GEO series
Genome-scale perturb-seq in primary human CD4+ T cells reveals genes regulating T cell programs and human immune traits.
GSE314342
Homo sapiens
Expression profiling by high throughput sequencing
577 samples
Submitted 2026/02/06
Platform GPL34762Platform GPL34284
Summary
CD4+ T cells orchestrate immune responses against infection and cancer, yet a comprehensive map of their gene regulatory networks has been lacking. Perturb-seq enables systematic mapping of such networks, but large-scale application in primary human T cells has been challenging. Here, we developed a scalable, probe-based Perturb-seq platform and performed genome-scale perturbations of all expressed genes across 22 million primary CD4+ T cells from four donors under three stimulation conditions. We demonstrate the utility of this dataset in three ways. First, we identify previously unrecognized regulators of the two important immune cytokines, IL-10 and IL-21. Second, we show that ex vivo perturbation signatures can model T cell states observed in population-scale atlases, revealing regulators of helper T cell polarization and T cell aging. Third, we leverage regulatory relationships to mechanistically explain gene–trait associations in immune-related diseases, nominating genes for uncharacterized immune functions. Thus genome-scale perturb-seq in primary human T cells provides a foundational resource for decoding immune variation in humans and reprogramming T cell states for next-generation precision therapies.
This dataset
Download
Direct links to NCBI, no account and no request form: the whole study as GSE314342_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 577 samples. Raw sequencing reads are also available from ENA.
Also filed as BioProject PRJNA1359008 and SRA study SRP643211. Searching any of these in the dataset finder brings you back here.
Study design
40 × scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim
Supports a between-group comparison across 40 samples.
1 replicated groups read from the first 40 of 577 sample titles; they account for 40 of them. Check it against the sample list below before relying on it.
Samples in this study
0 selected
- GSM9393828 CD4i_R1L01_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim
- GSM9393829 CD4i_R1L02_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim
- GSM9393830 CD4i_R1L03_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim
- GSM9393831 CD4i_R1L04_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim
- GSM9393832 CD4i_R1L05_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim
- GSM9393833 CD4i_R1L06_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim
- GSM9393834 CD4i_R1L07_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim
- GSM9393835 CD4i_R1L08_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim
- GSM9393836 CD4i_R1L09_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim
- GSM9393837 CD4i_R1L10_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim
- GSM9393838 CD4i_R1L11_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim
- GSM9393839 CD4i_R1L12_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim
- GSM9393840 CD4i_R1L13_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim
- GSM9393841 CD4i_R1L14_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim
- GSM9393842 CD4i_R1L15_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim
- GSM9393843 CD4i_R1L16_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim
- GSM9393844 CD4i_R1L17_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim
- GSM9393845 CD4i_R1L18_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim
- GSM9393846 CD4i_R1L19_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim
- GSM9393847 CD4i_R1L20_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim
- GSM9393848 CD4i_R1L21_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim
- GSM9393849 CD4i_R1L22_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim
- GSM9393850 CD4i_R1L23_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim
- GSM9393851 CD4i_R2L01_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim
- GSM9393852 CD4i_R2L02_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim
- GSM9393853 CD4i_R2L03_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim
- GSM9393854 CD4i_R2L04_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim
- GSM9393855 CD4i_R2L05_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim
- GSM9393856 CD4i_R2L06_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim
- GSM9393857 CD4i_R2L07_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim
- GSM9393858 CD4i_R2L08_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim
- GSM9393859 CD4i_R2L09_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim
- GSM9393860 CD4i_R2L10_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim
- GSM9393861 CD4i_R2L11_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim
- GSM9393862 CD4i_R2L12_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim
- GSM9393863 CD4i_R2L13_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim
- GSM9393864 CD4i_R2L14_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim
- GSM9393865 CD4i_R2L15_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim
- GSM9393866 CD4i_R2L16_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim
- GSM9393867 CD4i_R2L17_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim
+ 537 more — browse all 577 samples with per-sample file links →
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