scREAD A Single-cell RNA-Seq Database for Alzheimer's Disease
General information
Overview

scREAD Data ID: AD00106

Species: Human

Region: Prefrontal cortex

Condition: Control

Braak stage: 1 - 4; 1, 3, 4

Gender: Female

Age: 75-90+ years; 77-90+ years

Datasets from the same experiment
Dataset information

Number of cells from source: 56336

Number of cells in scREAD after filtering: 56329

Number of identified cell types: 7

Dataset source 1:

Title: Single-cell Transcriptomic Analysis of Alzheimer's Disease

Methodology: Single-nucleus RNA-seq

Protocol: 10x Genomics

GEO/synapse number: syn18485175

Pubmed ID: 31042697

Citation: Mathys, H., Davila-Velderrain, J., Peng, Z. et al. Single-cell transcriptomic analysis of Alzheimer’s disease. Nature 570, 332–337 (2019). 10.1038/s41586-019-1195-2

Dataset source 2:

Title: Human_and_Mouse Single-Nucleus Transcriptomics Reveal TREM2-dependent_and_TREM2-independent Cellular Responses in Alzheimer's Disease

Methodology: Single-nucleus RNA-seq

Protocol: 10x Genomics

GEO/synapse number: syn21125841

Pubmed ID: 31932797

Citation: Zhou Y, Song WM, Andhey PS, Swain A et al. Human_and_mouse single-nucleus transcriptomics reveal TREM2-dependent_and_TREM2-independent cellular responses in Alzheimer’s disease. Nat Med 2020 Jan;26(1):131-142.

Cell clustering

Cell type & subcluster:

Gene expression

Point size:

4
Differential expression (DE) / Gene set enrichment

Group:

Find differentially expressed genes in each cell type by comparing it to all of the others.

Cell type of interest:

Log2 fold-change cutoff:

0.5

Adjusted p-value cutoff:

10^-6
10^-5
10^-4
10^-3
0.01
0.05
0.1
1
DE direction:
CHI3L1 3.05977 0.298 0.054 0.00e+0
SLC1A2 2.81063 0.879 0.25 0.00e+0
GFAP 2.67174 0.85 0.109 0.00e+0
AQP4 2.37578 0.669 0.083 0.00e+0
ATP1A2 2.1107 0.686 0.105 0.00e+0
CST3 2.10118 0.879 0.239 0.00e+0
SLC1A3 2.0849 0.715 0.191 0.00e+0
GJA1 1.98208 0.538 0.035 0.00e+0
MT2A 1.97223 0.679 0.179 0.00e+0
ATP1B2 1.92475 0.633 0.139 0.00e+0
ANGPTL4 1.90442 0.408 0.016 0.00e+0
AHCYL1 1.86438 0.66 0.271 0.00e+0
APOE 1.83433 0.673 0.1 0.00e+0
F3 1.83164 0.457 0.026 0.00e+0
CLU 1.7663 0.921 0.593 0.00e+0