| This data was collected from the Nature publication | |
| "A single-cell transcriptomic atlas characterizes ageing tissues in the mouse" | |
| DOI: https://doi.org/10.1038/s41586-020-2496-1 | |
| Gene Expression Omnibus (GEO) Accession Code: GSE132042 | |
| In this study, researchers looked at how much certain genes were expressed in | |
| young and old mice so that they could compare gene expression between the groups. | |
| This provides data on how gene expression changes with age. Specifically, the | |
| samples were taken from male and female mice. The samples from 'young' mice came | |
| from mice at 1 and 3 months of age, and the samples from 'old' mice came from mice | |
| at 18, 21, 24, and 30 months of age. | |
| Also, the researchers used three different methods to measure gene expression: | |
| 1. FACS | |
| 2. Droplet | |
| 3. Bulk | |
| This redundancy helps cross-validate the data. FACS and droplet are both single-cell | |
| techniques, which means that gene expression is measured from each cell in a sample | |
| individually. In contrast, the bulk approach examines many cells together (in bulk) | |
| and basically finds their average expression rates. The metrics are reported by | |
| technique, and the researchers also reported the four metrics on the data combined | |
| from all three techniques. | |
| The methods provided four different metrics for gene expression: | |
| 1. raw_p: the p-value, a measure of significance that the difference in expression | |
| between the young and old groups is actually different | |
| 2. bh_p: the Benjamani-Hochberg p-value. This is a p-value adjusted for the huge | |
| number of hypotheses (genes) being tested at once. This is useful because by chance, | |
| some of the expression differences would appear random, and the BH p-value accounts | |
| for this | |
| 3. coef: the age coefficient. If you were to fit a line of best fit to how the | |
| gene expression rate changes with age, basically this would be the slope of the line. | |
| So if a gene increases in expression with age, the age coefficient is positive, and | |
| if a gene decreases in expression with age, the age coefficient would be negative. | |
| 4. fc: fold change. This quantifies how much the gene expression level differs | |
| between the young and old mice. P-value and BH p-value indicate *whether* there's | |
| a difference, and this metric quantifies the strength of the difference. | |
| The researchers also looked at how gene expression rates differed by tissue. This is | |
| useful because different tissues express genes at different rates. For example, | |
| tissue X might express gene G a *lot*, which tissue Y might express it very little | |
| or not at all. The tissues sampled were: | |
| - Aorta | |
| - BAT (brown adipose tissue) | |
| - Bladder | |
| - Brain myeloid | |
| - Brain non-myeloid | |
| - Diaphragm | |
| - GAT (gonadal adipose tissue) | |
| - Heart | |
| - Kidney | |
| - Large intestine | |
| - Limb muscle | |
| - Liver | |
| - Lung | |
| - MAT (marrow adipose tissue) | |
| - Mammary gland | |
| - Marrow | |
| - Pancreas | |
| - SCAT (SubCutaneous Adipose Tissue) | |
| - Skin | |
| - Small intestine | |
| - Spleen | |
| - Thymus | |
| - Tongue | |
| - Trachea | |
| Note that not every method was applied to each tissue type. | |
| The four metrics are also reported by cell type. For example, BAT.T Cell means | |
| that the sample was taken from T cells in BAT tissue. | |
| The comparison_summary table shows which methods provided data on which genes. | |
| For example, the cell in the FACS column and the Aorta row says 1001, and you'll | |
| see in the FACS_Aorta file that the four metrics are provided for 1001 genes. | |