|
| Status |
Public on Nov 24, 2021 |
| Title |
wild-type neonate scATAC-seq |
| Sample type |
SRA |
| |
|
| Source name |
trunk skin
|
| Organism |
Mus musculus |
| Characteristics |
tissue: trunk skin
strain: C57B16
genotype: wild-type
age: postnatal day 0 (P0)
|
| Treatment protocol |
No treatment or cell sorting were utilized.
|
| Growth protocol |
Cells were freshly isolated.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were isolated from mouse skin samples as in Jensen & Driskell et al. Nature Protocols (2010). Nuclei for scATAC-seq were isolated using an optimized version of 10x Genomics protocol CG000169 Rev D.
10x Genomics Chromium Single Cell 3' Kit V3.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
WT1 to WT4
Isolated cells were pooled from each sample prior to library construction; both scRNA-seq and scATAC-seq were run in parallel from the same pool of cells.
Accessible DNA fragments
|
| Data processing |
CellRanger 5.0.0's cellranger function to align Fastq files to mm10 for scRNA-seq.
cellranger-atac 1.2.0 function to align Fastq files to mm10 for scATAC-seq.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Cell Ranger 1.2.0 processing of FASTQ to standard scATAC-seq and scRNA-seq outputs.
Supplementary_files_format_and_content: peaks.bed: peak coordinates for scATAC from the P0 WT mice; default cell ranger output in filtered_peak_bc_matrix folder.
Supplementary_files_format_and_content: barcodes.tsv: single-cell barcodes for P0 WT scATAC; default cell ranger output in filtered_peak_bc_matrix folder.
Supplementary_files_format_and_content: matrix.mtx: filtered peak reads for P0 WT scATAC; default cell ranger output in filtered_peak_bc_matrix folder.
Supplementary_files_format_and_content: unpublished_peaks.bed: peak coordinates for scATAC from a currently unpublished dataset and experiment. This unpublished_peaks.bed is used to create a common set of peak coordinates in order to allow two scATAC-seq dataset Seurat objects to be merged into one Seurat object. The peak coordinates between the two Seurat objects must be the same, so we use these unpublished peak coordinates to create a common set of peak coordinates in order to allow direct merging of these unpublished samples with the P0 WT dataset that is analyzed in this study as part of a manuscript that is currently in progress. The peaks.bed file is genomic coordinates and does not affect the P0 WT sequencing data in any way.
Supplementary_files_format_and_content: singlecell.csv: metadata for P0 WT scATAC.
Supplementary_files_format_and_content: fragments.tsv.gz: peak reads for P0 WT scATAC.
Supplementary_files_format_and_content: fragments.tsv.gz.tbi: indices to quickly call P0 WT scATAC fragments.tsv data into R w/o reading the entire fragments.tsv.gz file into memory.
Supplementary_files_format_and_content: WT_filtered_feature_bc_matrix.h5: P0 WT scRNA reads, barcodes, metadata.
|
| |
|
| Submission date |
Nov 19, 2021 |
| Last update date |
Nov 24, 2021 |
| Contact name |
Sean Thompson |
| Organization name |
Washington State University
|
| Department |
School of Molecular Biosciences
|
| Lab |
Driskell Lab
|
| Street address |
BLS 240
|
| City |
Pullman |
| State/province |
WA |
| ZIP/Postal code |
99164 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE189210 |
Parallel single cell multi-omics analysis of neonatal skin reveals transitional fibroblast states that restrict differentiation into distinct fates |
|
| Relations |
| BioSample |
SAMN23309724 |
| SRA |
SRX13178720 |
