| We treated the human small cell lung cancer cell line H1092, a neuroendocrine line of the SCLC-ASCL1 subtype, with the autophagy inhibitor bafilomycin A1 (BafA1) in vitro. The `group` column, repeated in `treatment`, holds the condition: 'treated with 2 μM BafA1 for 24 hours' or 'treated with 5 μL DMSO for 24 hours', the solvent control; there are three cultures of each. All cultures were harvested at the end of the 24-hour treatment, 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 DMSO culture to a particular BafA1 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 BafA1-treated H1092 cells ('treated with 2 μM BafA1 for 24 hours') compared with DMSO-treated control cells ('treated with 5 μL DMSO for 24 hours'), using all six samples. | |