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| Status |
Public on Jan 13, 2022 |
| Title |
Analysis of tissue-derived alveolar and monocyte-derived alveolar macrophages at day 7 and day 14 post-nippostrongylus brasiliensis infection. |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Alveolar macrophages from Cx3cR1-CreER x Rosa26-tandem dimer Tomato(TdT) control and infected mice were sort-purified on live CD45+CD64+F4/80+CD11c+SiglecF+ and then sorted based on expression of TdT, with tissue-resident cells being TdT- and monocyte-derived cells TdT+. Illumina-compatible libraries were generated using the NEBNext Ultra II DNA Library Prep Kit for Illumina (catalog no. E7645S; New England BioLabs) and sequenced using an Illumina NextSeq 550 in a single-end 75-base pair (bp) read configuration. Bulk RNA-seq analysis was performed in accordance with the nf-core RNA-seq guidelines v.1.4.2. The output reads were aligned to the GRCm38 genome using STAR, followed by gene count generation using featureCounts and StringTie. Read counts were normalized and compared for differential gene expression using DESeq2 with significance at a false discovery rate-adjusted P<0.05. We report that at day 7 monocyte-derived alveolar macrophages had a gene expression profile distinct from tissue-derived alveolar macrophages while by day 14 the monocyte-derived macrophages had assumed gene expression profiles more similar to tissue-derived alveolar macrophages, as determine by pairwise Euclidean distance calculation and principal components analysis.
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| Overall design |
Examination and analysis of tissue-resident alveolar macrophages versus monocyte-derived macrophages at two different time points post-nippostrongylus brasiliensis infection.
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| Contributor(s) |
Ponessa JJ, Siracusa MC, Lemenze A, Gause WC |
| Citation(s) |
35021079 |
| |
| Submission date |
Nov 27, 2021 |
| Last update date |
Jan 13, 2022 |
| Contact name |
Alexander Lemenze |
| Organization name |
Rutgers
|
| Street address |
185 South Orange Ave
|
| City |
Newark |
| State/province |
New Jersey |
| ZIP/Postal code |
07103 |
| Country |
USA |
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| Platforms (1) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (21)
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| Relations |
| BioProject |
PRJNA784119 |
| SRA |
SRP348183 |
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