Fish Single-cell RNA Database

Species	Download Link
Danio rerio	Danio_rerio.txt
Astyanax mexicanus	Astyanax_mexicanus.txt
Gasterosteus aculeatus	Gasterosteus_aculeatus.txt
Nothobranchius furzeri	Nothobranchius_furzeri.txt
Oryzias latipes	Oryzias_latipes.txt
Oreochromis niloticus	Oreochromis_niloticus.txt
Monopterus albus	Monopterus_albus.txt
Mastacembelus armatus	Mastacembelus_armatus.txt
Oncorhynchus mykiss	Oncorhynchus_mykiss.txt

Expression

All expression profile data for each dataset are available.

Click on the node of the fold tree to expand the information of datasets.

The data table includes the gene ID, symbol, cell cluster ID, cell type and detail quantity of cells.

Danio rerio

heart

Dataset ID	Experiment Type	Sample	Source Dataset ID	Download Link
PRJNA608912 (wt_unjuried)	baseline	5mpf, wild type, uninjured	SRR11186432	SRR11186432.txt
PRJNA608912 (kit_14dpi)	regeneration	5mpf, kit mutant, 14 days post injury	SRR11186480	SRR11186480.txt
PRJNA608912 (kit_uninjuried)	regeneration	5mpf, kit mutant, uninjured	SRR11186457	SRR11186457.txt
PRJNA608912 (wt_2dpi)	regeneration	5mpf, wild type, 2 days post injury	SRR11186440	SRR11186440.txt
PRJNA608912 (kit_2dpi)	regeneration	5mpf, kit mutant, 2 days post injury	SRR11186464	SRR11186464.txt
PRJNA608912 (wt_7dpi)	regeneration	5mpf, wild type, 7 days post injury	SRR11186448	SRR11186448.txt
PRJNA608912 (kit_7dpi)	regeneration	5mpf, kit mutant, 7 days post injury	SRR11186472	SRR11186472.txt
PRJNA608912 (wt_14dpi)	regeneration	5mpf, wild type, 14 days post injury	SRR11186452	SRR11186452.txt

liver

Dataset ID	Experiment Type	Sample	Source Dataset ID	Download Link
GSE137784 (HCC, HepABC)	disease	6mpf, male, isolated from the Tg(fabp10a:pt-B-cat)(HepABC) zebrafish with HCC	GSM4087819	GSM4087819.txt
GSE137784 (HCC, CreLox)	disease	6mpf, male, isolated from the zebrafish without HCC	GSM4087820	GSM4087820.txt
GSE137784 (no HCC)	baseline	6mpf, male, isolated from the CreLox zebrafish with HCC	GSM4087821	GSM4087821.txt

intestine

Dataset ID	Experiment Type	Sample	Source Dataset ID	Download Link
GSE150498 (nod2-\|-, untreated)	disease	6dpf, nod2-/-, untreated	GSM4878623	GSM4878623.txt
GSE150498 (wildtype, 2X DSS+BZA)	disease	6dpf, wildtype, 2X DSS+BZA	GSM4878628	GSM4878628.txt
GSE150498 (untreated ctrl)	baseline	6dpf, untreated ctrl	GSM4551415	GSM4551415.txt
GSE150498 (wildtype, 1X DSS)	disease	6dpf, wildtype, 1X DSS	GSM4878624	GSM4878624.txt
GSE150498 (nod2-\|-, 2X DSS)	disease	6dpf, nod2-/-, 2X DSS	GSM4878630	GSM4878630.txt
GSE150498 (DSS treated)	disease	6dpf, DSS treated	GSM4551416	GSM4551416.txt
GSE150498 (nod2-\|-, 1X DSS)	disease	6dpf, nod2-/-, 1X DSS	GSM4878625	GSM4878625.txt
GSE150498 (nod2-\|-, 2X DSS+BZA)	disease	6dpf, nod2-/-, 2X DSS+BZA	GSM4878631	GSM4878631.txt
GSE150498 (wildtype, untreated)	baseline	6dpf, wildtype, untreated	GSM4878622	GSM4878622.txt
GSE150498 (wildtype, 2X DSS)	disease	6dpf, wildtype, 2X DSS	GSM4878627	GSM4878627.txt

