@AMPADDataReleaseUpdates The following data is now available. Study links are to the new [AMP-AD Knowledge Portal interface](https://adknowledgeportal.synapse.org/#/) * Please note that there will be a second fall release towards the end of December, and a MODEL-AD release winter 2020. ###Human [**The ROSMAP study**](https://adknowledgeportal.synapse.org/#/Explore/Studies?Study=syn3219045) * This study contains data generated from subjects participating in the Religious Orders Study (ROS) and Memory and Aging Project (MAP). These are longitudinal clinical-pathologic cohort studies of aging and AD run from Rush University. Previously released from these studies is GWAS, WGS, RNAseq on bulk and single nuclei from the dorsolateral prefrontal cortex, microglia RNAseq, array mRNA and miRNA expression, epigenetics, and metabolomics. * This release adds*: * RNAseq from single nuclei from the dorsolateral prefrontal cortex from an additional 24 samples for a total of 32 samples from 24 unique donors * RNAseq from bulk dorsolateral prefrontal cortex from an additional 252 samples for a total of 900 samples from 883 unique donors * RNAseq from bulk posterior cingulate cortex from 573 samples from 572 unique donors * RNAseq from bulk head of the caudate nucleus from 749 samples from 747 unique donors * Tandem Mass Tag proteomics from bulk dorsolateral prefrontal cortex from 400 samples * Metadata Update: A biospecimen metadata file has been created mapping all specimens used in ROSMAP assays to an individualID (R?). This individualID is mapped to the projid via the clinical file. Metadata files with assay variables linked to the specimenID can be found for most of the assays. *For bulk RNAseq this release + previous data provides 2222 bulk samples from 925 unique donors [**The snRNAseqPFC_BA10 study**](https://adknowledgeportal.synapse.org/#/Explore/Studies?Study=syn18485175) * This study provides single nuclei RNAseq from the dorsolateral prefrontal cortex as described in [Single-cell transcriptomic analysis of Alzheimer's disease](https://www.nature.com/articles/s41586-019-1195-2). The study uses 48 specimens from the ROSMAP study. Previously released is raw and processed RNAseq * This release adds: * The unfiltered count matrix * Metadata Update: A biospecimen metadata file has been created mapping all specimens used in this study to an individualID (R?). This individualID is mapped to the projid via the ROSMAP clinical file. See metadata file with RNAseq variables linked to the specimenID. [**The Emory_Vascular study**](https://adknowledgeportal.synapse.org/#/Explore/Studies?Study=syn18909507) * This is a new 2-year longitudinal, non-interventional cohort study conducted at Emory University. The objective is to investigate the contributions of vascular dysfunction in the systemic and cerebral circulations to the pathogenesis/progression of prodromal AD. Provided is baseline data on 200 individuals consisting of clinical, cognitive and cardiovascular assessments, processed MRI imaging, and metabolomics. ###Models [**The APOE-TR study**](https://adknowledgeportal.synapse.org/#/Explore/Studies?Study=syn8391648) * This study contains data from human APOE-targeted replacement mouse models. These models express each human APOE genotype (APOE2, APOE3 or APOE4) under the control of the mouse endogenous Apoe promoter. Previously released from this study is behavioral assessment, lab tests, metabolomics on serum and RNAseq from the cerebral cortex * This release adds: * Normalized gene counts from the previously released RNAseq data [**The 5XFAD study**]( https://adknowledgeportal.synapse.org/#/Explore/Studies?Study=syn16798076) * This study contains data from a familial Alzheimer?s disease mouse model expressing mutant human APP and PS1. The data is provided through the MODEL-AD (Model Organism Development & Evaluation for Late-Onset Alzheimer?s Disease) consortium. Previously released from this study is RNAseq on the cortex and hippocampus, behavioral data, immunoassays, immunofluorescence, pharmacokinetic data on acute and chronic levetiracetam treatment, and imaging (PET and Autorad) on levetiracetam treated mice. * This release adds: * Access to copies of the corrected and registered PET and probabilistic MRI images in Analyze single file format (i.e. .avw) upon request. * Electrochemiluminescence data at 12mo * Immunofluorescence raw images at ages 4 mo, 8 mo, and 12 mo; immunofluorescence processed data at ages 8 mo and 12 mo * LTP data at 4 mo, 8 mo, and 12 mo * Updated individual and biospecimen metadata files [**The GJA1_deficiency study**](https://adknowledgeportal.synapse.org/#/Explore/Studies?Study=syn21262226) * This is a new study that examines the effect of Gja1 (connexin43) deficiency on astrocyte function and the impact on co-cultured neurons as described in GJA1 (connexin43) is a key regulator of Alzheimer?s disease pathogenesis. It was done in order to characterize the impact of loss-of-Gja1-function in astrocyte and neuron/astrocyte co-culture using primary cells derived from neonatal and perinatal mice deficient in Gja1. Gja1 -/- astrocytes were generated from whole brains of perinatal litters obtained from mice homozygous for a Gja1 null mutation. Provided is RNAseq from astrocytes and neuron/astrocyte cocultures. ###[Tools](https://adknowledgeportal.synapse.org/#/Explore/Tools) This release adds a variety of computational and experimental tools **Computational** * WINA_Large-scale Weighted Integrative Gene Network Analysis * Software package: WINA implements an efficient pipeline for seamless coexpression network construction and module identification using weighted gene coexpression network analysis algorithm for very large gene sets. * Multiscale Embedded Gene Co-Expression Network Analysis (MEGENA) * Software package: Multiscale Embedded Gene Co-Expression Network Analysis (MEGENA) can efficiently construct and analyze large scale planar filtered co-expression networks. * SuperNOVA_ANOVA-based Differential Coexpression Analysis Between Two or More Group * Software package: SuperNova is an R package that implements an ANOVA test to quantify differential gene coexpression across two or more conditions simultaneously, and identifies differentially coexpressed genes, pathways, and modules, in parallel. * BrainQTL * A resource for genetic investigations of the human brain. **Experimental** * nanoString Mouse AD Panel * Gene expression panel: Panel of 770 standardized mouse genes covering 30 clinically derived AD-associated human expression modules discovered from an AMP-AD consortium study of human brain expression patterns. Developed by the MODEL-AD consortium and available through nanoString. * A variety of familial and LOAD mouse models from the MODEL-AD Consortium and grant U01AG046170 ###Changes * The ROSMAP study: The SRM proteomics data contained 17 samples from the Minority Aging Research Study. Data from this study is currently not released through the AMP-AD Knowledge Portal, and no clinical data is available on these donors in the portal. New SRM proteomics files have been provided that do not have data from these donors.