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| 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
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| 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.
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| 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.
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| 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 |
| E-mail(s) |
anastasiya.boersch@gmail.com
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| Organization name |
University of Basel
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| Department |
Biozentrum
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| Street address |
Klingelbergstrasse 50 / 70
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| City |
Basel |
| ZIP/Postal code |
4056 |
| Country |
Switzerland |
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| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (18)
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| GSM4222660 |
Huh7 cells, collagen_(0.5_mg/ml)_rep1 |
| GSM4222661 |
Huh7 cells, collagen_(0.5_mg/ml)_rep2 |
| GSM4222662 |
Huh7 cells, collagen_(0.5_mg/ml)_rep3 |
| GSM4222663 |
Huh7 cells, collagen_(1.0_mg/ml)_rep1 |
| GSM4222664 |
Huh7 cells, collagen_(1.0_mg/ml)_rep2 |
| GSM4222665 |
Huh7 cells, collagen_(1.0_mg/ml)_rep3 |
| GSM4222666 |
Huh7 cells, matrigel_(1.5_mg/ml)_rep1 |
| GSM4222667 |
Huh7 cells, matrigel_(1.5_mg/ml)_rep2 |
| GSM4222668 |
Huh7 cells, matrigel_(1.5_mg/ml)_rep3 |
| GSM4222669 |
Huh7 cells, matrigel_(3.0_mg/ml)_rep1 |
| GSM4222670 |
Huh7 cells, matrigel_(3.0_mg/ml)_rep2 |
| GSM4222671 |
Huh7 cells, matrigel_(3.0_mg/ml)_rep3 |
| GSM4222672 |
Huh7 cells, matrigel_(6.0_mg/ml)_rep1 |
| GSM4222673 |
Huh7 cells, matrigel_(6.0_mg/ml)_rep2 |
| GSM4222674 |
Huh7 cells, matrigel_(6.0_mg/ml)_rep3 |
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| Relations |
| BioProject |
PRJNA596217 |
| SRA |
SRP237940 |
| 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 |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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