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Series GSE136173 Query DataSets for GSE136173
Status Public on Sep 30, 2020
Title Epithelial cells in 2D and 3D culture exhibit significant differences in long-range genomic interactions [RNA-Seq]
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Recent studies have characterized the genomic structures of many eukaryotic cells, often with a focus on their relation to gene expression. So far, these studies have largely only investigated cells grown in 2D culture, although the transcriptomes of 3D cultured cells are generally closer to their in vivo phenotype. To examine the effects of spatial constraints on chromosome conformation, we investigated the genomic architecture of mouse hepatocytes grown in 2D and 3D cultures using in situ Hi-C. Our results reveal significant differences in long-range genomic interactions, notably in compartment identity and strength as well as in TAD-TAD interactions, but only minor differences at the TAD level. RNA-seq analysis reveals an up-regulation in the 3D cultured cells of those genes involved in physiological hepatocyte functions. We find that these genes are associated with only a subset of the structural changes, suggesting that the differences in genomic structure are indeed critically important for transcriptional regulation but also that there are major structural differences owing to other functions than gene expression. Overall, our results indicate that growth in 3D significantly alters longer-range genomic interactions, which may be consequential for a subset of genes that are important for the physiological functioning of the cell.
Overall design The genome-wide interactome were generated using in-situ Hi-C method in both ltwo-dimensional (2D) and three-dimensional (3D) cultured AML12 cells which were arrest at G1/S
Contributor(s) Liu X, Sun Q, Shao Z
Citation(s) 33631432
Submission date Aug 22, 2019
Last update date Feb 28, 2021
Contact name Xin Liu
Organization name Shanghai Jiaotong University
Department School of Biomedical Engineering
Street address 800 Dong Chuan Rd.
City Shanghai
State/province Shanghai
ZIP/Postal code 200240
Country China
Platforms (1)
GPL21273 HiSeq X Ten (Mus musculus)
Samples (4)
GSM4042106 2D RNA-seq rep1
GSM4042107 2D RNA-seq rep2
GSM4042108 3D RNA-seq rep1
This SubSeries is part of SuperSeries:
GSE136307 Epithelial cells in 2D and 3D culture exhibit significant differences in long-range genomic interactions
BioProject PRJNA561501
SRA SRP219431

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Supplementary file Size Download File type/resource
GSE136173_genes_diff_2d_vs_3d.txt.gz 1.1 Mb (ftp)(http) TXT
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