|
| Status |
Public on Jan 23, 2022 |
| Title |
Amyloid-β and tau aggregates are both necessary to induce novel Alzheimer’s disease stage-specific microglia subtypes |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Purpose: scRNA-Seq was performed to profile changes in microglia in our mouse AD models
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| |
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| Overall design |
Tissues (cerebral cortices, hypothalamus, and midbrain) were dissected into Hibernate-A media with a 2% B-27 and GlutaMAX supplement (0.5 mM final). Tissues were dissociated in papain (Worthington) and debris was removed using OptiPrep density gradient media following cell dissociation. Cells were then loaded into 10x Genomics Chromium Single Cell System (10x Genomics) and libraries were generated using v3 or v3.1 chemistry following the manufacturer’s instructions. Libraries were sequenced on Illumina NovaSeq. Sequencing data were first processed through the Cell Ranger (v.3.10, 10x Genomics) with default parameters, aligned to the mm10 genome (refdata-cellranger-mm10-3.0.0), and matrix files were used for subsequent bioinformatic analysis.
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| |
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| Contributor(s) |
Kim DW, Tu K, Wei A, Lau A, Gonzalez-Gil A, Ling JP, Troncoso JC, Blackshaw PW, Schnaar RL, Li T |
| Citation(s) |
36536457 |
| |
| Submission date |
May 25, 2021 |
| Last update date |
Dec 23, 2022 |
| Contact name |
Dong Won Thomas Kim |
| E-mail(s) |
kimtho87@gmail.com
|
| Organization name |
Johns Hopkins University
|
| Department |
Neuroscience
|
| Lab |
Blackshaw lab
|
| Street address |
733 N.Broadway, MRB building (Rm 332)
|
| City |
Baltimore |
| State/province |
Maryland |
| ZIP/Postal code |
21205 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
|
| Samples (12)
|
| GSM5341447 |
12 months old-Cortex-Tau4RΔK-AP-Female TL4 |
| GSM5341448 |
12 months old-Cortex-WT-Female TL9 |
| GSM5341449 |
12 months old-Cortex-Tau4RΔK-Female TL10 |
| GSM5341450 |
12 months old-Cortex-APP;PS1-Female TL11 |
| GSM5341451 |
12 months old-Cortex-Tau4RΔK-AP-Female TL12 |
| GSM5341452 |
6 months old-Cortex-WT-Female TL13 |
| GSM5341453 |
6 months old-Cortex-Tau4RΔK-Female TL14 |
| GSM5341454 |
6 months old-Cortex-APP;PS1-Female TL15 |
| GSM5341455 |
6 months old-Cortex-Tau4RΔK-AP-Female TL16 |
|
| Relations |
| BioProject |
PRJNA732698 |
| SRA |
SRP321313 |
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