| We study the testis of male mice with a conditional knockout of syna. Knockout mice carry Pbsn-cre with floxed syna (Pbsn-cre; syna f/f), and control mice carry floxed syna without Cre (syna f/f). The genotype is the grouping we compare, and it is in the `genotype` column: "syna knockout" for the 3 knockout mice and "wild type" for the 3 syna f/f controls (the `group` column is an exact copy of `genotype`). All mice were untreated, and whole testes were collected at 4 months of age, a single time point. | |
| Each of the six samples (KO1 to KO3 and WT1 to WT3 in `sample_id`) is the testis tissue of a different mouse, with one library per mouse, so no mouse contributed more than one sample and there are no technical replicates. The numbers only count the mice within each genotype; litters are not recorded, and there is no record that knockout and control mice were matched. The submitters recorded all six libraries in one batch (`src_batch` is 1 for every sample), so we have no batch variable, and we know of no other variable that matters; the remaining columns are GEO annotations. The GEO record says WT1 was judged an outlier and left out of the submitters' own analysis; it is still in our files and does not stand out in our own quality checks. | |
| The data are bulk mRNA-seq (oligo-dT selected), given as raw gene-level read counts for Ensembl genes, from HISAT2 alignment to GRCm39 and StringTie quantification. | |
| Our question is which genes are differentially expressed in the testes of syna knockout mice ("syna knockout" in `genotype`) compared with wild type syna f/f mice ("wild type"), using all six samples. | |