|
| Status |
Public on Aug 30, 2024 |
| Title |
sciMET-ATAC, human brain, BA46 |
| Sample type |
SRA |
| |
|
| Source name |
Brain BA46
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Brain BA46
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei were extracted using nuclei isolation buffer and gentle dounce homogenization
sciMET-ATAC libraries were prepared using 3-level single-cell combinatorial indexing workflow with an additional initial indexed tagmentation to capture chromatin accessibility prior to nucleosome disruption and genome-wide tagmentation
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
Cell-level methylation calls, amethyst analysis object, and fragments file for sciMET-ATAC technology
|
| Data processing |
Reads were processed using Premethyst and aligned to hg38
Methylation calls were analyzed using Amethyst
Assembly: hg38
Supplementary files format and content: Methylation calls in h5 format
Supplementary files format and content: Methylaiton metadata in amethyst object format
Supplementary files format and content: ATAC fragments in bed format
Library strategy: sciMET-ATAC
|
| |
|
| Submission date |
Jul 19, 2024 |
| Last update date |
Aug 30, 2024 |
| Contact name |
Andrew Adey |
| E-mail(s) |
adey@ohsu.edu
|
| Organization name |
Oregon Health & Science University
|
| Department |
MMG
|
| Lab |
Adey Lab
|
| Street address |
3181 S.W. Sam Jackson Park Rd, RHH, L103
|
| City |
Portland |
| State/province |
OR |
| ZIP/Postal code |
97239-3098 |
| Country |
USA |
| |
|
| Platform ID |
GPL30173 |
| Series (1) |
| GSE272699 |
sciMET-ATAC for simultaneous single-cell DNA methylation and chromatin accessibility analysis |
|
| Relations |
| BioSample |
SAMN41937078 |
| SRA |
SRX25272061 |
| SRA |
SRX25272062 |
| SRA |
SRX25272063 |
| SRA |
SRX25272064 |
