KEY RESOURCES TABLE.
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies (dilution) | ||
| mouse anti-Atp1A1 (1:250) | Developmental Studies Hybridoma Bank | A5 |
| mouse anti-β-Actin M2 (1:10000) | Sigma | AC-74 |
| rabbit anti-Barttin (1:1000) | Thomas Jentsch (Leibniz-Institut für Molekulare Pharmakologie) | N/A |
| rat anti-CD44 (1:200) | BD Parmingen | 550538 |
| rabbit anti-Claudin-11 (1:100 +AR) | Novex | 364500 |
| mouse anti-Connexin-26/Gjb2 (1:200) | Thermo Scientific | 71-0500 |
| mouse anti-E-cadherin (1:200 +AR) | BD Transduction Laboratories | 610181 |
| mouse anti-Esrp1 (1:200) | Russ Carstens (UPenn) | N/A |
| rabbit anti-Esrrβ/Nr3b2 (1:500 +AR) | Jeremy Nathans (Johns Hopkins Univ.) | N/A |
| goat anti-Kcnq1 (1:300) | Santa Cruz | SC-10646 |
| rabbit anti-MyosinVIIa (1:500) | Proteus Biosciences | 25-6790 |
| mouse anti-Neurofilament (1:200) | Developmental Studies Hybridoma Bank | 2H3 |
| rabbit anti-P27kip1 (1:400) | Thermo Scientific | PA5-27188 |
| mouse anti-Pou4F3/Brn-3c (1:200 +AR) | Santa Cruz | sc-81980 |
| rabbit anti-Prox1 (1:500) | Chemicon Billerica | AB5475 |
| rabbit anti-Otx2 (1:1000) | Flora Vaccarino (Yale University) | N/A |
| Mouse anti-Sox2 (1:200 +AR) | R&D Systems | MAB2018 |
| donkey anti-mouse IGG Alexa488 (1:200) | Molecular Probes | A-21202 |
| donkey anti-rabbit IGG Alexa594 (1:200) | Molecular Probes | A-21207 |
| rabbit anti-goat IGG Alexa488 (1:200) | Molecular Probes | A-11078 |
| donkey anti-rat Alexa488 (1:200) | Molecular Probes | A-21208 |
| *AR, antigen retrieval – boil for 6 minutes in 10mM citric acid buffer (pH 6.0) | ||
| Chemicals, Peptides, and Recombinant Proteins | ||
| Phalloidin conjugated Alexa488 (1:50) | Molecular Probes | A-12379 |
| Critical Commercial Assays | ||
| NEBNext® Poly(A) mRNA Magnetic Isolation Module | New England Biosystems | E7490S |
| Directional RNA Library Prep Kit for Illumina® | New England Biosystems | E7420S |
| Deposited Data | ||
| RNA-seq raw and analyzed data | This paper | GSE90821 |
| MAJIQ splicing analysis | This paper | http://majiq.biociphers.org/rohacek_2016/. |
| Experimental Models: Cell Lines | ||
| Human: patient derived IPSCs | This paper | N/A |
| Human: MDA-MB-231 cells | ATCC | HTB-26 |
| Mouse: Esrp1−/− embryonic stem cells | Cieply et al. 2016 | N/A |
| Experimental Models: Organisms/Strains | ||
| Mouse: Esrp1+/− | Bebee et al. 2015 | N/A |
| Mouse: Fgf9+/− - B6N(Cg)-Fgf9tm1b(KOMP)Wtsi/J | The Jackson Laboratories | 0224362 |
| Recombinant DNA | ||
| PMX-CFF-B | Modified from Toshio Kitamura | N/A |
| Sequence-Based Reagents | ||
| PCR Primers for human ESRP1 and ESRP2 exons see Table S3 | This paper | N/A |
| Primers used to detect gene specific alternative splicing switches by RT-PCR.see Table S4 | This paper | N/A |
| sgRNA oligos for ESRP1 (c.665_683 del)
CRISPR: F: caccGATGGAACTTATTGGGCACG R: aaacCGTGCCCAATAAGTTCCATC |
This paper | N/A |
| ESRP1 (c.665_683 del) repair template: TATTGAGTCCTTTGAAGAATCTTGCAATATCTTGATCTGAAGACTGCCATGGTAAACCTCGTGCCCTGACTACGGTGTTATCATCGATAAGTTCCATCTTGCTGCTGTGGATGAAGCAAAACTTCAGGTTGCATGATAAA | This paper | N/A |
| ESRP1 (c.665_683 del) repair PCR genotyping
primers: F: CACAGGCAGCCATGTTTCTA R: TAGGCAGTTGTCTTGCAGGG |
This paper | N/A |
| Software and Algorithms | ||
| RUM | Grant et al. 2011 | http://www.cbil.upenn.edu/RUM/ |
| edgeR | Robinson et al. 2010 | https://bioconductor.org/packages/release/bioc/html/edgeR.html |
| MAJIQ | Vaquero-Garcia et al., 2016 | http://majiq.biociphers.org/ |
| STAR | Dobin et al., 2013 | https://github.com/alexdobin/STAR |
| Other | ||