| We compared A375 human melanoma cells carrying a CRISPR/Cas9 knock-down of SIRT6 with wild-type A375 cells. The genotype is recorded in the `group` column, which holds our groups (`genotype` repeats it): SIRT6KD is a SIRT6 knock-down clone, picked by limiting dilution from a CRISPR/Cas9-edited pool, and WT is the wild-type parental A375 line (S6KO and WT in the sample names). There are three cultures of each, six samples in all, collected at a single time point during exponential growth, without any drug treatment. | |
| Each sample is one independent cell culture, made into its own library and sequenced once, so there are no technical replicates. No knock-down culture is matched to a particular wild-type culture: the numbers in the sample names (S6KO_1 to S6KO_3, WT_2 to WT_4) only count the cultures within each group. All six samples carry the same GEO batch date (`src_batch` is 11/1/2023 for every sample), so we have no batch differences, and we know of no other variable that matters; the remaining columns are GEO annotations. | |
| The data are bulk RNA-seq from total RNA (NEBNext Ultra II libraries), given as gene-level RSEM expected counts from the nf-core/rnaseq pipeline (STAR + RSEM), rounded to whole numbers; the features are NCBI gene symbols. | |
| Our question is which genes are differentially expressed in SIRT6 knock-down A375 cells (SIRT6KD) compared with wild-type cells (WT). All six samples are part of this question. | |