Danio rerio (zebrafish)


TISSUE / ORGAN


  • The figure above shows the number of datasets for tissues / organs at different growth time points. The larger the bubbles, the more datasets.


  • The figure above shows the number of cell types and markers in different tissues / organs.

CELL TYPE

  • The figure above shows the distribution of cell number of each cell type in different tissues / organs.

MARKER

  • The figure above shows the number of markers. Click on the image can browse the number of markers at the cell type level.
  • The word cloud figure above shows the frequency of markers.

DATASET LIST


Dataset ID Species Tissue / Organ Experiment type Sample Source dataset ID Project ID
1. PRJNA415636 (brain) Danio rerio brain baseline adult, Zebrabow M, brain SRR6811819 PRJNA415636
2. PRJNA554650 (6.5dpf) Danio rerio brain baseline 6.5dpf, whole brain of nr1d1:VNP fish SRR9685040 PRJNA554650
3. GSE158142 (8dpf) Danio rerio brain, eye baseline 8dpf, untreatment GSM4793234 GSE158142
4. GSE158142 (15dpf) Danio rerio brain, eye baseline 15dpf, untreatment GSM4793238 GSE158142
5. GSE158142 (5dpf) Danio rerio brain, eye baseline 5dpf, untreatment GSM4793216 GSE158142
6. GSE151354 (wild type) Danio rerio cartilage baseline 21dpf, wild type GSM4575942 GSE151354
7. GSE151354 (nkx3.2 mutant) Danio rerio cartilage growth 21dpf, nkx3.2 mutant GSM4575943 GSE151354
8. PRJNA610520 (3.5dpf) Danio rerio caudal hematopoietic tissue baseline 3.5dpf, the mixture of same amount of kdrl:mCherry+ cells, CD41:GFP+ cells and double negative cells. SRR11243177 PRJNA610520
9. PRJNA610520 (4.5dpf) Danio rerio caudal hematopoietic tissue baseline 4.5dpf, the mixture of same amount of kdrl:mCherry+ cells, CD41:GFP+ cells and double negative cells. SRR11243184 PRJNA610520
10. GSE144944 (fgfr3 +|+) Danio rerio cranial vault baseline 1mpf, fgfr3 +/+ GSM4301248 GSE144944
11. GSE144944 (fgfr3 -|-) Danio rerio cranial vault growth 1mpf, fgfr3 -/- GSM4301250 GSE144944
12. GSE130526 (fin) Danio rerio dorsal and anal fin baseline adult, fins were amputated from fish expressing both pnp4a:palmmCherry and tyrp1b:palmmCherry GSM3741778 GSE130526
13. PRJNA640816 (2dpf) Danio rerio embryo baseline 2dpf, FACS isolated -4.9sox10:EGFP+ cells SRR12060552 PRJNA640816
14. PRJNA734348 (shield, dnmt1) Danio rerio embryo growth 6hpf, shield, oocyte microinjection with Rhodamine B and dnmt1 MO at oogenesis III stage (GV) SRR14703474 PRJNA734348
15. PRJNA734348 (dome, control) Danio rerio embryo baseline 4.3hpf, dome, oocyte microinjection with Rhodamine B and control MO at oogenesis III stage (GV) SRR14703452 PRJNA734348
16. GSE126647 (Pbx4-depleted) Danio rerio embryo growth 1.17dpf, Pbx4-depleted nkx2.5:ZsYellow+ cells GSM3610371 GSE126647
17. PRJNA564810 (2dpf) Danio rerio embryo baseline 2dpf, a single-cell transcriptome atlas for zebrafish development SRR10095966 PRJNA564810
18. PRJNA706197 (18hpf) Danio rerio embryo baseline 18hpf, FACS sorted sox10:nEOS cells SRR13839979 PRJNA706197