tumor

Dataset ID	Experiment Type	Sample	Source Dataset ID	Download Link
PRJNA641144 (D_PRO)	disease	adult, ZMEL1-PRO cells in vitro individual culture	SRR12070788	SRR12070788.txt
GSE159709 (melanoma)	disease	adult, equal numbers of sorted GFP+ (tumor) and GFP- (macroenvironment) cells	GSM4838134	GSM4838134.txt
PRJNA641144 (M_INV)	disease	adult, ZMEL1-INV cells in vivo metastases	SRR12070746	SRR12070746.txt
PRJNA641144 (C_INV)	disease	adult, ZMEL1-INV cells in vitro co-culture	SRR12070794	SRR12070794.txt
PRJNA641144 (M_PRO)	disease	adult, ZMEL1-PRO cells in vivo metastases	SRR12070758	SRR12070758.txt
PRJNA641144 (C_PRO)	disease	adult, ZMEL1-PRO cells in vitro co-culture	SRR12070806	SRR12070806.txt
PRJNA641144 (P_INV)	disease	adult, ZMEL1-INV cells in vivo primary tumors	SRR12070722	SRR12070722.txt
PRJNA641144 (D_INV)	disease	adult, ZMEL1-INV cells in vitro individual culture	SRR12070771	SRR12070771.txt
PRJNA641144 (P_PRO)	disease	adult, ZMEL1-PRO cells in vivo primary tumors	SRR12070742	SRR12070742.txt

whole body

Dataset ID	Experiment Type	Sample	Source Dataset ID	Download Link
GSE158099 (WT)	baseline	16dpf, cd41:GFPlow-WT	GSM4792214	GSM4792214.txt
GSE158099 (runx1 -\|-)	hematopoietic	6dpf, cd41:GFPlow-runx1-/-	GSM4792211	GSM4792211.txt
GSE158099 (runx1 -\|-)	hematopoietic	16dpf, cd41:GFPlow-runx1-/-	GSM4792215	GSM4792215.txt
GSE158099 (WT)	baseline	2.5dpf, cd41:GFPlow-WT	GSM4792208	GSM4792208.txt
GSE158099 (WT)	baseline	10dpf, cd41:GFPlow-WT	GSM4792212	GSM4792212.txt
GSE158099 (runx1 -\|-)	hematopoietic	16dpf, cd41:GFPlow-runx1-/-	GSM4792216	GSM4792216.txt
GSE158099 (runx1 -\|-)	hematopoietic	2.5dpf, cd41:GFPlow-runx1-/-	GSM4792209	GSM4792209.txt
GSE176129 (pdgfrb-positive)	baseline	5dpf, FACS-isolated pdgfrb-positive cells	GSM5356650	GSM5356650.txt
GSE158099 (runx1 -\|-)	hematopoietic	10dpf, cd41:GFPlow-runx1-/-	GSM4792213	GSM4792213.txt
GSE158099 (WT)	baseline	6dpf, cd41:GFPlow-WT	GSM4792210	GSM4792210.txt

head

Dataset ID	Experiment Type	Sample	Source Dataset ID	Download Link
GSE158142 (20hpf)	baseline	20hpf, 21-22 somites, untreatment	GSM4793193	GSM4793193.txt
GSE158142 (3dpf)	baseline	3dpf, untreatment	GSM4793207	GSM4793207.txt
GSE158142 (14hpf)	baseline	14hpf, 10 somites, untreatment	GSM4793187	GSM4793187.txt
GSE158142 (24hpf)	baseline	24hpf, untreatment	GSM4793196	GSM4793196.txt
GSE158142 (16hpf)	baseline	16hpf, 14 somites, untreatment	GSM4793189	GSM4793189.txt
GSE158142 (1.5dpf)	baseline	1.5dpf, untreatment	GSM4793199	GSM4793199.txt
GSE158142 (18hpf)	baseline	18hpf, 18 somites, untreatment	GSM4793191	GSM4793191.txt
GSE158142 (2dpf)	baseline	2dpf, untreatment	GSM4793201	GSM4793201.txt
GSE158142 (12hpf)	baseline	12hpf, 6 somites, untreatment	GSM4793185	GSM4793185.txt

