| We study the liver of male C57BL/6J mice that lack Marchf6 in hepatocytes. Knockout mice carry floxed Marchf6 with Albumin-Cre (Marchf6 fl/fl AlbuminCre+), and their control littermates carry floxed Marchf6 without Cre (Marchf6 fl/fl AlbuminCre-). All mice were 10 weeks old, kept on standard chow and fasted for 4 hours before the liver was collected, so all samples come from one time point. The genotype is in the `genotype` column: Marchft liver KO marks the 6 hepatocyte-specific knockouts ('Marchft' is a typo for Marchf6 carried over from GEO), and WT marks the 6 control littermates. The `group` column repeats the same labels. | |
| Each of the 12 samples is the liver of a different mouse (mouse 1 to mouse 12 in `title_short`), and no mouse was sampled twice; each liver gave one library, so there are no technical replicates. The numbers WT1 to WT6 and LKO1 to LKO6 in `sample_id` only count the mice within each genotype. Litters and cages are not recorded, and there is no record that knockout and control mice were matched. The GEO field kept in `src_batch` holds the age (10-weeks-old) for every sample rather than a processing batch, and no technical batch is recorded, so we have no batch variable. All mice are male, as `sex` shows, and we know of no other variable that matters; the remaining columns are GEO annotations. | |
| The data are bulk mRNA-seq of total liver RNA, given as raw gene-level read counts from HTSeq-count for Ensembl release 93 genes (GRCm38). | |
| Our question is which genes are differentially expressed in the livers of the hepatocyte-specific Marchf6 knockout mice (Marchft liver KO) compared with their control littermates (WT), using all 12 samples. | |