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| Status |
Public on Jun 06, 2023 |
| Title |
The SWI/SNF subunit Dpf2 licenses Nrf2-dependent gene expression to enforce multilineage control of inflammation [ATAC-seq] |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Purpose: Multi-omics characterization of the consequences of deleting the SWI/SNF subunit Dpf2 in the transcriptome (RNAseq), accessibility of the genome (ATACseq) and binding of SWI/SNF subunits (CUT&RUN) in hematopoietic stem/progenitor cells, resting and polarized bone-marrow derived macrophages and resting and activated CD4+ T cells obtained from Dpf2f/f and Dpf2D/D mice.
Methods: Lin- cKit+ cells were sorted from bone marrow of 28-days old Dpf2f/f and Dpf2D/D mice. Bone-marrow derived macrophages were obtained from 28-days old Dpf2f/f and Dpf2D/D mice and polarized with IFNg and LPS, or IL-4 for 24hours. CD4+ splenic T helper cells were obtained from 28-days old Dpf2f/f and Dpf2D/D mice and activated by treatment with PMA and Ionomycin.
Methods: For ATACseq, Lin- cKit+ cells were processed following the OMIM-ATAC-seq protocol (Corces MR et al., Nature Methods 2017). Libraries were sequenced on a NextSeq (75bp, paired end reads) to obtain more than 40 million reads/sample.
Results: For ATACseq, we obtained more than 40 million reads per sample. ATAC-Seq chromatin accessible regions were determined using ENCODE pipeline standards (https://github.com/ENCODE-DCC/atac-seq-pipeline; git commit 2b693ab).
Conclusions: The absence of Dpf2 in LK cells results in downregulation of anti-oxidative and anti-inflammatory gene expression programs in bone marrow LK cells, bone-marrow derived macrophages and CD4+ T cells.
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| Overall design |
Samples were obtained from primary bone marrow or spleen cells isolated or sorted from Dpf2f/f and Dpf2D/D mice of approximately 28 days of age. For RNAseq and ATACseq datasets, each file corresponds to data from 1 independent mouse/genotype. At least 3 mice (independent biological replicates) per condition and genotype were used. CUT&RUN samples were obtained from a pool of LK cells
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| Contributor(s) |
Mas Martin G |
| Citation(s) |
37200093 |
| Submission date |
Dec 29, 2021 |
| Last update date |
Sep 05, 2023 |
| Contact name |
Gloria Mas Martin |
| E-mail(s) |
gloriamasmartin@gmail.com
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| Organization name |
University of Miami
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| Street address |
1501 NW 10th Avenue
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| City |
Miami |
| State/province |
Florida |
| ZIP/Postal code |
33136 |
| Country |
USA |
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| Platforms (1) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (7)
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| This SubSeries is part of SuperSeries: |
| GSE192779 |
The SWI/SNF subunit Dpf2 licenses Nrf2-dependent gene expression to enforce multilineage control of inflammation |
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| Relations |
| BioProject |
PRJNA793069 |
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