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Series GSE151737 Query DataSets for GSE151737
Status Public on Jun 04, 2020
Title E proteins orchestrate dynamic transcriptional cascades implicated in the suppression of the differentiation of group 2 innate lymphoid cells [ATAC-Seq]
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Group 2 innate lymphoid cells (ILC2s) represent a subset of newly discovered immune cells that are involved in immune reactions against microbial pathogens, host allergic reactions as well as tissue repair. The basic helix-loop-helix transcription factors collectively called E proteins powerfully suppress the differentiation of ILC2s from bone marrow and thymic progenitors while promoting the development of B and T lymphocytes. How E proteins exert the suppression is not well understood. Here we investigated the underlying molecular mechanisms using inducible gain and loss of function approaches in ILC2s and their precursors, respectively. Cross-examination of RNA sequencing and ATAC sequencing data obtained at different time points reveals a set of genes which are likely direct targets of E proteins. Consequently, a widespread down-regulation of chromatin accessibility occurs at a later time point, possibly due to the activation of transcriptional repressor genes such as Cbfa2t3 and Jdp2. The large number of genes repressed by gain of E protein function leads to the down-regulation of a transcriptional network important for ILC2 differentiation.
Overall design ATAC-seq was performed on thymic ILC2 cells isolated from Id1 transgenic mice, which were transduced with retroviruses expressing either GFP alone or together with an E47-ER fusion protein after stimulation with ILC2, IL-7, IL-25 and IL-33. Transduced cells were sorted for GFP and expanded in ILC2, IL-7, IL-25 and IL-33. The cells were then treated with 4-hydroxy-Tamoxifen for 4 or 16 hours before harvesting for DNA isolation.
Contributor(s) Sun X, Peng V
Citation(s) 32817168
Submission date Jun 03, 2020
Last update date Sep 04, 2020
Contact name Jonathan Wren
Phone (405) 271-6989
Organization name OMRF
Department Genes & Human Disease Research Program
Street address 825 N.E. 13th Street
City Oklahoma City
State/province OK
ZIP/Postal code 73104
Country USA
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (8)
GSM4589591 E47_16h_rep1
GSM4589592 E47_4h_rep1
GSM4589593 E47_16h_rep2
This SubSeries is part of SuperSeries:
GSE151739 E proteins orchestrate dynamic transcriptional cascades implicated in the suppression of the differentiation of group 2 innate lymphoid cells
BioProject PRJNA637071
SRA SRP265834

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Supplementary file Size Download File type/resource
GSE151737_E47-3_16h_S1_R1_001.trim.merged.nodup.no_chrM_MT.tn5.pooled.pval.signal.bigwig 674.9 Mb (ftp)(http) BIGWIG
GSE151737_E47-3_4h_S5_R1_001.trim.merged.nodup.no_chrM_MT.tn5.pooled.pval.signal.bigwig 790.5 Mb (ftp)(http) BIGWIG
GSE151737_E47_16h_idr.conservative_peak.narrowPeak.gz 2.3 Mb (ftp)(http) NARROWPEAK
GSE151737_E47_4h_idr.conservative_peak.narrowPeak.gz 2.8 Mb (ftp)(http) NARROWPEAK
GSE151737_GFP-3_16h_S2_R1_001.trim.merged.nodup.no_chrM_MT.tn5.pooled.pval.signal.bigwig 858.9 Mb (ftp)(http) BIGWIG
GSE151737_GFP-3_4h_S6_R1_001.trim.merged.nodup.no_chrM_MT.tn5.pooled.pval.signal.bigwig 875.7 Mb (ftp)(http) BIGWIG
GSE151737_GFP_16h_idr.conservative_peak.narrowPeak.gz 2.8 Mb (ftp)(http) NARROWPEAK
GSE151737_GFP_4h_idr.conservative_peak.narrowPeak.gz 2.4 Mb (ftp)(http) NARROWPEAK
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