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| Status |
Public on Jun 20, 2024 |
| Title |
MS3_NAWM, snATACSeq |
| Sample type |
SRA |
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| Source name |
white matter
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| Organism |
Homo sapiens |
| Characteristics |
tissue: white matter
lesion: NAWM
age: 61
postmortem delay: 21
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| Treatment protocol |
Fresh frozen tissue blocks
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
FANS-sorted nuclei from postmortem human brain tissue with anti-lamin A/C antibody
Guidelines from 10x Genomics (CG000209 Rev C, 10x Genomics)
Indexed adaptor pooling for transposase-accessible DNA sequencing with 1% PhIX
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
10x Genomics
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| Data processing |
Raw data processing was performed using cellranger-atac pipeline (version 2.0.0, with reference refdata-cellranger-arc-GRCh38-2020-A-2.0.0)
Data processing using Seurat in Signac, cells with fewer than 3000 or more that 20000 fragments per peak, blacklist ratio of more than 0.05, nucleosome signal of less than 4, TSS enrichment of more than 2, and predicted doublets (scDblFinder) were removed.
Batch integration and label transfer from matching scRNA data using harmony.
Differential accessibiliy, motifs and footprints where called using Signac
Assembly: GRCh38
Supplementary files format and content: filtered_peak_bc_matrix.h5; filtered_tf_bc_matrix.h5; the cellranger output
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| Submission date |
May 03, 2023 |
| Last update date |
Jun 20, 2024 |
| Contact name |
Anne Hartebrodt |
| E-mail(s) |
anne.hartebrodt@fau.de
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| Organization name |
University of Southern Denmark
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| Street address |
Campusvej 55
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| City |
Odense |
| ZIP/Postal code |
5230 |
| Country |
Denmark |
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| Platform ID |
GPL24676 |
| Series (2) |
| GSE231584 |
DNA accessibility profiling at the single nucleus level of post mortem white matter brain tissue of patients with progressive multiple sclerosis and non-neurological disease controls |
| GSE231587 |
Progressive multiple sclerosis |
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| Relations |
| BioSample |
SAMN34568972 |
| SRA |
SRX20209828 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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