Short read direct RNA-sequencing of mammalian bone marrow derived macrophages for chimeric RNA discovery
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: 4 × Control vs 4 × Inflammatory vs 4 × Tissue_ReparativeGroups 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.
Read the full summary ↓
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 GSE324139_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 PRJNA1433503 and SRA study SRP681777. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 3 replicated groups read from 12 sample titles; they account for 12 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.
- GSM9569458 Control_R1 Control
- GSM9569459 Control_R2 Control
- GSM9569460 Control_R3 Control
- GSM9569461 Control_R4 Control
- GSM9569462 Inflammatory_R1 Inflammatory
- GSM9569463 Inflammatory_R2 Inflammatory
- GSM9569464 Inflammatory_R3 Inflammatory
- GSM9569465 Inflammatory_R4 Inflammatory
- GSM9569466 Tissue_Reparative_R1 Tissue_Reparative
- GSM9569467 Tissue_Reparative_R2 Tissue_Reparative
- GSM9569468 Tissue_Reparative_R3 Tissue_Reparative
- GSM9569469 Tissue_Reparative_R4 Tissue_Reparative
- GSE201128 The response to lipopolysaccharide (LPS) of bone marrow derived macrophages treated with oxysterol binding protein (OSBP) inhibitors 30 samples shares macrophages, derived, marrow
- GSE331360 Bulk RNA sequencing of bone marrow-derived macrophages from WT and Ch25h-KO mice under different treatment conditions 24 samples shares macrophages, derived, marrow
- GSE279117 HIF1α deletion promotes mitochondrial repurposing in bone marrow-derived macrophages, but not in tissue-resident alveolar macrophages 24 samples shares macrophages, derived, marrow
- 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, derived
- GSE250551 Targeting inflammation with chimeric antigen receptor macrophages using a signal switch 32 samples shares macrophages, chimeric
- GSE237783 Complex interaction of tumor-derived factors instructs the niche specific phenotypes of tumor-associated macrophages [RNA-Seq] 28 samples shares macrophages, derived
- 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, derived
- GSE261139 Tumour-derived Extracellular Vesicle and Particle Reprogramming of Interstitial Macrophages in the Lung Pre-Metastatic Niche Enhances Vascular Permeability and Metastatic Potential 16 samples shares macrophages, derived
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.