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| Status |
Public on Sep 04, 2021 |
| Title |
sn-RNAseq of Pangolin Liver |
| Sample type |
SRA |
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| Source name |
Pangolin Liver
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| Organism |
Manis javanica |
| Characteristics |
tissue: Liver
age: Adult
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Tissue samples were obtained from a total of 11 animals, which included 1) four pet animals: a cat (Felis catus), a dog (Canis lupus familiaris), a hamster (Mesocricetus auratus) and a lizard (Anolis carolinensis); 2) two livestock species: a goat (Capra aegagrus hircus) and a rabbit (Oryctolagus cuniculus domesticus); 3) two poultry species: a duck (Anas platyrhynchos domesticus) and a pigeon (Columba livia domestica); 4) three wild animals: a tiger (Panthera tigris altaica), a pangolin (Manis javanica) and a deer (Cervus nippon). The Manis javanica samples were collected from a pangolin died of naturally cause in Guangdong Provincial Wildlife Rescue Center and were immediately stored in -80°C freezer after dissection. The samples from the tiger were obtained from a naturally dead tiger from the Siberian Tiger Park in Heilongjiang Province. Deer sample and corresponding genome assembly was kindly provided by institute of special animal and plant of sciences (ISAPS) of Chinese Academy of Agricultural Sciences. Other animals were obtained from farm market with the permissions from BGI Ethics Committee. Animals were kept in a pathogen-free environment and provided sufficient living space and adequate food and water. After the euthanasia of animals in accordance with the ethics of animal experiment guidelines issued by the Ministry of Science and Technology, China. Dissection was carried out quickly to separate each tissue. The collected tissues were rinsed by 1X PBS, then quick-frozen and stored in liquid nitrogen. The single cell nuclei of each tissue were separated by mechanical extraction method.85 Briefly, the tissues were first thawed, infiltrated by 1X homogenization buffer (containing 30mM CaCl2, 18mM Mg(Ac)2, 60mM Tris-HCl (pH 7.8), 320mM sucrose, 0.1% NP-40, 0.1mM EDTA and 0.2U/µl RNase inhibitor), then cut into smaller pieces, and the single nucleus was isolated by 2ml Dounce homogenizer set. After filtration with 30µm strainer, the nuclei extraction was resuspended by 1%BSA containing 0.2U/µl RNase inhibitor and span down at the speed of 500g for 10 min at 4°C (to carefully discard the cellular impurities within the supernatant). This step was repeated twice, and finally the nuclei were recollected with 0.1% BSA containing 0.2U/µl RNase inhibitor. Subsequently, DAPI was used to stain the nuclei, and the nucleus density was calculated under a fluorescence microscope to prepare for the subsequent library construction.
The separated single nucleus of different tissues were constructed using Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 (PN-1000075) following the standard user guide provided by manufacturer.
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
BGISEQ-500 |
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| Description |
single-cell gene expression of Manis javanica
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| Data processing |
Library strategy: snRNA-Seq
To facilitate the integration of cross-species lung single cell dataset, we converted genes from other species to mouse homologs. Firstly, we downloaded homologs between eight species (cat, tiger, dog, hamster, goat, rabbit, lizard, duck) and mouse using BioMart. As for pangolin, pigeon and deer, which lack homologs records on Ensemble. single-copy orthologs were identified from two species genomes, by cluster analysis of gene families using OrthoFinder (OrthoFinder version 2.3.3) with the default parameters. The single-copy genes were extracted from the OrthoFinder output file. Then, if a 1:1 match existed between a non-mouse gene and a mouse gene, the non-mouse gene name was converted to the mouse gene name.
Sequencing data were filtered using custom script and gene expression matrix were obtained by Cell Ranger 3.0.2 (10X Genomics).
Genome_build: dog: GCF_000002285.3; duck: GCA_002743455.1; tiger: GCF_000464555.1; hamster: GCA_000349665.1; lizard: GCA_000090745.1; pangolin: GCF_001685135.1; pigeon: GCF_000337935.1; goat: GCA_001704415.1; cat: GCA_000181335.4; rabbit: GCF_000003625.3.
Supplementary_files_format_and_content: tab-delimited text files include single cell-gene expression values for each Sample
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| Submission date |
Sep 02, 2021 |
| Last update date |
Sep 05, 2021 |
| Contact name |
CNSA CNGB |
| Organization name |
BGI
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| Street address |
BGI
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| City |
shenzhen |
| ZIP/Postal code |
518083 |
| Country |
China |
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| Platform ID |
GPL30582 |
| Series (1) |
| GSE183300 |
Single cell atlas for mammals, reptiles and birds |
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| Relations |
| BioSample |
SAMN20218756 |
| SRA |
SRX11506209 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5555225_Vthunter_0040_count_new_data_20210531.txt.gz |
10.0 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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