Analyzing Illumina Counts
The counts files for GSE89225 is the output of HTSeq-count as a large matrix. Unless you are developing a differential expression package yourself you should not attempt to directly use this. Rather, you should load it into R and use packages such as DESeq2, edgeR, or limma (those are the most popular ones).

For convenience, in DESeq2 you would want the DESeqDatasetFromMatrix() function after loading this.