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Series GSE141199 Query DataSets for GSE141199
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
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
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.
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
Phone (706)-723-4153
Organization name Augusta University
Department Georgia Cancer Center
Lab Cancer Immunology, Inflammation & Tolerance Program
Street address 1410 Laney Walker Blvd, CN 4120
State/province GA
ZIP/Postal code 30912
Country USA
Platforms (1)
GPL21493 Illumina HiSeq 3000 (Mus musculus)
Samples (6)
GSM4197059 CAFs rep1
GSM4197060 CAFs rep2
GSM4197061 CAFs rep3
BioProject PRJNA592566
SRA SRP234043

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Supplementary file Size Download File type/resource
GSE141199_RAW.tar 830.0 Kb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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