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| Status |
Public on Mar 28, 2017 |
| Title |
Next Generation Sequencing Facilitates Quantitative Analysis of Ern1f/f and Ern1f/fLyz2-Cre macrophage Transcriptomes |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Purpose: IRE1 are indicated to play important role in LPS-induced macrophage activation. The goals of this study are to investigate the effects of IRE1a abrogation in macrophages on Interleukin-4-induced alernative activation of macrophages.
Methods: Total cellular RNAs of M2-polarized BMDMs by IL-4 treatment were isolated and subjected to commercial RNA-seq analysis. RNA-seq data were uniquely mapped to mm10 reference genome by TopHat v1.4.1. Expression values were assigned to gene level by Cufflinks v1.3.0.
Results: Map ratios of all RNA-seq samples were above 80%. Merged expression values of all samples included 10,863 genes. Principle component analysis showed distinguished patterns between groups.
Conclusions: Our study represents detailed analysis of transcriptomes of IL-4-activated macrophages, with biologic replicates, generated by RNA-seq technology. Based on the analysis of our RNA-seq data, increased expression levels of marker genes of macrophage alternative activation were found in IRE1a-abrogated macrophages copared to control cells. Our results demonstrates the loss of ER stress sensor IRE1a in macrophages enhanced IL-4-induced alternative activation.
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| Overall design |
Macrophage mRNA profiles of 8-week old Ern1f/f and Ern1f/fLyz2-Cre mice were generated by deep sequencing, in duplicate, using Illumina HiSeq 2000
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| Contributor(s) |
Liu Y, Shan B, Xu C |
| Citation(s) |
28346409 |
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| Submission date |
Feb 08, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Yong Liu |
| E-mail(s) |
liuy@sibs.ac.cn
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| Organization name |
Wuhan University
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| Street address |
Wuhan 430072, China
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| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430072 |
| Country |
China |
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| Platforms (1) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
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| Samples (8)
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| Relations |
| BioProject |
PRJNA371750 |
| SRA |
SRP099049 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE94659_RAW.tar |
5.2 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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