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Series GSE87831 Query DataSets for GSE87831
Status Public on Nov 15, 2016
Title Nucleoporin-mediated regulation of cell identity genes
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary The organization of the genome in the three-dimensional space of the nucleus is coupled with cell type-specific gene expression. However, how nuclear architecture influences transcription that governs cell identity remains unknown. Here, we show that Nuclear Pore Complex (NPC) components Nup93 and Nup153 bind super-enhancers (SE), regulatory structures that drive the expression of key genes that specify cell identity. We found that nucleoporin-associated SEs localize preferentially to the nuclear periphery, and absence of Nup153 and Nup93 results in dramatic transcriptional changes of SE-associated genes. Our results reveal a crucial role of NPC components in the regulation of cell type specifying genes and highlight nuclear architecture as a regulatory layer of genome functions in cell fate.
 
Overall design DamID-Seq of Nup153 and Nup93 in human U2OS, DamID-Seq of Nup153 in IMR90 cells, RNA-seq of control and knocked-down populations in U2OS and IMR90 cells, ChIP-Seq of histone modifications in U2OS and IMR90 cells and DNAseI-Seq of U2OS cells.
 
Contributor(s) Ibarra A, Benner C, Hetzer MW
Citation(s) 27807035
Submission date Oct 11, 2016
Last update date May 15, 2019
Contact name Christopher Benner
E-mail(s) cbenner@ucsd.edu
Organization name University of California, San Diego (UCSD)
Department Medicine
Street address 9500 Gilman Dr. MC 0640
City La Jolla
State/province California
ZIP/Postal code 92093-0640
Country USA
 
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (33)
GSM2341623 GFP-DamID-forLBR
GSM2341624 LBR-DamID-r1
GSM2341625 LBR-DamID-r2
Relations
BioProject PRJNA347821
SRA SRP091382

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE87831_CTCF.peaks.bed.gz 333.3 Kb (ftp)(http) BED
GSE87831_DNase-Seq.r1.peaks.bed.gz 1.2 Mb (ftp)(http) BED
GSE87831_DNase-Seq.r2.peaks.bed.gz 982.4 Kb (ftp)(http) BED
GSE87831_H3K27ac.IMR90.SE.bed.gz 10.3 Kb (ftp)(http) BED
GSE87831_H3K27ac.U2OS.SE.bed.gz 5.3 Kb (ftp)(http) BED
GSE87831_H3K4me3-IMR90.peaks.bed.gz 226.9 Kb (ftp)(http) BED
GSE87831_H3K4me3.peaks.bed.gz 198.7 Kb (ftp)(http) BED
GSE87831_H3K9me2.peaks.bed.gz 1.5 Kb (ftp)(http) BED
GSE87831_LBR-DamID.LADs.bed.gz 14.2 Kb (ftp)(http) BED
GSE87831_Nup153-DamID-IMR90.peaks.bed.gz 337.2 Kb (ftp)(http) BED
GSE87831_Nup153-DamID-IMR90.toppeaks.bed.gz 26.3 Kb (ftp)(http) BED
GSE87831_Nup153-DamID.peaks.bed.gz 24.4 Kb (ftp)(http) BED
GSE87831_Nup93-DamID.peaks.bed.gz 14.3 Kb (ftp)(http) BED
GSE87831_fpkm.txt.gz 1.5 Mb (ftp)(http) TXT
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