19. GSE158849 (unlabeled) Danio rerio embryo baseline 6hpf, WT, 4sUTP injected (unlabeled) GSM4812182 GSE158849
20. PRJNA706197 (20hpf) Danio rerio embryo baseline 20hpf, FACS sorted sox10:nEOS cells SRR13839965 PRJNA706197
21. PRJNA656271 (24hpf) Danio rerio embryo baseline 24hpf, FACS-isolated EGFP+ cells SRR12424272 PRJNA656271
22. GSE173972 (WT, ezh1+|+) Danio rerio embryo baseline 1.25dpf, Kdrl-positive embryos GSM5283739 GSE173972
23. PRJNA640816 (2.9dpf) Danio rerio embryo baseline 2.9dpf, FACS isolated -4.9sox10:EGFP+ cells SRR12060555 PRJNA640816
24. PRJNA734348 (dome, dnmt1) Danio rerio embryo growth 4.3hpf, dome, oocyte microinjection with Rhodamine B and dnmt1 MO at oogenesis III stage (GV) SRR14703458 PRJNA734348
25. PRJNA564810 (1dpf) Danio rerio embryo baseline 1dpf, a single-cell transcriptome atlas for zebrafish development SRR10095968 PRJNA564810
26. PRJNA706197 (24hpf) Danio rerio embryo baseline 24hpf, FACS sorted sox10:nEOS cells SRR13839972 PRJNA706197
27. GSE106587 (WT) Danio rerio embryo baseline 12hpf, 6 somites, wild-type TLAB embryo GSM3084402 GSE106587
28. GSE168695 (5dpf) Danio rerio embryo baseline 5dpf, GFP+ cells isolated from 5 dpf cldnb:lyn-EGFP embryos GSM5158857 GSE168695
29. PRJNA656271 (1.5dpf) Danio rerio embryo baseline 1.5dpf, FACS-isolated EGFP+ cells SRR12424276 PRJNA656271
30. GSE173972 (HET, ezh1+|-) Danio rerio embryo hematopoietic 1.25dpf, Kdrl-positive embryos GSM5283741 GSE173972
31. PRJNA706197 (12hpf) Danio rerio embryo baseline 12hpf, FACS sorted sox10:nEOS cells SRR13839954 PRJNA706197
32. PRJNA734348 (shield, control) Danio rerio embryo baseline 6hpf, shield, oocyte microinjection with Rhodamine B and control MO at oogenesis III stage (GV) SRR14703469 PRJNA734348
33. GSE126647 (control) Danio rerio embryo baseline 1.17dpf, control nkx2.5:ZsYellow+ cells GSM3610370 GSE126647
34. PRJNA564810 (5dpf) Danio rerio embryo baseline 5dpf, a single-cell transcriptome atlas for zebrafish development SRR10095964 PRJNA564810
35. PRJNA706197 (1.25dpf) Danio rerio embryo baseline 1.25dpf, FACS sorted sox10:nEOS cells SRR13839973 PRJNA706197
36. GSE106587 (MZoep mutant) Danio rerio embryo baseline 12hpf, 6 somites, maternal zygotic oep tz57 mutant embryo GSM3084403 GSE106587
37. GSE158849 (labeled) Danio rerio embryo baseline 6hpf, WT, 4sUTP injected (labeled) GSM4812182 GSE158849
38. PRJNA706197 (14hpf) Danio rerio embryo baseline 14hpf, FACS sorted sox10:nEOS cells SRR13839958 PRJNA706197
39. PRJNA656271 (2dpf) Danio rerio embryo baseline 2dpf, FACS-isolated EGFP+ cells SRR12424278 PRJNA656271
40. GSE173972 (KO, ezh1-|-) Danio rerio embryo hematopoietic 1.25dpf, Kdrl-positive embryos GSM5283743 GSE173972
41. GSE161712 (M. marinum) Danio rerio granulomas disease adult, infected with bacteria of M. marinum GSM4913139 GSE161712
42. GSE158142 (2dpf) Danio rerio head baseline 2dpf, untreatment GSM4793201 GSE158142
43. GSE158142 (20hpf) Danio rerio head baseline 20hpf, 21-22 somites, untreatment GSM4793193 GSE158142
