Skip to main content
. 2018 Mar 12;44(5):597–610.e10. doi: 10.1016/j.devcel.2018.01.022
REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies
Mouse monoclonal anti-HA Sigma Cat#H9658; RRID: AB_260092
Mouse monoclonal anti-c-Myc Sigma Cat#M5546; RRID: AB_260581
Mouse monoclonal anti-α-tubulin Sigma Cat#T5168; RRID: AB_477579
Anti-mouse IgG (H+L) horse radish peroxidase conjugate Thermo Fisher Scientific Cat#31430; RRID: AB_228307
Fab fragments from polyclonal anti-digoxigenin conjugated to alkaline phosphatase Roche Cat#11093274910; RRID: AB_514497
Chemicals, Peptides, and Recombinant Proteins
PhosphoSafe extraction buffer Merck Cat#71296
complete EDTA-free protease inhibitors Roche Cat#11873580001
TRIzol Thermo Fisher Scientific Cat#15596018
digoxigenin-11-UTP Roche Cat#11277065910
RiboLock RNase inhibitor Thermo Fisher Scientific Cat#EO0381
4-Nitro-blue tetrazolium chloride (NBT) Roche Cat#11383213001
5-Bromo-4-chloro-3'-indolyphosphate (BCIP) Roche Cat#11383221001
digoxigenin-11-dUTP Roche Cat#11558706910
Critical Commercial Assays
mMessage mMachine T3 Transcription kit Thermo Fisher Scientific Cat#AM1348
mMessage mMachine SP6 Transcription kit Thermo Fisher Scientific Cat#AM1340
TruSeq RNA Library Prep Kit v2 Illumina Cat#RS-122-2001
KAPA HiFi HotStart ReadyMix Kapa Biosystems Cat#KK2602
TOPO TA cloning kit Thermo Fisher Scientific Cat#K4500
Zero-Blunt TOPO cloning kit Thermo Fisher Scientific Cat#K2800
Directional pENTR/TOPO cloning kit Thermo Fisher Scientific Cat#K2400
Turbo DNase Thermo Fisher Scientific Cat#AM2238
proteinase K Thermo Fisher Scientific Cat#AM2548
SP6 RNA polymerase Roche Cat#11487671001
T7 RNA polymerase Roche Cat#10881767001
Terminal deoxynucleotidyl transferase Thermo Fisher Scientific Cat#EP0161
RNase H minus and point-mutant M-MLV reverse transcriptase Promega Cat#M3681
SYBR Green I master mix Roche Cat#04707516001
Deposited Data
Raw sequencing data (FASTQ) This study GEO: GSE96655
Experimental Models: Organisms/Strains
Xenopus tropicalis te1.2D/+ This study EXRC: https://xenopusresource.org
Xenopus tropicalis te1.2D/+t2e3.7D/+ This study EXRC: https://xenopusresource.org
Oligonucleotides
Sulforhodamine-tagged morpholino, t MOsplice:
TGGAGAGACCCTGATCTTACCTTCC		 GeneTools Gentsch et al., 2013
Sulforhodamine-tagged morpholino, t MOtransl:
GGCTTCCAAGCGCACACACTGGG		 GeneTools Gentsch et al., 2013
Sulforhodamine-tagged morpholino, t2 MOsplice:
GAAAGGTCCATATTCTCTTACCTTC		 GeneTools Gentsch et al., 2013
Sulforhodamine-tagged morpholino, t2 MOtransl:
AGCTGTGCCTGTGCTCATTGTATTG		 GeneTools Gentsch et al., 2013
Untagged morpholino, standard control MO:
CCTCTTACCTCAGTTACAATTTATA		 GeneTools N/A
Biotin-tagged ttarget RNA:
[Btn]AAAAAAAAGGAAGGUAAGAUCAGGGUCUCUCCA		 IDT This study
Biotin-tagged dtymkoff-target RNA:
[Btn]AAAAAAAAGGAGGUAAGAGAUCAUUUGUAGGAU		 IDT This study
Biotin-tagged dtymkG>Coff-target RNA:
[Btn]AAAAAAAAGCAGGUAAGAGAUCAUUUGUAGGAU		 IDT This study
Biotin-tagged scrambled dtymkoff-target RNA:
[Btn]AAAAAAAAAGUUAUGGCGAGAGUGGAUAUUAGA		 IDT This study
Genotyping t (exon 1), forward and reverse primer:
AATCAGAGGAAGAGCTGCTG, CATTGGTGAGCTCCTTGAAC		 Sigma This study
Genotyping t2 (exon 3), forward and reverse primer:
