|
| Status |
Public on Sep 24, 2015 |
| Title |
Genome-wide maps of nuclear lamina interactions in single human cells (CEL-seq) |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Mammalian interphase chromosomes interact with the nuclear lamina (NL) through hundreds of large Lamina Associated Domains (LADs). We report a method to map NL contacts genome-wide in single human cells. Analysis of ~400 maps reveals a core architecture of gene-poor LADs that contact the NL with high cell-to-cell consistency, interspersed by LADs with more variable NL interactions. The variable contacts are more sensitive to a change in genome ploidy than the consistent contacts. Single-cell maps indicate that NL contacts involve multivalent interactions over hundreds of kilobases. Moreover, we observe extensive intra-chromosomal coordination of NL contacts, even over tens of megabases. Such coordinated loci exhibit preferential interactions as detected by Hi-C. Finally, single-cell gene expression and chromatin accessibility analysis shows that loci with consistent NL contacts are expressed at lower levels and are more consistently inaccessible than loci with lower contact frequencies. These results highlight fundamental principles of single cell chromatin organization.
|
| |
|
| Overall design |
In this dataset, single-cell mRNA sequencing results from 96 single KBM7 cells have been deposited
|
| |
|
| Contributor(s) |
Kind J, Dey SS, van Oudenaarden A, van Steensel B |
| Citation(s) |
26365489 |
| Submission date |
May 06, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Siddharth Subhas Dey |
| E-mail(s) |
s.dey@hubrecht.eu
|
| Organization name |
Hubrecht Institute
|
| Lab |
van Oudenaarden lab
|
| Street address |
Uppsalalaan 8
|
| City |
Utrecht |
| ZIP/Postal code |
3584 CT |
| Country |
Netherlands |
| |
|
| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
|
| Samples (1) |
| GSM1676569 |
Single cell mRNA sequencing data from KMB7 cells |
|
| Relations |
| BioProject |
PRJNA283181 |
| SRA |
SRP058046 |
