APOE U19 Publications Database

In Silico Investigation of Parkin-Activating Mutations Using Simulations and Network Modeling

Data and models will be made available upon request to the corresponding author.

https://www.mdpi.com/2218-273X/14/3/365

Cholesterol 25-hydroxylase mediates neuroinflammation and neurodegeneration in a mouse model of tauopathy

All sequencing data are available from the Gene Expression Omnibus under accession code GSE250277 (bulk RNA-seq) and GSE242896 (snRNA-seq). All other data are available in the main text or the supplementary material.

Apolipoprotein E secreted by astrocytes forms antiparallel dimers in discoidal lipoproteins
  • CryoEM electron density maps are deposited in EMDB (EMD-41830 and EMD-41831) and are publicly available at time of publication. Accession numbers are listed in the key resources table.

  • This paper does not report original code.

  • Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.

ABCA7 deficiency causes neuronal dysregulation by altering mitochondrial lipid metabolism

All data generated for this manuscript have been included in this article. The bulk RNA-seq data that support the findings of this study are deposited in the Gene Expression Omnibus repository under accession number GSE247360. All other data are available from the corresponding author upon reasonable request.

Amelioration of Tau and ApoE4-linked glial lipid accumulation and neurodegeneration with an LXR agonist
  • Mouse bulk (GEO:GSE242693) and snRNA-seq data (GEO:GSE242180) from this study are deposited in the Gene Expression Omnibus (GEO) database.

  • No custom code was used.

  • Any additional information required to reanalyze the data reported in this work paper is available from the lead contact upon request.

Regulation of cortical hyperexcitability in amyotrophic lateral sclerosis: focusing on glial mechanisms

The datasets during and/or analysed during the current study available from the corresponding author on reasonable request.

Cell-autonomous effects of APOE4 in restricting microglial response in brain homeostasis and Alzheimer’s disease

All datasets generated and/or analyzed in the current study are attached. The scRNA-seq data that support the findings of this study are deposited in the Gene Expression Omnibus repository under accession number https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE241553. Source data are provided with this paper.

Deconvolution reveals cell-type-specific transcriptomic changes in the aging mouse brain

The bulk transcriptomics data that were deconvoluted in this study are available on Synapse: https://doi.org/10.7303/syn20808171.

APOE deficiency impacts neural differentiation and cholesterol biosynthesis in human iPSC-derived cerebral organoids

The single-cell RNA-seq data are available via the AD Knowledge Portal (https://adknowledgeportal.synapse.org, Data reference number: syn30866487). The AD Knowledge Portal is a platform for accessing data, analyses, and tools generated by the Accelerating Medicines Partnership (AMPAD) Target Discovery Program and other National Institute on Aging (NIA)-supported programs to enable open-science practices and accelerate translational learning. The data, analyses, and tools are shared early in the research cycle without a publication embargo on secondary use. Data are available for general research use according to the following requirements for data access and data attribution [https://adknowledgeportal.synapse.org/DataAccess/Instructions]. All other data that support the findings of this study are available from the corresponding authors upon reasonable request.

Retrospective Evaluation of Neuropathologic Proxies of the Minimal Atrophy Subtype Compared With Corticolimbic Alzheimer Disease Subtypes

All requests for raw and analyzed data and related materials, excluding programming code, will be reviewed by Mayo Clinic’s Legal Department and Mayo Clinic Ventures to verify whether each request is subject to any intellectual property or confidentiality obligations. Any data and materials that can be shared will be released through a Data Use/Share Agreement or Material Transfer Agreement.

Dissecting Detergent-Insoluble Proteome in Alzheimer's Disease by TMTc-Corrected Quantitative Mass Spectrometry

Raw MS data have been submitted to the MassIVE repository with accession number MSV000091796. The dataset is also available in the PRIDE repository with number PXD038381.

LRP1 in vascular mural cells modulates cerebrovascular integrity and function in the presence of APOE4

The RNA-Seq data have been deposited in Gene Expression Omnibus DataSets (https://www.ncbi.nlm.nih.gov/gds; accession no. GSE225065).

