Dataset DOI: 10.5061/dryad.dv41ns295

Description of the data and file structure

This collection of datasets is from three cohorts of mice. Mice in cohort #1 had resting-state cerebral blood flow (CBF) measured with laser speckle imaging (LSI) across different age groups (12, 18, and 22 – 27 m.o.) in WT, hAβ-KI, and 3xTg-AD mice. Mice in cohort #2 utilized WT and hAβ-KI mice at 23 – 25 m.o. and had bulk RNA-sequencing performed to examine transcriptomics. Mice in cohort #3 utilized WT and hAβ-KI mice at 24 m.o. to examine cerebrovascular structure and neurovascular coupling (NVC). Datasets from cohorts #1 and #3 include the output data (e.g., resting-state CBF), mouse genotype, age group, and sex. Datasets from cohort #2 include results from differential gene expression analysis between genotypes and gene set enrichment analysis (GSEA) as .tsv files.

Files and variables

File: Resting-state_CBF__cohort__1.xlsx

Description: Output resting-state CBF data from cohort #1.

Variables

• Mouse number: Generic mouse ID for cohort #1
• Age group: Age group that a given mouse belongs to (i.e., 12, 18, or 22-27 month old)
• Sex (M/F): Whether a mouse is male or female
• Genotype: Whether the mouse is wild type (WT), hAB-KI, or 3xTg-AD
• Resting-state CBF: Output resting-state CBF value from laser speckle imaging in arbitrary units

File: AllGenes_hAB_vs_C57__cohort__2.tsv

Description: Data from all the genes from differential gene expression analysis from cohort #2.

Variables

• Gene: Names of the genes analyzed in the differential gene expression (DGE) analysis
• baseMean: The average of the normalized count values taken over all samples
• log2FoldChange: log fold-change of the average expression between WT and hAB-KI groups. Positive values indicate that the gene is more highly expressed in hAB-KI mice
• lfcSE: The standard error estimate for the log2FoldChange estimate
• stat: The value of the test statistic for the gene, calculated by log2FoldChange divided by lfcSE
• pvalue: The unadjusted pvalue for the gene
• padj: The adjusted pvalue accounting for multiple comparisons
• log10: Log base 10 of the adjusted pvalue
• signed: Log base 10 of the adjusted pvalue multipled by the sign of the log2FoldChange

File: SigGenes_hAB_vs_C57__cohort__2.tsv

Description: Data from only the significant genes from differential gene expression analysis from cohort #2.

Variables

• Gene: Names of the genes analyzed in the differential gene expression (DGE) analysis
• baseMean: The average of the normalized count values taken over all samples
• log2FoldChange: log fold-change of the average expression between WT and hAB-KI groups. Positive values indicate that the gene is more highly expressed in hAB-KI mice
• lfcSE: The standard error estimate for the log2FoldChange estimate
• stat: The value of the test statistic for the gene, calculated by log2FoldChange divided by lfcSE
• pvalue: The unadjusted pvalue for the gene
• padj: The adjusted pvalue accounting for multiple comparisons

File: Ranked_list_for_GSEA__cohort__2.tsv

Description: Ranked gene list for input into gene set enrichment analysis (GSEA).

Variables

• NAME: Names of the genes in the ranked order obtained from the Log base 10 of the adjusted pvalue multipled by the sign of the log2FoldChange
• SCORE: Log base 10 of the adjusted pvalue multipled by the sign of the log2FoldChange

File: GSEA_report_for_na_pos__cohort__2.tsv

Description: Output data of positive normalized enrichment scores from GSEA.

Variables

• NAME: Gene set name
• SIZE: Number of genes in the gene set after filtering out those genes not in the expression dataset
• ES: Enrichment score for the gene set.
• NES: Normalized enrichment score for the gene set.
• NOM p-val: Nominal p value; that is, the statistical significance of the enrichment score. The nominal p value is not adjusted for gene set size or multiple hypothesis testing.
• FDR q-val: False discovery rate; that is, the estimated probability that the normalized enrichment score represents a false positive finding.
• FWER p-val: Familywise-error rate.
• RANK AT MAX: The position in the ranked list at which the maximum enrichment score occurred.
• LEADING EDGE: Displays the tags, list, and signal used to describe the leading-edge subset of a single gene set.

File: GSEA_report_for_na_neg__cohort__2.tsv

Description: Output data of negative normalized enrichment scores from GSEA.

Variables

• NAME: Gene set name
• SIZE: Number of genes in the gene set after filtering out those genes not in the expression dataset
• ES: Enrichment score for the gene set.
• NES: Normalized enrichment score for the gene set.
• NOM p-val: Nominal p value; that is, the statistical significance of the enrichment score. The nominal p value is not adjusted for gene set size or multiple hypothesis testing.
• FDR q-val: False discovery rate; that is, the estimated probability that the normalized enrichment score represents a false positive finding.
• FWER p-val: Familywise-error rate.
• RANK AT MAX: The position in the ranked list at which the maximum enrichment score occurred.
• LEADING EDGE: Displays the tags, list, and signal used to describe the leading-edge subset of a single gene set.

File: Vascular_density_and_NVC__cohort__3.xlsx

Description: Output neurovascular coupling (NVC) and histological data from cohort #3.

Variables

• Mouse number: Generic mouse ID for cohort #3
• Age Group: All mice were 24 months old
• Sex (M/F): Whether a mouse is male or female
• Genotype: Whether the mouse is wild type (WT) or hAB-KI
• AUC during stim
• Percent increase in CBF (%)
• AUC during stim, delta CBF
• Peak delta CBF
• Time to 50% of max, rise
• Time to 50% of max, fall
• Total Cortical Vessel Density (1/mm)