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| Status |
Public on Jan 14, 2022 |
| Title |
Bulk RNA sequencing of WT and Batf-/- ILC2s sorted from lungs at day 9 after influenza virus infection |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Activated type 2 innate lymphoid cells (ILC2s) accumulate and promote inflammatory resolution and tissue repair in host defense against acute respiratory viral infections. However, whether an ILC2 subset that specializes in wound healing exists, and the mechanisms by which ILC2 cells contribute to tissue repair remain elusive. Using single-cell RNA-sequencing (scRNA-seq), we identified a transcriptionally distinct ILC2 subset that showed enrichment for wound healing signature genes and the transcription factor BATF. Notably, BATF promoted the proliferation and function of ILC2s and restricted their plasticity during infection with influenza virus. In the absence of BATF, ILC2s lost their immune protective properties and obtained pathogenic ILC3-like function, which led to persist neutrophil infiltration, tissue damage and lethality. Mechanistically, BATF directly bound the cis-regulatory elements of wound healing genes, maintained their chromatin accessibility and promoted their expression. Lastly, BATF played an important role in an IL-33-ST2 feed-forward loop that supports ILC2 cell identity and function. Collectively, our findings shed light on a BATF-dependent ILC2 program thereby providing a potential therapeutic target for terminating detrimental inflammation during acute viral infection.
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| Overall design |
Bulk RNA sequencing, 2 samples (WT and Batf-/- ILC2s), 3 biological replicates per sample, from lungs at day 9 after influenza virus infection.
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| Contributor(s) |
Chen Y, Wu X, Cui W |
| Citation(s) |
35030033 |
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| Submission date |
May 04, 2020 |
| Last update date |
Apr 15, 2022 |
| Contact name |
Weiguo Cui |
| E-mail(s) |
wcui04@gmail.com
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| Phone |
312-503-0332
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| Organization name |
Northwestern University
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| Department |
Pathology
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| Lab |
Cui
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| Street address |
303 E Chicago Ave
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| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60654 |
| Country |
USA |
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| Platforms (1) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA630274 |
| SRA |
SRP260046 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE149854_ILC2_Gene_Result_new.xlsx |
2.2 Mb |
(ftp)(http) |
XLSX |
| GSE149854_RAW.tar |
149.2 Mb |
(http)(custom) |
TAR (of BW) |
| GSE149854_fpkm_value.csv.gz |
1.2 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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