Available Animal Cohorts
This table lists several large studies that could either provide data for analysis, or collaborate by conducting desired analyses internally. This information can be used in helping to develop a pilot project in response to the request for applications. The table is a work in process, and will be updated regularly.
Should you wish to list your lab/name/data in this table, please write to: af2409@cumc.columbia.edu.
Investigator
Barnes, Carol
Bizon, Jennifer
Blalock, Eric
Burger, Corinna
Disterhoft, John
Foster, Tom
Gallagher, Michela
Kaczorowski, Catherine
Rapp, Peter
Martine Ammassari-Teule
Contact
Study 1
Study 2
Study 3
Study 1
Study 2
Study 3
Study 1
Study 2
Study 1
New study
Study 1
Study 2
Study 1
Study 2
Study 3
New data
Study 1 (AD project)
New study (Aging project)
Species
F344 rats
F344 rats
F344 rats
F344 rats
Fischer Brown Norway rats
Fischer Brown Norway rats
F344 rats (3 mo)
F344 rats (3 and 18 mo)
F344 rats
F344 rats
F344BN rats young adult (3-6 mo) and aged (27-32 mo)
F344 and TgF344-AD rats young adult (5-7 mo), middle-aged (12-14 mo), and aged (20-22 mo)
F344 rats
Long-Evans
Diversity Outbred (DO) mice
C57BL6/J mice
40+ genetically diverse, but reproducible, BXD strains and AD-BXDs strains that segregate for ~6 million DNA variants
Set of 10 genetically diverse,Collaborative Cross (CC) strains that segregate for ~50 million DNA variants
500+ female Diversity Outbred (DO) mice that segregate for ~50 million DNA variants.
1000+ female Diversity Outbred (DO) mice that segregate for ~50 million DNA variants.
Long-Evans
Pre-(2 Mo) and early-/3-Mo symptomatic Tg2576 (hAPPswe) mice on a B6/SJL background
B6/SJL wild-type
B6/SJL wild-type
Outbred CD1 young adults (6 Mo), middle-aged (12 Mo) and aged (18 Mo) mice
Sex
M
M
M
M
M
M
M, F
M
M
M
M
M, F
M, F
M
M
M, F
M, F
M, F
F
F
M
M
M, F
Behavioral Assay
Morris watermaze spatial, cued, working memory. I have large legacy datasets on these but do have other tests on smaller numbers of animals,the data are all cross sectional
Legacy data for: watermaze (spatial and cued), spatial working memory
Legacy data for: watermaze (spatial and cued) and odor detection threshold and discrimination learning
Legacy data for: watermaze (spatial and cued), delayed response, attentional set shifting
intertemporal choice, delayed response, attentional set shifting, instrumental responding on a progressive ratio
risky decision making, probabilistic reversal learning
Treatments (2x2): control vs 3 hour restraint; vehicle vs. progesterone. Morris water maze – spatial, cued, working memory
Morris water maze – spatial, cued, working memory. Transcriptional profiling of laser capture microdissected hippocampal CA1 (gray matter) and alveus (white matter). Gene signatures correlated to behavior
Nearly 30 published transcriptional profiling studies (we are actively growing the database). Raw transcriptional data downloaded from the Gene Expression Omnibus is reanalyzed for aging and AD-related transcriptional agreement across measurement platforms, labs, and animal models. We've built a comparison metric (the false concordance rate) that combines # found to agree vs # expected to agree by chance, as well as linear correlation of magnitudes of change among genes that do agree across studies. Additional pre-publication data can be compared with or added to the database
Morris Water Maze,-spatial, cued memory tests were carried out on 3 and 24 month old male rats. 24 month old male rats were categorized as superior and inferior learners.
Morris Water Maze,-spatial, cued memory tests were carried out on 3 and 24 month old male rats. 24 month old male rats were categorized as superior and inferior learners.
large Crossectional data: Morris watermaze – spatial, cued, working memory. Trace eyeblink conditioning – paired, pseudoconditioned
Morris watermaze – spatial, cued, working memory. Trace eyeblink conditioning – paired.
