| Series | GSE68596 |
| Title | Genome-wide maps of nuclear lamina interactions in single human cells (CEL-seq) |
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| Year | 2015 |
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| Country | Netherlands |
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| Article | van Steensel B,van Oudenaarden A,Dekker J,Jalink K,Mirny LA,Imakaev M,Fudenberg G,Amendola M,de Graaf CA,Lajoie B,Zhan Y,Bienko M,Dey SS,Nahidiazar L,de Vries SS,Pagie L,Kind J.Genome-wide maps of nuclear lamina interactions in single human cells.Cell.2015 Sep 24 |
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| PMID | 26365489 |
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| Bio Project | BioProject: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA283181 |
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| Sra | SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRP058046 |
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| Overall Desgin | In this dataset, single-cell mRNA sequencing results from 96 single KBM7 cells have been deposited |
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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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| Experimental Protocol | For single cell mRNA sequencing, single cells were sorted into 96-well plates containing trizol (life technologies).; The RNA was extracted using chloroform and precipitated with iso-propanol. The RNA-pellet was then processed using the CEL-seq protocol (Hashimshony et al., 2012) and sequenced on the Illumina Hiseq 2500 platform using 50 bp paired-end sequencing.
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| Data processing | After sequencing, the right mate was aligned to the hg19 RefSeq human transcriptome downloaded from the UCSC genome browser (Meyer et al., 2013) using bwa (Li and Durbin, 2010) with default parameters. The left mate contains a barcode identifying the single cell from which the read originated. Barcodes are listed in the README_barcodes.txt supplementary file.; Genome_build: hg19; Supplementary_files_format_and_content: csv files containing transcript counts from each single cell. mRNA count data for all single cells, each column is a single cell and each row is a gene.
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| Platform | GPL16791 |
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| Public On | Public on Sep 24 2015 |
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