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| Status |
Public on Dec 08, 2022 |
| Title |
Day_7_Antler_ATAC |
| Sample type |
SRA |
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| Source name |
Antler_Velvet
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| Organism |
Rangifer tarandus |
| Characteristics |
facs strategy: Dead cells excluded using the forward/side scatter gating and viability dye (Fixable Viability Dye eFluor™ 780)
library preparation: 10X Genomics Chromium Next GEM Chip H version 1
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| Growth protocol |
All Reindeer (Rangifer tarandus) used for this project were housed in an outdoor enclosure at the University of Calgary Veterinary Sciences Research station in Calgary, Alberta for the entire length of the procedure. All experiments were done in accordance with guidelines set out by the University Animal Welfare Committee (UAWC), the Animal Care Committee (ACC), and with the recommendations and regulations of the Canadian Council on Animal Care and the Province of Alberta Animal Protection Act and Regulation.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Following the collection of pedicle excision, the sample was minced and incubated in dispase (StemCell Technologies) for 10-15 minutes at 37°C to remove epidermis. Remaining dermis tissue was minced and digested using collagenase (0.2%, Sigma) in 37 degree C water bath for 1-3 hours. To further dissociate the tissue and liberate single cells, the gentleMACS™ Octo Dissociator (Miltenyi Biotec) was used for 6 minutes on a homogenization program. DNase I (1x - Sigma) was also added to the tissue for the last 30 minutes in the water bath. Single cell suspensions were resuspended in cold FACS staining buffer (1% bovine serum albumin in Hank’s Buffered Salt Solution, HBSS; Life Technologies), strained through 100 µm and 70 µm filters (Falcon) and centrifuged at 1200 rpm for 6 minutes. Cell pellets were resuspended in FACS staining buffer and quantified. Viability dye eFlour780 (eBiosciences) was used to exclude dead cells using FACSAria III (BD Biosciences). Of note, identical tissue processing steps were followed as described in GSE142854 to enable side-by-side comparisons with Day 0 Back and Day 0 Antler scRNA-Seq samples.
The sample was prepared according to 10X Genomics ChromiumTM Single Cell 3’ Reagent Guidelines v3 Chemistry. Briefly, single cells were sorted into 0.1% BSA–HBSS and partitioned into Gel Bead-In-EMulsions (GEMs) using 10xTM GemCodeTM Technology. This process lysed cells and enabled barcoded reverse transcription of RNA, generating full-length cDNA from poly-adenylated mRNA. DynaBeads® MyOneTM Silane magnetic beads were used to remove leftover biochemical reagents, then cDNA was amplified by PCR over 10 cycles. Quality control size gating was used to select cDNA amplicon size prior to library construction. Read 1 primer sequences were added to cDNA during GEM incubation. P5 primers, P7 primers, i7 sample index, and Read 2 primer sequences were added during library construction. Quality control and cDNA quantification was performed using Agilent High Sensitivity DNA Kit. Sequencing was performed using Illumina NovaSeq S2 flow cell at the Center for Health Genomics and Informatics at the University of Calgary.
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| Library strategy |
RNA-Seq |
| Library source |
genomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Recovered: 7,176 cells
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| Data processing |
All raw FASTQs reads were aligned to bovine (Bos_taurus.ARS-UCD1.2.103) genome using cellranger-atac count.
Genome_build: Bos_taurus (made cellranger compatible using cellranger-mkref pipeline; Reference Genome provided as part of the submission)
Supplementary_files_format_and_content: Filtered peak barcode matrix and filtered tf barcode matrix in hdf5 format from CellRanger-atac count (transcriptome = Bos_taurus)
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| Submission date |
Jun 08, 2021 |
| Last update date |
Dec 08, 2022 |
| 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 |
GPL27966 |
| Series (2) |
| GSE168748 |
Skin regeneration is enabled in the absence of fibroblast inflammatory priming |
| GSE176360 |
Single-cell chromatin landscapes supporting fibroblast polarization drives skin regeneration versus fibrosis in adult reindeer |
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| Relations |
| BioSample |
SAMN19605996 |
| SRA |
SRX11092315 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5363185_Day_7_Antler_ATAC_peaks.bed.gz |
1.3 Mb |
(ftp)(http) |
BED |
| GSM5363185_Day_7_Antler_filtered_peak_bc_matrix.h5 |
92.6 Mb |
(ftp)(http) |
H5 |
| GSM5363185_Day_7_Antler_filtered_tf_bc_matrix.h5 |
8.0 Mb |
(ftp)(http) |
H5 |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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