| We edited primary human NK cells by CRISPR with either a FLI1-targeting guide (FLI1 knockout) or a non-targeting control guide (NTC) and harvested them at a single time point after editing, so there is no time variable. The `group` column, repeated in `treatment`, holds the condition: FLI1 KO or NTC, three libraries each. | |
| Within each condition the libraries are numbered Rep1, Rep2 and Rep3, recorded in the `replicate` column. The FLI1 KO and NTC libraries that share a replicate number form a matched pair from the same NK-cell source, either the same donor or the same experiment (the records do not say which), so each replicate contributes one knockout and one control library. Each such pair is more alike in expression than libraries of the same condition with different numbers. Each library is one edited NK-cell culture, and there are no technical replicates. We have no record of processing or sequencing batches, and no other variable matters to us; the remaining columns are GEO annotations. | |
| The data are bulk RNA-seq (Illumina RNA Prep with Enrichment libraries from total RNA), aligned with STAR to hg38. The matrix holds raw gene-level read counts, one row per Ensembl gene ID. | |
| Our question is which genes are differentially expressed in FLI1 knockout NK cells (FLI1 KO) compared with NTC control cells (NTC), using all six libraries. | |