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Sample GSM7291236 Query DataSets for GSM7291236
Status Public on Jun 20, 2024
Title MS3_CA, snATACSeq
Sample type SRA
 
Source name white matter
Organism Homo sapiens
Characteristics tissue: white matter
lesion: CA
age: 61
postmortem delay: 21
Treatment protocol Fresh frozen tissue blocks
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
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Description 10x Genomics
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
 
Submission date May 03, 2023
Last update date Jun 20, 2024
Contact name Anne Hartebrodt
E-mail(s) anne.hartebrodt@fau.de
Organization name University of Southern Denmark
Street address Campusvej 55
City Odense
ZIP/Postal code 5230
Country Denmark
 
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
Relations
BioSample SAMN34568973
SRA SRX20209827

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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