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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Sep 19, 2023 |
| Title |
4DNES425UDGS - Replicate experiments of in situ Hi-C on immediate neuronal precursor cell with DpnII |
| Organism |
Mus musculus |
| Experiment type |
Other
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| Summary |
The genome is partitioned into topologically associated domains and genomic compartments with shared chromatin valence. This architecture is constrained by the DNA polymer, which precludes interactions between genes on different chromosomes. Here we report a marked divergence from this pattern of nuclear organization that occurs in mouse olfactory sensory neurons. Chromatin conformation capture using in situ Hi-C on fluorescence-activated cell-sorted olfactory sensory neurons and their progenitors shows that olfactory receptor gene clusters from 18 chromosomes make specific and robust interchromosomal contacts that increase with differentiation of the cells. These contacts are orchestrated by intergenic olfactory receptor enhancers, the 'Greek islands', which first contribute to the formation of olfactory receptor compartments and then form a multi-chromosomal super-enhancer that associates with the single active olfactory receptor gene. The Greek-island-bound transcription factor LHX2 and adaptor protein LDB1 regulate the assembly and maintenance of olfactory receptor compartments, Greek island hubs and olfactory receptor transcription, providing mechanistic insights into and functional support for the role of trans interactions in gene expression.
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| Overall design |
lab: Stavros Lomvardas, COLUMBIA
award: 1U01DA040582-01
accession: 4DNES425UDGS
condition: Immediate Neuronal Precursor cells
submitted_by: Adan Horta
dataset_label: Hi-C on Mouse Olfactory System cells
experiment_type: in situ Hi-C
url: https://data.4dnucleome.org/experiment-set-replicates/4DNES425UDGS/
number_of_experiments: 2
experiment: 4DNEXKO3TRJT; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEXTDMNUOO; replicate_number: Biorep 2, Techrep 1
Series supplementary files:
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workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/6aa74f2a-2d5f-4132-9cd0-ac178f752d4e/
genome_assembly: GRCm38
derived_from: 4DNFI3UBJ3HZ.chrom.sizes, 4DNFIDFRSE2G.pairs.gz, 4DNFIBO9M2WY.pairs.gz, 4DNFI3HVC1SE.txt
description: This is an output file of the Hi-C processing pipeline
file_type: contact list-combined
file_format: pairs
file name: 4DNFI1QBCSKR.pairs.gz
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workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/6aa74f2a-2d5f-4132-9cd0-ac178f752d4e/
genome_assembly: GRCm38
derived_from: 4DNFI3UBJ3HZ.chrom.sizes, 4DNFIDFRSE2G.pairs.gz, 4DNFIBO9M2WY.pairs.gz, 4DNFI3HVC1SE.txt
description: This is an output file of the Hi-C processing pipeline
file_type: contact matrix
file_format: mcool
file name: 4DNFICUQ1N7S.mcool
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workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/c8f95f43-1f95-4e07-8a82-647951bf7579/
genome_assembly: GRCm38
derived_from: 4DNFICUQ1N7S.mcool
description: Boundaries calls on Hi-C contact matrices
file_type: boundaries
file_format: bed
file name: 4DNFI2YHK51M.bed.gz
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workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/c8f95f43-1f95-4e07-8a82-647951bf7579/
genome_assembly: GRCm38
derived_from: 4DNFICUQ1N7S.mcool
description: Diamond insulation scores calls on Hi-C contact matrices
file_type: insulation score-diamond
file_format: bw
file name: 4DNFICXGHQP3.bw
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workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/96e31197-b1ca-4921-b833-9b6c1132d770/
genome_assembly: GRCm38
derived_from: 4DNFICUQ1N7S.mcool, 4DNFIOFXJOUA.bedGraph.gz
description: Compartments signals on Hi-C contact matrices
file_type: compartments
file_format: bw
file name: 4DNFIKXATLSH.bw
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| Citation(s) |
30626972 |
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| Submission date |
Sep 18, 2023 |
| Last update date |
Sep 20, 2023 |
| Contact name |
4DN DCIC |
| E-mail(s) |
support@4dnucleome.org
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| Organization name |
4D Nucleome - Data Coordination and Integration Center
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| Street address |
10 Shattuck St
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
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| Platforms (1) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (2) |
| GSM7789304 |
in situ Hi-C on immediate neuronal precursor cell with DpnII - 4DNEXKO3TRJT |
| GSM7789305 |
in situ Hi-C on immediate neuronal precursor cell with DpnII - 4DNEXTDMNUOO |
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| Relations |
| BioProject |
PRJNA1018570 |
| SRA |
SRP461485 |
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