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| Status |
Public on Dec 19, 2021 |
| Title |
pig_HMA2 |
| Sample type |
SRA |
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| Source name |
liver NPC
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| Organism |
Sus scrofa |
| Characteristics |
treatment: MGCD&AZA treatment after fibrosis
cell type: Non-Parenchymal Cells (NPC)
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| Extracted molecule |
total RNA |
| Extraction protocol |
liver were removed, NPC were isolated on ice, and
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
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).
The sequences from scRNA-Seq of pig and minipig liver NPCs were aligned to pig (Sus scrofa) transcriptome (Sscrofa11.1) and human (Homo sapiens) transcriptome (GRCh37)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
Genome_build: Sscrofa11.1/GRCh37
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
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| Submission date |
Dec 18, 2021 |
| Last update date |
Dec 19, 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 |
SAMN24195684 |
| SRA |
SRX13446173 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5741403_pig_HMA2.tar.gz |
32.3 Mb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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