embryo

Dataset ID	Experiment Type	Sample	Source Dataset ID	Download Link
PRJNA656271 (1.5dpf)	baseline	1.5dpf, FACS-isolated EGFP+ cells	SRR12424276	SRR12424276.txt
PRJNA706197 (14hpf)	baseline	14hpf, FACS sorted sox10:nEOS cells	SRR13839958	SRR13839958.txt
GSE173972 (KO, ezh1-\|-)	hematopoietic	1.25dpf, Kdrl-positive embryos	GSM5283743	GSM5283743.txt
GSE158849 (unlabeled)	baseline	6hpf, WT, 4sUTP injected (unlabeled)	GSM4812182	GSM4812182.txt
PRJNA564810 (1dpf)	baseline	1dpf, a single-cell transcriptome atlas for zebrafish development	SRR10095968	SRR10095968.txt
PRJNA706197 (18hpf)	baseline	18hpf, FACS sorted sox10:nEOS cells	SRR13839979	SRR13839979.txt
PRJNA734348 (shield, control)	baseline	6hpf, shield, oocyte microinjection with Rhodamine B and control MO at oogenesis III stage (GV)	SRR14703469	SRR14703469.txt
PRJNA656271 (2dpf)	baseline	2dpf, FACS-isolated EGFP+ cells	SRR12424278	SRR12424278.txt
PRJNA706197 (20hpf)	baseline	20hpf, FACS sorted sox10:nEOS cells	SRR13839965	SRR13839965.txt
GSE106587 (WT)	baseline	12hpf, 6 somites, wild-type TLAB embryo	GSM3084402	GSM3084402.txt
PRJNA640816 (2dpf)	baseline	2dpf, FACS isolated -4.9sox10:EGFP+ cells	SRR12060552	SRR12060552.txt
PRJNA734348 (shield, dnmt1)	growth	6hpf, shield, oocyte microinjection with Rhodamine B and dnmt1 MO at oogenesis III stage (GV)	SRR14703474	SRR14703474.txt
GSE173972 (WT, ezh1+\|+)	baseline	1.25dpf, Kdrl-positive embryos	GSM5283739	GSM5283739.txt
GSE126647 (control)	baseline	1.17dpf, control nkx2.5:ZsYellow+ cells	GSM3610370	GSM3610370.txt
PRJNA564810 (5dpf)	baseline	5dpf, a single-cell transcriptome atlas for zebrafish development	SRR10095964	SRR10095964.txt
PRJNA706197 (24hpf)	baseline	24hpf, FACS sorted sox10:nEOS cells	SRR13839972	SRR13839972.txt
PRJNA734348 (dome, control)	baseline	4.3hpf, dome, oocyte microinjection with Rhodamine B and control MO at oogenesis III stage (GV)	SRR14703452	SRR14703452.txt
GSE106587 (MZoep mutant)	baseline	12hpf, 6 somites, maternal zygotic oep tz57 mutant embryo	GSM3084403	GSM3084403.txt
PRJNA640816 (2.9dpf)	baseline	2.9dpf, FACS isolated -4.9sox10:EGFP+ cells	SRR12060555	SRR12060555.txt
PRJNA656271 (24hpf)	baseline	24hpf, FACS-isolated EGFP+ cells	SRR12424272	SRR12424272.txt
PRJNA706197 (12hpf)	baseline	12hpf, FACS sorted sox10:nEOS cells	SRR13839954	SRR13839954.txt
GSE173972 (HET, ezh1+\|-)	hematopoietic	1.25dpf, Kdrl-positive embryos	GSM5283741	GSM5283741.txt
GSE126647 (Pbx4-depleted)	growth	1.17dpf, Pbx4-depleted nkx2.5:ZsYellow+ cells	GSM3610371	GSM3610371.txt
GSE158849 (labeled)	baseline	6hpf, WT, 4sUTP injected (labeled)	GSM4812182	GSM4812182.txt
GSE168695 (5dpf)	baseline	5dpf, GFP+ cells isolated from 5 dpf cldnb:lyn-EGFP embryos	GSM5158857	GSM5158857.txt
PRJNA564810 (2dpf)	baseline	2dpf, a single-cell transcriptome atlas for zebrafish development	SRR10095966	SRR10095966.txt
PRJNA706197 (1.25dpf)	baseline	1.25dpf, FACS sorted sox10:nEOS cells	SRR13839973	SRR13839973.txt
PRJNA734348 (dome, dnmt1)	growth	4.3hpf, dome, oocyte microinjection with Rhodamine B and dnmt1 MO at oogenesis III stage (GV)	SRR14703458	SRR14703458.txt

