| We studied the basal ganglia of Sprague-Dawley rats 72 hours after an intracerebral hemorrhage (ICH) was induced or a sham operation was done. The groups are in the `group` column: "rat brain tissue, Sham" (sham-operated rats, 5 animals, named NC_1 to NC_5 in `sample_id`), "rat brain tissue, ICH" (ICH without drug treatment, 3 animals) and "rat brain tissue, ICH_MA" (ICH followed by treatment with the Sp1 inhibitor Mithramycin A, 3 animals). GEO registers five rats per group, but the deposited count table contains only these 11 samples. All rats were sampled at the same time after the operation, so time is not a variable here. | |
| Each sample is the basal ganglia tissue of one rat, and the three groups are different animals, so no rat contributes more than one sample. The numbers in the sample names and in the `treatment` column (for example "sham operation rep1") only count the rats within each group; there is no record linking samples with the same number across groups. Each sample was sequenced once, so there are no technical replicates. The GEO batch field in `src_batch` holds the same value ("6/15/2025") for every sample, so there is no known batch variable. We have no other variable we consider relevant; the remaining columns are GEO annotations. | |
| The data are bulk RNA-seq of brain tissue (Illumina NovaSeq 6000). The matrix holds the submitter's gene-level integer read counts for 15,094 Ensembl rat genes; GEO names RSEM as the quantification step. | |
| Our question is which genes are differentially expressed in Mithramycin A-treated ICH rats ("rat brain tissue, ICH_MA") compared with ICH rats that received no drug ("rat brain tissue, ICH"). All 11 samples, including the sham rats, are part of the analysis. | |