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| Status |
Public on Dec 29, 2023 |
| Title |
E4 5XFAD mice, 96weeks, scRNAseq |
| Sample type |
SRA |
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| Source name |
Hippocampal and cortical regions of brain
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| Organism |
Mus musculus |
| Characteristics |
tissue: Hippocampal and cortical regions of brain
cell type: Cd45+ cells
genotype: 5XFADhet APOE-knockin
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| Extracted molecule |
total RNA |
| Extraction protocol |
Briefly, mice were anesthetized with a ketamine/xylazine cocktail and perfused with 25 ml of Ca2+/Mg2+-free DPBS (Sigma). Cortex and hippocampus were removed and placed in FACS buffer (PBS containing 5% FBS and 10 mM HEPES), minced with scissors, and incubated with 80 U/mL of collagenase D (Roche, 11088858001) at 37°C for 30 min. Collagenase was inactivated by adding 10 mM EDTA for an additional 5-min incubation at 37°C. Digested material was passed through a 70μm cell strainer, centrifuged at 1500rpm for 10min, pellet was then resuspended in 7mL of 38% Percoll followed by a centrifugation at 2000rpm for 30 min. Nonspecific binding to FC receptors was blocked by incubation with a CD16- and CD32-specific antibody (BD-Pharmingen 553141) for 15 min. Lastly, cells were washed and stained with an anti-CD45 antibody (Invitrogen 56-0451-82) and 0.05 µg/mL DAPI and, then washed and resuspended in FACS buffer. Cells were sorted on an LSR-II flow cytometer (Becton Dickinson) for singlet DAPI- CD45+ cells.
Libraries were prepared according to manufacturer's instructions (3'v2, 5'v2, multiome; 10X Genomics). For 10-week and 20-week samples, hashed demultiplexing was performed using Cell Ranger multi, with read R2 and pattern 5PNNNNNNNNNN(BC)NNNNNNNNN. Samples from APOE2-bearing mice were barcoded with GGTCGAGAGCATTCA; samples from APOE3-bearing mice were barcoded with CTTGCCGCATGTCAT; samples from APOE4-bearing mice were barcoded with AAAGCATTCTTCACG.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
10X Genomics 3'v2
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| Data processing |
Counts matrices were produced using Cell Ranger version 6.1.1. For downstream processing steps, refer to code available at https://github.com/alonmillet/apoe-ad-age-atlas.
Assembly: mm10
Supplementary files format and content: HDF5 file containing tab-separated values and matrix files.
Supplementary files format and content: Tab-separated file containing ATAC fragment information and accompanying index file.
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| Submission date |
Feb 16, 2023 |
| Last update date |
Dec 29, 2023 |
| Contact name |
Alon Millet |
| E-mail(s) |
amillet@rockefeller.edu
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| Organization name |
The Rockefeller University
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| Lab |
Tavazoie Lab
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| Street address |
1230 York Ave
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE225503 |
scRNAseq and scATACseq of Cd45+ cells from brains of 5XFAD mice bearing distinct APOE alleles and across age |
| GSE239999 |
An Exhausted-Like Microglial Population Accumulates in Aged and APOE4 Genotype Alzheimer’s Brains |
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| Relations |
| BioSample |
SAMN33328736 |
| SRA |
SRX19394239 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7049634_96wk_E4_filtered_feature_bc_matrix.h5 |
8.2 Mb |
(ftp)(http) |
H5 |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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