| We established patient-derived colon organoids from colon biopsies of one histologically healthy donor (P12) and three patients with inflammatory bowel disease (P89, P90 and P99), and sequenced several independent culture wells of each donor's organoid line. The organoids received no treatment in vitro, and each well was harvested once, so there is no time variable. | |
| The donor's disease status is in the `group` column: normal means organoids from the healthy donor, and IBD means organoids from an IBD patient; the `disease` column repeats the same labels. Each sample is one culture well, and the donor of each well is in the `donor` column: 7 wells come from P12, 4 from P89, 3 from P90 and 6 from P99, 20 in all. The wells of one donor all come from that donor's organoid line, so they share their biological origin, and each donor belongs to only one group: all normal wells come from P12, and all IBD wells come from the three patients. For P12 and P99 the wells include early-passage and late-passage cultures, as the GEO titles in `original_sample_id` and `title_short` show; the titles of the P99 wells say Patient 90 instead of Patient 99, but P99 and P90 are two different patients. | |
| Each well is a separately grown culture and was sequenced once, so there are no technical replicates. We have no record of processing or sequencing batches and no other variable we consider relevant; the remaining columns are GEO annotations. The data are bulk RNA-seq, given as gene-level raw read counts from featureCounts (GRCh38). | |
| Our question is which genes are differentially expressed between IBD-derived and healthy-donor-derived organoids, that is, in IBD organoids compared with normal organoids. | |