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| Status |
Public on Nov 30, 2019 |
| Title |
Next Generation Sequencing Facilitates Quantitative Analysis of EG7-CAFs and MSCs Transcriptomes |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Purpose: The goals of this study are to compare EG7 - CAFs (cancer-associated fibroblasts) and MSCs (mesenchymal stem cells) transcriptome profiling (RNA-seq) generated from Next-generation Sequencing (NGS) to perform optimal high-throughput data analysis
Methods: mRNA profiles of CAFs were purified from EG7 tumor bearing mice and early passage (p6) murine MSCs purchased from Cyagen were cultured in DMEM for no more than 2 passages were generated by deep sequencing, in triplicate, using Illumina HiSeq 3000. The sequence reads that passed quality filters were analyzed at the transcript isoform level TopHat followed by Cufflinks
Results: Comparative high throughput RNA-sequencing (seq) analysis of purified EG7-CAFs and the early passage murine MSCs, which are thought to be precursors for some CAFs and used as the control for normal mesenchymal cells, by using an optimized data analysis workflow, we mapped about 50 million sequence reads per sample to the mouse genome (build mm10) and identified 11,839 transcripts with TopHat workflow. Approximately 1584 of the transcripts showed differential expression between the EG7 - CAFs and MSCs, with a fold change ≥ 2 and p value <0.01
Conclusions: Our results clearly support the notion that CAFs are transcriptionally different from MSCs in various pathways and biological processes associated with immune modulation, inflammation, hypoxia, and activation of oncogenic pathways
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| Overall design |
mRNA profiles of purified EG7-CAFs and the early passage murine MSCs were generated by deep sequencing, in triplicate, using Illumina HiSeq 3000.
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| Contributor(s) |
Yu M, Guo G, Cui Y |
| Citation(s) |
31980601 |
| Submission date |
Nov 29, 2019 |
| Last update date |
Jan 29, 2020 |
| Contact name |
YAN CUI |
| E-mail(s) |
ycui@augusta.edu
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| Phone |
(706)-723-4153
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| Organization name |
Augusta University
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| Department |
Georgia Cancer Center
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| Lab |
Cancer Immunology, Inflammation & Tolerance Program
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| Street address |
1410 Laney Walker Blvd, CN 4120
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| City |
AUGUSTA |
| State/province |
GA |
| ZIP/Postal code |
30912 |
| Country |
USA |
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| Platforms (1) |
| GPL21493 |
Illumina HiSeq 3000 (Mus musculus) |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA592566 |
| SRA |
SRP234043 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE141199_RAW.tar |
830.0 Kb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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