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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Sep 24, 2015 |
| Title |
Genome-wide maps of nuclear lamina interactions in single human cells. (DamID; LaminB1, clone-5-5, diploid) |
| Organism |
Homo sapiens |
| Experiment type |
Other
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| 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.
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| Overall design |
52 single cell LaminB1 DamID samples
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| Contributor(s) |
Kind J, Pagie L, de Vries S, van Steensel B |
| Citation(s) |
26365489 |
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| Submission date |
Apr 24, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Bas van Steensel |
| E-mail(s) |
b.v.steensel@nki.nl
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| Phone |
+ 31 20 512 2040
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| Fax |
+31 20 669 1383
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| URL |
http://www.nki.nl/nkidep/vansteensel
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| Organization name |
Netherlands Cancer Institute
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| Department |
division of Molecular Biology
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| Lab |
van Steensel group
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| Street address |
Plesmanlaan 121
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| City |
Amsterdam |
| ZIP/Postal code |
1066 CX |
| Country |
Netherlands |
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| Platforms (1) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
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| Samples (35)
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| GSM1666568 |
KBM7 cell line, clone 5-5, diploid, sample 001 |
| GSM1666569 |
KBM7 cell line, clone 5-5, diploid, sample 002 |
| GSM1666570 |
KBM7 cell line, clone 5-5, diploid, sample 003 |
| GSM1666571 |
KBM7 cell line, clone 5-5, diploid, sample 004 |
| GSM1666572 |
KBM7 cell line, clone 5-5, diploid, sample 005 |
| GSM1666573 |
KBM7 cell line, clone 5-5, diploid, sample 006 |
| GSM1666574 |
KBM7 cell line, clone 5-5, diploid, sample 007 |
| GSM1666575 |
KBM7 cell line, clone 5-5, diploid, sample 008 |
| GSM1666576 |
KBM7 cell line, clone 5-5, diploid, sample 009 |
| GSM1666577 |
KBM7 cell line, clone 5-5, diploid, sample 010 |
| GSM1666578 |
KBM7 cell line, clone 5-5, diploid, sample 011 |
| GSM1666579 |
KBM7 cell line, clone 5-5, diploid, sample 012 |
| GSM1666580 |
KBM7 cell line, clone 5-5, diploid, sample 013 |
| GSM1666581 |
KBM7 cell line, clone 5-5, diploid, sample 014 |
| GSM1666582 |
KBM7 cell line, clone 5-5, diploid, sample 015 |
| GSM1666583 |
KBM7 cell line, clone 5-5, diploid, sample 016 |
| GSM1666584 |
KBM7 cell line, clone 5-5, diploid, sample 017 |
| GSM1666585 |
KBM7 cell line, clone 5-5, diploid, sample 018 |
| GSM1666586 |
KBM7 cell line, clone 5-5, diploid, sample 019 |
| GSM1666587 |
KBM7 cell line, clone 5-5, diploid, sample 020 |
| GSM1666588 |
KBM7 cell line, clone 5-5, diploid, sample 021 |
| GSM1666589 |
KBM7 cell line, clone 5-5, diploid, sample 022 |
| GSM1666590 |
KBM7 cell line, clone 5-5, diploid, sample 023 |
| GSM1666591 |
KBM7 cell line, clone 5-5, diploid, sample 024 |
| GSM1666592 |
KBM7 cell line, clone 5-5, diploid, sample 025 |
| GSM1666593 |
KBM7 cell line, clone 5-5, diploid, sample 026 |
| GSM1666594 |
KBM7 cell line, clone 5-5, diploid, sample 027 |
| GSM1666595 |
KBM7 cell line, clone 5-5, diploid, sample 028 |
| GSM1666596 |
KBM7 cell line, clone 5-5, diploid, sample 029 |
| GSM1666597 |
KBM7 cell line, clone 5-5, diploid, sample 030 |
| GSM1666598 |
KBM7 cell line, clone 5-5, diploid, sample 031 |
| GSM1666599 |
KBM7 cell line, clone 5-5, diploid, sample 032 |
| GSM1666600 |
KBM7 cell line, clone 5-5, diploid, sample 033 |
| GSM1666601 |
KBM7 cell line, clone 5-5, diploid, sample 034 |
| GSM1666602 |
KBM7 cell line, clone 5-5, diploid, sample 035 |
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| This SubSeries is part of SuperSeries: |
| GSE69423 |
Genome-wide maps of nuclear lamina interactions in single human cells |
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| Relations |
| BioProject |
PRJNA282149 |
| SRA |
SRP057652 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE68261_Clone.5-5.2N.OE_LP150415.txt.gz |
3.3 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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