KEY RESOURCES TABLE.
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
|
| ||
| Bacterial and virus strains | ||
|
| ||
| Wt PA14 | Joao Xavier (MSKCC) | N/A |
|
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| Chemicals, peptides, and recombinant proteins | ||
|
| ||
| Blue-green (Cyan) fluorescent beads (Ex/Em=430/465) | Thermo Fisher | Cat#F13080 |
| Red fluorescent beads (Ex/Em=580/605) | Thermo Fisher | Cat#F8810 |
| Dextran, Fluorescein, 500,000 MW, Anionic, Lysine Fixable | Invitrogen | Cat#D7136 |
| Agarose LM | Gold Biotechnology | Cat#A-204-100 |
| 5-oxoETE | Cayman | Cat#34250 |
| Dimethyl sulfoxide (DMSO) | Sigma | Cat#D8418 |
| ethyl 3-aminobenzoate methanesulfonate (Tricaine) | Sigma | Cat#E10521 |
| Triton X-100 | Sigma | Cat#SLBW7103 |
| Phosphate buffered saline (PBS) | Sigma | Cat#79382 |
| FastDigest NotI restriction enzyme | Thermo Fisher | Cat#FD0593 |
| FastDigest BstXI restriction enzyme | Thermo Fisher | Cat#FD1024 |
| FastDigest BseLI restriction enzyme | Thermo Fisher | Cat#FD1204 |
| FastDigest MseI (Tru1I) restriction enzyme | Thermo Fisher | Cat#ER0981 |
| FastDigest BseNI restriction enzyme | Thermo Fisher | Cat#FD0884 |
| FastDigest HpaII restriction enzyme | Thermo Fisher | Cat#FD0514 |
| FastDigest Eco47I restriction enzyme | Thermo Fisher | Cat#FD0314 |
| FastDigest OliI restriction enzyme | Thermo Fisher | Cat#FD1634 |
| FastDigest PvuI restriction enzyme | Thermo Fisher | Cat#FD0624 |
| FastDigest Bsp1286I (SduI) restriction enzyme | Thermo Fisher | Cat#FD0654 |
| FastDigest SmlI (SmoI) restriction enzyme | Thermo Fisher | Cat#ER1981 |
| FastDigest SalI restriction enzyme | Thermo Fisher | Cat#FD0644 |
|
| ||
| Critical commercial assays | ||
|
| ||
| mMessage mMachine SP6 Kit | Thermo Fisher | Cat#AM1340 |
| Trizol reagent | Thermo Fisher | Cat#15596026 |
| RevertAid First Strand cDNA Synthesis Kit | Thermo Fisher | Cat#K1621 |
| RNeasy Plus Micro kit | QIAGEN | Cat#74034 |
| High-Capacity cDNA Reverse Transcript Kit | Thermo Fisher | Cat#4368814 |
| Maxima SYBR Green/Fluorescein qPCR Master Mix | Thermo Fisher | Cat#K0242 |
|
| ||
| Deposited data | ||
|
| ||
| RNA-seq | This paper | GSE201604 |
| Code | This paper | https://doi.org/10.5281/zenodo.7419586 |
|
| ||
| Experimental models: Organisms/strains | ||
|
| ||
| Zebrafish: wt casper | White et al., 200841 | https://doi.org/10.1016/j.stem.2007.11.002 |
| Zebrafish: TG(Iyz:pm2-mk2) | Stoddard et al., 201942 | https://doi.org/10.1038/s41598-018-36771-9 |
| Zebrafish: TG(mpeg1:eGFP) | Stoddard et al., 201942 | https://doi.org/10.1038/s41598-018-36771-9 |
| Zebrafish: hcar1–4mk213 +/+ | This paper | N/A |
| Zebrafish: hcar1–4mk213 −/− | This paper | N/A |
| Zebrafish: hcar1–4mk214 +/+ | This paper | N/A |
| Zebrafish: hcar1–4mk214 −/− | This paper | N/A |
|
| ||
| Oligonucleotides | ||
|
| ||
| See Table S3 for Oligonucleotides | This paper | N/A |
|
| ||
| Software and algorithms | ||
|
| ||
| ImageJ/FIJI (ImageJ 1.53t, v2.9.0.) | Johannes Schindelin | https://fiji.sc/ |
| MATLAB (9.12.0.1975300 (R2022a) Update 3) | Mathworks Inc., USA | http://mathworks.com |
| Bioinformatics Toolbox Version 4.16 (R2022a) | Mathworks Inc., USA | http://mathworks.com |
| Computer Vision Toolbox Version 10.2 (R2022a) | Mathworks Inc., USA | http://mathworks.com |
| Curve Fitting Toolbox Version 3.7 (R2022a) | Mathworks Inc., USA | http://mathworks.com |
| Deep Learning Toolbox Version 14.4 (R2022a) | Mathworks Inc., USA | http://mathworks.com |
| Fuzzy Logic Toolbox Version 2.9 (R2022a) | Mathworks Inc., USA | http://mathworks.com |
| Global Optimization Toolbox Version 4.7 (R2022a) | Mathworks Inc., USA | http://mathworks.com |
| Image Processing Toolbox Version 11.5 (R2022a) | Mathworks Inc., USA | http://mathworks.com |
| MATLAB Compiler Version 8.4 (R2022a) | Mathworks Inc., USA | http://mathworks.com |
| Mapping Toolbox Version 5.3 (R2022a) | Mathworks Inc., USA | http://mathworks.com |
| Optimization Toolbox Version 9.3 (R2022a) | Mathworks Inc., USA | http://mathworks.com |
| Parallel Computing Toolbox Version 7.6 (R2022a) | Mathworks Inc., USA | http://mathworks.com |
| Partial Differential Equation Toolbox Version 3.8 (R2022a) | Mathworks Inc., USA | http://mathworks.com |
| Sensor Fusion and Tracking Toolbox (R2022a) | Mathworks Inc., USA Version 2.3 | http://mathworks.com |
| Signal Processing Toolbox Version 9.0 (R2022a) | Mathworks Inc., USA | http://mathworks.com |
| Statistics and Machine Learning Toolbox Version 12.3 (R2022a) | Mathworks Inc., USA | http://mathworks.com |
| NIS imaging software (Nikon, v5.11.01) | Nikon Microscope Product | https://www.microscope.healthcare.nikon.com/products/software/nis-elements |
| Prism (GraphPad, v8.3.0) | GraphPad Software | https://www.graphpad.com/scientific-software/prism |
| Imaris (Bitplane, v9.6.0) | Molecular Cytology Core Facility at MSKCC |
https://imaris.oxinst.com/ |