Key resources table.
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Gene (zebrafish, Danio rerio) | mitfa | Ensembl | ENSDARG00000003732 | |
| Gene (zebrafish, Danio rerio) | sox10 | Ensembl | ENSDARG00000077467 | |
| Gene (zebrafish, Danio rerio) | si:ch73-308m11.1 | Ensembl | ENSDARG00000039752 | |
| Gene (zebrafish, Danio rerio) | myhc4 | Ensembl | ENSDARG00000035438 | |
| Gene (zebrafish, Danio rerio) | slc4a4a | Ensembl | ENSDARG00000013730 | |
| Gene (zebrafish, Danio rerio) | polr3h | Ensembl | ENSDARG00000102590 | |
| Gene (zebrafish, Danio rerio) | vasnb | Ensembl | ENSDARG00000102565 | |
| Gene (zebrafish, Danio rerio) | gata3 | Ensembl | ENSDARG00000016526 | |
| Gene (zebrafish, Danio rerio) | ahsa1a | Ensembl | ENSDARG00000028664 | |
| Gene (zebrafish, Danio rerio) | BX537296.1 | Ensembl | ENSDARG00000110416 | |
| Gene (zebrafish, Danio rerio) | cygb1 | Ensembl | ENSDARG00000099371 | |
| Gene (zebrafish, Danio rerio) | BX000701.1 | Ensembl | ENSDARG00000099172 | |
| Gene (zebrafish, Danio rerio) | syngr1a | Ensembl | ENSDARG00000002564 | |
| Gene (zebrafish, Danio rerio) | hlfa | Ensembl | ENSDARG00000074752 | |
| Gene (zebrafish, Danio rerio) | coro7 | Ensembl | ENSDARG00000089616 | |
| Gene (zebrafish, Danio rerio) | kctd13 | Ensembl | ENSDARG00000044769 | |
| Gene (zebrafish, Danio rerio) | RF00091 | Ensembl | ENSDARG00000084991 | |
| Gene (zebrafish, Danio rerio) | trir | Ensembl | ENSDARG00000104178 | |
| Gene (zebrafish, Danio rerio) | tfap4 | Ensembl | ENSDARG00000103923 | |
| Gene (zebrafish, Danio rerio) | CU138547.1 | Ensembl | ENSDARG00000074231 | |
| Gene (zebrafish, Danio rerio) | CABZ01019904.1 | Ensembl | ENSDARG00000104193 | |
| Gene (zebrafish, Danio rerio) | traf7 | Ensembl | ENSDARG00000060207 | |
| Gene (zebrafish, Danio rerio) | polr2f | Ensembl | ENSDARG00000036625 | |
| Gene (zebrafish, Danio rerio) | CR394546.5 | Ensembl | ENSDARG00000112755 | |
| Gene (zebrafish, Danio rerio) | FP326649.1 | Ensembl | ENSDARG00000088820 | |
| Gene (zebrafish, Danio rerio) | AL953907.2 | Ensembl | ENSDARG00000113960 | |
| Gene (zebrafish, Danio rerio) | CR388047.2 | Ensembl | ENSDARG00000109888 | |
| Gene (zebrafish, Danio rerio) | CABZ01040998.1 | Ensembl | ENSDARG00000111638 | |
| Gene (zebrafish, Danio rerio) | si:dkey-175d9.2 | Ensembl | ENSDARG00000093476 | |
| Strain, strain background (zebrafish, Danio rerio) | AB | ZIRC | ZDB-GENO-960809–7 | |
| Strain, strain background (zebrafish, Danio rerio) | Tübingen | ZIRC | ZDB-GENO-990623–3 | |
| Strain, strain background (zebrafish, Danio rerio) | SAT | ZIRC | ZDB-GENO-100413–1 | |
| Genetic reagent (zebrafish, Danio rerio) |
ENSDAR G00000089358sa19600 |
PMID:23594742 | ZDB-ALT-190501–298 | |
| Genetic reagent (zebrafish, Danio rerio) | bace2hu3332 | PMID:23594742 | ZDB-ALT-100723–4 | |
| Genetic reagent (zebrafish, Danio rerio) | bmp7asa1343 | PMID:23594742 | ZDB-ALT-120411–112 | |
