scATAC-seq

Question

[Bogdan]

Dear all,

for a successful scATAC-seq experiment, would you please let me know :

whet is the standard number of cells,

standard value of ATAC-seq median fragments per cell,

standard value of GEX median genes per cell ?

Thanks a lot,

Bogdan

Answer 1

[Bogdan]

I have found an answer :

• All Multiome ATAC + GEX datasets

  Fresh embryonic E18 mouse brain (5k)

  Estimated number of cells: 4,878 ATAC Mean raw read pairs per cell: 39,755 ATAC Median high-quality fragments per cell: 16,446 ATAC Number of peaks: 172,193 GEX Mean raw reads per cell: 97,172 GEX Median genes per cell: 3,120 GEX Median UMI counts per cell: 7,984 Linked genes: 10,481 Linked peaks: 56,250

  Fresh Frozen Lymph Node with B-cell Lymphoma (14k sorted nuclei)

  Estimated number of cells: 14,566 ATAC Mean raw read pairs per cell: 32,248 ATAC Median high-quality fragments per cell: 8,396 ATAC Number of peaks: 109,789 GEX Mean raw reads per cell: 25,917 GEX Median genes per cell: 1,186 GEX Median UMI counts per cell: 1,671 Linked genes: 12,382 Linked peaks: 58,474

  Frozen human healthy brain tissue (3k)

  Estimated number of cells: 3,233 ATAC Mean raw read pairs per cell: 95,897 ATAC Median high-quality fragments per cell: 22,881 ATAC Number of peaks: 134,030 GEX Mean raw reads per cell: 122,335 GEX Median genes per cell: 2,600 GEX Median UMI counts per cell: 6,966 Linked genes: 13,629 Linked peaks: 88,843

  PBMC from a healthy donor - granulocytes removed through cell sorting (3k)

  Estimated number of cells: 2,711 ATAC Mean raw read pairs per cell: 28,482 ATAC Median high-quality fragments per cell: 14,479 ATAC Number of peaks: 98,319 GEX Mean raw reads per cell: 60,701 GEX Median genes per cell: 1,791 GEX Median UMI counts per cell: 3,790 Linked genes: 8,664 Linked peaks: 53,127

  PBMC from a healthy donor - no cell sorting (10k)

  Estimated number of cells: 12,012 ATAC Mean raw read pairs per cell: 38,103 ATAC Median high-quality fragments per cell: 11,769 ATAC Number of peaks: 111,857 GEX Mean raw reads per cell: 69,129 GEX Median genes per cell: 1,719 GEX Median UMI counts per cell: 3,300 Linked genes: 13,958 Linked peaks: 79,187