metadata: run_metadata: 86 rows where devstage_curation = "Juvenile" and tissue_curation

86 rows where devstage_curation = "Juvenile" and tissue_curation_coarse = "All anatomical structures"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.description	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
42301	42301	SRR5579865	SRX2837982	SRS2212147	SRP107584	PRJNA387320	Danio rerio 1207 Raw sequence reads	PRJNA387320	Other						1207 2	breed:not applicable\|strain:not applicable\|age:1 month\|biomaterial provider:not applicable\|sex:not collected\|tissue:Embyro\|treatment:1207 2\|BioSampleModel:Model organism or animal									2002 2	1207 2 S1 L001	1207 2 S1 L001	The embryos were subjected to RNA isolation. Ten embryos per group n = 10 from wild type control embryos n = 10 from mibnn2002 mutants and n = 10 from mibta52b mutants were used to prepare a pooled RNA sample. Three biological replicates per group were prepared. Total RNA from pooled samples was extracted by using the mirVanaTM RNA isolation kit Applied Biosystems according to the manufacturers protocol as previously described. RNA quality was assessed by using the Agilent 2100 Bioanalyzer system and samples with a RNA Integrity Number RIN greater than 8 were used for RNA library construction.			RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina MiSeq	SRP107584				1531873131.0	5203504.0	1207 2 S2 L001 2 paired.fq.gz	0:148.34 1:146.06	A:384469512;C:380138079;G:381661689;T:385603823;N:28	148	146	384469512	380138079	381661689	385603823	28	SRX2837982	SRS2212147	SRA563090	The Chinese University of Hong Kong\|School of Life Sciences	The Chinese University of Hong Kong	2	0.97313	0.97391	0.03931	0.03966	0.73675	0.74186	0.47243	0.47819	151	150	B	B	biological fallback assumption	illumina	miseq	unknown	random_priming	unknown	bulk	unknown	unknown	China	2017-05-20	Juvenile	Juvenile	Embryo Imprecise	All anatomical structures
42302	42302	SRR5579866	SRX2837981	SRS2212146	SRP107584	PRJNA387320	Danio rerio 1207 Raw sequence reads	PRJNA387320	Other						1207 1	breed:not applicable\|strain:not applicable\|age:1 month\|biomaterial provider:not applicable\|sex:not collected\|tissue:Embyro\|treatment:1207 1\|BioSampleModel:Model organism or animal									2002 1	1207 1 S1 L001	1207 1 S1 L001	The embryos were subjected to RNA isolation. Ten embryos per group n = 10 from wild type control embryos n = 10 from mibnn2002 mutants and n = 10 from mibta52b mutants were used to prepare a pooled RNA sample. Three biological replicates per group were prepared. Total RNA from pooled samples was extracted by using the mirVanaTM RNA isolation kit Applied Biosystems according to the manufacturers protocol as previously described. RNA quality was assessed by using the Agilent 2100 Bioanalyzer system and samples with a RNA Integrity Number RIN greater than 8 were used for RNA library construction.			RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina MiSeq	SRP107584				1250178633.0	4243308.0	1207 1 S1 L001 2 paired.fq.gz	0:148.83 1:145.79	A:314820390;C:308887372;G:310674271;T:315796566;N:34	148	145	314820390	308887372	310674271	315796566	34	SRX2837981	SRS2212146	SRA563090	The Chinese University of Hong Kong\|School of Life Sciences	The Chinese University of Hong Kong	2	0.97174	0.9719	0.04506	0.04505	0.73154	0.73683	0.4817	0.48252	150	148	B	B	biological fallback assumption	illumina	miseq	unknown	random_priming	unknown	bulk	unknown	unknown	China	2017-05-20	Juvenile	Juvenile	Embryo Imprecise	All anatomical structures
42303	42303	SRR5579867	SRX2837980	SRS2212145	SRP107584	PRJNA387320	Danio rerio 1207 Raw sequence reads	PRJNA387320	Other						AB 1	breed:not applicable\|strain:not applicable\|age:1 month\|biomaterial provider:not applicable\|sex:not collected\|tissue:Embyro\|treatment:AB1\|BioSampleModel:Model organism or animal									WT1	AB1 S1 L001	AB1 S1 L001	The embryos were subjected to RNA isolation. Ten embryos per group n = 10 from wild type control embryos n = 10 from mibnn2002 mutants and n = 10 from mibta52b mutants were used to prepare a pooled RNA sample. Three biological replicates per group were prepared. Total RNA from pooled samples was extracted by using the mirVanaTM RNA isolation kit Applied Biosystems according to the manufacturers protocol as previously described. RNA quality was assessed by using the Agilent 2100 Bioanalyzer system and samples with a RNA Integrity Number RIN greater than 8 were used for RNA library construction.			RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina MiSeq	SRP107584				1819768909.0	6190653.0	AB1 S1 L001 2 paired.fq.gz	0:148.08 1:145.88	A:465877977;C:442905762;G:444673127;T:466312043;N:0	148	145	465877977	442905762	444673127	466312043	0	SRX2837980	SRS2212145	SRA563090	The Chinese University of Hong Kong\|School of Life Sciences	The Chinese University of Hong Kong	2	0.97169	0.97078	0.03527	0.03575	0.72823	0.73338	0.48283	0.48226	151	151	B	B	biological fallback assumption	illumina	miseq	unknown	random_priming	unknown	bulk	unknown	unknown	China	2017-05-20	Juvenile	Juvenile	Embryo Imprecise	All anatomical structures
