We grew the soil bacterium Arthrobacter sp. AZCC_0090 on filters kept in two humidity chambers for 16 days. The control chamber stayed at 99-100% relative humidity throughout. In the treatment chamber the humidity stayed at 100% until day 2, was lowered step by step to about 25% by day 14, and the filters were then rehydrated with water vapour until day 16. The chamber is in the `group` column (hydrated control or desiccated-rehydrated); the `treatment` column repeats it.

Filters were sampled destructively on days 2, 8, 14 and 16, recorded in the `day` column (days since the filters entered the chambers). On day 2 both chambers were still at 100% humidity, so day 2 is the baseline; day 8 is during drying, day 14 the dry state, and day 16 about 48 hours after rehydration began. There are 3 filters per chamber and day (4 desiccated-rehydrated filters on day 8), 25 in all. Each sample is a different filter, sequenced once, so the samples are independent and there are no technical replicates. The replicate numbers in `sample_id` only label filters within one chamber and day; the same number elsewhere is a different filter.

GEO also lists a batch field (`batch`, repeated in `src_batch`) whose meaning is not documented. Its values are day labels that match the sampling day for the desiccated-rehydrated filters but not for the controls (the day 2 controls are labelled "day 16"), and every chamber-and-day combination falls entirely within one of its values. It matches no processing step we know of, so we have no batch variable, and we have no other variable we consider relevant. The data are bulk rRNA-depleted total RNA-seq, given as featureCounts raw read counts per protein-coding gene (CDS locus tags).

Our question is how the change over time differs between the two chambers: which genes have a difference of desiccated-rehydrated filters relative to hydrated control filters on day 8, 14 or 16 that departs from the difference on day 2. We would like to use all 25 samples.