GEO series

Resf1 is a compound G4 quadruplex-associated tumor suppressor for triple negative breast cancer I

GSE255388 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2024/03/27 Platform GPL21103

At a glance

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
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: Resf1 is a compound G4 quadruplex-associated tumor suppressor for triple negative breast cancerPLoS genetics · 2024

Summary (written by the submitters)

Patients with ER-negative breast cancer have the worst prognosis of all breast cancer subtypes, often experiencing rapid recurrence or progression to metastatic disease shortly after diagnosis. Given that metastasis is the primary cause of mortality in most solid tumors, understanding metastatic biology is crucial for effective intervention.

Read the full summary ↓

Using a mouse systems genetics approach, we previously identified 12 genes associated with metastatic susceptibility. Here, we extend those studies to identify Resf1, a poorly characterized gene, as a novel metastasis susceptibility gene in ER- breast cancer. Resf1 is a large, unstructured protein with an evolutionarily conserved intron-exon structure, but with poor amino acid conservation. CRISPR or gene trap mouse models crossed to the PyMT GEMM demonstrated that reduction of Resf1 resulted in a significant increase in tumor growth, a shortened overall survival time, and increased incidence and number of lung metastases, consistent with patient data. Furthermore, an analysis of matched tail and primary tissues revealed loss of the wildtype copy in tumor tissue, consistent with Resf1 being a tumor suppressor. Mechanistic analysis revealed a potential role of Resf1 in transcriptional control through association with compound G4 quadruplexes in expressed sequences, particularly those associated with ribosomal biogenesis. These results suggest that loss of Resf1 enhances tumor progression in ER- breast cancer through multiple alterations in both transcriptional and translational control.

Published in

Resf1 is a compound G4 quadruplex-associated tumor suppressor for triple negative breast cancer

Majocha MR, Jackson DE, Ha NH et al. · PLoS genetics 2024 · PMID 38722825 · doi:10.1371/journal.pgen.1011236

This dataset

Open GSE255388 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 GSE255388_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 PRJNA1074794 and SRA study SRP489027. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38722825) ↗

Samples in this study

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+ 12 more — browse all 12 samples with per-sample file links →

Datasets on a similar topic

GSE255391 Resf1 is a compound G4 quadruplex-associated tumor suppressor for triple negative breast cancer IV 16 samples shares resf1, quadruplex-associated, suppressor, compound, negative, triple, breast
GSE255389 Resf1 is a compound G4 quadruplex-associated tumor suppressor for triple negative breast cancer II 9 samples shares resf1, quadruplex-associated, suppressor, compound, negative, triple, breast
GSE255390 Resf1 is a compound G4 quadruplex-associated tumor suppressor for triple negative breast cancer III 8 samples shares resf1, quadruplex-associated, suppressor, compound, negative, triple, breast
GSE296217 The promyelocytic leukemia PML protein is a key immune suppressor in triple-negative breast cancer 2 samples shares suppressor, negative, triple, breast
GSE223029 Increase of blood CSF3R+ myeloid-derived suppressor cell predicts breast cancer recurrence 24 samples shares suppressor, breast
GSE267037 MEF2D functions as a tumor suppressor in breast cancer 5 samples shares suppressor, breast
GSE260878 EHF is an essential regulator of mammary alveolar lineage differentiation and putative suppressor of breast tumorigenesis 8 samples shares suppressor, breast
GSE308515 Resf1 is required for normal placental development and configuration of trophoblast cell-specific heterochromatin [RNA-seq] 17 samples shares resf1

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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.