| Genetic reagent (zebrafish, Danio rerio) | cacna1csa6050 | PMID:23594742 | ZDB-ALT-161003–17955 | |
| Genetic reagent (zebrafish, Danio rerio) | capza1bta253a | PMID:23594742 | Allele not cryopreserved | |
| Genetic reagent (zebrafish, Danio rerio) | capzbhi1858bTg | PMID:23594742 | ZDB-ALT-040907–2 | |
| Genetic reagent (zebrafish, Danio rerio) | cax1sa10712 | PMID:23594742 | ZDB-ALT-130411–634 | |
| Genetic reagent (zebrafish, Danio rerio) | cdan1sa5902 | PMID:23594742 | ZDB-ALT- 161003–17833 |
|
| Genetic reagent (zebrafish, Danio rerio) | cep192sa875 | PMID:23594742 | ZDB-ALT-120411–491 | |
| Genetic reagent (zebrafish, Danio rerio) | clp1sa6358 | PMID:23594742 | ZDB-ALT- 161003–18184 |
|
| Genetic reagent (zebrafish, Danio rerio) | copb1sa3636 | PMID:23594742 | Allele not cryopreserved | |
| Genetic reagent (zebrafish, Danio rerio) | cyfip2sa1556 | PMID:23594742 | ZDB-ALT-120411–193 | |
| Genetic reagent (zebrafish, Danio rerio) | cyldasa21010 | PMID:23594742 | ZDB-ALT-161003–11078 | |
| Genetic reagent (zebrafish, Danio rerio) | dag1hu3072 | PMID:23594742 | ZDB-ALT-070315–1 | |
| Genetic reagent (zebrafish, Danio rerio) | dhx15sa7108 | PMID:23594742 | ZDB-ALT- 161003–18741 |
|
| Genetic reagent (zebrafish, Danio rerio) | dmdta222a | PMID:23594742 | ZDB-ALT-980413–693 | |
| Genetic reagent (zebrafish, Danio rerio) | dnmt3aasa3105 | PMID:23594742 | Allele not cryopreserved | |
| Genetic reagent (zebrafish, Danio rerio) | dnmt3aasa617 | PMID:23594742 | ZDB-ALT-120411–432 | |
| Genetic reagent (zebrafish, Danio rerio) | dnmt3basa14480 | PMID:23594742 | ZDB-ALT-130411–3189 | |
| Genetic reagent (zebrafish, Danio rerio) | dnmt3bb.1sa15458 | PMID:23594742 | ZDB-ALT-130411–4030 | |
| Genetic reagent (zebrafish, Danio rerio) | frem2asa21742 | PMID:23594742 | ZDB-ALT- 161003–11257 |
|
| Genetic reagent (zebrafish, Danio rerio) | glra1sa3896 | PMID:23594742 | Allele not cryopreserved | |
| Genetic reagent (zebrafish, Danio rerio) | gmdsp31erb | PMID:23594742 | ZDB-ALT-051012–8 | |
| Genetic reagent (zebrafish, Danio rerio) | gpaa1sa2042 | PMID:23594742 | ZDB-ALT- 161003–10931 |
|
| Genetic reagent (zebrafish, Danio rerio) | greb1sa1260 | PMID:23594742 | ZDB-ALT-120411–60 | |
| Genetic reagent (zebrafish, Danio rerio) | grin2b (2 of 2)sa19927 | PMID:23594742 | ZDB-ALT-190501–603 | |
| Genetic reagent (zebrafish, Danio rerio) | hsp90aa1.1u45 | PMID:18256191 | ZDB-ALT-080401–1 | |
| Genetic reagent (zebrafish, Danio rerio) | jak2bsa20578 | PMID:23594742 | ZDB-ALT-161003–10984 | |
| Genetic reagent (zebrafish, Danio rerio) | kdm2aasa898 | PMID:23594742 | ZDB-ALT-120727–213 | |
| Genetic reagent (zebrafish, Danio rerio) | kdm2aasa9360 | PMID:23594742 | ZDB-ALT-161003–20015 | |
| Genetic reagent (zebrafish, Danio rerio) | kitlgatc244b | PMID:23364329 | ZDB-ALT-980203–1317 | |
| Genetic reagent (zebrafish, Danio rerio) | lamb2tm272a | PMID:19736328 | ZDB-ALT-980203–1438 | |
