KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Mouse anti-EGFP(1) | MSKCC | Clone 19F7; RRID: AB_2716736 |
| Mouse anti-EGFP(2) | MSKCC | Clone 19C8; RRID: AB_2716737 |
| Chicken anti-GFP | AVES | GFP-1020; RRID: AB_10000240 |
| Mouse anti-TH | MilliporeSigma | MAB318; RRID: AB_2201528 |
| Rabbit anti-FGF13 | Geoffrey Pitt lab | N/A |
| Goat anti-cFOS | Santa Cruz | sc-52-g; RRID: AB_2629503 |
| Alexa Fluor 488 Donkey anti-Mouse | ThermoFisher | A21202; RRID: AB_141607 |
| Alexa Fluor 546 Donkey anti-Rabbit | ThermoFisher | A10040; RRID: AB_2534016 |
| Alexa Fluor 647 Donkey anti-Goat | ThermoFisher | A21447; RRID: AB_2535864 |
| Horseradish Peroxidase Goat anti-chicken IgY | AVES | H-1004; RRID: AB_2313517 |
| Bacterial Strains | ||
| NEB® 5-alpha Competent E. coli (High Efficiency) | New England Biolabs | C2987 |
| Deposited Data | ||
| CLIP-Seq raw data | This paper | GEO: GSE118623 |
| PTRE-Seq raw data | This paper | GEO: GSE118623 |
| Experimental Models: Cell Lines | ||
| Human: SH-SY5Y (female, age 4 years) | ATCC | CRL-2266 |
| Experimental Models: Organisms/Strains | ||
| Mouse: CELF6-HA/YFP | Dougherty Lab | JD2078 |
| Mouse: CeH6−/− (“KO”) | Dougherty Lab | Brj56 |
| Oligonucleotides | ||
| See Table S9 | Integrated DNA Technologies | N/A |
| Recombinant DNA | ||
| His/Xpress-CELF3 plasmid | Thomas Cooper lab | N/A |
| His/Xpress-CELF4 plasmid | Thomas Cooper lab | N/A |
| His/Xpress-CELF5 plasmid | Thomas Cooper lab | N/A |
| His/Xpress-CELF6 plasmid | Thomas Cooper lab | N/A |
| EGFP-CELF6 | This paper | N/A |
| pEGFP-C1 | Clontech | N/A |
| pcDNA3.1 His-A | Thermo Fisher | V38520 |
| EGFP-RPL10a | Heiman et al., 2008 | N/A |
| pQC membrane TdTomato IX | Addgene | 37351 |
| pmrPTRE-AAV | This paper | N/A |
| pmrPTRE-AAV with CELF6 CLIP target UTR library | This paper | N/A |
| Software and Algorithms | ||
| Trimmomatic | Bolger et al., 2014 | http://www.usadellab.org/cms/?page=trimmomatic |
| STAR | Dobin et al., 2013 | https://github.com/alexdobin/STAR |
| FGBio | Fulcrum Genomics | https://github.com/fulcrumgenomics/fgbio |
| Picard Tools | Broad Institute | https://broadinstitute.github.io/picard |
| Samtools | Li et al., 2009 | http://samtools.sourceforge.net/ |
| Bedtools | Quinlan and Hall, 2010 | https://github.com/arq5x/bedtools2/blob/master/docs/content/overview.rst |
| Piranha | Uren et al., 2012 | http://smithlabresearch.org/software/piranha/ |
| Subread (featureCounts for read counting) | Liao et al., 2013 | http://subread.sourceforge.net/ |
| R | R Core Team, 2014 | https://www.r-project.org/ |
| edgeR (R package) | Robinson et al., 2010 | https://bioconductor.org/packages/release/bioc/html/edgeR.html |
| Discriminative Regular Expression Motif Elicitation (DREME) | Bailey, 2011 | http://meme-suite.org/tools/dreme |
| Analysis of Motif Enrichment (AME) | McLeay and Bailey, 2010 | http://meme-suite.org/tools/ame |
| Find Individual Motif Occurences (FIMO) | Grant et al., 2011 | http://meme-suite.org/tools/fimo |
| CISBP-RNA Database: Catalog of Inferred Sequence Binding Preferences of RNA binding proteins | Ray et al., 2013 | http://cisbp-rna.ccbr.utoronto.ca/index.php |
| lme4 (R package) | Bates et al., 2015 | https://cran.r-project.org/web/packages/lme4/index.html |
| multcomp (R package) | Hothorn et al., 2008 | https://cran.r-project.org/web/packages/multcomp/index.html |
| car (R package) | Fox and Weisberg, 2019 | https://cran.r-project.org/web/packages/car/index.html |
| limma (R package) | Ritchie et al., 2015 | https://bioconductor.org/packages/release/bioc/html/limma.html |
| ImageJ | NIH | https://imagej.nih.gov/ |
| lsmeans (R package) | Lenth, 2016 | https://cran.r-project.org/web/packages/lsmeans/ |