A Glycosylation-Dependent Checkpoint Restrains Intestinal Intra-Epithelial Lymphocyte Activation

Experimental design:

1. Lm-OVA infection and OTI cell transfer system was used in this project. We transferred CD45.1 OTI cells into CD45.2 WT recipient mice, followed by oral infection with Kisteria-OVA. At day 30 post infection, memory OTI cells from spleen and small intestine epithelium (SI-IEL) were sorted and subjected to bulk RNA-seq. Differential gene expression was analyzed between these two groups. (SP1, SP2, SP3, SI_IEL_1, SI_IEL_2, SI_IEL_3 are the raw data)
2. CD8aa+ and CD8ab+ natural SI-IELs from Gcnt2 Het control and Gcnt2 KO mice were sorted out and subjected to bulk RNA-seq to compare there gene expression pattern under steady state.
3. 3. I-Ag+ and I-Ag- CD8aa+ SI-IEL cells were sorted out for ATAC-seq to detect chromatin accessibility in these two subpopulations.

Processed data:

1. Rawcount_OTImemory_cells.xlsx-----> raw counts of the sequencing data in Experimental design 1. Table_SI_IEL_vs_Spleen.tsv---> differential gene expression result of SI-IEL Trm cells vs spleen memory OT-I cells.
2. Raw_counts_IEL.tsv----> raw counts of the sequencing data in Experimental design 2. Table_KOCD8aa_vs_HetCD8aa.tsv---->differential gene expression result of Gcnt2 KO  vs  Gcnt2 Het CD8aa+ SI-IEL at steady state. Metacore_table_KOCD8ab_vs_HetCD8ab.tsv-----> differential gene expression result of Gcnt2 KO  vs  Gcnt2 Het CD8ab+ SI-IEL at steady state.
3. LQ-AgP.rep2468.avg.bw-----> averaged peaks of I-Ag+ population in Experimental design 3;  LQ-AgN.rep1357.avg.bw-----> averaged peaks of I-Ag- population in Experimental design 3.
4. ATAC.Tcells.downregulated_in_P.3col.bed-------->downregulated peaks in I-Ag+ population in Experimental design 3; ATAC.Tcells.upregulated_in_P.3col.bed------->upregulated peaks in I-Ag+ population compared to I-Ag- in Experimental design 3.