Table 1.

Gene expression by RNA sequencing of colonic and small intestinal GFP^High stem cells and non-stem cell (GFP negative) populations. Values are expressed as RPKM (reads per kilobase per million mapped reads). Cells were sorted from two pooled mice.

Colon
Gene	Expression in stem cell population (GFP high)	Expression in non stem cell population (GFP negative)	Fold Change (GFP high/negative)
Adam9	18.665	5.991	3.116
Ascl2	0	0.132	0
Axin2	1.646	2.023	0.814
Bmi1	0	1.783	0
Bmp4	0.758	0.016	47.844
Cdx2	44.720	7.527	5.941
Dclk1	0	0.282	0
Ephb3	21.991	0.622	35.344
Foxn1	1.224	0.077	15.948
Hes1	46.953	5.296	8.866
Hopx	0.317	2.477	0.128
Hoxc8	1.230	0.024	51.831
Igf1	0.028	0.004	7.974
Lgr5	2.599	0.862	3.015
Lgr6	0	0	0
Lrig1	0.856	5.031	0.170
Lrig2	0.020	2.548	0.008
Lrig3	0.527	4.684	0.112
Notch4	0.106	0.067	1.595
Omlf4	0	0.041	0
Prom1	6.541	40.642	0.161
Rspo-1	0	0	0
Runx3	0.042	0.007	5.980
Smoc2	10.571	1.452	7.280
Snai2	0.588	0.052	11.296
Sox4	4.910	2.816	1.744
Sox9	51.631	4.288	12.040
Stat3	0.347	3.722	0.093
Tert	0.017	0.216	0.077
Tgfbr2	4.761	2.454	1.940

Small Intestine
Gene	Expression in stem cell population (GFP high)	Expression in non stem cell population (GFP negative)	Fold Change (GFP high/negative)
Adam9	1.448	2.858	0.506
Ascl2	5.776	1.064	5.426
Axin2	27.925	16.477	1.695
Bmi1	2.333	3.054	0.764
Bmp4	0.070	0	0
Cdx2	7.731	8.247	0.938
Dclk1	0.360	0.212	1.696
Ephb3	13.987	2.026	6.904
Foxn1	0.012	0.100	0.122
Hes1	42.973	8.090	5.312
Hopx	9.810	9.202	1.066
Hoxc8	0.053	0.024	2.198
Igf1	0.004	0	0
Lgr5	13.870	3.575	3.880
Lgr6	0	0	0
Lrig1	7.571	8.813	0.859
Lrig2	0.710	2.207	0.321
Lrig3	3.226	3.230	0.999
Notch4	0.108	0.103	1.051
Olfm4	647.212	678.583	0.954
Prom1	36.511	29.596	1.234
Rspo-1	0.020	0	0
Runx3	0	0.057	0
Smoc2	38.483	12.751	3.018
Snai2	0.327	0.105	3.114
Sox4	17.097	6.821	2.506
Sox9	15.853	8.702	1.822
Stat3	1.511	4.083	0.370
Tert	1.551	0.512	3.027
Tgfbr2	1.441	1.219	1.182