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| Status |
Public on Oct 12, 2021 |
| Title |
Ctrl |
| Sample type |
SRA |
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| Source name |
Biopsy operation liver
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| Organism |
Sus scrofa |
| Characteristics |
cell type: Non-Parenchymal Cells (NPC)
treatment: Oil
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Liver tissues minipig were washed twice with cold PBS, minced, and incubated in a digestive mixture (1 mg/ml collagenase I and 1mg/ml dispase II in PBS) on an orbital shaker at 37 °C, for 15 min. After 15 min, liver tissues were suspended to ensure complete dissociation. Digested liver sample was homogenous with minimal chunks. Digested tissues were filtered through cell strainer multiple times, and cells were collected at 400 g for 5 min. After red blood cells were removed with RBC lysis buffer ( Solarbio) and washed once, hepatocytes and NPCs were separated by an additional centrifugation step at 50 g for 5 min at 4 °C.
Single cells were processed in the following steps: GEM generation & Barcoding, GEM-RT cleanup & cDNA amplification, and library construction, and finally were sequenced on an Illumina Nova-seq 6000 (Illumina).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
one sample form pig liver
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| Data processing |
The sequences from scRNA-Seq of pig and minipig liver NPCs were aligned to pig (Sus scrofa) transcriptome (Sscrofa11.1) using Hisat2 v2.0.5
Low-quality cells expressing less than 200 genes as well as genes expressed in less than 3 cells were filtered. Mitochondrial gene content percentage thresholds were set to filter pig liver NPCs.
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: matrix files
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| Submission date |
Aug 04, 2021 |
| Last update date |
Oct 12, 2021 |
| Contact name |
Bi-Sen Ding |
| E-mail(s) |
bsding@outlook.com
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| Organization name |
Weill Cornell
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| Street address |
York Avenue
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
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| Platform ID |
GPL26351 |
| Series (1) |
| GSE181483 |
Therapeutic landscape of targeting epigenetically reprogrammed vascular adaptome in the fibrotic liver of multiple species |
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| Relations |
| BioSample |
SAMN20585100 |
| SRA |
SRX11651008 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5503300_Ctrl_barcodes.tsv.gz |
71.5 Kb |
(ftp)(http) |
TSV |
| GSM5503300_Ctrl_genes.tsv.gz |
146.4 Kb |
(ftp)(http) |
TSV |
| GSM5503300_Ctrl_matrix.mtx.gz |
36.4 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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