neuromast

Dataset ID	Experiment Type	Sample	Source Dataset ID	Download Link
PRJNA605021 (supporting cells)	baseline	7dpf, posterior lateral-line neuromast cells were isolated from the dissociated trunks of Tg[Et(krt4:EGFP)sqgw57A] transgenic zebrafish larvae	SRR11031289	SRR11031289.txt
GSE123241 (fgf3 mutants)	regeneration	5dpf, fgf3 mutants during sensory hair cell regeneration, lateral line sensory	GSM3498553	GSM3498553.txt
PRJNA605021 (hair cells)	baseline	7dpf, posterior lateral-line neuromast cells were isolated from the dissociated trunks of Tg[myo6b:actb1-EGFP] transgenic zebrafish larvae	SRR11031290	SRR11031290.txt
GSE123241 (fgf3 siblings)	regeneration	5dpf, fgf3 siblings during sensory hair cell regeneration, lateral line sensory	GSM3498554	GSM3498554.txt
GSE123241 (wild type)	baseline	5dpf, wild type during sensory hair cell regeneration, lateral line sensory	GSM3498552	GSM3498552.txt

brain, eye

Dataset ID	Experiment Type	Sample	Source Dataset ID	Download Link
GSE158142 (15dpf)	baseline	15dpf, untreatment	GSM4793238	GSM4793238.txt
GSE158142 (5dpf)	baseline	5dpf, untreatment	GSM4793216	GSM4793216.txt
GSE158142 (8dpf)	baseline	8dpf, untreatment	GSM4793234	GSM4793234.txt

brain

Dataset ID	Experiment Type	Sample	Source Dataset ID	Download Link
PRJNA415636 (brain)	baseline	adult, Zebrabow M, brain	SRR6811819	SRR6811819.txt
PRJNA554650 (6.5dpf)	baseline	6.5dpf, whole brain of nr1d1:VNP fish	SRR9685040	SRR9685040.txt

retina

Dataset ID	Experiment Type	Sample	Source Dataset ID	Download Link
GSE122680 (1.5dpf)	baseline	1.5dpf, WT, untreatment	GSM3478014	GSM3478014.txt
GSE122680 (3dpf)	baseline	3dpf, WT, untreatment	GSM3478018	GSM3478018.txt
PRJNA672101 (nrl-KO)	growth	5mpf, three retinas from nrl-KO zebrafsih	SRR12899703	SRR12899703.txt
GSE122680 (14dpf)	baseline	14dpf, WT, untreatment	GSM3478019	GSM3478019.txt
PRJNA672101 (WT)	baseline	5mpf, three retinas from WT zebrafsih	SRR12899698	SRR12899698.txt
GSE122680 (24hpf)	baseline	24hpf, WT, untreatment	GSM3478013	GSM3478013.txt
GSE175929 (5mpf)	baseline	5mpf, GFP-positive cells collected from two transgenic zebrafish, Tg(rho:EGFP)ja2Tg and Tg(gnat2:EGFP)ja23Tg	GSM5351368	GSM5351368.txt
GSE122680 (2dpf)	baseline	2dpf, WT, untreatment	GSM4233148	GSM4233148.txt

cranial vault

Dataset ID	Experiment Type	Sample	Source Dataset ID	Download Link
GSE144944 (fgfr3 +\|+)	baseline	1mpf, fgfr3 +/+	GSM4301248	GSM4301248.txt
GSE144944 (fgfr3 -\|-)	growth	1mpf, fgfr3 -/-	GSM4301250	GSM4301250.txt