42304	42304	SRR5579868	SRX2837979	SRS2212143	SRP107584	PRJNA387320	Danio rerio 1207 Raw sequence reads	PRJNA387320	Other						1207 3	breed:not applicable\|strain:not applicable\|age:1 month\|biomaterial provider:not applicable\|sex:not collected\|tissue:Embyro\|treatment:1207 3\|BioSampleModel:Model organism or animal									2002 3	1207 3 S1 L001	1207 3 S1 L001	The embryos were subjected to RNA isolation. Ten embryos per group n = 10 from wild type control embryos n = 10 from mibnn2002 mutants and n = 10 from mibta52b mutants were used to prepare a pooled RNA sample. Three biological replicates per group were prepared. Total RNA from pooled samples was extracted by using the mirVanaTM RNA isolation kit Applied Biosystems according to the manufacturers protocol as previously described. RNA quality was assessed by using the Agilent 2100 Bioanalyzer system and samples with a RNA Integrity Number RIN greater than 8 were used for RNA library construction.			RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina MiSeq	SRP107584				1045991851.0	3554741.0	1207 3 S3 L001 2 paired.fq.gz	0:148.38 1:145.87	A:263998819;C:257909132;G:259440555;T:264643331;N:14	148	145	263998819	257909132	259440555	264643331	14	SRX2837979	SRS2212143	SRA563090	The Chinese University of Hong Kong\|School of Life Sciences	The Chinese University of Hong Kong	2	0.97252	0.97273	0.0409	0.04037	0.74213	0.74574	0.48248	0.48634	151	151	B	B	biological fallback assumption	illumina	miseq	unknown	random_priming	unknown	bulk	unknown	unknown	China	2017-05-20	Juvenile	Juvenile	Embryo Imprecise	All anatomical structures
42305	42305	SRR5579869	SRX2837978	SRS2212142	SRP107584	PRJNA387320	Danio rerio 1207 Raw sequence reads	PRJNA387320	Other						AB 3	breed:not applicable\|strain:not applicable\|age:1 month\|biomaterial provider:not applicable\|sex:not collected\|tissue:Embyro\|treatment:AB3\|BioSampleModel:Model organism or animal									WT3	AB3 S1 L001	AB3 S1 L001	The embryos were subjected to RNA isolation. Ten embryos per group n = 10 from wild type control embryos n = 10 from mibnn2002 mutants and n = 10 from mibta52b mutants were used to prepare a pooled RNA sample. Three biological replicates per group were prepared. Total RNA from pooled samples was extracted by using the mirVanaTM RNA isolation kit Applied Biosystems according to the manufacturers protocol as previously described. RNA quality was assessed by using the Agilent 2100 Bioanalyzer system and samples with a RNA Integrity Number RIN greater than 8 were used for RNA library construction.			RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina MiSeq	SRP107584				1126218531.0	3826972.0	AB3 S3 L001 1 paired.fq.gz	0:148.46 1:145.83	A:285650942;C:276774884;G:276765238;T:287027467;N:0	148	145	285650942	276774884	276765238	287027467	0	SRX2837978	SRS2212142	SRA563090	The Chinese University of Hong Kong\|School of Life Sciences	The Chinese University of Hong Kong	2	0.97355	0.97389	0.03977	0.04012	0.71999	0.72506	0.47576	0.4728	149	151	B	B	biological fallback assumption	illumina	miseq	unknown	random_priming	unknown	bulk	unknown	unknown	China	2017-05-20	Juvenile	Juvenile	Embryo Imprecise	All anatomical structures
42306	42306	SRR5579870	SRX2837977	SRS2212144	SRP107584	PRJNA387320	Danio rerio 1207 Raw sequence reads	PRJNA387320	Other						AB 2	breed:not applicable\|strain:not applicable\|age:1 month\|biomaterial provider:not applicable\|sex:not collected\|tissue:Embyro\|treatment:AB2\|BioSampleModel:Model organism or animal									WT2	AB2 S1 L001	AB2 S1 L001	The embryos were subjected to RNA isolation. Ten embryos per group n = 10 from wild type control embryos n = 10 from mibnn2002 mutants and n = 10 from mibta52b mutants were used to prepare a pooled RNA sample. Three biological replicates per group were prepared. Total RNA from pooled samples was extracted by using the mirVanaTM RNA isolation kit Applied Biosystems according to the manufacturers protocol as previously described. RNA quality was assessed by using the Agilent 2100 Bioanalyzer system and samples with a RNA Integrity Number RIN greater than 8 were used for RNA library construction.			RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina MiSeq	SRP107584				1716453669.0	5815815.0	AB2 S2 L001 1 paired.fq.gz	0:148.63 1:146.50	A:430519895;C:426826400;G:426635292;T:432472082;N:0	148	146	430519895	426826400	426635292	432472082	0	SRX2837977	SRS2212144	SRA563090	The Chinese University of Hong Kong\|School of Life Sciences	The Chinese University of Hong Kong	2	0.97735	0.97725	0.02854	0.02833	0.73196	0.73484	0.48256	0.4861	151	151	B	B	biological fallback assumption	illumina	miseq	unknown	random_priming	unknown	bulk	unknown	unknown	China	2017-05-20	Juvenile	Juvenile	Embryo Imprecise	All anatomical structures
42350	42350	SRR7410374	SRX4281985	SRS3446891	SRP151068	PRJNA387484	RNA Seq of a Zebrafish Fanconi Mutant	PRJNA387484	Transcriptome Analysis	We conducted RNA seq analysis of zebrafish fancl mutants and wild type siblings at 4dpf 10dpf 14dpf 18dpf 22dpf 26dpf and 30dpf. RNA was extracted from the whole organism and libraries were prepared with the BIOO NEXTflex Rapid Directional qRNA Seq Kit.			RNA seq library	fancl wildtype 30dpf	fancl wildtype 30dpf	strain:AB\|age:30 dpf\|sex:not applicable\|tissue:whole organism\|biomaterial provider:John H. Postlethwait University of Oregon\|genotype:fancl nkhg10aEt +/+\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: 30dpf fancl wild type sample 30 29	30dpf fancl wild type 30 29	30dpf fancl wild type 30 29	Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP151068				2995334748.0	11886249.0	fancl wt 30 29 R1.fq.gz	0:126 1:126	A:744191069;C:728333183;G:750401765;T:772070330;N:338401	126	126	744191069	728333183	750401765	772070330	338401	SRX4281985	SRS3446891	SRA726408	University of Oregon\|Institute of Neuroscience	University of Oregon	2	0.94282	0.94989	0.10261	0.10127	0.72119	0.72498	0.56397	0.58255	126	126	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2018-06-21	Juvenile	Juvenile	Whole Organism	All anatomical structures
42353	42353	SRR7410377	SRX4281982	SRS3446891	SRP151068	PRJNA387484	RNA Seq of a Zebrafish Fanconi Mutant	PRJNA387484	Transcriptome Analysis	We conducted RNA seq analysis of zebrafish fancl mutants and wild type siblings at 4dpf 10dpf 14dpf 18dpf 22dpf 26dpf and 30dpf. RNA was extracted from the whole organism and libraries were prepared with the BIOO NEXTflex Rapid Directional qRNA Seq Kit.			RNA seq library	fancl wildtype 30dpf	fancl wildtype 30dpf	strain:AB\|age:30 dpf\|sex:not applicable\|tissue:whole organism\|biomaterial provider:John H. Postlethwait University of Oregon\|genotype:fancl nkhg10aEt +/+\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: 30dpf fancl wild type sample 30 23	30dpf fancl wild type 30 23	30dpf fancl wild type 30 23	Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP151068				4941076140.0	19607445.0	fancl wt 30 23 R1.fq.gz	0:126 1:126	A:1238002112;C:1200211717;G:1228052007;T:1274235738;N:574566	126	126	1238002112	1200211717	1228052007	1274235738	574566	SRX4281982	SRS3446891	SRA726408	University of Oregon\|Institute of Neuroscience	University of Oregon	2	0.94867	0.95506	0.10325	0.10339	0.72683	0.72961	0.58661	0.58503	126	126	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2018-06-21	Juvenile	Juvenile	Whole Organism	All anatomical structures
42376	42376	SRR7410400	SRX4281959	SRS3446891	SRP151068	PRJNA387484	RNA Seq of a Zebrafish Fanconi Mutant	PRJNA387484	Transcriptome Analysis	We conducted RNA seq analysis of zebrafish fancl mutants and wild type siblings at 4dpf 10dpf 14dpf 18dpf 22dpf 26dpf and 30dpf. RNA was extracted from the whole organism and libraries were prepared with the BIOO NEXTflex Rapid Directional qRNA Seq Kit.			RNA seq library	fancl wildtype 30dpf	fancl wildtype 30dpf	strain:AB\|age:30 dpf\|sex:not applicable\|tissue:whole organism\|biomaterial provider:John H. Postlethwait University of Oregon\|genotype:fancl nkhg10aEt +/+\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: 30dpf fancl wild type sample 30 02	30dpf fancl wild type 30 02	30dpf fancl wild type 30 02	Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP151068				5095936944.0	20221972.0	fancl wt 30 02 R1.fq.gz	0:126 1:126	A:1263289375;C:1249199634;G:1278613652;T:1304252815;N:581468	126	126	1263289375	1249199634	1278613652	1304252815	581468	SRX4281959	SRS3446891	SRA726408	University of Oregon\|Institute of Neuroscience	University of Oregon	2	0.94816	0.95396	0.10228	0.10104	0.72616	0.72654	0.57393	0.58353	126	126	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2018-06-21	Juvenile	Juvenile	Whole Organism	All anatomical structures