TCACATCATTAAAATAGTGGCCTGCT, TCCATGAAATGTGAATTGTGGGCT		 Sigma This study
Cloning t and te1.2D for N-terminal tagging, forward and reverse primer:
CACCATGAGTGTAAGTGCCACCGAGA, TTAGATTGACGGCGGTGCAAC		 Sigma This study
Cloning t and te1.2D for C-terminal tagging, forward and reverse primer:
CACCATGAGTGTAAGTGCCACCGAGA, GATTGACGGCGGTGCAACTG		 Sigma This study
Cloning t2 for N-terminal tagging, forward and reverse primer:
CACCATGAGTACAGGAACAGCTG,
CTATAATGATGGAGGTGTCACAGA		 Sigma This study
Cloning t2 for C-terminal tagging, forward and reverse primer:
CACCCAGAAGAGGCATCAGCAATAC,
TAATGATGGAGGTGTCACAGAAG		 Sigma This study
Cloning t2e3.7D for N-terminal tagging, forward and reverse primer:
CACCATGAGCACAGGCACAGCTGAGA,
CTATAATGATGGAGGTGTCACAGA		 Sigma This study
Cloning t2e3.7D for C-terminal tagging, forward and reverse primer:
CACCATGAGCACAGGCACAGCTGAGA,
TAATGATGGAGGTGTCACAGAAGC		 Sigma This study
Generating c3ar1 in situ probe template (1,020 bp), forward and reverse primer:
GAGAGAGTGCCCGTTACAGC,
ATGAGGCAGTTTGTGCCAAG		 Sigma This study
Generating tp53 in situ probe template (999 bp), forward and reverse primer:
TGTGGAGTCTGTTGCCTGAC,
CCAGCAGCTTCTTTCCTTTC		 Sigma This study
Generating tp53inp1 in situ probe template (1,002 bp), forward and reverse primer:
TCGTCTACCTCACCCGTTTC,
TGCAAGTCGCTCTGCTACTC		 Sigma This study
RT-qPCR for abi1 (exon 1), forward and reverse primer:
CGGGTGTGGACTTAGCTGTT,
CGGGGATCTCCTCCTCTAGT		 Sigma This study
RT-qPCR for abi1 (ˆ, joining exon 7 and 11 by alternative splicing), forward and reverse primer:
TATTGGACAAGˆTTGCGGACA,
GGAGGTGGAGGAGGAGAATC		 Sigma This study
RT-qPCR for bloc1s4 (exon 1 to 2), forward and reverse primer:
CCAGTCTCCTGACCGAAGAG,
AATCTCTGCATTTCCGCTGT		 Sigma This study
RT-qPCR for bloc1s4 (ˆ, joining exon 4 and 6 by alternative splicing), forward and reverse primer:
TGCTTGAGˆAAACAAACACCTG,
CTGCTGCTGGGAAAGAAATC		 Sigma This study
RT-qPCR for c3ar1 (exon 1 to 2), forward and reverse primer:
TTGATGGTCAGGAGACAGAGG,
CGTCCCATTCCTGATATTGC		 Sigma This study
RT-qPCR for dtymk (exon 1), forward and reverse primer:
TGCGAGGTGCTTTAATTGTG,
CTTGTAACCCCGCTCTTTCA		 Sigma This study
RT-qPCR for dtymk (ˆ, joining exon 2 and 5 by alternative splicing), forward and reverse primer:
CGCTGGGAACAAGTˆCTCATT,
TCGGTTTATCTTTGGCATCC		 Sigma This study
RT-qPCR for odc1, forward and reverse primer:
GGGCAAAAGAGCTTAATGTGG,
CATCGTGCATCTGAGACAGC		 Sigma Gentsch et al., 2013
RT-qPCR for t (exon 1 to 2), forward and reverse primer:
CCTGTGGATGAGGTTCAAGG,
CACGCTCACCTTTAGAACTGG		 Sigma Gentsch et al., 2013
RT-qPCR for t (exon 6), forward and reverse primer:
TCTTTATGTTCGCCCAATCC,
CGAGCGGTGGTTTCTTAGAG		 Sigma This study
RT-qPCR for t (ˆ, joining exon 1 and 2 by cryptic splicing), forward and reverse primer:
GAGCTGAAGˆGCGAATGTTTC,
TTGTCAGCTGCCACAAAATC		 Sigma This study
RT-qPCR for t2, forward and reverse primer:
CACAAGCCATTCATTTCCAG,
TCTTTGGCATCAAGGAAAGC		 Sigma Gentsch et al., 2013
RT-qPCR for tbx6, forward and reverse primer:
ACCTCCTACGGGATGAGACC,
AACAGCCCATCAAACCTCTG		 Sigma Gentsch et al., 2013
RT-qPCR for tp53, forward and reverse primer:
GGATCGTCGCACAGAAGAAG,
AAGTGGAGGGTCACTGGATG		 Sigma This study
RT-qPCR for tp53inp1, forward and reverse primer:
CACAGGATATAAAGCGACCAAAG,
