GEO series

YTHDF1 functions as a non-canonical nuclear checkpoint that couples R-loop homeostasis to innate immune restraint and adaptive immune resistance in cancer（RNA-seq II）

GSE319703 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2026/07/15 Platform GPL24676

At a glance

RNA-seq (gene expression) · human · 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: Homo sapiens (human)
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.

Summary (written by the submitters)

Innate immune signaling within cancer cells plays an important role in shaping antitumor immunity, yet the nuclear mechanisms that restrain inappropriate immune activation remain incompletely defined. YTHDF1 is an mRNA-binding protein previously characterized as a cytoplasmic m⁶A reader. Emerging evidence indicates that YTHDF1 also functions in the nucleus, where it associates with chromatin and contributes to the regulation of R-loop homeostasis.

Read the full summary ↓

Loss of YTHDF1 results in R-loop accumulation, genomic instability, cytosolic DNA release, and activation of the cGAS–STING–type I interferon pathway. Mechanistically, YTHDF1 interacts with the chromatin remodeler ARID1A at immune-associated genomic regions, suggesting a cooperative role in maintaining genome stability and regulating immune-related transcriptional programs. To investigate the transcriptomic and chromatin-level consequences of YTHDF1 and ARID1A perturbation, we generated RNA sequencing (RNA-seq) and R-loop CUT&Tag datasets in A549 human lung cancer cells. RNA-seq was performed in two experimental settings: (1) wild-type (WT) and YTHDF1 knockout (YTHDF1-KO) cells; and (2) WT, YTHDF1-KO, ARID1A knockdown (siARID1A), and combined YTHDF1-KO with ARID1A knockdown cells. In parallel, R-loop CUT&Tag profiling was conducted under the same respective conditions to assess genome-wide R-loop distribution. These datasets provide integrated transcriptomic and chromatin profiling resources for studying the roles of YTHDF1 and ARID1A in regulating R-loop dynamics and tumor-intrinsic innate immune signaling

This dataset

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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 GSE319703_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 PRJNA1424980 and SRA study SRP677765. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Samples in this study

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

Datasets on a similar topic

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GSE270047 Analytical performance of OncoPrism-HNSCC, an RNA-based assay to inform immune checkpoint inhibitor treatment decisions for recurrent/metastatic head and neck squamous cell carcinoma 434 samples shares checkpoint
GSE318645 Dual Immune Checkpoint Blockade Induces Distinct Systemic and Intratumoral Immune Activation in Recurrent Glioblastoma 226 samples shares checkpoint

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