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README.md

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+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.
+