42396	42396	SRR7410420	SRX4281939	SRS3446903	SRP151068	PRJNA387484	RNA Seq of a Zebrafish Fanconi Mutant	PRJNA387484	Transcriptome Analysis	We conducted RNA seq analysis of zebrafish fancl mutants and wild type siblings at 4dpf 10dpf 14dpf 18dpf 22dpf 26dpf and 30dpf. RNA was extracted from the whole organism and libraries were prepared with the BIOO NEXTflex Rapid Directional qRNA Seq Kit.			RNA seq library	fancl mutant 30dpf	fancl mutant 30dpf	strain:AB\|age:30 dpf\|sex:not applicable\|tissue:whole organism\|biomaterial provider:John H. Postlethwait University of Oregon\|genotype:fancl nkhg10aEt / \|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: 30dpf fancl mutant sample 30 17	30dpf fancl mutant 30 17	30dpf fancl mutant 30 17	Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP151068				7715826468.0	30618359.0	fancl mut 30 17 R2.fq.gz	0:126 1:126	A:1807986336;C:2002774910;G:2035877968;T:1868285117;N:902137	126	126	1807986336	2002774910	2035877968	1868285117	902137	SRX4281939	SRS3446903	SRA726408	University of Oregon\|Institute of Neuroscience	University of Oregon	2	0.96709	0.97354	0.08768	0.08676	0.74152	0.7447	0.58802	0.57631	126	126	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2018-06-21	Juvenile	Juvenile	Whole Organism	All anatomical structures
42397	42397	SRR7410421	SRX4281938	SRS3446903	SRP151068	PRJNA387484	RNA Seq of a Zebrafish Fanconi Mutant	PRJNA387484	Transcriptome Analysis	We conducted RNA seq analysis of zebrafish fancl mutants and wild type siblings at 4dpf 10dpf 14dpf 18dpf 22dpf 26dpf and 30dpf. RNA was extracted from the whole organism and libraries were prepared with the BIOO NEXTflex Rapid Directional qRNA Seq Kit.			RNA seq library	fancl mutant 30dpf	fancl mutant 30dpf	strain:AB\|age:30 dpf\|sex:not applicable\|tissue:whole organism\|biomaterial provider:John H. Postlethwait University of Oregon\|genotype:fancl nkhg10aEt / \|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: 30dpf fancl mutant sample 30 08	30dpf fancl mutant 30 08	30dpf fancl mutant 30 08	Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP151068				5683582044.0	22553897.0	fancl mut 30 08 R1.fq.gz	0:126 1:126	A:1407291490;C:1395013891;G:1423770166;T:1456844244;N:662253	126	126	1407291490	1395013891	1423770166	1456844244	662253	SRX4281938	SRS3446903	SRA726408	University of Oregon\|Institute of Neuroscience	University of Oregon	2	0.9455	0.95135	0.1075	0.10757	0.71912	0.72196	0.57287	0.55078	126	126	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2018-06-21	Juvenile	Juvenile	Whole Organism	All anatomical structures
42398	42398	SRR7410422	SRX4281937	SRS3446903	SRP151068	PRJNA387484	RNA Seq of a Zebrafish Fanconi Mutant	PRJNA387484	Transcriptome Analysis	We conducted RNA seq analysis of zebrafish fancl mutants and wild type siblings at 4dpf 10dpf 14dpf 18dpf 22dpf 26dpf and 30dpf. RNA was extracted from the whole organism and libraries were prepared with the BIOO NEXTflex Rapid Directional qRNA Seq Kit.			RNA seq library	fancl mutant 30dpf	fancl mutant 30dpf	strain:AB\|age:30 dpf\|sex:not applicable\|tissue:whole organism\|biomaterial provider:John H. Postlethwait University of Oregon\|genotype:fancl nkhg10aEt / \|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: 30dpf fancl mutant sample 30 01	30dpf fancl mutant 30 01	30dpf fancl mutant 30 01	Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP151068				8917768188.0	35387969.0	fancl mut 30 01 R1.fq.gz	0:126 1:126	A:2184330162;C:2213012086;G:2262881514;T:2256511021;N:1033405	126	126	2184330162	2213012086	2262881514	2256511021	1033405	SRX4281937	SRS3446903	SRA726408	University of Oregon\|Institute of Neuroscience	University of Oregon	2	0.95002	0.95663	0.11136	0.11179	0.72502	0.72815	0.57109	0.54445	126	126	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2018-06-21	Juvenile	Juvenile	Whole Organism	All anatomical structures
