DOI: 10.5061/dryad.dv41ns295
title: Cerebrovascular alterations in a mouse model of late-onset Alzheimer's disease

description: 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.
description: # Cerebrovascular alterations in a mouse model of late-onset
 Alzheimer's disease Dataset DOI:
 [10.5061/dryad.dv41ns295](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)