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| Status |
Public on Jan 30, 2019 |
| Title |
Differential expression analysis of wildtype and zip-3(gk3164) mutant with next generation sequencing |
| Organism |
Caenorhabditis elegans |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
ZIP-3 has been shown to repress the mitochondrial-UPR genes and immune response during P. aeruginosa infection. To identify genes repressed by ZIP-3, we compared transcript profiles from wildtype and zip-3(gk3164) worms raised on P. aeruginosa or E. coli.
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| Overall design |
RNA samples were prepared from wild-type(wt) and zip-3(gk3164)(mutant) worms fed either E. coli or P. aeruginosa. Worms were synchronized by bleaching, starved on empty NGM plates for 48h, transferred to E. coli or P. aeruginosa seeded NGM plates for 18h and then harvested. Each experiment was performed in triplicate indicated as 1,2 and 3.
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| Contributor(s) |
Deng P, Haynes C |
| Citation(s) |
30850535 |
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| Submission date |
Mar 01, 2018 |
| Last update date |
Jul 10, 2019 |
| Contact name |
Cole Haynes |
| Organization name |
U Mass Medical School
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| Street address |
364 Plantation Street, 425
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| City |
Worcester |
| State/province |
Massachusetts |
| ZIP/Postal code |
01605 |
| Country |
USA |
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| Platforms (1) |
| GPL13657 |
Illumina HiSeq 2000 (Caenorhabditis elegans) |
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| Samples (12)
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| GSM3028518 |
wildtype fed with E. coli, biological rep1 |
| GSM3028519 |
wildtype fed with E. coli, biological rep2 |
| GSM3028520 |
wildtype fed with E. coli, biological rep3 |
| GSM3028521 |
wildtype fed with P. aeruginosa, biological rep1 |
| GSM3028522 |
wildtype fed with P. aeruginosa, biological rep2 |
| GSM3028523 |
wildtype fed with P. aeruginosa, biological rep3 |
| GSM3028524 |
zip-3 (gk3164) fed with E. coli, biological rep1 |
| GSM3028525 |
zip-3 (gk3164) fed with E. coli, biological rep2 |
| GSM3028526 |
zip-3 (gk3164) fed with E. coli, biological rep3 |
| GSM3028527 |
zip-3 (gk3164) fed with P. aeruginosa, biological rep1 |
| GSM3028528 |
zip-3 (gk3164) fed with P. aeruginosa, biological rep2 |
| GSM3028529 |
zip-3 (gk3164) fed with P. aeruginosa, biological rep3 |
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| Relations |
| BioProject |
PRJNA436589 |
| SRA |
SRP133787 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE111325_counts.txt.gz |
1.8 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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