42404	42404	SRR7410428	SRX4281931	SRS3446903	SRP151068	PRJNA387484	RNA Seq of a Zebrafish Fanconi Mutant	PRJNA387484	Transcriptome Analysis	We conducted RNA seq analysis of zebrafish fancl mutants and wild type siblings at 4dpf 10dpf 14dpf 18dpf 22dpf 26dpf and 30dpf. RNA was extracted from the whole organism and libraries were prepared with the BIOO NEXTflex Rapid Directional qRNA Seq Kit.			RNA seq library	fancl mutant 30dpf	fancl mutant 30dpf	strain:AB\|age:30 dpf\|sex:not applicable\|tissue:whole organism\|biomaterial provider:John H. Postlethwait University of Oregon\|genotype:fancl nkhg10aEt / \|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: 30dpf fancl mutant sample 30 25	30dpf fancl mutant 30 25	30dpf fancl mutant 30 25	Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP151068				10430314776.0	41390138.0	fancl mut 30 25 R1.fq.gz	0:126 1:126	A:2601755089;C:2535322569;G:2600718638;T:2691288565;N:1229915	126	126	2601755089	2535322569	2600718638	2691288565	1229915	SRX4281931	SRS3446903	SRA726408	University of Oregon\|Institute of Neuroscience	University of Oregon	2	0.94533	0.95212	0.10271	0.10301	0.71549	0.71823	0.57327	0.58016	126	126	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2018-06-21	Juvenile	Juvenile	Whole Organism	All anatomical structures
42405	42405	SRR7410429	SRX4281930	SRS3446903	SRP151068	PRJNA387484	RNA Seq of a Zebrafish Fanconi Mutant	PRJNA387484	Transcriptome Analysis	We conducted RNA seq analysis of zebrafish fancl mutants and wild type siblings at 4dpf 10dpf 14dpf 18dpf 22dpf 26dpf and 30dpf. RNA was extracted from the whole organism and libraries were prepared with the BIOO NEXTflex Rapid Directional qRNA Seq Kit.			RNA seq library	fancl mutant 30dpf	fancl mutant 30dpf	strain:AB\|age:30 dpf\|sex:not applicable\|tissue:whole organism\|biomaterial provider:John H. Postlethwait University of Oregon\|genotype:fancl nkhg10aEt / \|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: 30dpf fancl mutant sample 30 19	30dpf fancl mutant 30 19	30dpf fancl mutant 30 19	Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP151068				5726761488.0	22725244.0	fancl mut 30 19 R2.fq.gz	0:126 1:126	A:1417828651;C:1399791137;G:1432389082;T:1476078215;N:674403	126	126	1417828651	1399791137	1432389082	1476078215	674403	SRX4281930	SRS3446903	SRA726408	University of Oregon\|Institute of Neuroscience	University of Oregon	2	0.94187	0.95012	0.10759	0.10798	0.71944	0.71928	0.57165	0.52896	126	126	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2018-06-21	Juvenile	Juvenile	Whole Organism	All anatomical structures
42416	42416	SRR7410440	SRX4281919	SRS3446900	SRP151068	PRJNA387484	RNA Seq of a Zebrafish Fanconi Mutant	PRJNA387484	Transcriptome Analysis	We conducted RNA seq analysis of zebrafish fancl mutants and wild type siblings at 4dpf 10dpf 14dpf 18dpf 22dpf 26dpf and 30dpf. RNA was extracted from the whole organism and libraries were prepared with the BIOO NEXTflex Rapid Directional qRNA Seq Kit.			RNA seq library	brca2 wildtype 30dpf	brca2 wildtype 30dpf	strain:AB\|age:30 dpf\|sex:not applicable\|tissue:whole organism\|biomaterial provider:John H. Postlethwait University of Oregon\|genotype:brca2 ZM 00057434 +/+\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: 30dpf brca2 wild type sample 30 27	30dpf brca2 wild type 30 27	30dpf brca2 wild type 30 27	Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP151068				10335588808.0	34223804.0	brca2 wt 30 27 TATGTGGC R2.fq.gz	0:151 1:151	A:2578068515;C:2550705556;G:2592943796;T:2612664094;N:1206847	151	151	2578068515	2550705556	2592943796	2612664094	1206847	SRX4281919	SRS3446900	SRA726408	University of Oregon\|Institute of Neuroscience	University of Oregon	2	0.91509	0.92944	0.1198	0.09246	0.72794	0.73476	0.50295	0.55616	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2018-06-21	Juvenile	Juvenile	Whole Organism	All anatomical structures
42417	42417	SRR7410441	SRX4281918	SRS3446900	SRP151068	PRJNA387484	RNA Seq of a Zebrafish Fanconi Mutant	PRJNA387484	Transcriptome Analysis	We conducted RNA seq analysis of zebrafish fancl mutants and wild type siblings at 4dpf 10dpf 14dpf 18dpf 22dpf 26dpf and 30dpf. RNA was extracted from the whole organism and libraries were prepared with the BIOO NEXTflex Rapid Directional qRNA Seq Kit.			RNA seq library	brca2 wildtype 30dpf	brca2 wildtype 30dpf	strain:AB\|age:30 dpf\|sex:not applicable\|tissue:whole organism\|biomaterial provider:John H. Postlethwait University of Oregon\|genotype:brca2 ZM 00057434 +/+\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: 30dpf brca2 wild type sample 30 19	30dpf brca2 wild type 30 19	30dpf brca2 wild type 30 19	Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP151068				16971362932.0	56196566.0	brca2 wt 30 19 TTCAGCTC R1.fq.gz	0:151 1:151	A:4261370563;C:4149954129;G:4237743108;T:4320302899;N:1992233	151	151	4261370563	4149954129	4237743108	4320302899	1992233	SRX4281918	SRS3446900	SRA726408	University of Oregon\|Institute of Neuroscience	University of Oregon	2	0.90172	0.92611	0.10946	0.08762	0.71551	0.71993	0.50428	0.59503	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2018-06-21	Juvenile	Juvenile	Whole Organism	All anatomical structures
