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| Status |
Public on Dec 11, 2018 |
| Title |
RNAseq profiling of zebrafish larval macrophages reveals similarities with human M1 and M2 transcriptome signatures |
| Organism |
Danio rerio |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
We used different zebrafish transgenic lines to sort macrophages, neutrophils and immature lymphoid cells from 5-6 day old zebrafish larvae and analyzed their transcriptomes. Comparison between the different transcriptomes and gene ontology analysis revealed specificities for each cell population. Comparison with previously published data showed that zebrafish larval macrophages expressed several known human M1 and M2 macrophages. Transcriptome analysis of uninfected and infected macrophages from embryos infected by of Mycobacterium marinum revealed infection induced transcriptional changes and a shift towards M1 transcriptomic signature.
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| Overall design |
For infection experiments, zebrafish embryos were manually dechorionated at 24 hours post fertilization (hpf) and were infected by injection in the caudal vein of 125 colony forming unit of Mycobacterium marinum M strain expressing GFP. Embryos were grown into egg water refresh every day and incubated for 5 days at 28°C. 0.003% 1-phenyl-2-thiourea (Sigma-Aldrich) was added after 1 day to prevent melanisation. After the incubation period, embryos were dissociated into single cell suspension by Trypsin treatment and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer. cDNA synthesis, amplification and library preparation were performed as previously described. (Rougeot et al., 2014, Methods Mol Biol 1197:41-66).
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| Contributor(s) |
Rougeot J, Zakrzewska A, Torraca V, Kanwal Z, Jansen H, Spaink HP, Meijer AH |
| Citation(s) |
31832066 |
| |
| Submission date |
May 15, 2015 |
| Last update date |
Dec 17, 2019 |
| Contact name |
Julien Rougeot |
| E-mail(s) |
julien.rougeot@wur.nl
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| Phone |
0031655778095
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| Organization name |
Wageningen University and Research
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| Department |
Plant Science Group
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| Lab |
Entomology
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| Street address |
Droevendaalsesteeg 1 Building 107
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| City |
Wageningen |
| State/province |
Gerlderland |
| ZIP/Postal code |
6708 PB |
| Country |
Netherlands |
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| Platforms (1) |
| GPL14875 |
Illumina HiSeq 2000 (Danio rerio) |
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| Samples (6)
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| GSM1686454 |
6dpf mpeg1:mCherryPos_MmarinumGFPNeg_rep1 |
| GSM1686455 |
6dpf mpeg1:mCherryPos_MmarinumGFPNeg_rep2 |
| GSM1686456 |
6dpf mpeg1:mCherryPos_MmarinumGFPNeg_rep3 |
| GSM1686457 |
6dpf mpeg1:mCherryPosMmarinumGFPPos_rep1 |
| GSM1686458 |
6dpf mpeg1:mCherryPosMmarinumGFPPos_rep2 |
| GSM1686459 |
6dpf mpeg1:mCherryPosMmarinumGFPPos_rep3 |
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| Relations |
| BioProject |
PRJNA284108 |
| SRA |
SRP058376 |
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