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Series GSE141846 Query DataSets for GSE141846
Status Public on Feb 11, 2020
Title Genetic Variations in Type 1 Diabetes Reconfigure the 3D Chromatin Organization of T Cells [ChIP-seq]
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Despite overwhelming evidence supporting the role of genetics in susceptibility tocomplex diseases, such as autoimmune disorders, a fundamental unresolved questionis whether large numbers of sequence variants with small effect sizes can alter thespatial genome organization. Here, we provide the first report on the reconfiguration ofthe 3D genome due to nucleotide differences associated with type 1 diabetes, anautoimmune disorder. We show that the chromatin organization at T cell identity genesis identical between diabetes-susceptible and diabetes-resistant mouse strains despitethousands of sequence polymorphisms, suggesting that these loci are epigeneticallyresilient to genetic variation. However, molecular and optical mapping of genomefolding demonstrate that diabetes risk-conferring loci coalesce into close spatialproximity in T cells of diabetes-susceptible mice, forming regulatory cliques, andresulting in aberrant gene expression. Our data uncover 3D chromatin architecture asa new dimension in understanding complex diseases
 
Overall design Cells were chemically cross-linked by 1% formaldehyde. Samples were sonicated and protein-DNA complexes were isolated with antibody.
 
Contributor(s) Fasolino M, Goldman N, Wang W, Cattau B, Zhou Y, Petrovic J, Link VM, Cote A, Silverman M, Joyce EF, Little SC, Raj A, Henao-Mejia J, Faryabi RB, Vahedi G
Citation(s) 32049053
Submission date Dec 11, 2019
Last update date May 12, 2020
Contact name Naomi Goldman
Organization name University of Pennsylvania
Lab Golnaz Vahedi
Street address 324 BRB II/III, 421 Curie Blvd
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
 
Platforms (1)
GPL21626 NextSeq 550 (Mus musculus)
Samples (16)
GSM4214137 ChIP-seq_K27ac_DP_BL6_Rep1B
GSM4214138 ChIP-seq_K27ac_DP_BL6_Rep2B
GSM4214139 ChIP-seq_K27ac_DP_NOD_Rep1B
This SubSeries is part of SuperSeries:
GSE141853 Genetic Variations in Type 1 Diabetes Reconfigure the 3D Chromatin Organization of T Cells
Relations
BioProject PRJNA594961
SRA SRP236884

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Supplementary file Size Download File type/resource
GSE141846_RAW.tar 9.3 Gb (http)(custom) TAR (of BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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