|
| Status |
Public on Dec 11, 2018 |
| Title |
Walking along chromosomes with super-resolution imaging, contact maps, and integrative modelling |
| Organism |
Homo sapiens |
| Experiment type |
Other
|
| Summary |
Using the super-resolution microscopy methods of OligoSTORM and OligoDNA-PAINT, we trace 8 megabases of human chromosome 19, visualizing structures ranging in size from a few kilobases to over a megabase. Focusing on chromosomal regions that contribute to compartments identified with chromosome conformation capture, with our imaging we discover distinct structures that, in spite of considerable variability, can predict whether such regions correspond to active (A-type) or inactive (B-type) compartments. Imaging through the depths of an entire nuclei, we capture pairs of homologous regions in diploid cells, obtaining evidence that maternal and paternal homologous regions can be differentially organized. Finally, using restraint-based modeling to integrate imaging and Hi-C data, we implement a method – integrative modeling of genomic regions (IMGR) – to increase the genomic resolution of our traces to 10 kb.
Grant: 1DP2OD008540: Exploring how the genome folds through proximity ligation and sequencing
Grant: 4DP2OD008540: Exploring how the genome folds through proximity ligation and sequencing
Grant: U01HL130010: Beyond Pairwise DNA Contacts: Exploring Higher-order Genome Structure Using Proximity Ligation NIH/4D Nucleome Consortium
Grant: UM1HG009375: Genome-wide mapping of loops using in situ Hi-C
|
| |
|
| Overall design |
Hi-C maps of 10 library replicates and a mega map
|
| |
|
| Contributor(s) |
Pérez Estrada C, Lieberman Aiden E, Russel S |
| Citation(s) |
30586358 |
| Submission date |
Dec 10, 2018 |
| Last update date |
May 14, 2019 |
| Contact name |
Cynthia Perez Estrada |
| E-mail(s) |
cynthiperez.estrada@gmail.com
|
| Phone |
8572428558
|
| Organization name |
Baylor College of Medicine
|
| Department |
Molecular and Human Genetics
|
| Lab |
Aiden lab
|
| Street address |
1 Baylor Plaza Room 906B
|
| City |
houston |
| State/province |
TEXAS |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platforms (1) |
|
| Samples (10)
|
|
| Relations |
| BioProject |
PRJNA509222 |
| SRA |
SRP173234 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE123552_PGP1F_mega_090118.hic |
24.9 Gb |
(ftp)(http) |
HIC |
| GSE123552_PGP1F_mega_090118_30.hic |
23.4 Gb |
(ftp)(http) |
HIC |
| GSE123552_RAW.tar |
98.9 Gb |
(http)(custom) |
TAR (of HIC) |
| GSE123552_enriched_pixels_10000.bedpe.gz |
1.6 Mb |
(ftp)(http) |
BEDPE |
| GSE123552_enriched_pixels_5000.bedpe.gz |
297.8 Kb |
(ftp)(http) |
BEDPE |
| GSE123552_merged_loops.bedpe.gz |
333.5 Kb |
(ftp)(http) |
BEDPE |
| GSE123552_postprocessed_pixels_10000.bedpe.gz |
327.5 Kb |
(ftp)(http) |
BEDPE |
| GSE123552_postprocessed_pixels_5000.bedpe.gz |
87.6 Kb |
(ftp)(http) |
BEDPE |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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