| We treated the human small cell lung cancer cell line DMS114, a non-neuroendocrine line of the SCLC-YAP1 subtype, with the autophagy activator trehalose in vitro. The `group` column, repeated in `treatment`, holds the condition: 'treated with 200 mM trehalose for 12 hours' or 'WT', which here means untreated control cultures, not a genotype; there are three cultures of each. There is a single dose and a single time point, so there is no time variable. | |
| Each sample is one culture sequenced as one library, no two libraries are recorded as coming from the same culture, and there are no technical replicates. The GEO series title calls the comparison 'paired', but no record says what this refers to, and the numbers 1 to 3 at the end of the sample names only count the cultures within each condition: nothing links a control culture to a particular treated culture, and same-numbered cultures are no more alike in expression than other combinations. 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 poly(A) RNA-seq (stranded, paired-end reads). The matrix holds raw gene-level integer read counts, one row per Ensembl gene ID (hg38). | |
| Our question is which genes are differentially expressed in trehalose-treated DMS114 cells ('treated with 200 mM trehalose for 12 hours') compared with untreated control cells ('WT'), using all six samples. | |