|
| Status |
Public on Dec 29, 2023 |
| Title |
E2/E3/E4 5XFAD mice, 60 weeks, high and low abeta uptake, scRNAseq |
| Sample type |
SRA |
| |
|
| Source name |
Hippocampal and cortical regions of brain
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Hippocampal and cortical regions of brain
cell type: Cd45+ cells
genotype: 5XFADhet APOE-knockin
|
| 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 (5'v2, multiome; 10X Genomics).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| 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: Feature barcode matrix output from Cell Ranger.
|
| |
|
| Submission date |
Aug 03, 2023 |
| Last update date |
Dec 29, 2023 |
| Contact name |
Alon Millet |
| E-mail(s) |
amillet@rockefeller.edu
|
| Organization name |
The Rockefeller University
|
| Lab |
Tavazoie Lab
|
| Street address |
1230 York Ave
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE239974 |
scRNAseq of Cd45+ cells from brains of ApoE-variant Alzheimer's mice sorted by ex-vivo amyloid beta uptake |
| GSE239999 |
An Exhausted-Like Microglial Population Accumulates in Aged and APOE4 Genotype Alzheimer’s Brains |
|
| Relations |
| BioSample |
SAMN36825687 |
| SRA |
SRX21236942 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7679367_abeta_allcells.rds.gz |
1019.2 Mb |
(ftp)(http) |
RDS |
| GSM7679367_abeta_mglia.rds.gz |
766.6 Mb |
(ftp)(http) |
RDS |
| GSM7679367_sample_feature_bc_matrix_e2_hi.h5 |
5.6 Mb |
(ftp)(http) |
H5 |
| GSM7679367_sample_feature_bc_matrix_e2_lo.h5 |
4.8 Mb |
(ftp)(http) |
H5 |
| GSM7679367_sample_feature_bc_matrix_e3_hi.h5 |
5.7 Mb |
(ftp)(http) |
H5 |
| GSM7679367_sample_feature_bc_matrix_e3_lo.h5 |
5.3 Mb |
(ftp)(http) |
H5 |
| GSM7679367_sample_feature_bc_matrix_e4_hi.h5 |
5.5 Mb |
(ftp)(http) |
H5 |
| GSM7679367_sample_feature_bc_matrix_e4_lo.h5 |
4.4 Mb |
(ftp)(http) |
H5 |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
