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

scREAD Data ID: AD00201

Species: Human

Region: Entorhinal Cortex

Condition: Control

Braak stage: NA; 0

Gender: Male

Age: mean age 77.6, range 67.3-91 years; 50-91 years

Datasets from the same experiment
Dataset information

Number of cells from source: 29993

Number of cells in scREAD after filtering: 29993

Number of identified cell types: 6

Dataset source 1:

Title: A Single-Cell Atlas of Entorhinal Cortex From Individuals With Alzheimer's Disease Reveals Cell-Type-Specific Gene Expression Regulation

Methodology: Single-nucleus RNA-seq

Protocol: DroNc-seq

GEO/synapse number: GSE138852

Pubmed ID: 31768052

Citation: Grubman A, Chew G, Ouyang JF, Sun G et al. A single-cell atlas of entorhinal cortex from individuals with Alzheimer’s disease reveals cell-type-specific gene expression regulation. Nat Neurosci 2019 Dec;22(12):2087-2097.

Dataset source 2:

Title: Molecular characterization of selectively vulnerable neurons in Alzheimer’s Disease

Methodology: Single-nucleus RNA-seq

Protocol: 10x Genomics

GEO/synapse number: GSE147528

Pubmed ID: NA

Citation: Leng K, Li E, Eser R, et al. Molecular characterization of selectively vulnerable neurons in Alzheimer’s Disease. bioRxiv; 2020. 10.1101/2020.04.04.025825.

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:
SLC1A2 3.098 0.834 0.106 0.00e+0
ADGRV1 2.86821 0.797 0.059 0.00e+0
RNF219-AS1 2.76788 0.704 0.024 0.00e+0
SLC1A3 2.54543 0.85 0.091 0.00e+0
APOE 2.50028 0.722 0.069 0.00e+0
GPC5 2.28437 0.816 0.163 0.00e+0
MT2A 2.2798 0.582 0.043 0.00e+0
FGFR3 2.2429 0.605 0.029 0.00e+0
NKAIN3 2.11467 0.679 0.093 0.00e+0
PITPNC1 2.10437 0.793 0.126 0.00e+0
DTNA 2.08441 0.827 0.171 0.00e+0
CST3 2.08133 0.617 0.073 0.00e+0
EMX2 2.04195 0.463 0.007 0.00e+0
GFAP 2.04057 0.418 0.04 0.00e+0
GJA1 1.99003 0.429 0.014 0.00e+0