GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE89520 Query DataSets for GSE89520
Status Public on Nov 01, 2017
Title Lamins organize the three dimensional genome from nuclear periphery in ES cells
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Lamins are the major structural components of the nuclear lamina (NL) beneath the inner nuclear membrane. Although lamins are believed to regulate genome organization and transcription, how they perform these functions remains poorly understood. Combining Hi-C with fluorescence in situ hybridization (FISH) and Histone and Lamina landscape (HiLands) analyses of chromatin domains, we show that lamins differentially regulate the NL-associated HiLands-P and -B domains in mouse ES cells (mESCs). Lamin loss leads to HiLands-P expansion at the NL, detachment of HiLands-B from the NL, and genome-wide changes of 3D chromatin interactions in NL-associated and interior HiLands in mESCs. Further epigenome and transcriptome analyses show that lamins can function from the NL to maintain the boundaries of active and repressive chromatin domains, thereby influencing gene expression throughout the genome. These findings should provide the basis to further understand how changes in the NL-associated chromatin influence transcription in development and NL-associated diseases.
Overall design Comparison of transcriptome (RNA-seq, 2 replicates), histone modifications(H3K4me3, H3K27me3, H3K9me3, H3K4me1, H3K27Ac, each 3-4 replicates), and 3D genome organization (Hi-C, 2 replicates) in WT and lamin-B1/B2/A triple knockout mESCs.
Contributor(s) Zheng X, Hu J, Kim Y, Zheng Y
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date Nov 03, 2016
Last update date May 15, 2019
Contact name Yixian Zheng
Organization name Carnegie Institution for Science
Department Embryology
Lab Yixian Zheng
Street address 3520 San Martin Drive
City Baltimore
State/province MD
ZIP/Postal code 21218
Country USA
Platforms (2)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (40)
GSM2375116 ESC_RNASeq_TKO_Rep1
GSM2375117 ESC_RNASeq_TKO_Rep2
GSM2375118 ESC_RNASeq_WT_Rep1
BioProject PRJNA352471
SRA SRP092589

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
GSE89520_RAW.tar 6.5 Gb (http)(custom) TAR (of BEDGRAPH, TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap