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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jun 09, 2023 |
| Title |
CH-Head_3 |
| Sample type |
SRA |
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| Source name |
head skin
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| Organism |
Sus scrofa |
| Characteristics |
breed: Chenghua
tissue: head skin
cell type: Skin cells
Sex: female
age: 180 days old
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| Extracted molecule |
total RNA |
| Extraction protocol |
Single-cell transcriptome analyze from three CH pigs at six different anatomical body areas (head, ear, shoulder, back, abdomen, leg) and three LW pigs with one region (back).The fresh skin samples were thoroughly scraped off the hair and subcutaneous fat and were washed thrice with ice-cold Dulbecco’s Phosphate-Buffered Salline (1ｘDPBS).
Single-cell suspension were subjected to a series of progress, including droplet encapsulation, emulsion breakage, mRNA captured bead collection, reverse transcription, and cDNA amplification and purification, to generate barcoded libraries
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-G400 |
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| Description |
Skin, replicate 3
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| Data processing |
Cells genes were expressed in less than three cells, and cells were removed on the basis of detected genes number with a minimal of 200. Mitochondrial gene expression was set at a threshold of 5% for per cell
Assembly: Sus scrofa11.1
Supplementary files format and content: Tab-separated values files and matrix files
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| Submission date |
Feb 16, 2023 |
| Last update date |
Jun 09, 2023 |
| Contact name |
Qin Zou |
| E-mail(s) |
zouqin182023@126.com
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| Organization name |
Sichuan Agricultural University
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| Street address |
No.211, Huimin Road
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| City |
Chengdu |
| ZIP/Postal code |
611130 |
| Country |
China |
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| Platform ID |
GPL29847 |
| Series (1) |
| GSE225416 |
A single-cell transcriptome atlas of pig skin characterizes anatomic positional heterogeneity |
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| Relations |
| BioSample |
SAMN33325484 |
| SRA |
SRX19391821 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7048219_Head_3_barcodes.tsv.gz |
30.3 Kb |
(ftp)(http) |
TSV |
| GSM7048219_Head_3_features.tsv.gz |
153.9 Kb |
(ftp)(http) |
TSV |
| GSM7048219_Head_3_matrix.mtx.gz |
37.9 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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