Table 1.
GEO datasets
| Dataset | Experiment | Patient samples | Anatomical site | Sample preparation | Country | Year |
|---|---|---|---|---|---|---|
| GSE38713 | Microarray (Affymetrix Human Genome U133 Plus 2.0) |
15 inflamed (active UC) 8 remission (UC in remission) |
colon (n = 23) | Samples were obtained with mucosal pinch biopsies, treated with RNAlater and stored frozen. | Spain | 2012 |
| GSE95437 | CAGE-seq |
45 inflamed (25 active UC, 20 active CD) 20 remission (17 UC in remission, 3 CD in remission) |
colon (n = 65) | Samples were obtained with mucosal pinch biopsies, treated with RNAlater and stored frozen. | Denmark | 2018 |
| GSE179285 | Microarray (Agilent 4 × 44K Whole Human Genome) |
136 inflamed (46 active UC + 90 active CD) 225 uninflamed (48 uninflamed regions in UC patients +177 uninflamed regions in CD patients) |
colon (n = 236), ileum (n = 125) | Samples were obtained with mucosal biopsies, treated with RNAlater and stored frozen. | USA | 2021 |
| GSE75214 | Microarray (Affymetrix Human Gene 1.0 ST) |
125 inflamed (74 active UC + 51 active CD) 39 remission (23 UC in remission, 16 CD in remission) |
colon (n = 97), ileum (n = 67) | Samples were obtained with mucosal biopsies, immediately snap-frozen in liquid nitrogen and stored frozen. | Belgium | 2017 |
| GSE59071 | Microarray (Affymetrix Human Gene 1.0 ST) |
82 inflamed (74 active UC+8 active CD) 23 remission (23 UC in remission) |
colon (n = 105) | Samples were obtained with mucosal biopsies, immediately snap-frozen in liquid nitrogen and stored frozen | Belgium | 2015 |
| GSE83687 | RNA-seq |
74 inflamed (32 active UC + 42 active CD) 60 uninflamed (59 normal control+1 UC in remission) |
ileum (n = 42), colon (n = 86), rectum (n = 6) | Samples were obtained with surgical specimen, immediately snap-frozen in liquid nitrogen and stored frozen | USA | 2017 |