Mannose-Modified Tobacco Mosaic Virus-Mediated Macrophage Regulation Inhibits Pulmonary Fibrosis Progression
RNA-seq (gene expression) · mouse · 9 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
- 9 samples: 3 × BMDMs, M2, vs 3 × BMDMs, M0, vs 3 × BMDMs, TMV-OEG8-Man regulated M2,Groups 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 GSE309156_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 PRJNA1334241 and SRA study SRP627069. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 9 samples.
How we read this: 3 replicated groups read from 9 sample titles; they account for 9 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.
- GSM9262198 BMDMs, M2, rep 1 BMDMs, M2,
- GSM9262199 BMDMs, M2, rep 2 BMDMs, M2,
- GSM9262200 BMDMs, M2, rep 3 BMDMs, M2,
- GSM9262201 BMDMs, M0,rep 1 BMDMs, M0,
- GSM9262202 BMDMs, M0,rep 2 BMDMs, M0,
- GSM9262203 BMDMs, M0,rep 3 BMDMs, M0,
- GSM9262204 BMDMs, TMV-OEG8-Man regulated M2, rep 1 BMDMs, TMV-OEG8-Man reg…
- GSM9262205 BMDMs, TMV-OEG8-Man regulated M2, rep 2 BMDMs, TMV-OEG8-Man reg…
- GSM9262206 BMDMs, TMV-OEG8-Man regulated M2, rep 3 BMDMs, TMV-OEG8-Man reg…
- GSE280003 Gpnmb and Spp1 mark a conserved macrophage injury response masking fibrosis-specific programming in the lung 81 samples shares macrophage, fibrosis
- GSE316023 AI digital pathology as a key tool providing in-depth understanding of the progression and regression of MASH and fibrosis in male mouse models 77 samples shares progression, fibrosis
- GSE220691 Kidney Single-Cell Atlas Reveals Macrophage Heterogeneity in Progression and Regression of Cisplatin Induced AKI. 22 samples shares progression, macrophage
- GSE179812 Macrophage Heterogeneity in Progression and Regression Phases of Cisplatin Induced AKI Mice Model - A single-cell RNA sequencing study 17 samples shares progression, macrophage
- GSE220675 Kidney Single-Cell Atlas Reveals Macrophage Heterogeneity in Progression and Regression of Cisplatin Induced AKI [scRNA-seq] 11 samples shares progression, macrophage
- GSE295293 Single-cell fixed RNAseq of liver fibrosis progression and regression 9 samples shares progression, fibrosis
- GSE159911 “Bench-to-Bedside and Back” analysis of NAFLD model reveals common transcriptomic shifts between mouse and human during disease progression 152 samples shares progression
- GSE269191 ZEB2 is a Master Switch Controlling the Tumor-Associated Macrophage Program [in vivo] 145 samples shares macrophage
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.