GTGTAGCAAGGTGGCACAAG		 Sigma This study
Recombinant DNA
t TALEN Cellectis Bioresearch N/A
t2 TALEN This study N/A
Golden Gate TALEN and TAL Effector Kit 2.0 Cermak et al., 2011 Addgene: goldengatev2
t2 cDNA clone Source BioScience IMAGE 5307982
RCIscript-GoldyTALEN plasmid Carlson et al., 2012 Addgene: 38142
N-terminal 3xHA pCS2+ destination vector Nigel Messenger Smith lab
C-terminal 3xHA pCS2+ destination vector Nigel Messenger Smith lab
myc-tagged fam83g pCS2+ Kevin Dingwell Smith lab
X. laevis tp53 pCS105 Cordenonsi et al., 2007 N/A
X. laevis actc1 pSP21 Mohun et al., 1984 N/A
X. tropicalis cav1 pExpress1 Gentsch et al., 2013 IMAGE: 7024946
X. tropicalis c3ar1 pCRII-TOPO This study N/A
X. tropicalis hoxd8 pCR2.1-TOPO Gentsch et al., 2013 N/A
X. tropicalis myh6 pCRII-TOPO Abu-Daya et al., 2009 N/A
X. laevis tal1 pGEM-7Zf+ N/A EXRC
X. laevis tbx6 pBluescript KS- Uchiyama et al., 2001 N/A
X. tropicalis tp53 pCRII-TOPO This study N/A
X. tropicalis tp53inp1 pCRII-TOPO This study N/A
Software and Algorithms
TAL Effector Nucleotide Targeter 2.0 Cermak et al., 2011, Doyle et al., 2012 https://tale-nt.cac.cornell.edu
Bowtie2 v2.1.0 Langmead and Salzberg, 2012 http://bowtie-bio.sourceforge.net/bowtie2
Tophat v2.0.10 Kim et al., 2013 https://ccb.jhu.edu/software/tophat
STAR v2.5.2a Dobin et al., 2013 https://github.com/alexdobin/STAR
Samtools v1.3.1 Li et al., 2009 http://www.htslib.org
RSeQC v2.6.4 (Python) Wang et al., 2012 http://rseqc.sourceforge.net
IGV genome browser v2.3.92 Robinson et al., 2011 http://software.broadinstitute.org/software/igv/
HOMER v4.8.3 Heinz et al., 2010 http://homer.ucsd.edu/homer/index.html
LeafCutter v1.0 (Python/R package) Li et al., 2018 https://github.com/davidaknowles/leafcutter
splAdder v1.0 (Python) Kahles et al., 2016 https://github.com/ratschlab/spladder
Julia: Bio.Seq module BioJulia Project https://github.com/BioJulia
HTSeq-count v0.5.4p3 (Python) Anders et al., 2015 http://www-huber.embl.de/HTSeq/doc/count.html
DESeq2 v1.14.1 (Bioconductor package) Love et al., 2014 https://bioconductor.org/packages/release/bioc/html/DESeq2.html
limma v3.30.13 (Bioconductor package) Ritchie et al., 2015 https://bioconductor.org/packages/release/bioc/html/limma.html
edgeR v3.16.5 (Bioconductor package) Robinson et al., 2010 https://bioconductor.org/packages/release/bioc/html/edgeR.html
GOstats v2.40.0 (Bioconductor package) Falcon and Gentleman, 2007 https://bioconductor.org/packages/release/bioc/html/GOstats.html
GSEABase v1.36.0 (Bioconductor package) Morgan et al., 2017 http://bioconductor.org/packages/release/bioc/html/GSEABase.html
igraph v1.0.1 (R package) Csárdi and Nepusz, 2006 https://cran.r-project.org/web/packages/igraph/index.html
seriation v1.2-1 (R package) Hahsler et al., 2008 https://cran.r-project.org/web/packages/seriation/index.html
Matching v4.9-2 (R package) Sekhon, 2011 https://cran.r-project.org/web/packages/Matching/index.html
R v3.3.1 The R Foundation https://www.r-project.org
Bioconductor v3.5 Bioconductor http://www.bioconductor.org
Perl v5.18.2 The Perl Foundation https://www.perl.org
Python v2.7.12 Python Software Foundation http://www.python.org
Julia v0.5 The Julia Community https://julialang.org