trunk

Dataset ID	Experiment Type	Sample	Source Dataset ID	Download Link
GSE152982 (wild type)	baseline	1.25dpf, untreatment	GSM4631066	GSM4631066.txt
GSE163907 (24hpf)	baseline	24hpf, trunk tg(sox10:GFP) positive cells	GSM4990514	GSM4990514.txt

pituitary

Dataset ID	Experiment Type	Sample	Source Dataset ID	Download Link
GSE148591 (3mpf)	transplant	3mpf, graft transplantation during early embryogenesis	GSM4474605	GSM4474605.txt
GSE148591 (6mpf)	baseline	6mpf, male, Sox17:CreERT2	GSM4474603	GSM4474603.txt

thyroid gland

Dataset ID	Experiment Type	Sample	Source Dataset ID	Download Link
PRJNA551501 (8mpf)	baseline	8mpf, Tg(tg:mVenus-T2A-NTR)	SRR9609654	SRR9609654.txt
PRJNA551501 (2mpf)	baseline	2mpf, Tg(tg:mVenus-T2A-NTR)	SRR9609653	SRR9609653.txt

caudal hematopoietic tissue

Dataset ID	Experiment Type	Sample	Source Dataset ID	Download Link
PRJNA610520 (4.5dpf)	baseline	4.5dpf, the mixture of same amount of kdrl:mCherry+ cells, CD41:GFP+ cells and double negative cells.	SRR11243184	SRR11243184.txt
PRJNA610520 (3.5dpf)	baseline	3.5dpf, the mixture of same amount of kdrl:mCherry+ cells, CD41:GFP+ cells and double negative cells.	SRR11243177	SRR11243177.txt

hypothalamus

Dataset ID	Experiment Type	Sample	Source Dataset ID	Download Link
PRJNA754013 (zebrafish)	baseline	adult, male, female, untreatment	SRR15422672	SRR15422672.txt

olfactory rosette

Dataset ID	Experiment Type	Sample	Source Dataset ID	Download Link
PRJNA668529 (3d)	disease	3mpf, intranasal 100ng r-Spike 3 days	SRR12858254	SRR12858254.txt
PRJNA668529 (3h)	disease	3mpf, intranasal 100ng r-Spike 3 hours	SRR12858255	SRR12858255.txt
PRJNA668529 (control)	baseline	3mpf, intranasal PBS	SRR12858259	SRR12858259.txt

primary pancreatic islet

Dataset ID	Experiment Type	Sample	Source Dataset ID	Download Link
PRJNA415636 (primary pancreatic islet)	baseline	adult, Zebrabow M, primary pancreatic islet	SRR6811821	SRR6811821.txt

cartilage

Dataset ID	Experiment Type	Sample	Source Dataset ID	Download Link
GSE151354 (wild type)	baseline	21dpf, wild type	GSM4575942	GSM4575942.txt
GSE151354 (nkx3.2 mutant)	growth	21dpf, nkx3.2 mutant	GSM4575943	GSM4575943.txt

dorsal and anal fin

Dataset ID	Experiment Type	Sample	Source Dataset ID	Download Link
GSE130526 (fin)	baseline	adult, fins were amputated from fish expressing both pnp4a:palmmCherry and tyrp1b:palmmCherry	GSM3741778	GSM3741778.txt

hepatopancreas

Dataset ID	Experiment Type	Sample	Source Dataset ID	Download Link
PRJNA415636 (pancreas, liver)	baseline	adult, Zebrabow M, pancreas and liver	SRR6211488	SRR6211488.txt

granulomas

Dataset ID	Experiment Type	Sample	Source Dataset ID	Download Link
GSE161712 (M. marinum)	disease	adult, infected with bacteria of M. marinum	GSM4913139	GSM4913139.txt

trunk, skin

Dataset ID	Experiment Type	Sample	Source Dataset ID	Download Link
GSE131136 (all)	baseline	5dpf, sox10:CRE positive cells from 5dpf and post-embryonic zebrafish trunks with and without thyroid hormone	GSE131136	GSE131136.txt

heart, blood

Dataset ID	Experiment Type	Sample	Source Dataset ID	Download Link
PRJNA415636 (heart, blood)	baseline	adult, Zebrabow M, heart and blood	SRR6211492	SRR6211492.txt

