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. Author manuscript; available in PMC: 2022 Nov 8.
Published in final edited form as: Curr Biol. 2021 Sep 7;31(21):4800–4809.e9. doi: 10.1016/j.cub.2021.08.030

KEY RESOURCES TABLE

REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies
Primary: rabbit anti-SYCP3 Abcam Cat# ab15093; RRID: AB_301639
Primary: mouse anti-MLH1 Abcam Cat# ab14206: RRID: AB_300987
Secondary: goat anti-rabbit IgG H&L Alexa488 Abcam Cat# ab150077; RRID: AB_2630356
Secondary: goat anti-mouse IgG H&L Alexa555 Abcam Cat# ab150114; RRID: AB_2687594
Chemicals, peptides, and recombinant proteins
Tricaine methanesulfonate (MS 22) Sigma-Aldrich Cat# E10521
2-phenoxyethanol Sigma-Aldrich Cat# 77699
Ribonuclease A from bovine pancreas Sigma-Aldrich Cat# R6513
Formamide Sigma-Aldrich Cat# 47671
Cas9 protein Tacgene No reference
Hematoxylin Microm Microtech Cat# F/HAQ999
Mountant and DAPI (4′,6-diamidino-2-phenolindole) Cambio Cat# 1124-MD-1250
Spectrum-Orange-dUTP Vysis Cat# 02N33-050
Spectrum-Green-dUTP Vysis Cat# 02N32-050
Bovine Serum Albumin (BSA) Vector Cat# SP-5050
Pepsin Chemos CZ Cat# A4289.0100
Giemsa stain Giemsa stain Giemsa stain
Critical commercial assays
NucleoSpin plasmid DNA purification kit Machery-Nagel Cat# 740588.50
NucleoSpin Kits for Tissue Machery-Nagel Cat# 740952.50
HiDi Taq DNA polymerase myPOLS Biotec No reference
AccuPrime Taq DNA polymerase Thermofisher Cat# 12339016
AccuPrime Taq DNA Polymerase, High Fidelity Thermofisher Cat# 12346086
TOPO TA cloning Kit XL Thermofisher Cat# K8050-20
ProLong Gold Antifade Mountant Thermofisher Cat# P10144
MAXIscript T7 Transcription Kit Thermofisher Cat# AM1312
Jumpstart Taq DNA polymerase Sigma-Aldrich Cat# D9307
Chromium Genome Reagent Kits v2 10X genomics Cat# PN-120258
KAPA library Amplification kit Roche Diagnostics Cat# KK2620
Kapa Library Quantification Kit Roche Diagnostics Cat# KK4824
Illumina HiSeq3000 sequencing kits Illumina Cat# FC-410-101
Illumina NovaSeq Reagent Kits Illumina Cat# 20012860
Truseq DNA PCR-Free kit Illumina Cat# 20015962
TruSeq Nano DNA HT Library Prep Kit Illumina Cat# 20015965
SP flow cell Illumina Cat# 20027464
S4 Novaseq flow cell Illumina Cat #20012866
AMPure XP beads Beckman Coulter Cat# A63881
Nanopore Ligation Sequencing Kit Oxford Nanopore Cat# SQK-LSK109
SMRTbell Express Template Prep Kit 2.0 PacBio Cat# 101-685-400
Binding kit 2.0 kit PacBio Cat# 102-089-000
Sequencing kit 2.0 PacBio Cat# 101-829-200
Arima-HiC kit Arima Cat# 510008
Cy3 NT Labeling Kit Jena Bioscience Cat# PP-305L-CY3
Multiplex Fluorescent Reagent Kit v2 ACD Biotechne Cat# 323100
MagAttract HMW DNA kit (48) QIAGEN Cat# 67563
Deposited data
Structure of proprotein complex of human GDF2 55 PDB: 4YCG
Structure of the proprotein complex of human activin A 56 PDB: 5HLY
Structure of the growth factor domain of human GDF5 in complex with repulsive guidance molecule B 57 PDB: 6Z3J
Structure of the growth factor domain of human GDF5 in complex with repulsive guidance molecule B and neogenin 57 PDB: 6Z3M
Structure of the growth factor domain of human GDF5 in complex with BMP receptor 1A 58 PDB: 3QB4
Pachón cavefish, Astyanax mexicanus, genome assembly and annotation This study GenBank: PRJNA734455
Experimental models: Organisms/strains
A. mexicanus Pachón cavefish wild-type Jeffery laboratory, University of Maryland, College Park, MD N/A
A. mexicanus Pachón cavefish gdf6b KO This study N/A
Oligonucleotides
