Table 1. Bulk RNA-seq on CD4 T cells from the FRTs of RORɣt mutant mice show few differences from wild-type mice.

Gene Name	Log2 Fold Change	Average Expression	Adjusted p value	Gene Description
Il1r1	-3.08	5.26	0.0071	interleukin 1 receptor, type I [Source:MGI Symbol;Acc:MGI:96545]
Il17re	-2.53	5.43	0.0148	interleukin 17 receptor E [Source:MGI Symbol;Acc:MGI:1889371]
Ramp1	-3.13	4.56	0.0148	receptor (calcitonin) activity modifying protein 1 [Source:MGI Symbol;Acc:MGI:1858418]
Il22	-5.48	2.58	0.0876	interleukin 22 [Source:MGI Symbol;Acc:MGI:1355307]
Ighg2c	2.73	2.29	0.1707	immunoglobulin heavy constant gamma 2C [Source:MGI Symbol;Acc:MGI:2686979]
Myl12b	-0.97	6.71	0.2665	myosin, light chain 12B, regulatory [Source:MGI Symbol;Acc:MGI:107494]
Nrgn	-3.04	4.03	0.3077	neurogranin [Source:MGI Symbol;Acc:MGI:1927184]
Tmem176a	-2.13	5.33	0.3077	transmembrane protein 176A [Source:MGI Symbol;Acc:MGI:1913308]
Ccl5	0.85	7.45	0.3077	chemokine (C-C motif) ligand 5 [Source:MGI Symbol;Acc:MGI:98262]
Ccdc66	1.87	4.15	0.308	coiled-coil domain containing 66 [Source:MGI Symbol;Acc:MGI:2443639]

At 17 days post infection, CD4+ T cells were FACS sorted from infected FRTs of RORɣt mutant and wild-type mice and underwent RNA sequencing. This table lists differential gene expression analysis of RORɣt mutants compared to wild-type, including the top 10 genes as ordered by adjusted p-value. Bold values are p<0.05. Average expression is across all samples in log2 counts per million reads and the adjusted p-value uses the Benjamini-Hochberg false discovery rate.