44. GSE158142 (14hpf) Danio rerio head baseline 14hpf, 10 somites, untreatment GSM4793187 GSE158142
45. GSE158142 (3dpf) Danio rerio head baseline 3dpf, untreatment GSM4793207 GSE158142
46. GSE158142 (24hpf) Danio rerio head baseline 24hpf, untreatment GSM4793196 GSE158142
47. GSE158142 (16hpf) Danio rerio head baseline 16hpf, 14 somites, untreatment GSM4793189 GSE158142
48. GSE158142 (1.5dpf) Danio rerio head baseline 1.5dpf, untreatment GSM4793199 GSE158142
49. GSE158142 (18hpf) Danio rerio head baseline 18hpf, 18 somites, untreatment GSM4793191 GSE158142
50. GSE158142 (12hpf) Danio rerio head baseline 12hpf, 6 somites, untreatment GSM4793185 GSE158142
51. PRJNA608912 (kit_7dpi) Danio rerio heart regeneration 5mpf, kit mutant, 7 days post injury SRR11186472 PRJNA608912
52. PRJNA608912 (wt_14dpi) Danio rerio heart regeneration 5mpf, wild type, 14 days post injury SRR11186452 PRJNA608912
53. PRJNA608912 (wt_unjuried) Danio rerio heart baseline 5mpf, wild type, uninjured SRR11186432 PRJNA608912
54. PRJNA608912 (kit_14dpi) Danio rerio heart regeneration 5mpf, kit mutant, 14 days post injury SRR11186480 PRJNA608912
55. PRJNA608912 (kit_uninjuried) Danio rerio heart regeneration 5mpf, kit mutant, uninjured SRR11186457 PRJNA608912
56. PRJNA608912 (wt_2dpi) Danio rerio heart regeneration 5mpf, wild type, 2 days post injury SRR11186440 PRJNA608912
57. PRJNA608912 (kit_2dpi) Danio rerio heart regeneration 5mpf, kit mutant, 2 days post injury SRR11186464 PRJNA608912
58. PRJNA608912 (wt_7dpi) Danio rerio heart regeneration 5mpf, wild type, 7 days post injury SRR11186448 PRJNA608912
59. PRJNA415636 (heart, blood) Danio rerio heart, blood baseline adult, Zebrabow M, heart and blood SRR6211492 PRJNA415636
60. PRJNA415636 (pancreas, liver) Danio rerio hepatopancreas baseline adult, Zebrabow M, pancreas and liver SRR6211488 PRJNA415636
61. PRJNA754013 (zebrafish) Danio rerio hypothalamus baseline adult, male, female, untreatment SRR15422672 PRJNA754013
62. GSE150498 (wildtype, 2X DSS+BZA) Danio rerio intestine disease 6dpf, wildtype, 2X DSS+BZA GSM4878628 GSE150498
63. GSE150498 (wildtype, 1X DSS) Danio rerio intestine disease 6dpf, wildtype, 1X DSS GSM4878624 GSE150498
64. GSE150498 (DSS treated) Danio rerio intestine disease 6dpf, DSS treated GSM4551416 GSE150498
65. GSE150498 (nod2-|-, 2X DSS) Danio rerio intestine disease 6dpf, nod2-/-, 2X DSS GSM4878630 GSE150498
66. GSE150498 (nod2-|-, 1X DSS) Danio rerio intestine disease 6dpf, nod2-/-, 1X DSS GSM4878625 GSE150498
67. GSE150498 (wildtype, untreated) Danio rerio intestine baseline 6dpf, wildtype, untreated GSM4878622 GSE150498
68. GSE150498 (nod2-|-, 2X DSS+BZA) Danio rerio intestine disease 6dpf, nod2-/-, 2X DSS+BZA GSM4878631 GSE150498
69. GSE150498 (wildtype, 2X DSS) Danio rerio intestine disease 6dpf, wildtype, 2X DSS GSM4878627 GSE150498
70. GSE150498 (nod2-|-, untreated) Danio rerio intestine disease 6dpf, nod2-/-, untreated GSM4878623 GSE150498
71. GSE150498 (untreated ctrl) Danio rerio intestine baseline 6dpf, untreated ctrl GSM4551415 GSE150498
