We grew the human T-ALL cell line Jurkat for 72 hours in custom RPMI medium with either the standard histidine concentration or a quarter of it. The condition is recorded in the `group` column, which holds our groups (`treatment` repeats it, and `genotype` codes it as his100 and his25): 100% histidine is the control medium with the standard RPMI histidine concentration (about 97 µM), and 25 % histidine is histidine restriction to 25% of that concentration (about 24 µM). There are five cultures in 100% histidine and four in 25 % histidine, nine samples in all, all harvested at 72 hours, so there is a single time point.

Each sample is one culture under one histidine condition, made into its own library and sequenced once, so there are no technical replicates, and with a cell line there are no donors or animals. The RNA was taken from the same lysates as ribosome-profiling libraries (hence "rpf_matched" in the sample names), which are not part of these data. The rep numbers in the sample names only count the cultures within each condition, and the 25 % histidine group has no rep4 library; nothing records that cultures with the same number were grown or processed together. No batch is recorded, and we know of no other variable that matters; the remaining columns are GEO annotations that are constant or repeat the condition.

The data are bulk poly(A) RNA-seq (TruSeq mRNA libraries), given as gene-level integer counts with Ensembl gene IDs from Salmon quantification imported with tximeta, which the submitters deposited as raw counts.

Our question is which genes differ in expression in Jurkat cells grown in 25 % histidine compared with cells grown in 100% histidine for 72 hours. All nine samples are part of this question.