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Sample GSM7049627 Query DataSets for GSM7049627
Status Public on Dec 29, 2023
Title E2/E3/E4 5XFAD mice, 10weeks, 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 (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.
 
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description 10X Genomics 5'v2
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.
 
Submission date Feb 16, 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)
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
Relations
BioSample SAMN33328743
SRA SRX19394233

Supplementary file Size Download File type/resource
GSM7049627_10wk_E2_sample_feature_bc_matrix.h5 9.3 Mb (ftp)(http) H5
GSM7049627_10wk_E3_sample_feature_bc_matrix.h5 9.1 Mb (ftp)(http) H5
GSM7049627_10wk_E4_sample_feature_bc_matrix.h5 10.1 Mb (ftp)(http) H5
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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