72. GSE137784 (HCC, CreLox) Danio rerio liver disease 6mpf, male, isolated from the zebrafish without HCC GSM4087820 GSE137784
73. GSE137784 (no HCC) Danio rerio liver baseline 6mpf, male, isolated from the CreLox zebrafish with HCC GSM4087821 GSE137784
74. GSE137784 (HCC, HepABC) Danio rerio liver disease 6mpf, male, isolated from the Tg(fabp10a:pt-B-cat)(HepABC) zebrafish with HCC GSM4087819 GSE137784
75. GSE123241 (fgf3 siblings) Danio rerio neuromast regeneration 5dpf, fgf3 siblings during sensory hair cell regeneration, lateral line sensory GSM3498554 GSE123241
76. GSE123241 (wild type) Danio rerio neuromast baseline 5dpf, wild type during sensory hair cell regeneration, lateral line sensory GSM3498552 GSE123241
77. PRJNA605021 (supporting cells) Danio rerio neuromast baseline 7dpf, posterior lateral-line neuromast cells were isolated from the dissociated trunks of Tg[Et(krt4:EGFP)sqgw57A] transgenic zebrafish larvae SRR11031289 PRJNA605021
78. GSE123241 (fgf3 mutants) Danio rerio neuromast regeneration 5dpf, fgf3 mutants during sensory hair cell regeneration, lateral line sensory GSM3498553 GSE123241
79. PRJNA605021 (hair cells) Danio rerio neuromast baseline 7dpf, posterior lateral-line neuromast cells were isolated from the dissociated trunks of Tg[myo6b:actb1-EGFP] transgenic zebrafish larvae SRR11031290 PRJNA605021
80. PRJNA668529 (3h) Danio rerio olfactory rosette disease 3mpf, intranasal 100ng r-Spike 3 hours SRR12858255 PRJNA668529
81. PRJNA668529 (control) Danio rerio olfactory rosette baseline 3mpf, intranasal PBS SRR12858259 PRJNA668529
82. PRJNA668529 (3d) Danio rerio olfactory rosette disease 3mpf, intranasal 100ng r-Spike 3 days SRR12858254 PRJNA668529
83. GSE148591 (6mpf) Danio rerio pituitary baseline 6mpf, male, Sox17:CreERT2 GSM4474603 GSE148591
84. GSE148591 (3mpf) Danio rerio pituitary transplant 3mpf, graft transplantation during early embryogenesis GSM4474605 GSE148591
85. PRJNA415636 (primary pancreatic islet) Danio rerio primary pancreatic islet baseline adult, Zebrabow M, primary pancreatic islet SRR6811821 PRJNA415636
86. PRJNA672101 (WT) Danio rerio retina baseline 5mpf, three retinas from WT zebrafsih SRR12899698 PRJNA672101
87. GSE122680 (14dpf) Danio rerio retina baseline 14dpf, WT, untreatment GSM3478019 GSE122680
88. GSE122680 (24hpf) Danio rerio retina baseline 24hpf, WT, untreatment GSM3478013 GSE122680
89. GSE122680 (2dpf) Danio rerio retina baseline 2dpf, WT, untreatment GSM4233148 GSE122680
90. GSE122680 (1.5dpf) Danio rerio retina baseline 1.5dpf, WT, untreatment GSM3478014 GSE122680
91. GSE175929 (5mpf) Danio rerio retina baseline 5mpf, GFP-positive cells collected from two transgenic zebrafish, Tg(rho:EGFP)ja2Tg and Tg(gnat2:EGFP)ja23Tg GSM5351368 GSE175929
92. PRJNA672101 (nrl-KO) Danio rerio retina growth 5mpf, three retinas from nrl-KO zebrafsih SRR12899703 PRJNA672101
93. GSE122680 (3dpf) Danio rerio retina baseline 3dpf, WT, untreatment GSM3478018 GSE122680