42418	42418	SRR7410442	SRX4281917	SRS3446900	SRP151068	PRJNA387484	RNA Seq of a Zebrafish Fanconi Mutant	PRJNA387484	Transcriptome Analysis	We conducted RNA seq analysis of zebrafish fancl mutants and wild type siblings at 4dpf 10dpf 14dpf 18dpf 22dpf 26dpf and 30dpf. RNA was extracted from the whole organism and libraries were prepared with the BIOO NEXTflex Rapid Directional qRNA Seq Kit.			RNA seq library	brca2 wildtype 30dpf	brca2 wildtype 30dpf	strain:AB\|age:30 dpf\|sex:not applicable\|tissue:whole organism\|biomaterial provider:John H. Postlethwait University of Oregon\|genotype:brca2 ZM 00057434 +/+\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: 30dpf brca2 wild type sample 30 14	30dpf brca2 wild type 30 14	30dpf brca2 wild type 30 14	Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP151068				6864849882.0	22731291.0	brca2 wt 30 14 TTGCGTAC R2.fq.gz	0:151 1:151	A:1727616237;C:1676798537;G:1712647063;T:1746990291;N:797754	151	151	1727616237	1676798537	1712647063	1746990291	797754	SRX4281917	SRS3446900	SRA726408	University of Oregon\|Institute of Neuroscience	University of Oregon	2	0.92049	0.93514	0.11	0.08759	0.73511	0.74349	0.51728	0.58993	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2018-06-21	Juvenile	Juvenile	Whole Organism	All anatomical structures
42420	42420	SRR7410444	SRX4281915	SRS3446900	SRP151068	PRJNA387484	RNA Seq of a Zebrafish Fanconi Mutant	PRJNA387484	Transcriptome Analysis	We conducted RNA seq analysis of zebrafish fancl mutants and wild type siblings at 4dpf 10dpf 14dpf 18dpf 22dpf 26dpf and 30dpf. RNA was extracted from the whole organism and libraries were prepared with the BIOO NEXTflex Rapid Directional qRNA Seq Kit.			RNA seq library	brca2 wildtype 30dpf	brca2 wildtype 30dpf	strain:AB\|age:30 dpf\|sex:not applicable\|tissue:whole organism\|biomaterial provider:John H. Postlethwait University of Oregon\|genotype:brca2 ZM 00057434 +/+\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: 30dpf brca2 wild type sample 30 17	30dpf brca2 wild type 30 17	30dpf brca2 wild type 30 17	Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP151068				8432584732.0	27922466.0	brca2 wt 30 17 TGCGTGAA R2.fq.gz	0:151 1:151	A:2132479978;C:2035633473;G:2088942653;T:2174550395;N:978233	151	151	2132479978	2035633473	2088942653	2174550395	978233	SRX4281915	SRS3446900	SRA726408	University of Oregon\|Institute of Neuroscience	University of Oregon	2	0.91011	0.9287	0.1076	0.08793	0.70627	0.71431	0.49536	0.58516	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2018-06-21	Juvenile	Juvenile	Whole Organism	All anatomical structures
42421	42421	SRR7410445	SRX4281914	SRS3446900	SRP151068	PRJNA387484	RNA Seq of a Zebrafish Fanconi Mutant	PRJNA387484	Transcriptome Analysis	We conducted RNA seq analysis of zebrafish fancl mutants and wild type siblings at 4dpf 10dpf 14dpf 18dpf 22dpf 26dpf and 30dpf. RNA was extracted from the whole organism and libraries were prepared with the BIOO NEXTflex Rapid Directional qRNA Seq Kit.			RNA seq library	brca2 wildtype 30dpf	brca2 wildtype 30dpf	strain:AB\|age:30 dpf\|sex:not applicable\|tissue:whole organism\|biomaterial provider:John H. Postlethwait University of Oregon\|genotype:brca2 ZM 00057434 +/+\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: 30dpf brca2 wild type sample 30 16	30dpf brca2 wild type 30 16	30dpf brca2 wild type 30 16	Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP151068				5787544912.0	19164056.0	brca2 wt 30 16 TTGACTCT R1.fq.gz	0:151 1:151	A:1470953427;C:1394911620;G:1427129077;T:1493879392;N:671396	151	151	1470953427	1394911620	1427129077	1493879392	671396	SRX4281914	SRS3446900	SRA726408	University of Oregon\|Institute of Neuroscience	University of Oregon	2	0.90129	0.91879	0.11795	0.09608	0.69909	0.70818	0.49724	0.5781	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2018-06-21	Juvenile	Juvenile	Whole Organism	All anatomical structures