Astyanax mexicanus

hypothalamus

Dataset ID	Experiment Type	Sample	Source Dataset ID	Download Link
PRJNA754013 (Molino cave)	baseline	male, female, adult, untreatment	SRR15422671, SRR15422704	SRR15422671_SRR15422704.txt
PRJNA754013 (Pachon cave)	baseline	male, female, adult, untreatment	SRR15422680, SRR15422698	SRR15422680_SRR15422698.txt
PRJNA754013 (Tinaja cave)	baseline	male, female, adult, untreatment	SRR15422699, SRR15422703	SRR15422699_SRR15422703.txt
PRJNA754013 (Choy surface)	baseline	male, female, adult, untreatment	SRR15422711, SRR15422691	SRR15422711_SRR15422691.txt

Gasterosteus aculeatus

embryo

Dataset ID	Experiment Type	Sample	Source Dataset ID	Download Link
PRJNA797645	baseline	70 hpf, whole embryo, untreatment	SRR17665713	SRR17665713.txt

Nothobranchius furzeri

caudal fin

Dataset ID	Experiment Type	Sample	Source Dataset ID	Download Link
PRJNA559885	regeneration	adult, 2-month old, untreatment	SRR11886701, SRR11917464	SRR11886701_SRR11917464.txt

Oryzias latipes

pituitary

Dataset ID	Experiment Type	Sample	Source Dataset ID	Download Link
GSE162787 (male)	baseline	male, adult, untreatment	GSM4959938	GSM4959938.txt
GSE162787 (female)	baseline	female, adult, untreatment	GSM4959937	GSM4959937.txt

Oreochromis niloticus

anterior kidney

Dataset ID	Experiment Type	Sample	Source Dataset ID	Download Link
PRJNA766837	baseline	male, adult, untreatment	SRR16095434	SRR16095434.txt

Monopterus albus

gonad

Dataset ID	Experiment Type	Sample	Source Dataset ID	Download Link
GSE153961 (intersex)	baseline	adult, untreatment	GSM4661001	GSM4661001.txt

Mastacembelus armatus

ovotestes

Dataset ID	Experiment Type	Sample	Source Dataset ID	Download Link
GSE175406	baseline	The ovotestes of three individual 2-year-old zig-zag eels	GSM5333024	GSM5333024.txt

Oncorhynchus mykiss

blood

Dataset ID	Experiment Type	Sample	Source Dataset ID	Download Link
GSE158102 (3 fishes)	baseline	MHC-II+ B cells in blood	GSM4792223, GSM4792224, GSM4792225	GSM4792223_GSM4792224_GSM4792225.txt

DOWNLOAD

Marker

All marker/potential marker gene data for each species are available.

The data table includes the gene ID, symbol, chromosome location, scientific name of the species, marker class, tissue/organ, cell type, p value, and evidence.

Expression

All expression profile data for each dataset are available.

Click on the node of the fold tree to expand the information of datasets.

The data table includes the gene ID, symbol, cell cluster ID, cell type and detail quantity of cells.

copyright 2021-present@Lab of Aquatic Bioinfomatics, Institute of Hydrobiology, Chinese Academy of Sciences

DOWNLOAD

Marker

All marker/potential marker gene data for each species are available. The data table includes the gene ID, symbol, chromosome location, scientific name of the species, marker class, tissue/organ, cell type, p value, and evidence.

Expression

All expression profile data for each dataset are available. Click on the node of the fold tree to expand the information of datasets. The data table includes the gene ID, symbol, cell cluster ID, cell type and detail quantity of cells.

copyright 2021-present@Lab of Aquatic Bioinfomatics, Institute of Hydrobiology, Chinese Academy of Sciences

All marker/potential marker gene data for each species are available.

The data table includes the gene ID, symbol, chromosome location, scientific name of the species, marker class, tissue/organ, cell type, p value, and evidence.

All expression profile data for each dataset are available.

Click on the node of the fold tree to expand the information of datasets.

The data table includes the gene ID, symbol, cell cluster ID, cell type and detail quantity of cells.