Description
Data Available
To access this data, please log into DSS and submit an application.
Within the application, add this dataset (accession NG00121) in the “Choose a Dataset” section.
Once approved, you will be able to log in and access the data within the DARM portal.
Description
Single-neuron amplified genome libraries were sequenced (WGS) on Illumina instruments and aligned to the human reference genome GRCh37. Linked-read analysis (LiRA) and SCAN-SNV were used to identify single-cell somatic mutations. The single-cell dataset includes a total of 319 single-neuron genome sequences (172 PFC-MDA, 78 HC-MDA, 69 PFC-PTA). Sequence files are in .bam format.
Sample Summary per Data Type
| Sample Set | Accession | Data Type | Number of Samples |
|---|---|---|---|
| Alzheimer’s disease single-neuron whole-genome sequencing – Miller 2022 | snd10029 | Single-Neuron WGS | 29 |
Available Filesets
| Name | Accession | Latest Release | Description |
|---|---|---|---|
| AD WGS – Miller: Single-neuron WGS BAM files | fsa000024 | NG00121.v1 | Single-neuron WGS BAM files |
| AD WGS – Miller: Phenotype files | fsa000025 | NG00121.v1 | Phenotype files |
View the File Manifest for a full list of files released in this dataset.
Subject Information
This study performed whole-genome sequencing of single neurons isolated from prefrontal cortex (PFC) and hippocampus CA1 (HC) of postmortem human brain of individuals with Alzheimer’s disease (AD)(Braak stage V-VI) or non-disease control, along with bulk whole-genome sequencing performed on each individual as a reference genome for variant calling. Single neuron genomes were amplified using multiple-displacement amplification (MDA) or primary template-directed amplification (PTA).
| Sample Set | Accession | Number of Subjects |
|---|---|---|
| Alzheimer’s disease single-neuron whole-genome sequencing – Miller 2022 | snd10029 | n = 29 |
Consent Levels
| Consent Level | Number of Subjects |
|---|---|
| HMB-IRB-PUB | n = 22 |
| DS-NEURO-IRB-PUB | n = 7 |
Visit the Data Use Limitations page for definitions of the consent levels above.
Acknowledgement
Acknowledgment statement for any data distributed by NIAGADS:
Data for this study were prepared, archived, and distributed by the National Institute on Aging Alzheimer’s Disease Data Storage Site (NIAGADS) at the University of Pennsylvania (U24-AG041689), funded by the National Institute on Aging.
Use the study-specific acknowledgement statements below (as applicable):
For investigators using any data from this dataset:
Please cite/reference the use of NIAGADS data by including the accession NG00121.
For investigators using AD Single-Neuron WGS - Miller (sa000022) data:
NIH Sponsoring Institute: NIA
Grant funding: NIH K08 AG065502