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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jul 12, 2022 |
| Title |
Ultra-deep 3D genome structure mapping with Region Capture Micro-C |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
Other
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| Summary |
In an effort to map the deeply map the structure of the genome at loci of interest, we applied Region Capture Micro-C and revealed focal patterns of contact between enhancers & promoters that we term microcompartments. We have mapped genomic structure at 0.4-1.9 Mb-sized regions at the Klf1, Ppm1g, Fbn2, Sox2, and Nanog loci across 4 conditions: wild-type and transcriptionally inhibited mouse Embryonic Stem Cells (mESCs), and cohesin-depletion & control treatments in a RAD21-AID genome-edited mESC line.
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| Overall design |
Micro-C with capture of five genomic regions in mouse embryonic stem cells, including triptolide treatment and depletion of cohesin subunit RAD21 using the AID system and IAA treatment.
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| Contributor(s) |
Goel VY, Huseyin MK, Hansen AS |
| Citation(s) |
37157000 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| DP2 GM140938 |
DYNAMIC BOTTOM-UP DISSECTION OF CHROMATIN LOOPING AND GENE REGULATION |
MASSACHUSETTS INSTITUTE OF TECHNOLOGY |
Anders Sejr Hansen |
| R33 CA257878 |
Super-resolution microscopy for dynamic analysis of focal enhancer amplifications in cancer |
MASSACHUSETTS INSTITUTE OF TECHNOLOGY |
Anders Sejr Hansen |
| UM1 HG011536 |
Center for 3D Structure and Physics of the Genome |
UNIV OF MASSACHUSETTS MED SCHOOL |
Job Dekker |
| F32 GM140548 |
Mechanistic dissection of dynamics of transcriptional regulation by chromatin looping |
MASSACHUSETTS INSTITUTE OF TECHNOLOGY |
Miles Kocur Huseyin |
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| Submission date |
Jun 29, 2022 |
| Last update date |
Jun 26, 2023 |
| Contact name |
Viraat Y Goel |
| E-mail(s) |
viraat@mit.edu
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| Organization name |
Massachusetts Institute of Technology
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| Department |
Biological Engineering
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| Lab |
Anders Hansen
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| Street address |
Building 56 Room 787B, 32 Vassar Street
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
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| Platforms (2) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
| GPL25526 |
Illumina NovaSeq 6000 (Homo sapiens; Mus musculus) |
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| Samples (18)
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| GSM6281852 |
JM8.N4 mESC, F1 RAD21-mAID IAA 3hr, RCMC, rep1 |
| GSM6809971 |
JM8.N4 mESC, Triptolide 4hr, RCMC, rep1 |
| GSM6809972 |
JM8.N4 mESC, WT, RCMC, rep2 |
| GSM6809973 |
JM8.N4 mESC, Triptolide 45min, RCMC, rep2 |
| GSM6809974 |
JM8.N4 mESC, F1 RAD21-mAID DMSO, RCMC, rep2 |
| GSM6809975 |
JM8.N4 mESC, F1 RAD21-mAID IAA 3hr, RCMC, rep2 |
| GSM6809976 |
JM8.N4 mESC, Triptolide 4hr, RCMC, rep2 |
| GSM6809977 |
JM8.N4 mESC, WT, Xinput, rep2 |
| GSM6809978 |
JM8.N4 mESC, Triptolide 45min, XInput, rep2 |
| GSM6809979 |
JM8.N4 mESC, Triptolide 4hr, XInput, rep1 |
| GSM6809980 |
JM8.N4 mESC, Triptolide 4hr, XInput, rep2 |
| GSM6809981 |
JM8.N4 mESC, WT, RNAPolIIXChIP, rep2 |
| GSM6809982 |
JM8.N4 mESC, Triptolide 45min, RNAPolIIXChIP, rep2 |
| GSM6809983 |
JM8.N4 mESC, Triptolide 4hr, RNAPolIIXChIP, rep1 |
| GSM6809984 |
JM8.N4 mESC, Triptolide 4hr, RNAPolIIXChIP, rep2 |
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| Relations |
| BioProject |
PRJNA854190 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE207225_RAW.tar |
2.1 Gb |
(http)(custom) |
TAR (of BW, MCOOL) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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