Gene Expression
Nebulas
Gene Expression NebulasSummary: We investigated the effect of IL-13 neutralization on COVID-19 disease progression in mice.
Overall Design: We analyzed the bulk lung tissue transcriptomes in Covid19 infected mice treated with anti-IL-13 or isotype (IgG) control antibodies and uninfected mice as an additional control group. 8-16 week-old male Tg(K18-hACE2) 2Prlmn (Jackson Laboratories) mice were challenged with 5000 plaque forming units (PFUs) of SARS-CoV-2 Hong Kong/VM20001061/2020 (BEI 14 Resources) in 50 μL by an intranasal route under 100 μL ketamine/xylazine sedation. Mice were given 150 μg of anti-IL-13(Thermofisher, clone eBio1316H; cat # 16-7135-85) or an isotype matched control IgG (Thermofisher, clone eBRG1; cat # 16-4301-85) administered on day 0, 2, and 4 pi. Mice were euthanzied at 5 days post-infection and lung tissue was resected for RNA-sequencing analysis.
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| Treatment Protocol: | - |
| Extract Protocol: | Snip from lower inferior lobe was taken and RNA was extracted from murine lung tissue preserved in trizol by bead beating (tissuelyserII, Qiagen), followed by a phenol-chloroform extraction and RNA Isolation Kit (Qiagen). RNA quality was assessed using Agilent Tape station. Ribosomal RNA was depleted using the rRNA depletion kit (NEB E6310). |
| Library Construction Protocol: | Following rRNA 2 depletion cDNA libraries were prepared using the NEB ultra-directional library preparation kit 3 2.0 (NEB E7760) and indexed using the NEBNext Multiplex Oligos for Illumina (NEB E7335, E7500). Libraries were diluted and pooled. 15 libraries were sequenced on the Illumina Nextseq 500 using a 150 high output kit (400 Million 8 reads, 2x75bp paired end, 150 cycles) |
| Molecule Type: | rRNA- RNA |
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| Library Layout: | PAIRED |
| Library Strand: | Forward; - |
| Platform: | ILLUMINA |
| Instrument Model: | Illumina NextSeq 500 |
| Strand-Specific: | Specific; Unspecific |
| Data Resource | GEN Sample ID | GEN Dataset ID | Project ID | BioProject ID | Sample ID | Sample Name | BioSample ID | Sample Accession | Experiment Accession | Release Date | Submission Date | Update Date | Species | Race | Ethnicity | Age | Age Unit | Gender | Source Name | Tissue | Cell Type | Cell Subtype | Cell Line | Disease | Disease State | Development Stage | Mutation | Phenotype | Case Detail | Control Detail | Growth Protocol | Treatment Protocol | Extract Protocol | Library Construction Protocol | Molecule Type | Library Layout | Strand-Specific | Library Strand | Spike-In | Strategy | Platform | Instrument Model | Cell Number | Reads Number | Gbases | AvgSpotLen1 | AvgSpotLen2 | Uniq Mapping Rate | Multiple Mapping Rate | Coverage Rate |
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