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| Status |
Public on Sep 23, 2020 |
| Title |
E844-LoM-Naive |
| Sample type |
SRA |
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| Source name |
Lung organoid
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| Organisms |
Homo sapiens; Mus musculus |
| Characteristics |
mouse model: LoM
time point (days post infection): Naive
disease state: Naive
tissue: Lung organoid
cell lining: Epithelial
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| Treatment protocol |
SARS-CoV-2 infected LoM
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| Growth protocol |
Viruses were directly injected into the human lung tissue of LoMs and lung tissue collected either 2, 6, or 14 days post-exposure for virus titer determination and/or analysis by histology, electron microscopy, or RNA-seq
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Trizol Plus RNA extraction kit (Thermo Fisher)
NEBNext Ultra II library prep kit with polyA RNA selection
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
E844-LoM-Naive
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| Data processing |
Sequence quality was assessed using FASTQC (v).
No issues were detected with the data and quality was typical for RNA extracted from fresh frozen material.
A small amount of index hopping was detected (0.09%) due to the single indices used in the library preparation.
Raw reads were mapped to the human, mouse, and SARS-CoV-2 reference genomes simultaneously (GRCh38.p13, GRCm38.p6 M25, NC_045512, respectively) using the BBsplit function in BBmap (version 38.86). This step minimized cross mapping of reads among genomes.
We then mapped and quantified on a transcript and gene model basis using STAR (version 2.7.5a) and Salmon (version 1.2.1)
Reads mapping to multiple locations were dropped from analysis.
Genome_build: GRCh38.p13, GRCm38.p6 M25, NC_045512
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
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| Submission date |
Jul 28, 2020 |
| Last update date |
Sep 23, 2020 |
| Contact name |
Paul O Grant |
| E-mail(s) |
paul_grant@med.unc.edu
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| Phone |
7043145422
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| Organization name |
UNC SOM
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| Department |
BARC
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| Street address |
3105 Neuoscience Research Building
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| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27516 |
| Country |
USA |
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| Platform ID |
GPL25526 |
| Series (1) |
| GSE155286 |
SARS-CoV-2 infection is effectively treated and prevented by EIDD-2801 |
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| Relations |
| BioSample |
SAMN15660599 |
| SRA |
SRX8839385 |
| 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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