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Iron oxide nanoparticles inhibit tumor progression and suppress lung metastases in mouse models of breast cancer

GSE261780 Mus musculus (mouse) RNA-seq (gene expression) 72 samples Submitted 2024/03/22 Platform GPL25652Platform GPL17021
At a glance

RNA-seq (gene expression) · mouse · 72 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
72 samples: 24 conditions, mostly in triplicateGroups 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
Iron Oxide Nanoparticles Inhibit Tumor Progression and Suppress Lung Metastases in Mouse Models of Breast CancerACS nano · 2024
SuperSeries — this record groups several sub-series.
Summary (written by the submitters)
This SuperSeries is composed of the SubSeries listed below.
Published in
Iron Oxide Nanoparticles Inhibit Tumor Progression and Suppress Lung Metastases in Mouse Models of Breast Cancer
Korangath P, Jin L, Yang CT et al. · ACS nano 2024 · PMID 38564478 · doi:10.1021/acsnano.3c12064
This dataset
Open GSE261780 in finder → Find more mouse RNA-seq datasets →
Download · which file do I need?

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.

1 · Just have a look

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.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE261780_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

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.

Raw reads on ENA ↗

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 PRJNA1088850 and SRA study SRP495947. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38564478) ↗
Study design
24 conditions, mostly in triplicate
Bone Marrow from BP Treated Mouse ×3 Lymph Nodes from BP Treated Mouse ×3 Lung from BP Treated Mouse ×3 Nanoparticle Associated Cells in Bone Marrow … ×3 Nanoparticle Associated Cells in Liver from B… ×3 Nanoparticle Associated Cells in Spleen from … ×3 Nanoparticle Associated Cells in Tumor from B… ×3 Spleen from BP Treated Mouse ×3 +19 more

Supports a between-group comparison across 69 samples.

How we read this: 24 replicated groups read from 72 sample titles; they account for 69 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.

Samples in this study

+ 32 more — browse all 72 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

Share this dataset

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.