GEO series
A unified network systems approach uncovers a core program underlying T follicular helper cell differentiation [CUT&RUN]
GSE303343
Homo sapiens
Genome binding/occupancy profiling by high throughput sequencing
48 samples
Submitted 2026/08/02
Platform GPL21697
Summary
We investigated Tfh cell differentiation across multiple levels of biological organization by integrating diverse data types through interpretable network-based approaches. Our multi-scale network framework successfully combines transcriptomic and epigenetic datasets, capturing known regulators of Tfh differentiation identified in numerous prior studies. Through this approach, we identify a core set of Tfh-associated genes that is conserved across various tissues and disease conditions. Although individual components of this core set have been reported previously, a central contribution of our study is the unbiased discovery and in-depth characterization of this conserved gene signature.
Published in
Omelchenko AA, Rahman SA, Viswanadham VV et al.
· bioRxiv : the preprint server for biology 2025
· PMID 40894583
· doi:10.1101/2025.08.19.670906
This dataset
Download
Direct links to NCBI, no account and no request form: the whole study as GSE303343_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 48 samples. Raw sequencing reads are also available from ENA.
Also filed as BioProject PRJNA1294876 and SRA study SRP602784. Searching any of these in the dataset finder brings you back here.
Study design
40 conditions, each sampled once — no replicated groups
Read from the first 40 of 48 sample titles: 40 distinct titles with little repetition. Check it against the sample list below before relying on it.
Samples in this study
0 selected
- GSM9123845 S01_CD4_naive_H3K4me1
- GSM9123846 S02_CD4_naive_H3K4me1
- GSM9123847 S03_CD4_naive_H3K4me1
- GSM9123848 S04_CD4_naive_H3K4me1
- GSM9123849 S05_CD4_CXCR5pos_PD1neg_H3K4me1
- GSM9123850 S06_CD4_CXCR5pos_PD1neg_H3K4me1
- GSM9123851 S07_CD4_CXCR5pos_PD1neg_H3K4me1
- GSM9123852 S08_CD4_CXCR5pos_PD1neg_H3K4me1
- GSM9123853 S09_CD4_naive_H3K4me3
- GSM9123854 S10_CD4_naive_H3K4me3
- GSM9123855 S11_CD4_naive_H3K4me3
- GSM9123856 S12_CD4_naive_H3K4me3
- GSM9123857 S13_CD4_CXCR5pos_PD1neg_H3K4me3
- GSM9123858 S14_CD4_CXCR5pos_PD1neg_H3K4me3
- GSM9123859 S15_CD4_CXCR5pos_PD1neg_H3K4me3
- GSM9123860 S16_CD4_CXCR5pos_PD1neg_H3K4me3
- GSM9123861 S17_CD4_naive_H3K27Ac
- GSM9123862 S18_CD4_naive_H3K27Ac
- GSM9123863 S19_CD4_naive_H3K27Ac
- GSM9123864 S20_CD4_naive_H3K27Ac
- GSM9123865 S21_CD4_CXCR5pos_PD1neg_H3K27Ac
- GSM9123866 S22_CD4_CXCR5pos_PD1neg_H3K27Ac
- GSM9123867 S23_CD4_CXCR5pos_PD1neg_H3K27Ac
- GSM9123868 S24_CD4_CXCR5pos_PD1neg_H3K27Ac
- GSM9123869 S25_CD4_CXCR5pos_PD1int_H3K4me1
- GSM9123870 S26_CD4_CXCR5pos_PD1int_H3K4me1
- GSM9123871 S27_CD4_CXCR5pos_PD1int_H3K4me1
- GSM9123872 S28_CD4_CXCR5pos_PD1int_H3K4me1
- GSM9123873 S29_CD4_CXCR5hi_PD1hi_H3K4me1
- GSM9123874 S30_CD4_CXCR5hi_PD1hi_H3K4me1
- GSM9123875 S31_CD4_CXCR5hi_PD1hi_H3K4me1
- GSM9123876 S32_CD4_CXCR5hi_PD1hi_H3K4me1
- GSM9123877 S33_CD4_CXCR5pos_PD1int_H3K4me3
- GSM9123878 S34_CD4_CXCR5pos_PD1int_H3K4me3
- GSM9123879 S35_CD4_CXCR5pos_PD1int_H3K4me3
- GSM9123880 S36_CD4_CXCR5pos_PD1int_H3K4me3
- GSM9123881 S37_CD4_CXCR5hi_PD1hi_H3K4me3
- GSM9123882 S38_CD4_CXCR5hi_PD1hi_H3K4me3
- GSM9123883 S39_CD4_CXCR5hi_PD1hi_H3K4me3
- GSM9123884 S40_CD4_CXCR5hi_PD1hi_H3K4me3
+ 8 more — browse all 48 samples with per-sample file links →
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