The November 2018 Data Release includes additional Data for ROSMAP and MayoRNAseq, plus a new human study of 470 individuals and a model study from the Jackson Laboratory. Data Updates to MSBB, Banner, and Emory studies.
Human
November 2018
Compare the AMP-AD Knowledge Portal – All Studies_October28.2018.freeze to the AMP-AD Knowledge Portal – All Studies_November24.2018.freeze for the full set of new files that have been added for the November 2018 release.
The ROSMAP study
Targeted proteomics by Selected Reaction Monitoring (SRM). A new version of the SRM data matrix file (syn10468857) adds protein measures on the DLPFC from an additional 385 individuals, resulting in the measure of 67 proteins on 1226 individuals. This set has been termed Round 1. A new set of 119 protein measures on the DLPFC has been generated in Round 2* on 1227 individuals. The assay description has been updated to reflect the difference in protocols between Round 1 and Round 2.
Single-nucleus RNA-sequencing. Raw data has been provided from sequencing of single nuclei isolated from the DLPFC of 8 individuals
ChIPSeq. Processed data including H3K9ac peaks and read counts has been provided for 669 samples that passed quality control and had complete pathologic characterization.Differential Expression – merged differential expression (Ad/Control) resuts from the three rnaSeqReprocessing reprocessing cohorts (Mayo, MSBB, ROSMAP)
eQTL analysis of the Mayo and ROSMAP cohortsThe MayoRNAseq study.
Modules from WGCNA network analysis enriched for GO Biological Process term “ImmuneResponse” (GO:0006955) for the temporal cortex and the cerebellum
Protein validation of the nodes in the temporal cortex immune network
Replication of key immune network nodes in other AMP-AD expression datasets: The rnaSeqReprocessing Differential Expression – for the temporal cortex and the cerebellum – The rnaSeqReprocessing eQTL – temporal cortex and the cerebellumNew Human Study
The ADMC_ADNI2-GO study. This includes Bile Acids and metabolomics data on the p180 platform across 470 individuals from the ADNI cohort. Data is stored on the ADNI website within the Laboratory of Neuro Imaging (LONI). ADNI has additional data access requirements. Researchers interested in ADNI data should apply for data access through LONI.
Models
New Model Study
The AD Cross Species study: This study examines the overlaps between gene expression changes in human AD brains and those from mouse models AD or other models relevant to neurodegenerative diseases. 30 AD-associated gene coexpression modules were examined for overlap with 234 curated differentially-expressed gene sets from mouse brain RNA-sequencing experiments, reprocessed from 99 studies total (GEO and AMP-AD Knowledge Portal). Processed data from all studies and analysis results are provided.
The JAX_B6J.APPPS1_PlaqueOnset study.This study examines plaque formation in APP/PS1 and wild-type mice from the Jackson laboratory. Provided is RNAseq from 60 animals
The UFL Cxcl10 study. This study provides RNAseq data on non-tg littermates of TgCRND8 mice injected with rAAV-CXCL10 or rAAV—GFP
Updates
The MSBB_ArrayTissuePanel study. An update has been done to replace previous individual IDs with new identifiers
The Mount Sinai Brain Bank study.An update has been done to the following metadata files to reflect the results of a comprehnsive sample identity QC: RNAseq (syn6100548), WES (syn6101472), WGS (syn11384608). Additional RNAseq files have been added to the study
The Banner study. An update has been made to the study description providing additional information
The Emory_ADRC study. An update has been made to the study description clarifying the number of donors
The UPPpilot study. An update has been made to the study description clarifying that this is a pilot for a more extensive study that will be released in May