| 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. | |