Comment[ArrayExpressAccession] E-GEOD-74459 MAGE-TAB Version 1.1 Public Release Date 2016-01-07 Investigation Title Translation State Array Assay for C elegans IFE-1-dependent mRNAs Comment[Submitted Name] Translation State Array Assay for C elegans IFE-1-dependent mRNAs Experiment Description Relative polysomal loading changes for wild type (N2) versus ife-1(bn127) C. elegans strains Strain ife-1(bn127) is null for the gene encoding one of five eIF4E isoforms in the worm, IFE-1. Only this isoform associates with P granules. Resolution of translating and non-translating mRNAs from WT and mutant worms on 10-45% sucrose gradients. Comparision was by ratios of polysomal content. Please note that each sample data table contains raw signal directly imported from the Affymetrix files and the ratio of signals, P/(NP+P), and fold-changes were further calculated. The TSAA_overview.xls contains more datails about the TSAA procedure and 'complete_data.xlsx' contains complete TSAA data output. Term Source Name ArrayExpress EFO Term Source File http://www.ebi.ac.uk/arrayexpress/ http://www.ebi.ac.uk/efo/efo.owl Person Last Name Keiper Keiper Friday Henderson Morrison Hoffman Person First Name Brett Brett Andrew Melissa J Jenna Person Mid Initials D D J A K L Person Email keiperb@ecu.edu Person Affiliation Brody School of Med at ECU Person Phone 252-744-2656 Person Address Biochem and Mol Biol, Brody School of Med at ECU, 600 Moye Blvd, Greenville, NC, USA Person Roles submitter Protocol Name P-GSE74459-1 P-GSE74459-5 P-GSE74459-6 P-GSE74459-2 P-GSE74459-3 P-GSE74459-4 P-GSE74459-7 Protocol Description Custom Excel spreadsheets were created by AJF for calculating translation ratios, relative (fold) translation changes, and statistics (provided in the 'complete_data.xls) Comparisons: Samples were paired (WT and ife-1) for each biological growth set. Replicate 1 includes samples from gradients for an ife-1 set and a wild type set. The set includes a wild type non-polysomal measurement (NPw), a wild type polysomal measurement (Pw), an ife-1 non-polysomal measurement (NPi), and an ife-1 polysomal measurement (Pi). each set of replicate measurements, P values, present/absent calls, and subsequent calculated columns are color coded. Green header columns are data from Replicate 1, blue are Replicate 2, and orange are Replicate 3. P and A for present/absent calls were replaced by 1 and 0, respectively, for clarity and for mathematical culling. Data calculations: [Pw/(NPw+Pw)]=Rw, [Pi/(NPi+Pi)]=Ri, [Rw/Ri]= Relative Fold Change in R (MFR). Summing the non-polysomal and polysomal signals (NP+P) from single replicates allowed similar calculation of mean fold change in total mRNA (MFT). Affymetrix returned a probe signal output value for each of 22,625 genes. Each gene was tagged as being statistically “present” or “absent” for each of 4 samples (Pw, NPw, Pi, and NPi). Signals flagged as “absent” by Affymetrix in 3 or more of the 4 samples for a single replicate were removed. This analysis was performed in three biological replicates. Any mRNAs that did not pass the “present”/”absent” test in all three replicates were removed from the data set, leaving a representative group of 13,372 mRNAs. ID_REF = VALUE = raw signal P/A = p-val = Labelled cRNA were prepared according to the standard protocol at UNC Functional Genomics core (www.med.unc.edu/corefacilities/functionalgenomics) Hybridization according to the standard protocol at UNC Functional Genomics core Worms were isolated, lysed and resolved on 10-45% sucrose gradients as described in detail in the tsaa overview sheet. Three day final passage growth at 20C on agar plates with OP50 E coli supplemented with chicken egg yolk. Trizol extraction of RNA from each sucrose fraction, pooling, re-extraction with chloroform, and reprecipitation as described in the tsaa overview sheet. GeneChips were scanned at the UNC Functional Genomics core, Chapel Hill, NC. Protocol Type normalization data transformation protocol labelling protocol hybridization protocol sample treatment protocol growth protocol nucleic acid extraction protocol array scanning protocol Experimental Factor Name molecule subtype genotype Experimental Factor Type molecule subtype genotype Publication Title Spatial and temporal translational control of germ cell mRNAs mediated by the eIF4E isoform IFE-1. Publication Author List Friday AJ, Henderson MA, Morrison JK, Hoffman JL, Keiper BD PubMed ID 26542024 Publication DOI 10.1242/jcs.172684 Comment[SecondaryAccession] GSE74459 Comment[GEOReleaseDate] 2016-01-07 Comment[ArrayExpressSubmissionDate] 2015-10-28 Comment[GEOLastUpdateDate] 2016-01-07 Comment[AEExperimentType] transcription profiling by array Comment[AdditionalFile:Data1] GSE74459_TSAA_overview.xls Comment[AdditionalFile:Data2] GSE74459_complete_data.xlsx SDRF File E-GEOD-74459.sdrf.txt