account for 18 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.
- GSM7890534 IAIE_Healthy_1 IAIE_Healthy
- GSM7890535 CD11c_Healthy_1 CD11c_Healthy
- GSM7890536 Lyve1_Healthy_1 Lyve1_Healthy
- GSM7890537 IAIE_Healthy_2 IAIE_Healthy
- GSM7890538 CD11c_Healthy_2 CD11c_Healthy
- GSM7890539 Lyve1_Healthy_2 Lyve1_Healthy
- GSM7890540 IAIE_Healthy_3 IAIE_Healthy
- GSM7890541 CD11c_Healthy_3 CD11c_Healthy
- GSM7890542 Lyve1_Healthy_3 Lyve1_Healthy
- GSM7890543 IAIE_IC_1 IAIE_IC
- GSM7890544 CD11c_IC_1 CD11c_IC
- GSM7890545 Lyve1_IC_1 Lyve1_IC
- GSM7890546 IAIE_IC_2 IAIE_IC
- GSM7890547 CD11c_IC_2 CD11c_IC
- GSM7890548 Lyve1_IC_2 Lyve1_IC
- GSM7890549 IAIE_IC_3 IAIE_IC
- GSM7890550 CD11c_IC_3 CD11c_IC
- GSM7890551 Lyve1_IC_3 Lyve1_IC
- GSE272970 Bulk liver RNA-sequencing of mice co-exposed to simvastatin and 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) 60 samples shares rna-sequencing, bulk
- GSE331360 Bulk RNA sequencing of bone marrow-derived macrophages from WT and Ch25h-KO mice under different treatment conditions 24 samples shares macrophages, bulk
- 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 wild-type, bulk
- GSE262879 Single-cell RNA-sequencing of murine pancreatic tumors derived from the orthotopic transplantation of Smad4 wild-type (WT) or Smad4 knockout (KO) pancreatic ductal adenocarcinoma (PDAC) KPC organoids in nu/nu mice. 18 samples shares rna-sequencing, wild-type
- 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
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.