42441	42441	SRR7410465	SRX4281894	SRS3446892	SRP151068	PRJNA387484	RNA Seq of a Zebrafish Fanconi Mutant	PRJNA387484	Transcriptome Analysis	We conducted RNA seq analysis of zebrafish fancl mutants and wild type siblings at 4dpf 10dpf 14dpf 18dpf 22dpf 26dpf and 30dpf. RNA was extracted from the whole organism and libraries were prepared with the BIOO NEXTflex Rapid Directional qRNA Seq Kit.			RNA seq library	brca2 mutant 30dpf	brca2 mutant 30dpf	strain:AB\|age:30 dpf\|sex:not applicable\|tissue:whole organism\|biomaterial provider:John H. Postlethwait University of Oregon\|genotype:brca2 ZM 00057434 / \|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: 30dpf brca2 mutant sample 30 13	30dpf brca2 mutant 30 13	30dpf brca2 mutant 30 13	Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP151068				7614746082.0	25214391.0	brca2 mut 30 13 GTGTCCTT R2.fq.gz	0:151 1:151	A:1953796672;C:1825224132;G:1858553376;T:1976291422;N:880480	151	151	1953796672	1825224132	1858553376	1976291422	880480	SRX4281894	SRS3446892	SRA726408	University of Oregon\|Institute of Neuroscience	University of Oregon	2	0.90472	0.92046	0.1248	0.1051	0.69836	0.70745	0.43736	0.58121	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2018-06-21	Juvenile	Juvenile	Whole Organism	All anatomical structures
42442	42442	SRR7410466	SRX4281893	SRS3446892	SRP151068	PRJNA387484	RNA Seq of a Zebrafish Fanconi Mutant	PRJNA387484	Transcriptome Analysis	We conducted RNA seq analysis of zebrafish fancl mutants and wild type siblings at 4dpf 10dpf 14dpf 18dpf 22dpf 26dpf and 30dpf. RNA was extracted from the whole organism and libraries were prepared with the BIOO NEXTflex Rapid Directional qRNA Seq Kit.			RNA seq library	brca2 mutant 30dpf	brca2 mutant 30dpf	strain:AB\|age:30 dpf\|sex:not applicable\|tissue:whole organism\|biomaterial provider:John H. Postlethwait University of Oregon\|genotype:brca2 ZM 00057434 / \|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: 30dpf brca2 mutant sample 30 12	30dpf brca2 mutant 30 12	30dpf brca2 mutant 30 12	Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP151068				6609294160.0	21885080.0	brca2 mut 30 12 TGTTCTCC R1.fq.gz	0:151 1:151	A:1663996252;C:1611724064;G:1649391730;T:1683416159;N:765955	151	151	1663996252	1611724064	1649391730	1683416159	765955	SRX4281893	SRS3446892	SRA726408	University of Oregon\|Institute of Neuroscience	University of Oregon	2	0.92261	0.93707	0.12282	0.10062	0.72555	0.73655	0.50213	0.55978	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2018-06-21	Juvenile	Juvenile	Whole Organism	All anatomical structures
42443	42443	SRR7410467	SRX4281892	SRS3446892	SRP151068	PRJNA387484	RNA Seq of a Zebrafish Fanconi Mutant	PRJNA387484	Transcriptome Analysis	We conducted RNA seq analysis of zebrafish fancl mutants and wild type siblings at 4dpf 10dpf 14dpf 18dpf 22dpf 26dpf and 30dpf. RNA was extracted from the whole organism and libraries were prepared with the BIOO NEXTflex Rapid Directional qRNA Seq Kit.			RNA seq library	brca2 mutant 30dpf	brca2 mutant 30dpf	strain:AB\|age:30 dpf\|sex:not applicable\|tissue:whole organism\|biomaterial provider:John H. Postlethwait University of Oregon\|genotype:brca2 ZM 00057434 / \|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: 30dpf brca2 mutant sample 30 11	30dpf brca2 mutant 30 11	30dpf brca2 mutant 30 11	Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP151068				3609770062.0	11952881.0	brca2 mut 30 11 ATCACGTT R2.fq.gz	0:151 1:151	A:910534494;C:877404076;G:898143524;T:923267603;N:420365	151	151	910534494	877404076	898143524	923267603	420365	SRX4281892	SRS3446892	SRA726408	University of Oregon\|Institute of Neuroscience	University of Oregon	2	0.90353	0.92062	0.11856	0.09432	0.72809	0.73669	0.44186	0.57479	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2018-06-21	Juvenile	Juvenile	Whole Organism	All anatomical structures
42447	42447	SRR7410471	SRX4281888	SRS3446892	SRP151068	PRJNA387484	RNA Seq of a Zebrafish Fanconi Mutant	PRJNA387484	Transcriptome Analysis	We conducted RNA seq analysis of zebrafish fancl mutants and wild type siblings at 4dpf 10dpf 14dpf 18dpf 22dpf 26dpf and 30dpf. RNA was extracted from the whole organism and libraries were prepared with the BIOO NEXTflex Rapid Directional qRNA Seq Kit.			RNA seq library	brca2 mutant 30dpf	brca2 mutant 30dpf	strain:AB\|age:30 dpf\|sex:not applicable\|tissue:whole organism\|biomaterial provider:John H. Postlethwait University of Oregon\|genotype:brca2 ZM 00057434 / \|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: 30dpf brca2 mutant sample 30 36	30dpf brca2 mutant 30 36	30dpf brca2 mutant 30 36	Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP151068				6899944698.0	22847499.0	brca2 mut 30 36 GAGGTGCT R1.fq.gz	0:151 1:151	A:1745582542;C:1669300984;G:1707455172;T:1776814198;N:791802	151	151	1745582542	1669300984	1707455172	1776814198	791802	SRX4281888	SRS3446892	SRA726408	University of Oregon\|Institute of Neuroscience	University of Oregon	2	0.91438	0.93255	0.11037	0.09276	0.72088	0.73024	0.50255	0.57014	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2018-06-21	Juvenile	Juvenile	Whole Organism	All anatomical structures
