RNA sequencing for endoscopic biopsy tissue samples from controls and Crohn's disease patients, and organoids derived from these specimens.

RNA sequencing for endoscopic biopsy tissue samples from controls (jejunum [S170], n=1; ileum [SN2], n=1) and patients with Crohn's disease (jejunum [non-inflamed area, A2/L2+L4/B2, infliximab maintenance therapy, S93], n=1; ileum, [non-inflamed area, A2/L2/B2, infliximab maintenance therapy, S95], n=1). Organoid culture was performed using intestinal crypts derived from these specimens, as described previously (Sato et al. Nature 2009; 459: 262–265]. Organoids were sub-cultured at least 6 passages. RNA sequencing was conducted for organoids on day 3, day 6, and day 9 [S170 and S93], and organoids treated with TNFɑ 30 ng/ml on day 3, day 6, and day 9 [S170 and S93]. RNA sequencing was conducted for organoids on day 6 and day 9 [N2 and S95], and organoids treated with TNFɑ 30 ng/ml on day 6 and day 9. RNA sequencing for tissue samples: Examination of 4 RNA samples of endoscopic biopsy tissue specimens obtained from control (n=2 [S170, SN2]) and patients with Crohn’s disease (n=2 [S93, S95]). RNA sequencing for organoid samples: Examination of 10 RNA samples of control organoids (5 pair of RNA samples of 2 control organoids treated with and without TNFɑ 30 ng/ml) - control organoids on day 3 [S170_0_D3], day 6 [S170_0_D6, SN2_0_D6], and day 9 [S170_0_D9, SN2_0_D9]), and control organoids treated with TNFɑ 30 ng/ml on day 3 [S170_30_D3], day 6 [S170_30_D6, SN2_30_D6], and day 9 [S170_30_D9, SN2_30_D9]). Examination of 10 RNA samples of organoids derived from Crohn’s disease patients (5 pair of RNA samples of 2 organoids derived from Crohn’s disease patients treated with and without TNFɑ 30 ng/ml) - organoids derived Crohn’s disease patients on day 3 [S93_0_D3], day 6 [S93_0_D6, S95_0_D6], and day 9 [S93_0_D9, S95_0_D9]), and organoids derived Crohn’s disease patients treated with TNFɑ 30 ng/ml on day 3 [S93_30_D3], day 6 [S93_30_D6, S95_30_D6], and day 9 [S93_30_D9, S95_30_D9]). Note from submitter: Our data were derived from material obtained from patients at Samsung Medical Center Therefore, based on the hospital policy and Korean raw, it is difficult to upload raw data because they contained the patient information.