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Series GSE151504 Query DataSets for GSE151504
Status Public on May 31, 2020
Title E proteins orchestrate dynamic transcriptional cascades implicated in the suppression of the differentiation of group 2 innate lymphoid cells [RNA-Seq]
Organism Mus musculus
Experiment type Expression 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 RNA-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 harvested for RNA isolation.
 
Contributor(s) Sun X, Georgescu C
Citation(s) 32817168
Submission date May 30, 2020
Last update date Sep 04, 2020
Contact name Jonathan Wren
E-mail(s) Jonathan-Wren@omrf.org
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)
GPL16417 Illumina MiSeq (Mus musculus)
Samples (8)
GSM4579751 ILC2 cells , GFP_4h_1
GSM4579752 ILC2 cells , GFP_4h_2
GSM4579753 ILC2 cells , E47_4h_1
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
Relations
BioProject PRJNA636093
SRA SRP265355

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Supplementary file Size Download File type/resource
GSE151504_RawCounts_Matrix.txt.gz 464.6 Kb (ftp)(http) TXT
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Processed data are available on Series record

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