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| Status |
Public on Feb 20, 2020 |
| Title |
Next Generation Sequencing Facilitates Quantitative Analysis of Taurine Promoted Transcriptomes |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Purpose: Taurine promotes the activation of plasmacytoid dendritic cells. The goals of this study are to identify genes and pathways invovled in the regulation.
Methods: Mouse plasmacytoid dendritic cells were stimulated with R837, together with or without taurine for 12 hours. Then, the next-generation libraries of mRNA were prepared using VAHTS mRNA-seq v2 Library Prep Kit for Illumina® (Vazyme, Nanjing, China). The Library quality was determined by Bioanalyzer 4200 (Agilent, Santa Clara, CA, USA). Then the mRNA-seq libraries were sequenced in HiSeq ⅹ10 system (Illumina, San Diego, CA, USA) on a 150bp paired-end run. The differentially expressed genes were selected as having more than 1 fold difference in their geometrical mean expression between the compared groups and a statistically significant p-value (<0.05) by analysis of DEseq2. The GO analysis on differentially expressed genes was performed with an R package: Clusterprofiler using a p<0.05 to define statistically enriched GO categories. Pathway analysis was used to determine the significant pathway of the differential genes according to Kyoto Encyclopedia of Genes and Genomes Database (http://www.genome.jp/kegg/) and DAVID Bioinformatics Resources 6.8 (https://david.ncifcrf.gov/).
Results: Genes in the TLR7-IRF7 pathway were augmented by taurine. As a result, the production of type I IFNs increased upon taurine treatment.
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| Overall design |
MRNA profiles of R837 stimulated and R837 plus taurine treated pDCs were generated by deep sequencing, in triplicate, using illumina HiSeq ⅹ10 system
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| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Feb 19, 2020 |
| Last update date |
Feb 23, 2020 |
| Contact name |
Haibo Zhou |
| E-mail(s) |
hbzhou1984@gmail.com
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| Phone |
+8602168385620
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| Organization name |
Renji Hospital
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| Department |
Department of Rheumatology
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| Street address |
No.160, Pujian Road
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| City |
Shanghai |
| ZIP/Postal code |
200127 |
| Country |
China |
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| Platforms (1) |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA607531 |
| SRA |
SRP250015 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE145546_RAW.tar |
6.8 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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