Morris watermaze – spatial, cued, working memory. 5-choice serial reaction time task. Beacon discrimination (pattern separation). Physical measures (mainly grip strength). Most studies are cross sectional with some repeated testing (6-18 months) or twice with various delays (10 days to 1-2 months)
Legacy water maze data, spatial and non-spatial. Data from a variety of smaller, purpose-designed behavioral studies
Water maze data, spatial and non-spatial
Large cross-sectional legacy datasets: Y-maze working memory, contextual fear conditioning, elevated plus maze, motor composite (incline screen, narrow beam, and grip strength) at 6 and 14 mo. New studies are adding 3 mo and 22 mo time points
Large cross-sectional legacy datasets: Y-maze working memory, contextual fear conditioning, elevated plus maze, motor composite (incline screen, narrow beam, and grip strength) at 6 and 14 mo. New studies are adding 3 mo and 22 mo time points
Large cross-sectional legacy datasets: Contextual fear conditioning at 6, 12 and 18 mo.
Large cross-sectional legacy datasets
Large longitudinal (up to 24 mo) legacy datasets: Y-maze working memory (10 and 22 mo) and contextual fear conditioning at 24 mo. Diet groups: 2 and 3-day fast, 20% and 40% caloric restriction, ad lib chow.
Legacy water maze data, spatial and non-spatial. Data from a variety of far smaller, purpose designed behavioral studies
Contextual fear conditioning
Morris water maze
Systems consolidation (recent and remote fear memory)
Morris water maze
Systems consolidation (recent and remote fear memory)
Working and recognition memory (high memory load 6-different objects test)
Contextual fear conditioning
Sociability (3-chamber test, social interaction in pairs (SIP) test)
Contextual fear conditioning
Sociability (3-chamber test, social interaction in pairs (SIP) test)
Biological Data collected from all or a subset of animals
awake, behaving electrophysiology, molecular imaging (catFISH), microbiome samples, immunohistochemistry, RNAseq, and MRI scans
biochemistry (GABA/GLU mRNA and protein expression), CORT
RNAseq, optogentic data, pharmacology, serum cytokine
resting state fMRI
Plasma for hormone measures; brain tissue for IHC and laser capture microdissected hippocampal subregions for transcriptional profiling.
Microarray analysis of CA1 area of the hippocampus was performed for both young and aged rats. Analysis of differences between aged superior and inferior learners, and aged versus young. Raw data available at the NCBI Gene Expression Omnibus (GEO) database.
Microarray analysis of dentate area of the hippocampus was performed for both young and aged rats. Analysis of differences between aged superior and inferior learners, and aged versus young. Raw data available at the NCBI Gene Expression Omnibus (GEO) database.
Brains micro-dissected/flash frozen; Brains perfused and fixed in PFA; Mass Spectrometry Proteomic Profiling; Biophysical data from CA1 and CA3 pyramidal neurons and Layer III and Layer V Lateral Entorhinal Cortex neurons
In vitro electrophysiology (IO curves for AMPA and NMDA receptors, synaptic plasticity), considerable RNAseq from hippocampal subregions and mPFC and fMRI scans (one published study and some preliminary data
Gene microarray datasets (open access data is provided to repositories (e.g. the raw uncurated data from microarray gene profiling has been deposited in the NCBI Gene Expression Omnibus (GEO) database). plasma samples, brain microdissected samples, in situ hybridization and immunohistochemical samples and analysis
Plasma samples, brain microdissected samples, in situ hybridization and immunohistochemical samples
Bulk RNAseq of hippocampus and prefrontal cortex (PFC). Cerebellum, hypothalamus and midbrain micro-dissected/flash frozen; peripheral organs flash frozen, hemi-brains fixed in PFA; Mass Spectrometry Proteomic Profiling; MRI (structural, functional and DTI).
Brains typically prepared and frozen for immunohistochemical/quantitative morphometry analysis; brains microdissected/flash frozen; plasma sample, limited other tissues
Immunohistochemistry (c-fos, Abeta oligomers, dendritic spines) in hippocampus (CA1) amygdala (BLA), medial Prefrontal Cortex (aCC) Entorhinal cortex (LEC)
Chemogenetic (DREADD) manipulations of neural activity
Transcranial Direct Current Stimulation
Chemogenetic (DREADD) manipulations of neural activity
Transcranial Direct Current Stimulation
Predictive markers of early vs late cognitive decline