GEO series
Step-wise signal integration governs adaptive programming of lymphocytes [bulkRNA-seq and ATAC-seq]
GSE292377
Mus musculus
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
41 samples
Submitted 2026/01/22
Platform GPL24247
Summary
Lymphocyte differentiation depends on activation via antigen and cytokines during the immune response to infection. How the timing and integration of these signals program the epigenetic and functional fate of these cells is not completely understood. In this study, we find that inflammatory cytokine signals received by innate and adaptive lymphocytes have a context-dependent role for immune memory formation. Without preceding and sufficient antigen receptor signaling, inflammatory cytokines drive terminal differentiation into short-lived effector cells. In contrast, sufficient antigen-receptor signaling redirects inflammatory cytokine signals to promote memory differentiation via cooperation of STAT and AP-1 transcription factors. By this crucial epigenetic mechanism, optimally equipped lymphocytes are selected for memory formation rather than a terminal effector cell fate. Whereas T cells are hardwired to be shielded from premature inflammatory signals, NK cells rely on coincidental early antigen receptor signaling for adaptive responses. Together, step-wise integration of antigen and cytokine signaling optimizes both effector and memory differentiation, allowing for promiscuous recruitment into the acute immune response while promoting avidity maturation in memory populations of both innate and adaptive lymphocytes.
Published in
Grassmann S, Santosa EK, Kim H et al.
· Immunity 2026
· PMID 41619729
· doi:10.1016/j.immuni.2026.01.004
This dataset
Download
Direct links to NCBI, no account and no request form: the whole study as GSE292377_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 41 samples. Raw sequencing reads are also available from ENA.
Also filed as BioProject PRJNA1238266 and SRA study SRP571580. 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 41 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
- GSM8857729 RNA_TotalNK_NK11_3hr_1_12001_5
- GSM8857730 RNA_TotalNK_NK11_3hr_2_12001_6
- GSM8857731 RNA_TotalNK_NK11_3hr_3_12001_7
- GSM8857732 RNA_TotalNK_Unstim_3hr_1_12001_1
- GSM8857733 RNA_TotalNK_Unstim_3hr_2_12001_2
- GSM8857734 ATAC_TotalNK_NK11_3hr_1_12002_B_8
- GSM8857735 ATAC_TotalNK_NK11_3hr_2_12002_B_9
- GSM8857736 ATAC_TotalNK_NK11_3hr_3_12002_B_10
- GSM8857737 ATAC_TotalNK_Unstim_3hr_1_12002_B_1
- GSM8857738 ATAC_TotalNK_Unstim_3hr_2_12002_B_2
- GSM8857739 RNA_NK_Spleen_D1_Ly49D_Nur77GFP_All_2_12637_4
- GSM8857740 RNA_NK_Spleen_D1_Ly49D_Nur77GFP_All_3_12637_7
- GSM8857741 RNA_NK_Spleen_D1_Ly49D_Nur77GFP_All_4_12637_10
- GSM8857742 RNA_NK_Spleen_D1_Ly49H_Nur77GFP_GFPneg_2_12637_6
- GSM8857743 RNA_NK_Spleen_D1_Ly49H_Nur77GFP_GFPneg_3_12637_9
- GSM8857744 RNA_NK_Spleen_D1_Ly49H_Nur77GFP_GFPneg_4_12637_12
- GSM8857745 RNA_NK_Spleen_D1_Ly49H_Nur77GFP_GFPpos_2_12637_5
- GSM8857746 RNA_NK_Spleen_D1_Ly49H_Nur77GFP_GFPpos_3_12637_8
- GSM8857747 RNA_NK_Spleen_D1_Ly49H_Nur77GFP_GFPpos_4_12637_11
- GSM8857748 ATAC_NK_Spleen_D1_Ly49D_Nur77GFP_All_1_2_12669_13
- GSM8857749 ATAC_NK_Spleen_D1_Ly49D_Nur77GFP_All_2_2_12669_16
- GSM8857750 ATAC_NK_Spleen_D1_Ly49D_Nur77GFP_All_3_2_12669_19
- GSM8857751 ATAC_NK_Spleen_D1_Ly49D_Nur77GFP_All_4_2_12669_22
- GSM8857752 ATAC_NK_Spleen_D1_Ly49H_Nur77GFP_GFPneg_1_2_12669_15
- GSM8857753 ATAC_NK_Spleen_D1_Ly49H_Nur77GFP_GFPneg_3_2_12669_21
- GSM8857754 ATAC_NK_Spleen_D1_Ly49H_Nur77GFP_GFPneg_4_2_12669_24
- GSM8857755 ATAC_NK_Spleen_D1_Ly49H_Nur77GFP_GFPpos_1_2_12669_14
- GSM8857756 ATAC_NK_Spleen_D1_Ly49H_Nur77GFP_GFPpos_2_2_12669_17
- GSM8857757 ATAC_NK_Spleen_D1_Ly49H_Nur77GFP_GFPpos_3_2_12669_20
- GSM8857758 ATAC_NK_Spleen_D1_Ly49H_Nur77GFP_GFPpos_4_2_12669_23
- GSM8857759 RNA_IL12_1_13538_3
- GSM8857760 RNA_IL12_2_13538_4
- GSM8857761 RNA_NK11_1_13538_5
- GSM8857762 RNA_NK11_2_13538_6
- GSM8857763 RNA_NK11_IL12_1_13538_7
- GSM8857764 RNA_NK11_IL12_2_13538_8
- GSM8857765 RNA_untreated_1_13538_1
- GSM8857766 RNA_untreated_2_13538_2
- GSM9760780 RNA_TotalNK_Ly49H_3hr_1_12001_9
- GSM9760781 RNA_TotalNK_Ly49H_3hr_2_12001_10
+ 1 more — browse all 41 samples with per-sample file links →
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