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Series GSE142206 Query DataSets for GSE142206
Status Public on Jul 07, 2020
Title The transcriptional landscapes of a hepatoma cell line grown on scaffolds of Extracellular Matrix proteins
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary The in vivo microenvironment of cells is complex and highly dynamic, resulting from an interplay between matrix proteins with several other cues and biomolecules. Although the effects of the cellular niche have been investigated for a number of cell types using different molecular approaches, a comprehensive information on the global transcriptome at various stiffness levels of 3D scaffolds resulting derived from components of the extracellular matrix (ECM) are still lacking. In this study, we explored the effect of the biomechanical parameters of Collagen I and Matrigel (ECM) on transcriptional gene regulation in a cell culture system. Using Huh7 cells cultured on traditional cell culture plates or on the component of the ECM, we have generated transcriptome sequencing data that may be further explored to understand the differentiation and growth potential of this cell for the development of 3D cultures. Assessment of the hepatocyte phenotype in our data set would also be useful for the development of systems mimicking the in vivo structure and function of liver cells which still remains a challenge.
Overall design 3 Biological replicates of each growth type were sequenced. There were 6 conditions of matrix scaffolds. A total of 18 samples were sequenced.
Contributor(s) Ghosh S, Börsch A, Zavolan M
Citation(s) 33823809
Submission date Dec 17, 2019
Last update date Apr 13, 2021
Contact name Anastasiya Boersch
Organization name University of Basel
Department Biozentrum
Street address Klingelbergstrasse 50 / 70
City Basel
ZIP/Postal code 4056
Country Switzerland
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (18)
GSM4222657 Huh7 cells, control_rep1
GSM4222658 Huh7 cells, control_rep2
GSM4222659 Huh7 cells, control_rep3
BioProject PRJNA596217
SRA SRP237940

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Supplementary file Size Download File type/resource
GSE142206_counts.txt.gz 772.5 Kb (ftp)(http) TXT
GSE142206_tpms.txt.gz 3.2 Mb (ftp)(http) TXT
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