94. PRJNA551501 (2mpf) Danio rerio thyroid gland baseline 2mpf, Tg(tg:mVenus-T2A-NTR) SRR9609653 PRJNA551501
95. PRJNA551501 (8mpf) Danio rerio thyroid gland baseline 8mpf, Tg(tg:mVenus-T2A-NTR) SRR9609654 PRJNA551501
96. GSE163907 (24hpf) Danio rerio trunk baseline 24hpf, trunk tg(sox10:GFP) positive cells GSM4990514 GSE163907
97. GSE152982 (wild type) Danio rerio trunk baseline 1.25dpf, untreatment GSM4631066 GSE152982
98. GSE131136 (all) Danio rerio trunk, skin baseline 5dpf, sox10:CRE positive cells from 5dpf and post-embryonic zebrafish trunks with and without thyroid hormone GSE131136 GSE131136
99. PRJNA641144 (C_INV) Danio rerio tumor disease adult, ZMEL1-INV cells in vitro co-culture SRR12070794 PRJNA641144
100. PRJNA641144 (P_INV) Danio rerio tumor disease adult, ZMEL1-INV cells in vivo primary tumors SRR12070722 PRJNA641144
101. PRJNA641144 (M_PRO) Danio rerio tumor disease adult, ZMEL1-PRO cells in vivo metastases SRR12070758 PRJNA641144
102. PRJNA641144 (C_PRO) Danio rerio tumor disease adult, ZMEL1-PRO cells in vitro co-culture SRR12070806 PRJNA641144
103. PRJNA641144 (D_INV) Danio rerio tumor disease adult, ZMEL1-INV cells in vitro individual culture SRR12070771 PRJNA641144
104. PRJNA641144 (P_PRO) Danio rerio tumor disease adult, ZMEL1-PRO cells in vivo primary tumors SRR12070742 PRJNA641144
105. GSE159709 (melanoma) Danio rerio tumor disease adult, equal numbers of sorted GFP+ (tumor) and GFP- (macroenvironment) cells GSM4838134 GSE159709
106. PRJNA641144 (D_PRO) Danio rerio tumor disease adult, ZMEL1-PRO cells in vitro individual culture SRR12070788 PRJNA641144
107. PRJNA641144 (M_INV) Danio rerio tumor disease adult, ZMEL1-INV cells in vivo metastases SRR12070746 PRJNA641144
108. GSE158099 (runx1 -|-) Danio rerio whole body hematopoietic 16dpf, cd41:GFPlow-runx1-/- GSM4792215 GSE158099
109. GSE158099 (WT) Danio rerio whole body baseline 10dpf, cd41:GFPlow-WT GSM4792212 GSE158099
110. GSE158099 (runx1 -|-) Danio rerio whole body hematopoietic 2.5dpf, cd41:GFPlow-runx1-/- GSM4792209 GSE158099
111. GSE176129 (pdgfrb-positive) Danio rerio whole body baseline 5dpf, FACS-isolated pdgfrb-positive cells GSM5356650 GSE176129
112. GSE158099 (runx1 -|-) Danio rerio whole body hematopoietic 16dpf, cd41:GFPlow-runx1-/- GSM4792216 GSE158099
113. GSE158099 (WT) Danio rerio whole body baseline 6dpf, cd41:GFPlow-WT GSM4792210 GSE158099
114. GSE158099 (runx1 -|-) Danio rerio whole body hematopoietic 10dpf, cd41:GFPlow-runx1-/- GSM4792213 GSE158099
115. GSE158099 (WT) Danio rerio whole body baseline 16dpf, cd41:GFPlow-WT GSM4792214 GSE158099
116. GSE158099 (runx1 -|-) Danio rerio whole body hematopoietic 6dpf, cd41:GFPlow-runx1-/- GSM4792211 GSE158099
117. GSE158099 (WT) Danio rerio whole body baseline 2.5dpf, cd41:GFPlow-WT GSM4792208 GSE158099

  • The figure above shows the distribution of cell number of each cell type in different datasets.
  • Click on the links in the table to view more specific information. Click on the cell type on the x-axis in the figure to browse the detailed information of the cell type.