Dataset
NOTE: Processed data from Synapse was not available.
IMPORTANT: If you are unable to download, please try to right click the ‘download’ link and select ‘save link as’.
| 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
- Front-end: https://github.com/OSU-BMBL/scread/
- Back-end: https://github.com/OSU-BMBL/scread-backend
- Processing workflow: https://github.com/OSU-BMBL/scread/tree/master/script
- STAR Protocols: https://github.com/OSU-BMBL/scread-protocol
Code tutorials
Please check the following GitHub link for full tutorials, including:
- Calculating overlapping DEGs from the same cell type across datasets
- 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?