| Genetic reagent (zebrafish, Danio rerio) | lamc1sa379 | PMID:23594742 | ZDB-ALT-120411–351 | |
| Genetic reagent (zebrafish, Danio rerio) | las1lsa674 | PMID:23594742 | ZDB-ALT-120727–150 | |
| Genetic reagent (zebrafish, Danio rerio) | ldlrsa16375 | PMID:23594742 | ZDB-ALT-130411–4850 | |
| Genetic reagent (zebrafish, Danio rerio) | maptasa22009 | PMID:23594742 | ZDB-ALT-161003–11315 | |
| Genetic reagent (zebrafish, Danio rerio) | mdn1sa1349 | PMID:23594742 | ZDB-ALT-120411–117 | |
| Genetic reagent (zebrafish, Danio rerio) | megf10sa6166 | PMID:23594742 | ZDB-ALT-161003–18049 | |
| Genetic reagent (zebrafish, Danio rerio) | meis1sa9839 | PMID:23594742 | ZDB-ALT-130411–5422 | |
| Genetic reagent (zebrafish, Danio rerio) | mitfaw2 | PMID:10433906 | ZDB-ALT-990423–22 | |
| Genetic reagent (zebrafish, Danio rerio) | nebhu2849 | PMID:23594742 | ZDB-ALT-070730–10 | |
| Genetic reagent (zebrafish, Danio rerio) | bufti209 | PMID:9007258 | ZDB-ALT-980203–1049 | |
| Genetic reagent (zebrafish, Danio rerio) | nod2sa18880 | PMID:23594742 | ZDB-ALT-161003–10423 | |
| Genetic reagent (zebrafish, Danio rerio) | nol9sa1022 | PMID:23594742 | ZDB-ALT-120411–10 | |
| Genetic reagent (zebrafish, Danio rerio) | nol9sa1029 | PMID:23594742 | ZDB-ALT-160721–33 | |
| Genetic reagent (zebrafish, Danio rerio) | nup88sa2206 | PMID:23594742 | ZDB-ALT-120727–92 | |
| Genetic reagent (zebrafish, Danio rerio) | pax2asa24936 | PMID:23594742 | ZDB-ALT-161003–12106 | |
| Genetic reagent (zebrafish, Danio rerio) | pcnasa8962 | PMID:23594742 | ZDB-ALT-161003–19656 | |
| Genetic reagent (zebrafish, Danio rerio) | pla2g12bsa659 | PMID:23594742 | ZDB-ALT-161003–18374 | |
| Genetic reagent (zebrafish, Danio rerio) | pld1sa1311 | PMID:23594742 | ZDB-ALT-120411–91 | |
| Genetic reagent (zebrafish, Danio rerio) | polr1asa1376 | PMID:23594742 | ZDB-ALT-120411–135 | |
| Genetic reagent (zebrafish, Danio rerio) | ptf1asa126 | PMID:23594742 | ZDB-ALT-100506–17 | |
| Genetic reagent (zebrafish, Danio rerio) | rpl13sa638 | PMID:23594742 | ZDB-ALT-161003–18201 | |
| Genetic reagent (zebrafish, Danio rerio) | rps24sa2681 | PMID:23594742 | ZDB-ALT-161003–12995 | |
| Genetic reagent (zebrafish, Danio rerio) | ryr1sa23341 | PMID:23594742 | ZDB-ALT-161003–11675 | |
| Genetic reagent (zebrafish, Danio rerio) | ryr1sa6529 | PMID:23594742 | ZDB-ALT-161003–18326 | |
| Genetic reagent (zebrafish, Danio rerio) | sh3gl2sa19508 | PMID:23594742 | ZDB-ALT-161003–10694 | |
| Genetic reagent (zebrafish, Danio rerio) | si:ch211-168k14.2sa6115 | PMID:23594742 | ZDB-ALT-161003–18015 | |
| Genetic reagent (zebrafish, Danio rerio) | slc22a7bsa365 | PMID:23594742 | ZDB-ALT-120411–342 | |
| Genetic reagent (zebrafish, Danio rerio) | slc2a11bsa1577 | PMID:23594742 | ZDB-ALT-120411–200 | |
| Genetic reagent (zebrafish, Danio rerio) | smarce1sa18758 | PMID:23594742 | Allele not cryopreserved | |
