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Zebrafish marker genes
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| tissue | subtissue | gene | |
|---|---|---|---|
| Endoderm | Endoderm | PRDX5 | |
| Endoderm | Endoderm | FOXA1 | |
| Endoderm | Endoderm | FOXA2 | |
| Endoderm | Pharyngeal endoderm | NKX2.7 | |
| Endoderm | Pharyngeal endoderm | IRX7 | |
| Endoderm | Posterior (pancreatic and interstinal endoderm) | CDX4 | |
| Axial Mesoderm | Prechordal plate | HE1A | |
| Axial Mesoderm | Prechordal plate | HE1B | |
| Axial Mesoderm | Prechordal plate | CTSLB | |
| Axial Mesoderm | Notochord | COL2A1A | |
| Axial Mesoderm | Notochord | COL8A1A | |
| Axial Mesoderm | Notochord | P4HA1B | |
| Axial Mesoderm | Notochord | TA | |
| Axial Mesoderm | Notochord | NOTO | |
| Axial Mesoderm | Notochord | NTD5 | |
| Intermediate / Lateral Mesoderm | Celphalic mesoderm | FOXF2A | |
| Intermediate / Lateral Mesoderm | Celphalic mesoderm | FSTA | |
| Intermediate / Lateral Mesoderm | Hematopoietic | TAL1 | |
| Intermediate / Lateral Mesoderm | Hematopoietic | LMO2 | |
| Intermediate / Lateral Mesoderm | ICM/erythroid | GATA1A | |
| Intermediate / Lateral Mesoderm | Rostral blood island (myeloid) | SPI1B | |
| Intermediate / Lateral Mesoderm | Pronephric progenitors | FOXJ1A | |
| Intermediate / Lateral Mesoderm | Pronephric progenitors | PAX2A | |
| Intermediate / Lateral Mesoderm | Heart primordium | HAND2 | |
| Paraxial mesoderm | Adaxial | MYL10 | |
| Paraxial mesoderm | Adaxial | MYOD1 | |
| Paraxial mesoderm | Adaxial | MYOG | |
| Paraxial mesoderm | Somites | MEOX1 | |
| Paraxial mesoderm | Somites | RIPPLY1 | |
| Paraxial mesoderm | Somites | ALDH1A2 | |
| Paraxial mesoderm | Forming somites | MESPBA | |
| Paraxial mesoderm | Forming somites | RIPPLY2 | |
| Paraxial mesoderm | Forming somites | TBX6 | |
| Paraxial mesoderm | Presomitic mesoderm | TBX6L | |
| Paraxial mesoderm | Tailbud | SOX2 | |
| Paraxial mesoderm | Tailbud | TA | |
| Paraxial mesoderm | Tailbud | NOTO | |
| Paraxial mesoderm | Tailbud | FGF8A | |
| Paraxial mesoderm | Tailbud | WNT8A | |
| Neural | Neural crest | FOXD3 | |
| Neural | Neural crest | SOX9B | |
| Neural | Neural crest | SOX10 | |
| Neural | Floor plate | SHHA | |
| Neural | Floor plate | SHHB | |
| Neural | Floor plate | FOXJ1A | |
| Neural | Floor plate | FOXA2 | |
| Neural | Spinal cord | ELAVL3 | |
| Neural | Spinal cord | NEUROD1 | |
| Neural | Spinal cord | NEUROD4 | |
| Neural | Spinal cord | NEUROG1 | |
| Fore/mid-brain | Midbrain | ENG2A | |
| Fore/mid-brain | Midbrain | ENG2B | |
| Fore/mid-brain | Midbrain | HER5 | |
| Fore/mid-brain | Midbrain | HER11 | |
| Fore/mid-brain | Midbrain | PAX2A | |
| Fore/mid-brain | Telencephalon | FOXG1A | |
| Fore/mid-brain | Telencephalon | EMX3 | |
| Fore/mid-brain | Optic cup | RX3 | |
| Fore/mid-brain | Optic cup | RX2 | |
| Fore/mid-brain | Optic cup | PAX6B | |
| Fore/mid-brain | Ventral diencephalon | DBX1A | |
| Fore/mid-brain | Ventral diencephalon | DBX1B | |
| Fore/mid-brain | Ventral diencephalon | NKX2.2B | |
| Fore/mid-brain | Dorsal diencephalon | LHX5 | |
| Fore/mid-brain | Dorsal diencephalon | PAX6A | |
| Fore/mid-brain | Dorsal diencephalon | FOXD1 | |
| Fore/mid-brain | Dorsal diencephalon | OLIG3 | |
| Hindbrain | Rhombomeres 5&6 | MAFBA | |
| Hindbrain | Rhombomere 3 | EGR2B | |
| Hindbrain | Rhombomere 4 | FGF8A | |
| Hindbrain | Rhombomere 7 | HOXD4A | |
| Hindbrain | Rhombomere 7 | HOXA3A | |
| Non-neural ectoderm | Integument | FOXI3A | |
| Non-neural ectoderm | Integument | FOXI3B | |
| Non-neural ectoderm | Integument | MYB | |
| Non-neural ectoderm | Integument | GCM2 | |
| Non-neural ectoderm | Neural plate border | CRABP2A | |
| Non-neural ectoderm | Neural plate border | DLX3B | |
| Non-neural ectoderm | Epidermis | GATA2A | |
| Non-neural ectoderm | Epidermis | TBX2B | |
| Non-neural ectoderm | Epidermis | CYP2K16 | |
| Pre-placodal ectoderm | Lens placode | PITX3 | |
| Pre-placodal ectoderm | Olfactory placode | FOXN4 | |
| Pre-placodal ectoderm | Olfactory placode | EBF2 | |
| Pre-placodal ectoderm | Olfactory placode | SIX3B | |
| Pre-placodal ectoderm | Olfactory placode | DLX4B | |
| Pre-placodal ectoderm | Adenohypophyseal placode | SIX3B | |
| Pre-placodal ectoderm | Adenohypophyseal placode | DLX4B | |
| Pre-placodal ectoderm | Adenohypophyseal placode | HESX1 | |
| Pre-placodal ectoderm | Epibranchail placode | FOXI1 | |
| Pre-placodal ectoderm | Epibranchail placode | PAX8 | |
| Pre-placodal ectoderm | Otic placode | ATOH1B | |
| Pre-placodal ectoderm | Otic placode | TBX2B | |
| Pre-placodal ectoderm | Otic placode | PAX2A | |
| Pre-placodal ectoderm | Trigeminal placode | KLF17 | |
| Pre-placodal ectoderm | Trigeminal placode | IRX1A | |
| Pre-placodal ectoderm | Trigeminal placode | P2RX3A | |
| Non-blastoderm | EVL/Periderm | KRT18 | |
| Non-blastoderm | EVL/Periderm | KRT92 | |
| Non-blastoderm | EVL/Periderm | KRT4 | |
| Non-blastoderm | EVL/Periderm | KRT5 | |
| Non-blastoderm | EVL/Periderm | KRT17 | |
| Non-blastoderm | Primordial germ cells | DDX4 | |
| Non-blastoderm | Primordial germ cells | H1M | |
| Non-blastoderm | Primordial germ cells | NANOS3 | |
| Non-blastoderm | Yolk Syncitial Layer | CYP11A1 | |
| Non-blastoderm | Yolk Syncitial Layer | MXTX2 | |
| Non-blastoderm | Yolk Syncitial Layer | GATA3 | |
| Non-blastoderm | Yolk Syncitial Layer | HNF4A |
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