Bulk RNA-sequencing of synovial macrophages (CGRP stimulation)
RNA-seq (gene expression) · mouse · 12 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
- 12 samples: 12 samples, each with a distinct title — no replicated groupsGroups 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 GSE247477_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 PRJNA1038753 and SRA study SRP471256. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 12 sample titles: 12 distinct titles with little repetition. 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.
- GSM7890569 IAIE_Healthy_1 [Jointmac13797714]
- GSM7890570 IAIE_Healthy_2 [Jointmac13797715]
- GSM7890571 IAIE_Healthy_3 [Jointmac13797716]
- GSM7890572 CD11c_Healthy_1 [Jointmac13797717]
- GSM7890573 CD11c_Healthy_2 [Jointmac13797718]
- GSM7890574 CD11c_Healthy_3 [Jointmac13797719]
- GSM7890575 IAIE_CGRP_1 [Jointmac13797723]
- GSM7890576 IAIE_CGRP_2 [Jointmac13797724]
- GSM7890577 IAIE_CGRP_3 [Jointmac13797725]
- GSM7890578 CD11c_CGRP_1 [Jointmac13797726]
- GSM7890579 CD11c_CGRP_2 [Jointmac13797727]
- GSM7890580 CD11c_CGRP_3 [Jointmac13797728]
- GSE283700 RNA-sequencing of SVF-derived preadipocytes from inguinal adipose tissue of male mice differentiating under control conditions or treated with CGRP 15 samples shares cgrp, rna-sequencing
- GSE331360 Bulk RNA sequencing of bone marrow-derived macrophages from WT and Ch25h-KO mice under different treatment conditions 24 samples shares macrophages, bulk
- GSE271362 CGRP-Related Neuropeptide Adrenomedullin 2 Promotes Tissue-Protective ILC2 Responses and Limits Intestinal Inflammation 11 samples shares cgrp
- GSE272755 Transcriptional effects of lysosome stress on mouse bone marrow-derived macrophages and primary microglia 263 samples shares macrophages
- GSE255004 Sensory Flicker Stimulation of 5xFAD Mice Activates Immune Pathways in a Frequency and Time Dependent Manner 176 samples shares stimulation
- 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.