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| Status |
Public on Mar 25, 2019 |
| Title |
Extracellular matrix (ECM) stiffness and collagen-1 (col-1) responsive genes in 3D cultured mammary epithelial cells |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
We report the expression profiles of MCF10A cells encapsulated in hydrogels of varying stiffness and composition. Cells were encapsulated for 7 days in either 1.) soft alginate and reconstituted basement membrane (rBM), 2.) stiff alginate and rBM, 3,) soft col-1 and rBM, or 4.) stiff col-1. We find global gene expression changes in response to enhanced ECM stiffness, independent of expression changes in response to col-1 exposure. These results provide a comprehensive study of the gene expression changes associated with increased ECM stiffness in addition to the gene expression changes associated with increased col-1 concentration in combination with, and independent of, ECM stiffness.
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| Overall design |
Expression profiling of MCF10A cells in four hydrogel conditions were sequenced in duplicate via Illumina HiSeq.
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| Contributor(s) |
Lee JY, Chaudhuri O |
| Citation(s) |
31015465 |
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Joanna Y. Lee, Jessica Chang, Antonia A. Dominguez, Sungmin Nam, Julie Chang, Hong-pyo Lee, Sushama Varma, Lei S. Qi, Robert B. West, Ovijit Chaudhuri. YAP-independent mechanotransduction drives breast cancer progression. bioRxiv 495499. doi:10.1101/495499
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| Submission date |
Aug 10, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Jessica Kay Chang |
| Organization name |
Stanford University
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| Department |
Genetics
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| Lab |
Baker
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| Street address |
300 Pasteur Drive, Alway Building M311
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| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (8)
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| Relations |
| BioProject |
PRJNA397902 |
| SRA |
SRP115218 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE102506_JYL_Count.Data.txt.gz |
296.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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