Tumour-derived Extracellular Vesicle and Particle Reprogramming of Interstitial Macrophages in the Lung Pre-Metastatic Niche Enhances Vascular Permeability and Metastatic Potential
RNA-seq (gene expression) · mouse · 16 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
- 16 samples: 7 conditions, mostly in duplicateGroups 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
- Tumour-derived Extracellular Vesicle and Particle Reprogramming of Interstitial Macrophages in the Lung Pre-Metastatic Niche Enhances Vascular Permeability and Metastatic PotentialResearch square · 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 GSE261139_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 PRJNA1085343 and SRA study SRP494016. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 15 samples.
How we read this: 7 replicated groups read from 16 sample titles; they account for 15 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.
- GSM8135716 IMs ,B16F10 CON KO EVP, rep1 IMs ,B16F10 CON KO EVP,
- GSM8135717 IMs ,B16F10 CON KO EVP, rep2 IMs ,B16F10 CON KO EVP,
- GSM8135718 IMs ,B16F10 ITGA5 KO EVP, rep1 IMs ,B16F10 ITGA5 KO EV…
- GSM8135719 IMs ,B16F10 ITGA5 KO EVP, rep2 IMs ,B16F10 ITGA5 KO EV…
- GSM8135720 IMs ,K7M2 CON KO EVP, rep1 IMs ,K7M2 CON KO EVP,
- GSM8135721 IMs ,K7M2 CON KO EVP, rep2 IMs ,K7M2 CON KO EVP,
- GSM8135722 IMs ,K7M2 ITGA5 KO EVP, rep1 IMs ,K7M2 ITGA5 KO EVP,
- GSM8135723 IMs ,K7M2 ITGA5 KO EVP, rep2 IMs ,K7M2 ITGA5 KO EVP,
- GSM8135724 IMs .control, rep1 IMs .control,
- GSM8135725 IMs .control, rep2 IMs .control,
- GSM8135726 IMs ,B16F10 EVP, in vivo, rep1 IMs ,B16F10 EVP, in viv…
- GSM8135727 IMs ,B16F10 EVP, in vivo, rep2 IMs ,B16F10 EVP, in viv…
- GSM8135728 IMs .B16F10 EVP, in vivo, rep3
- GSM8135729 IMs .control, in vivo, rep1 IMs .control, in vivo,
- GSM8135730 IMs .control, in vivo, rep2 IMs .control, in vivo,
- GSM8135731 IMs .control, in vivo, rep3 IMs .control, in vivo,
- GSE282695 STAT3 regulates pathogen control and clearance in macrophages by reprogramming inflammation-induced microbial defense response 18 samples shares reprogramming, macrophages
- GSE301501 Extracellular matrix reprogramming by the YAP/TAZ/TGF-ß2 axis drives immune exclusion in cholangiocarcinoma models 45 samples shares extracellular, reprogramming
- GSE268822 Transcriptional landscapes underlying Notch-induced lineage conversion and reprogramming of mammary cells 840 samples shares reprogramming
- GSE295428 Spaceflight induces systemic effects on extracellular matrix and immune system in different age-stages 229 samples shares extracellular
- GSE330865 Multiorgan transcriptomics and circulating extracellular vesicle profiling reveal age-dependent systemic vulnerability to isoflurane anesthesia and surgery 120 samples shares extracellular
- GSE302857 Multi-tier signaling and epigenomic reprogramming drive microglial inflammatory states and functions associated with demyelination [RNA-seq] 81 samples shares reprogramming
- GSE242731 Class switch recombination regulation by extracellular vesicles mediated intercellular epigenomic signaling 48 samples shares extracellular
- GSE283571 Circadian reprogramming of protein homeostasis and glycolipid metabolism in diabetic nephropathy 47 samples shares reprogramming
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.