| Genetic reagent (zebrafish, Danio rerio) | sox10baz1 | PMID:17065232 | ZDB-ALT-070131–1 | |
| Genetic reagent (zebrafish, Danio rerio) | sox10t3 | PMID:11684650 | ZDB-ALT-980203–1827 | |
| Genetic reagent (zebrafish, Danio rerio) | srpk3sa18907 | PMID:23594742 | ZDB-ALT-161003–10436 | |
| Genetic reagent (zebrafish, Danio rerio) | sucla2sa20646 | PMID:23594742 | ZDB-ALT-161003–11003 | |
| Genetic reagent (zebrafish, Danio rerio) | tcf7l1am881 | PMID:11057671 | ZDB-ALT-001107–2 | |
| Genetic reagent (zebrafish, Danio rerio) | tfap2asa24445 | PMID:23594742 | ZDB-ALT-131217–17748 | |
| Genetic reagent (zebrafish, Danio rerio) | tfap2csa18857 | PMID:23594742 | Allele not cryopreserved | |
| Genetic reagent (zebrafish, Danio rerio) | tfip11sa3219 | PMID:23594742 | ZDB-ALT-120727–140 | |
| Genetic reagent (zebrafish, Danio rerio) | tmod4hu3530 | PMID:23594742 | ZDB-ALT-070914–1 | |
| Genetic reagent (zebrafish, Danio rerio) | top1lsa2597 | PMID:23594742 | ZDB-ALT-161003–12704 | |
| Genetic reagent (zebrafish, Danio rerio) | ttnasa1029 | PMID:23594742 | ZDB-ALT-160721–33 | |
| Genetic reagent (zebrafish, Danio rerio) | ttnasa787 | PMID:23594742 | ZDB-ALT-120411–459 | |
| Genetic reagent (zebrafish, Danio rerio) | ttnbsa5562 | PMID:23594742 | Allele not cryopreserved | |
| Genetic reagent (zebrafish, Danio rerio) | vps16sa7027 | PMID:23594742 | ZDB-ALT-161003–18689 | |
| Genetic reagent (zebrafish, Danio rerio) | vps16sa7028 | PMID:23594742 | ZDB-ALT-161003–18690 | |
| Genetic reagent (zebrafish, Danio rerio) | vps51p9emcf | PMID:16581006 | ZDB-ALT-060602–2 | |
| Genetic reagent (zebrafish, Danio rerio) | wu:fj82b07sa24599 | PMID:23594742 | ZDB-ALT-161003–20235 | |
| Genetic reagent (zebrafish, Danio rerio) | yap1sa25458 | PMID:23594742 | ZDB-ALT-200207–2 | |
| Genetic reagent (zebrafish, Danio rerio) | zgc:171,763sa22031 | PMID:23594742 | ZDB-ALT-161003–11320 | |
| Software, algorithm | HISAT2 | PMID:31375807 | RRID:SCR_015530version 2.1.0 | https://github.com/DaehwanKimLab/hisat2 |
| Software, algorithm | featureCounts | PMID:24227677 | ||
| Software, algorithm | DESeq2 | PMID:25516281 | ||
| Software, algorithm | BCFTools | PMID:33590861 | RRID:SCR_002105version 1.4 | https://samtools.github.io/bcftools/bcftools.html |
| Software, algorithm | statsmodels | http://conference.scipy.org/proceedings/scipy2010/pdfs/seabold.pdf | https://www.statsmodels.org/stable/index.html | |
| Software, algorithm | DeTCT | PMID:26238335 | ||
| Software, algorithm | BWA | https://arxiv.org/abs/1303.3997 | ||
| Software, algorithm | biobambam | https://gitlab.com/german.tischler/biobambam2 | ||
| Software, algorithm | mpileup | PMID:21903627 | ||
| Software, algorithm | QCALL | PMID:20980557 | ||
| Software, algorithm | GATK | PMID:21478889 | ||
| Software, algorithm | Tophat | PMID:23618408 | ||
| Software, algorithm | QoRTs | PMID:26187896 |