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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 22, 2022 |
| Title |
infected, lung, male, rep2 |
| Sample type |
SRA |
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| Source name |
lung
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| Organism |
Macaca mulatta |
| Characteristics |
tissue: lung
infection: SARS-CoV-2
Sex: male
animal: infected animal #2
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Tissue blocks that stored at -80 refrigerators were homogenized and performed density gradient centrifugation to cleanup, single-nucleus suspension is the final product for 10X Genomics system.
Library construction was carried out in according to manufacturer's protocol.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
infected animal #2, male
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| Data processing |
Illumina Casava1.8 software used for basecalling
Reads were aligned to macaca mulatta pre-mRNA reference genome by Cell Ranger count (v3.1.0).
Alignment results of macaque data were aggragated by Cell Ranger aggr (v3.1.0).
Aggragated data of macaque were read into scanpy.
Assembly: macaca mulatta (release 95) pre-mRNA
Supplementary files format and content: The file Macaca_global_integration.h5ad is formatted by h5ad (created by scanpy), contains all samples in this study.
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| Submission date |
Nov 07, 2022 |
| Last update date |
Dec 22, 2022 |
| Contact name |
Qiang Ma |
| E-mail(s) |
[email protected]
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| Organization name |
Institute of Biophysics, Chinese Academy of Sciences
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| Street address |
Datun Road, #15
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| City |
Beijing |
| ZIP/Postal code |
100101 |
| Country |
China |
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| Platform ID |
GPL27943 |
| Series (1) |
| GSE217483 |
Single-nucleus transcriptomic profiling of multiple organs from rhesus macaque model with SARS-CoV-2 infection |
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| Relations |
| BioSample |
SAMN31647823 |
| SRA |
SRX18200610 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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