Gene Expression
Nebulas
Gene Expression NebulasSummary: We used Drop-seq and next generation sequencing to determine gene expression differences in dogs with atopic dermatitis and healthy dogs in peripheral blood mononuclear cells in an unbiased way. Using Seurat, we find 13 discrete immune cells clusters, including a cluster enriched for Gata3 expressing T cells with 95 differentially expressed genes between healthy and allergic dogs.
Overall Design: PBMCs from 5 dogs diagnosed with atopic dermatitis and 5 matched healthy dogs were analyzed using Drop-seq and Seurat, and analyzed on a NextSeq500.
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| Growth Protocol: | - |
| Treatment Protocol: | - |
| Extract Protocol: | PBMCs were isolated from canine blood using density gradient centrifugation with Ficoll- Paque Premium (GE Healthcare, Chicago, IL, USA) and washed in flow cytometry buffer. |
| Library Construction Protocol: | Drop-seq protocol provided online by MacCarroll lab (version 3.1, 12/28/2015). Nextera XT Library Preparation Kit; Drop-seq protocol provided online by MacCarroll lab (version 3.1, 12/28/2016). Nextera XT Library Preparation Kit; Drop-seq protocol provided online by MacCarroll lab (version 3.1, 12/28/2017). Nextera XT Library Preparation Kit; Drop-seq protocol provided online by MacCarroll lab (version 3.1, 12/28/2018). Nextera XT Library Preparation Kit; Drop-seq protocol provided online by MacCarroll lab (version 3.1, 12/28/2019). Nextera XT Library Preparation Kit; Drop-seq protocol provided online by MacCarroll lab (version 3.1, 12/28/2021). Nextera XT Library Preparation Kit; Drop-seq protocol provided online by MacCarroll lab (version 3.1, 12/28/2022). Nextera XT Library Preparation Kit; Drop-seq protocol provided online by MacCarroll lab (version 3.1, 12/28/2023). Nextera XT Library Preparation Kit; Drop-seq protocol provided online by MacCarroll lab (version 3.1, 12/28/2024). Nextera XT Library Preparation Kit |
| Molecule Type: | poly(A)+ RNA |
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| Library Layout: | PAIRED |
| Library Strand: | Forward |
| Platform: | ILLUMINA |
| Instrument Model: | Illumina NextSeq 500 |
| Strand-Specific: | Specific |
| 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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