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Series GSE68596 Query DataSets for GSE68596
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
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
BioProject PRJNA283181
SRA SRP058046

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Supplementary file Size Download File type/resource
GSE68596_RAW.tar 690.0 Kb (http)(custom) TAR (of CSV)
GSE68596_README_barcodes.txt 1.6 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data provided as supplementary file

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