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| Status |
Public on Mar 29, 2021 |
| Title |
Hyaluronan-CD44 signaling promotes pro-tumor inflammation in breast cancer |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
We report the application of next-generation sequencing (NGS) technology for high-throughput profiling of RNA expression in human breast cancer cells. The goal of this study was to compare NGS-derived transcriptome profiling (RNA-seq) from cells expressing either wildtype or knockout CD44 to identify key downstream signaling events of HA-CD44 interactions.
Methods: This experiment was repeated for a total of three times and replicate RNA samples were extracted and submitted for Illumina Sequencing. Twelve dual-indexed Illumina TruSeq stranded mRNA libraries were pooled for sequencing on 1 lane of a HiSeq 2500 using v4 chemistry to generate 2x50 bp paired-end reads. After applying the Benjamini-Hochberg multiple hypothesis adjustment to raw p-values, differentially expressed genes were identified requiring that they had a log2 fold change > 0 and an adjusted p-value ≤ 0.01.
Results: A total of 1,530 and 320 genes were impacted by CD44 KO in the Hs578T cells and MDA-MB-231 cells, respectively. When comparing each of these data sets, 40 genes were differentially expressed in both Hs578T and MDA-MB-231 cells upon deletion of CD44.
Conclusions: Gene ontology (GO) analysis revealed that CD44 KO in breast cancer cells altered expression of genes involved in both cell adhesion and cytokine activity. This study provides a framework for the application of NGS to compare differential gene expression between genetically edited mammalian cell populations.
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| Overall design |
Determining the effects of CD44 KO in 2 different human breast cancer cell lines. Three replicates were prepared for each of the four experimental conditions.
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| Contributor(s) |
Schwertfeger K, Witschen P, Munro S |
| Citation(s) |
32455980 |
| |
| Submission date |
Apr 14, 2020 |
| Last update date |
Mar 29, 2021 |
| Contact name |
Sarah Munro |
| Organization name |
University of Minnesota
|
| Street address |
117 Pleasant Street SE
|
| City |
Minneapolis |
| State/province |
MN |
| ZIP/Postal code |
55455 |
| Country |
USA |
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| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (12)
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| Relations |
| BioProject |
PRJNA625295 |
| SRA |
SRP256345 |
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