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| Status |
Public on Aug 04, 2020 |
| Title |
D14 Large Wound Center scATAC-Seq |
| Sample type |
SRA |
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| Source name |
14 days post injury skin wound
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| Organism |
Mus musculus |
| Characteristics |
transgenic strain: Hic1CreERT2:TDTmt
background: C57BL/6J
tissue: skin wound
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| Treatment protocol |
Despite our experiments being performed on Hic1CreERT2:TDTmt transgenics, cre-recombination was not initiated as no tamoxifen was applied.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Large wounds from adult mice (n = 3) were dissected and enzymatically dissociated with dispase (StemCell Technologies) for 20 mins at 37 oC to remove the epidermis. Remaining dermis was dissociated using 0.2% collagenase for 2 hours at 37oC. Cell suspensions were diluted with cold Hank’s Buffered Salt Solution (HBSS; Life Technologies), strained through 40 µm cell filters (Falcon) and centrifuged at 280 X g. Liberated single cells were re-suspended in bovine serum album in HBSS before FACS purification. For FACS purification, a stringent forward and side scatter gates were used to exclude debris, and cell doublets. Following FACS, single nucleus was isolated, washed, and counted prior to use with the Chromium Single Cell ATAC protocol (as described in CG000169, Demonstrated Protocol for Nuclei Isolation ATAC Sequencing Rev B document at: https://support.10xgenomics.com/single-cell-atac/sample-prep/doc/demonstrated-protocol-nuclei-isolation-for-single-cell-atac-sequencing).
Libraries were prepared according to 10X Genomics Chromium Single Cell ATAC Library & Gel Bead Kit Chemistry. Briefly, single nuclei were first treated in bulk with Tn5 transposase to preferentially insert sequencing adaptors into accessible DNA regions. Transposed nuclei are then partitioned into GEMs in the 10x Chromium Controller. All the DNA fragments from the same nucleus share a common 10x barcode. The barcoded, accessible DNA fragments are subsequently pooled for downstream processing and library preparation. Next generation sequencing was performed using Illumina HiSeq 4000 PE with a targeted sequencing depth of >10,000 median fragments per cell. 77.4% of the fragments overlapped a targeted region and fraction of transposition events in peaks was 53.2%.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
FACS strategy: No FACS Enrichment for TDTmt. Hic1CreERT2:TDTmt transgenic strain is utilized to corroberate this dataset with our previous scRNA-Seq studies (GEO Deposits: GSE108677, GSE115543).
FACS sorted cells: 10,000 cells; Recovered: 1,578 cells
single-cell ATAC-Seq
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| Data processing |
All raw base call (BCL) files generated by Illumina® sequencers were converted to FASTQ files using cellranger-atac mkfastq function, a wrapper around bcl2fastq from Illumina®, with additional 10x Genomics-specific features. Next, read filtering and alignment, barcode counting, and identification of transposase cut sites were detected using cellranger-atac count function using the cellranger-atac-specific mm10 reference package. The resulting filtered peak-barcode matrix was imported into Cicero, an R toolkit specifically designed for analyzing single-cell chromatin accessibility experiments.
Genome_build: refdata-cellranger-atac-mm10-1.0.0 (mm10 with pre-generated indices and other data required to run CellRanger-ATAC)
Supplementary_files_format_and_content: Filtered peak-barcode matrix output from CellRanger-ATAC (containing only detected cellular barcodes)
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| Submission date |
May 21, 2019 |
| Last update date |
Aug 04, 2020 |
| Contact name |
Jeff Biernaskie |
| E-mail(s) |
jabierna@ucalgary.ca
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| Phone |
4032107306
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| Organization name |
University of Calgary
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| Department |
Comparative Biology and Experimental Medicine
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| Lab |
Biernaskie Lab
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| Street address |
3330 Hospital Drive NW
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| City |
Calgary |
| State/province |
Alberta |
| ZIP/Postal code |
T2N4N1 |
| Country |
Canada |
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| Platform ID |
GPL21103 |
| Series (2) |
| GSE131600 |
Single-cell ATAC-Seq of cells recruited to regenerative portions of large skin wounds. |
| GSE155678 |
Distinct Regulatory Programs Control the Latent Regenerative Potential of Dermal Fibroblasts during Wound Healing |
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| Relations |
| BioSample |
SAMN11811224 |
| SRA |
SRX5880163 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3790766_sample_1_barcodes.tsv.gz |
7.0 Kb |
(ftp)(http) |
TSV |
| GSM3790766_sample_1_matrix.mtx.gz |
42.3 Mb |
(ftp)(http) |
MTX |
| GSM3790766_sample_1_peaks.bed.gz |
756.4 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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