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| Status |
Public on Jul 09, 2024 |
| Title |
LAA, AF, CF93, snATACseq |
| Sample type |
SRA |
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| Source name |
Left atrial appendage
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Left atrial appendage
Sex: M
rhythm: AF
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| Extracted molecule |
other |
| Extraction protocol |
Left atrial appendage biopsies were collected before cardiopulmonary bypass and immediately, rinsed of blood, towel-dried and snap-frozen in liquid nitrogen until use for subsequent experiments.
Chromium Next GEM Single Cell Multiome ATAC + Gene Expression
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| Library strategy |
OTHER |
| Library source |
other |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
10X Genomics
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| Data processing |
We aligned FASTQ to Cellranger’s GRCh38-2020-A reference using the count function of cellranger-arc-2.0.0 for each sample. We then aggregated all samples using cellranger-arc aggr function. For downstream analyses, we used Seurat v4 and Signac. We kept ATAC peaks present in at least 10 cells. We removed low quality cells using the following thresholds: > 200 detected genes, > 400 detected peaks, <10% mitochondrial reads, > 2 transcription start site enrichment score and > 10% ATAC reads in peaks. We integrated the data using Harmony. We removed doublets using both scDblFinder scores and manual sub-clustering curation. We then re-clustered cells using seurat’s function FindMultiModalNeighbors() with the first 20 PCs of the RNAseq data and PCs 2-20 of the ATACseq data. Finally, we refined ATACseq peaks with cell-type labels using Signac’s CallPeaks function.
Assembly: hg38
Supplementary files format and content: Tab separated values matrix files
Library strategy: Single Cell Multiome ATAC + Gene Expression
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| Submission date |
Jul 25, 2023 |
| Last update date |
Jul 09, 2024 |
| Contact name |
Guillaume Lettre |
| E-mail(s) |
guillaume.lettre@mhi-humangenetics.org
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| Organization name |
Montreal Heart Institute
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| Street address |
5000 Belanger
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| City |
Montreal |
| State/province |
Quebec |
| ZIP/Postal code |
H1T 1C8 |
| Country |
Canada |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE238242 |
Atrial fibrillation variant-to-gene prioritization through cross-ancestry eQTL and single-nucleus multiomic analyses |
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| Relations |
| BioSample |
SAMN36705107 |
| SRA |
SRX21156248 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7661001_CF93ATAC.counts.tsv.gz |
15.4 Mb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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