DOI: 10.5061/dryad.0zpc8672f
title: scATAC data from: Organization of the human intestine at single cell resolution

description: The human adult intestinal system is a complex organ that is approximately
 9 meters long and performs a variety of complex functions including
 digestion, nutrient absorption, and immune surveillance. We performed
 snATAC-seq on 8 regions of of the human intestine (duodenum,
 proximal-jejunum, mid-jejunum, ileum, ascending colon, transverse colon,
 descending colon, and sigmoid colon) from 9 donors (B001, B004, B005,
 B006, B008, B009, B010, B011, and B012). In the corresponding paper, we
 find cell compositions differ dramatically across regions of the intestine
 and demonstrate the complexity of epithelial subtypes. We map gene
 regulatory differences in these cells suggestive of a regulatory
 differentiation cascade, and associate intestinal disease heritability
 with specific cell types. These results describe the complexity of the
 cell composition, regulation, and organization in the human intestine, and
 serve as an important reference map for understanding human biology and
 disease.
description: For a detailed description of each of the steps of
 protocols and processes to obtain this data see the detailed materials and
 methods in the associated manuscript. Briefly, intestine pieces from 8
 different sites across the small intestine and colon were flash frozen.
 Nuclei were isolated from each sample and the resulting nuclei were
 processed with either 10x scRNA-seq using Chromium Next GEM Single Cell 3’
 Reagent Kits v3.1 (10x Genomics, 1000121) or Chromium Next GEM Chip G
 Single Cell Kits (10x Genomics, 1000120) or 10x multiome sequencing using
 Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Kits (10x
 Genomics, 1000283).   Initial processing of snATAC-seq data was done with
 the Cell Ranger ATAC pipeline and initial processing of the mutiome data,
 including alignment and generation of fragments files and expression
 matrices, was performed with the Cell Ranger ARC pipeline. The fragments
 files from these pipelines are included here. Downstream processing was
 performed in R.
description: The dataset includes the fragments file generated by Cell Ranger
 ATAC or Cell Ranger ARC for each individual sample included in the study.
 For each sample there is a ***_atac_fragments.tsv.gz file and a
 ***_atac_fragments.tsv.gz.tbi file.  In addition to the
 individual fragments files, we include peak barcode matrices. These are
 divided into separate matrices for the duodenum epithelial cells, jejunum
 epithelial cells, ileum epithelial cells, colon epithelial cells, stromal
 cells, and immune cells. Each peak matrix is stored in three files. The
 ***_peak_matrix.mtx file contains the matrix data, the
 ***_peak_matrix_cells.tsv file contains the cell barcodes represented in
 the matrix, and the ***_peaks.bed contains the peaks represented in the
 matrix. They are also divided into separate matrices for cells from the
 multiome and non-multiome samples, with the non-multiome files having the
 "non_multiome_" prefix. The list of all the peak matrix files is
 outlined in the peak_matrix_metadata.csv file. These files can be opened
 with any programming language.  A list of the final
 cell annotations are also included. Note that the multiome annotations are
 the same as the multiome RNA annotations. These files are titled
 scATAC_non_multiome_cell_types_***.tsv for the non-multiome cells and
 scATAC_multiome_cell_types_***.tsv for the multiome cells. Each of these
 files has a column for the cell ID consisting of the sample and barcode
 (Cell) and the cell type annotation of the corresponding cell (CellType).
 These files can be opened with any programming language. 
 A metadata file (atac_sample_location_metadata.csv) is also
 included that contains columns for the ATAC sample name, the RNA sample
 name, the sample name without location replicates indicated, the donor the
 sample was collected from, the location in the intestine the sample was
 collected from, the fragments file name, and the index file
 name. See the README for additional details on files
 included in the submission.