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| Status |
Public on Mar 01, 2012 |
| Title |
Microarray analysis of TAP::ALG-1 associated RNAs isolated from synchronized 'wild-type' animals and 'mir-58' mutants |
| Organism |
Caenorhabditis elegans |
| Experiment type |
Other
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| Summary |
To discover new miRNA targets, we generated a C. elegans transgenic line expressing a functional N-terminally Tandem Affinity Purification (TAP) tagged ALG-1 protein (C. elegans strain WS4303). We crossed the TAP::ALG-1 transgene into the mir-58(n4640) mutant background to generate the strain WS5041. For simplicity, we will hereafter term the TAP::ALG-1 transgenic animals as wild typeand the transgenic WS5041 animals as mir-58.
We compared the mRNA population that coimmunopurified with TAP::ALG-1 from synchronized L4 stage wild-type animals with that from synchronized L4 stage mir-58 mutant animals by one-color Affymetrix gene arrays. miR-58 target mRNAs should be specifically underrepresented in the latter samples.
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| Overall design |
Strains WS4303 (wt) and WS5041 (mir-58) were used for TAP::ALG-1 IPs. All experiments were conducted in three independent replicates. For each replicate, WS4303 and WS5041 were grown in parallel. 150 ng of TAP::ALG-1 associated RNA isolated from synchronized late L4 animals were sent to the GeneCore facilty in Heidelberg, Germany (http://www.genecore.embl.de/index.cfm), and the microarray data were generated according to their standard protocol (Weinmann et al. 2009).
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| Contributor(s) |
Marko J, Michael HO, Andre GP, Ruedi A, Hubert R |
| Citation(s) |
22454234 |
| |
| Submission date |
Oct 12, 2011 |
| Last update date |
Jul 06, 2016 |
| Contact name |
Marko Jovanovic |
| E-mail(s) |
markojov@broadinstitute.org
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| Organization name |
Broad Institute of MIT and Harvard
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| Department |
Core Group (Regev group) member
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| Lab |
Regev lab
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| Street address |
7 Cambridge Center
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
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| Platforms (1) |
| GPL200 |
[Celegans] Affymetrix C. elegans Genome Array |
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| Samples (6)
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| GSM815851 |
WS5041 (mir 58(n4640); alg 1(tm492); opIs205). Replicate 1 |
| GSM815852 |
WS4303 (alg 1(tm492); opIs205). Replicate 1 |
| GSM815853 |
WS5041 (mir 58(n4640); alg 1(tm492); opIs205). Replicate 2 |
| GSM815854 |
WS4303 (alg 1(tm492); opIs205). Replicate 2 |
| GSM815855 |
WS5041 (mir 58(n4640); alg 1(tm492); opIs205). Replicate 3 |
| GSM815856 |
WS4303 (alg 1(tm492); opIs205). Replicate 3 |
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| This SubSeries is part of SuperSeries: |
| GSE32944 |
Identification of miRNA target genes in C. elegans by RIP-chip-SRM |
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| Relations |
| BioProject |
PRJNA154407 |
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