Primers for the amplification of the gdf6b FISH Probe, see Data S1E Eurofins N/A
Primers for B genotyping, see Data S1E Eurofins N/A
Primers for screening gdf6b-KO, see Data S1E Eurofins N/A
Primers for RT-QPCR for gdf6b, see Data S1E Eurofins N/A
Forward primer containing sgRNAs target sequences for #site 1 GAAATTAATACGACTCACTATAGGAGTCTGAAACCGGTTCTGGTTTTAGAGCTAGAAATAGCAAG Eurofins N/A
Forward primer containing sgRNAs target sequences for #site 2 GAAATTAATACGACTCACTATAGGGAGCTGGGCTGGGACGACGTTTTAGAGCTAGAAATAGCAAG Eurofins N/A
Universal Reverse primer: AAAAGCACCGACTCGGTGCCACT Eurofins N/A
Truseq DNA UD Indexes Illumina Cat# 20020590
DOP primer (10 μM) GAGGATGAGGTTGAGNNNNNNGTGG KRD, Prague, Czech Republic N/A
RNAScope probe for cavefish Gdf6b ACD Biotechne N/A
RNAScope probe for cavefish gsdf ACD Biotechne N/A
Recombinant DNA
DR274 vector 59 Addgene plasmid #42250
Gdf6b genomic FISH probe This study N/A
Software and algorithms
Hifiasm version 0.9 60 https://github.com/chhylp123/hifiasm
Long Ranger v2.1.1 10X Genomics https://support.10xgenomics.com/genome-exome/software/pipelines/latest/advanced/other-pipelines
Juicer 61 https://github.com/aidenlab/juicer
3D-DNA pipeline 62 https://github.com/aidenlab/3d-dna
Juicebox 62 https://github.com/aidenlab/Juicebox/wiki/Juicebox-Assembly-Tools
Minimap2 v2.11 63 https://github.com/lh3/minimap2
RepeatModeler Smit, AFA, Hubley, R. Unpublished http://www.repeatmasker.org/
RepeatMasker Smit, AFA, Hubley, R & Green, P. Unpublished http://www.repeatmasker.org/
Genewise 64 https://www.ebi.ac.uk/seqdb/confluence/display/THD/GeneWise
Exonerate European Bioinformatics Institute. Unpublished https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate
Hisat 65 http://www.ccb.jhu.edu/software/hisat/index.shtml
StringTie 66 https://ccb.jhu.edu/software/stringtie/
Trinity 67 https://github.com/trinityrnaseq/trinityrnaseq/wiki
Pasa 68 https://github.com/PASApipeline/PASApipeline/wiki
Augustus 69 https://github.com/Gaius-Augustus/Augustus
karyoploteR 70 https://bernatgel.github.io/karyoploter_tutorial/
Primer3web software version 4.1.0 71 https://primer3.ut.ee/
NovaSeq Control Software and Real-Time Analysis component (v3.4.4) PacBio N/A
Illumina’s conversion software (bcl2fastq v2.20) Illumina N/A
FastQC (v0.11.8) 72 https://github.com/s-andrews/FastQC
BWA mem version 0.7.17 73 https://github.com/lh3/bwa
Picard tools version 2.18.2 Broad Institute http://broadinstitute.github.io/picard
samtools mpileup version 1.8 74 https://sourceforge.net/projects/samtools/files/samtools/
popoolation2 75 https://sourceforge.net/projects/popoolation2/
PSASS version 2.0.0 Feron R. unpublished https://doi.org/10.5281/zenodo.2615936
Yasara 76 http://www.yasara.org
Yasara hm_build.mcr macro 76 http://www.yasara.org/hm_build.mcr
RStudio (Open Source version) RStudio team http://www.rstudio.com/
Ikaros software MetaSystems N/A
DP Manager imaging software Olympus N/A
Olympus Acquisition Software Olympus N/A
Adobe Photoshop CS6 Adobe N/A
ZiFiT software 77 http://zifit.partners.org/ZiFiT/Disclaimer.aspx
Other
Nalgene Freezing Container (Mr. Frosty) Merck Cat# C1562-1EA
Megaruptor1 system Diagenode Cat# B06010001
Qubit3 fluorometer Invitrogen ThermoFisher Cat# Q33216
poly-l-lysine slides ThermoFisher Cat# J2800AMNZ
BluePippin Size Selection system Sage Science No reference
M220 Focused-ultrasonicator Covaris Cat# 500295
Sequence data a whole genome assembly of Pachón This study PRJNA734455