Apolipoprotein E4 has extensive conformational heterogeneity in lipid-free and lipid-bound forms

The code for the kinetic Monte Carlo simulation of photon trajectories has been developed as a command line app and is distributed via the enspara GitHub (https://github.com/bowman-lab/enspara). The Markov state model used for this paper is publicly available at: https://osf.io/7jqyz/ (51). The main experimental data are available in SI AppendixSupplementary Tables. Raw single-molecule photon trajectories and simulation data will be provided upon request. Plasmid of created constructs will be provided upon request. Code for analysis of single-molecule and computational data is publicly available through the sources indicated in the corresponding sections in SI Appendix, Methods.

Alzheimer’s disease-associated U1 snRNP splicing dysfunction causes neuronal hyperexcitability and cognitive impairment

ROSMAP data can be download from this website (https://adknowledgeportal.synapse.org/) and mapped to human transcriptome (hg19). All mouse RNA-seq data were deposited in the GEO database under accession codes GSE115177 (mouse brain) and GSE196873 containing two sub-series IDs, GSE196871 (mouse brain) and GSE196872 (mouse neuronal culture) and mapped to the mouse transcriptome (mm9). The MS proteomics data were deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifiers PXD031587 (human aggregated proteome), PXD031581 (mouse aggregated proteome), PXD031546 (mouse neuronal culture) and PXD023395 and PXD031545 (mouse brain). Both hg19 and mm9 can be download from UCSC website (https://genome.ucsc.edu/index.html). Other data underlying the paper are provided as source data files or are available from the corresponding author upon reasonable request.

APOE2 Exacerbates TDP-43 Related Toxicity in the Absence of Alzheimer Pathology

All data in the project are contained in the manuscript. Further information can be provided upon reasonable request to the corresponding authors.

https://onlinelibrary.wiley.com/doi/10.1002/ana.26580

Opposing effects of apoE2 and apoE4 on microglial activation and lipid metabolism in response to demyelination

All data generated in this study are included in this published article. Raw RNA-seq data (fastq files) has been deposited in the Synapse with the dataset identifier https://www.synapse.org/#!Synapse:syn27717736.

TREM2-independent microgliosis promotes tau-mediated neurodegeneration in the presence of ApoE4
  • Mouse snRNA-seq data that support the findings of this study have been deposited in the Gene Expression Omnibus (GEO) database with accession number GSE206368.

For Human data: http://ngi.pub/SNARE/

Sequence files, quantified gene expression and clean data from the Knight ADRC are available in NIAGADS (https://dss.niagads.org/datasets/ng00108/).

For the evaluation of the CLEAR network in the microglial upregulated genes in TE4-T2KO mice, we used the interactive TFEBexplorer (https://tfeb.tigem.it/help.php) to identify genes that are predicted to be upregulated by the master regulator TFEB.

  • This study did not generate new original code.

  • Any additional information required to reanalyze the data reported in this work paper is available from the Lead Contact upon request.

Suppression of Wnt/?-Catenin Signaling Is Associated with Downregulation of Wnt1, PORCN, and Rspo2 in Alzheimer’s Disease

All data generated during this study are included in this article or are available on reasonable request from the corresponding author.

https://link.springer.com/article/10.1007/s12035-022-03065-1#data-availability

JUMPptm: Integrated software for sensitive identification of post-translational modifications and its application in Alzheimer's disease study

The data that supports the findings of this study are available in the supplementary material of this article. The JUMPptm tool is freely available for the research community (https://github.com/surPoudel/JUMP-ptm).

https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/pmic.202100369

Astrocyte-secreted glypican-4 drives APOE4-dependent tau hyperphosphorylation

All study data are included in the main text and SI Appendix. Data will be shared and made available by request from a qualified academic investigator.

https://www.pnas.org/doi/full/10.1073/pnas.2108870119

Cholesterol and matrisome pathways dysregulated in astrocytes and microglia

The data discussed in this publication have been deposited in NCBI’s Gene Expression Omnibus (GEO) and are publicly available as of the date of publication. Accession numbers are listed in the key resources table. We have used the software and algorithms cited in the key resource table in this manuscript with default parameters or minor changes, thus the paper does not report original code, but the code for these analyses is available upon request. Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.

https://www.sciencedirect.com/science/article/pii/S0092867422006481?via%3Dihub#da0010

29-Plex tandem mass tag mass spectrometry enabling accurate quantification by interference correction

The MS proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the iProX partner repository with the dataset identifier PXD033865.

https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/pmic.202100243