scREAD A Single-cell RNA-Seq Database for Alzheimer's Disease

Dataset

NOTE: Processed data from Synapse was not available.

scREAD data ID Description Gene expression matrix (.txt.gz) Cell type label (.txt.gz) Processed Seurat object (.rds)
AD00101 H-H-Prefrontal cortex-Male syn18485175;syn21125841 NA NA
AD00102 H-AD.late-Prefrontal cortex-Male_001 syn18485175 NA NA
AD00103 H-AD.late-Prefrontal cortex-Female_001 syn18485175 NA NA
AD00104 H-AD.early-Prefrontal cortex-Male_001 syn18485175 NA NA
AD00105 H-AD.early-Prefrontal cortex-Female_001 syn18485175 NA NA
AD00106 H-H-Prefrontal cortex-Female syn18485175;syn21125841 NA NA
AD00107 H-AD-Prefrontal cortex-Male_001 syn21125841 NA NA
AD00108 H-AD-Prefrontal cortex-Male_002 syn21125841 NA NA
AD00109 H-AD-Prefrontal cortex-Female_001 syn21125841 NA NA
AD00110 H-AD-Prefrontal cortex-Female_002 syn21125841 NA NA
AD00201 H-H-Entorhinal Cortex-Male Download Download Download
AD00202 H-H-Entorhinal Cortex-Female Download Download Download
AD00203 H-AD-Entorhinal Cortex-Male_001 Download Download Download
AD00204 H-AD-Entorhinal Cortex-Female_001 Download Download Download
AD00205 H-AD.Braak 2-Entorhinal cortex -Male_001 Download Download Download
AD00206 H-AD.Braak 6-Entorhinal cortex -Male_001 Download Download Download
AD00301 M-H-Cortex-Male-7m Download Download Download
AD00302 M-H-Cortex-Male-15m Download Download Download
AD00303 M-AD-Cortex-Male-7m_001 Download Download Download
AD00304 M-AD-Cortex-Male-7m_002 Download Download Download
AD00305 M-AD-Cortex-Male-7m_003 Download Download Download
AD00306 M-AD-Cortex-Male-7m_004 Download Download Download
AD00307 M-AD-Cortex-Male-15m_001 Download Download Download
AD00308 M-AD-Cortex-Male-15m_002 Download Download Download
AD00309 M-AD-Cortex-Male-15m_003 Download Download Download
AD00401 M-H-Cerebral cortex-Female-15m Download Download Download
AD00402 M-AD-Cerebral cortex-Female-15m_001 Download Download Download
AD00403 M-AD-Cerebral cortex-Female-15m_002 Download Download Download
AD00404 M-AD-Cerebral cortex-Male-15m_001 Download Download Download
AD00405 M-AD-Cerebral cortex-Male-15m_002 Download Download Download
AD00501 M-H-Cerebellum-Male-7m Download Download Download
AD00502 M-AD-Cerebellum-Male-7m_001 Download Download Download
AD00601 M-H-Prefrontal cortex-Male-7m Download Download Download
AD00602 M-H-Prefrontal cortex-Male-15m Download Download Download
AD00603 M-AD-Prefrontal cortex-Male-7m_001 Download Download Download
AD00604 M-AD-Prefrontal cortex-Male-15m_001 Download Download Download
AD00702 M-H-Hippocampus-Male-7m Download Download Download
AD00703 M-H-Hippocampus-Male-15m Download Download Download
AD00704 M-H-Hippocampus-Female-7m Download Download Download
AD00705 M-H-Hippocampus-Female-20m Download Download Download
AD00708 M-AD-Hippocampus-Male-7m_001 Download Download Download
AD00709 M-AD-Hippocampus-Male-7m_002 Download Download Download
AD00710 M-AD-Hippocampus-Male-7m_003 Download Download Download
AD00711 M-AD-Hippocampus-Male-15m_001 Download Download Download
AD00712 M-AD-Hippocampus-Male-15m_002 Download Download Download
AD00713 M-AD-Hippocampus-Male-15m_003 Download Download Download
AD00714 M-AD-Hippocampus-Male-15m_006 Download Download Download
AD00715 M-AD-Hippocampus-Male-15m_007 Download Download Download
AD00716 M-AD-Hippocampus-Male-15m_008 Download Download Download
AD00717 M-AD-Hippocampus-Male-20m_002 Download Download Download
AD00718 M-AD-Hippocampus-Female-7m_001 Download Download Download
AD00719 M-AD-Hippocampus-Female-20m_001 Download Download Download
AD00801 H-H-Superior frontal gyrus-Male Download Download Download
AD00802 H-AD.Braak 2-Superior frontal gyrus-Male_001 Download Download Download
AD00803 H-AD.Braak 6-Superior frontal gyrus-Male_001 Download Download Download
AD00901 M-H-cortex_and_hippocampus-Female-7m_001 Download Download Download
AD00902 M-H-cortex_and_hippocampus-Female-7m_002 Download Download Download
AD00903 M-AD-cortex_and_hippocampus-Female-7m_001 Download Download Download
AD00904 M-AD-cortex_and_hippocampus-Female-7m_002 Download Download Download
AD01001 M-H-subventricular_zone_and_hippocampus-Female-7m_001 Download Download Download
AD01002 M-H-subventricular_zone_and_hippocampus-Female-7m_002 Download Download Download
AD01003 M-AD-subventricular_zone_and_hippocampus-Female-7m_001 Download Download Download
AD01004 M-AD-subventricular_zone_and_hippocampus-Female-7m_002 Download Download Download
AD01101 H-H-Prefrontal_cortex-Male_BA9 Download Download Download
AD01102 H-H-Prefrontal_cortex-Female_BA9 Download Download Download
AD01103 H-AD-Prefrontal_cortex_BA9-Male_001 Download Download Download
AD01104 H-AD-Prefrontal_cortex_BA9-Female_001 Download Download Download
AD01201 H-H-Superior_parietal_lobe-Male Download Download Download
AD01202 H-H-Superior_parietal_lobe-Female Download Download Download
AD01203 H-AD-Superior_parietal_lobe-Male_001 Download Download Download
AD01204 H-AD-Superior_parietal_lobe-Female_001 Download Download Download
AD01205 H-AD-Superior_parietal_lobe-Male_002 Download Download Download
AD01206 H-AD-Superior_parietal_lobe-Female_002 Download Download Download

Source code

Code tutorials

Please check the following GitHub link for full tutorials, including:

  1. Calculating overlapping DEGs from the same cell type across datasets
  2. Running scREAD backend analysis workflow locally

https://github.com/OSU-BMBL/scread-protocol

More methods details about the pipeline can be found in What is the scREAD overall pipeline?