Bulk RNAseq analysis of Cx3cr1+ macrophages with and without IL4Ra deletion during bleomycin-induced lung fibrosis.
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 × saline_IL4Ra WT vs 4 × Bleomycin_IL4Ra WT vs 4 × Bleomycin_IL4Ra KOGroups 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 GSE272105_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 PRJNA1135117 and SRA study SRP519547. 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.
- GSM8393302 saline_IL4Ra WT_1 saline_IL4Ra WT
- GSM8393303 saline_IL4Ra WT_2 saline_IL4Ra WT
- GSM8393304 saline_IL4Ra WT_3 saline_IL4Ra WT
- GSM8393305 saline_IL4Ra WT_4 saline_IL4Ra WT
- GSM8393306 Bleomycin_IL4Ra WT_1 Bleomycin_IL4Ra WT
- GSM8393307 Bleomycin_IL4Ra WT_2 Bleomycin_IL4Ra WT
- GSM8393308 Bleomycin_IL4Ra WT_3 Bleomycin_IL4Ra WT
- GSM8393309 Bleomycin_IL4Ra WT_4 Bleomycin_IL4Ra WT
- GSM8393310 Bleomycin_IL4Ra KO_1 Bleomycin_IL4Ra KO
- GSM8393311 Bleomycin_IL4Ra KO_2 Bleomycin_IL4Ra KO
- GSM8393312 Bleomycin_IL4Ra KO_3 Bleomycin_IL4Ra KO
- GSM8393313 Bleomycin_IL4Ra KO_4 Bleomycin_IL4Ra KO
- GSE309348 Whole transcriptome sequencing of UPEC-infected testis and epididymis (5d) following depletion of CX3CR1+ macrophages 18 samples shares cx3cr1, macrophages
- GSE309471 Single-cell RNA sequencing of lung cells from bleomycin-induced and doxycycline-inducible TGF-β transgenic mouse models of pulmonary fibrosis 46 samples shares bleomycin-induced, fibrosis
- GSE308578 Consistent lack of efficacy of nintedanib in a spirometry-confirmed and bleomycin-induced mouse model of idiopathic pulmonary fibrosis 43 samples shares bleomycin-induced, fibrosis
- GSE331360 Bulk RNA sequencing of bone marrow-derived macrophages from WT and Ch25h-KO mice under different treatment conditions 24 samples shares macrophages, bulk
- GSE279117 HIF1α deletion promotes mitochondrial repurposing in bone marrow-derived macrophages, but not in tissue-resident alveolar macrophages 24 samples shares macrophages, deletion
- GSE289939 Gene expression profiling of mouse lung tissue in a bleomycin-induced pulmonary fibrosis model 15 samples shares bleomycin-induced, fibrosis
- GSE210004 Activin A and CCR2 regulate the function of macrophages in testicular fibrosis caused by experimental autoimmune orchitis 12 samples shares macrophages, fibrosis
- GSE263892 Single-cell analysis reveals Mycobacterium tuberculosis ESX-1-mediated accumulation of permissive macrophages in infected mouse lungs 6078 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.