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Series GSE125729 Query DataSets for GSE125729
Status Public on Apr 30, 2019
Title Chromatin immunoprecipitation sequencing (ChIP-Seq) for Bhlhe40 from naïve and IL-4c-stimulated large peritoneal macrophages (LPMs)
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Most tissue-resident macrophage populations develop during embryogenesis, self-renew in the steady state, and can expand during type 2 immunity. Whether shared mechanisms regulate macrophage proliferation in homeostasis and disease is unclear. We found that the transcription factor Bhlhe40 was cell-intrinsically required in large peritoneal macrophages (LPMs) for self-renewal and maintenance, but was not required in other resident macrophages. Bhlhe40 was selectively necessary in LPMs for proliferation, but not polarization, in response to IL-4. During a helminth infection,
Bhlhe40 was required for normal LPM cell cycling. Bhlhe40 repressed the expression of Maf and Mafb and directly promoted expression of cell cycle-related transcripts to enable proliferation of LPMs. Genomic sites bound by Bhlhe40 in LPMs included some co-bound by the macrophage lineage-determining factor PU.1 and others uniquely bound by Bhlhe40, including Maf and cell cycle-related loci. Our findings demonstrate a tissue-specific control mechanism regulating resident macrophage proliferation in homeostasis and type 2 immunity.
Overall design LPMs were sorted from pooled naïve and pooled IL-4c-treated C57BL/6 mice. Chromatin was crosslinked and immunoprecipitation (Novus Biologicals, anti-Dec1, catalog NB100-1800, Lot C1) was performed for Bhlhe40-bound genomic regions, which were sequenced along with input DNA controls from the same samples.
DNA from 1 naïve LPM ChIP and 1 IL-4c-stimulated ChIP were sequenced, as well as input DNA. Cells were pooled from multiple mice for each immunoprecipitation.
Contributor(s) Jarjour NN, Shchukina I, Edelson BT
Citation(s) 31061528
Submission date Jan 28, 2019
Last update date Jul 30, 2019
Contact name Brian T Edelson
Organization name Washington University in St. Louis
Department Pathology and Immunology
Lab Rm. 8304
Street address 425 S. Euclid Ave.
City St. Louis
State/province MO
ZIP/Postal code 63110
Country USA
Platforms (1)
GPL21493 Illumina HiSeq 3000 (Mus musculus)
Samples (4)
GSM3581127 naïve LPM input DNA
GSM3581128 naïve LPM Bhlhe40 ChIP
GSM3581129 IL-4c-stimulated LPM input DNA
This SubSeries is part of SuperSeries:
GSE125730 Bhlhe40 mediates tissue-specific control of macrophage proliferation in homeostasis and type 2 immunity
BioProject PRJNA517407
SRA SRP182643

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Supplementary file Size Download File type/resource
GSE125729_RAW.tar 598.3 Mb (http)(custom) TAR (of BED, BW, XLSX)
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Raw data are available in SRA
Processed data provided as supplementary file

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