42448	42448	SRR7410472	SRX4281887	SRS3446892	SRP151068	PRJNA387484	RNA Seq of a Zebrafish Fanconi Mutant	PRJNA387484	Transcriptome Analysis	We conducted RNA seq analysis of zebrafish fancl mutants and wild type siblings at 4dpf 10dpf 14dpf 18dpf 22dpf 26dpf and 30dpf. RNA was extracted from the whole organism and libraries were prepared with the BIOO NEXTflex Rapid Directional qRNA Seq Kit.			RNA seq library	brca2 mutant 30dpf	brca2 mutant 30dpf	strain:AB\|age:30 dpf\|sex:not applicable\|tissue:whole organism\|biomaterial provider:John H. Postlethwait University of Oregon\|genotype:brca2 ZM 00057434 / \|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: 30dpf brca2 mutant sample 30 18	30dpf brca2 mutant 30 18	30dpf brca2 mutant 30 18	Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP151068				9162516316.0	30339458.0	brca2 mut 30 18 GTAAGGTG R2.fq.gz	0:151 1:151	A:2312465867;C:2223181568;G:2268715689;T:2357087788;N:1065404	151	151	2312465867	2223181568	2268715689	2357087788	1065404	SRX4281887	SRS3446892	SRA726408	University of Oregon\|Institute of Neuroscience	University of Oregon	2	0.91218	0.93164	0.10691	0.08773	0.73464	0.74306	0.50561	0.58578	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2018-06-21	Juvenile	Juvenile	Whole Organism	All anatomical structures
42450	42450	SRR7410474	SRX4281885	SRS3446891	SRP151068	PRJNA387484	RNA Seq of a Zebrafish Fanconi Mutant	PRJNA387484	Transcriptome Analysis	We conducted RNA seq analysis of zebrafish fancl mutants and wild type siblings at 4dpf 10dpf 14dpf 18dpf 22dpf 26dpf and 30dpf. RNA was extracted from the whole organism and libraries were prepared with the BIOO NEXTflex Rapid Directional qRNA Seq Kit.			RNA seq library	fancl wildtype 30dpf	fancl wildtype 30dpf	strain:AB\|age:30 dpf\|sex:not applicable\|tissue:whole organism\|biomaterial provider:John H. Postlethwait University of Oregon\|genotype:fancl nkhg10aEt +/+\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: 30dpf fancl wild type sample 30 30	30dpf fancl wild type 30 30	30dpf fancl wild type 30 30	Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP151068				10131111648.0	40202824.0	fancl wt 30 30 R1.fq.gz	0:126 1:126	A:2542923952;C:2446585748;G:2508652587;T:2631768070;N:1181291	126	126	2542923952	2446585748	2508652587	2631768070	1181291	SRX4281885	SRS3446891	SRA726408	University of Oregon\|Institute of Neuroscience	University of Oregon	2	0.94391	0.95296	0.107	0.10797	0.72786	0.73115	0.58931	0.57476	126	126	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2018-06-21	Juvenile	Juvenile	Whole Organism	All anatomical structures
54727	54727	SRR10150436	SRX6875873	SRS5411730	SRP222654	PRJNA571187	single cell RNA Seq of juvenile zebrafish	PRJNA571187	Other	single cell RNA Seq of juvenile zebrafish using the 10x Genomics platform with Chromium Single Cell three prime v2 Reagent Kit				whole organism single cell RNA seq of juvenile zebrafish	SC2S3	strain:AB\|age:30 dpf\|sex:not collected\|tissue:whole organism\|genotype:WT\|BioSampleModel:Model organism or animal									single cell RNA Seq of zebrafish: whole organism of juvenile	I4S2	I4S2	A single Juvenile fish at about 30 dpf was anesthetized in tricaine and euthanized on ice. Then it was washed three times with 200 L ice cold HBSS supplemented with 1% BSA and transferred into 200 L Dissociation buffer 1 TrypLE Thermo Fisher Scientific in 1 HBSS [Ca+/Mg+ free] GIBCO. Next the solution was incubated for 20 minutes and mixed occasionally with a pipette. 120 L HBSS and 80 L Digestion cocktail stock 5 mg/mL collagenase Sigma Aldrich 10 mg/mL pronase Sigma Aldrich 10 mg/mL proteinase K Sigma Aldrich were added and the suspension was pipetted until the larva was invisible. The cell suspension was washed with wash buffer twice and pelleted by centrifuging at 600g for 8 minutes at 4 C and resuspended in wash buffer. The cells were filtered through a 35 m strainer and processed using the 10x Genomics platform with Chromium Single Cell 3 v2 Reagent Kit.			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	HiSeq X Ten	SRP222654		S3-I4-Hiseq_S2_L001_R1_001.fastq.gz S3-I4-Hiseq_S2_L001_R2_001.fastq.gz	fastq fastq	3487596300.0	11625321.0	S3 I4 Hiseq S2 L001 R1 001.fastq.gz	0:150 1:150	A:892777135;C:554604922;G:602698080;T:1437353489;N:162674	150	150	892777135	554604922	602698080	1437353489	162674	SRX6875873	SRS5411730	SRA965192	Sun Yat- sen University\|Life Sicence School	Sun Yat- sen University	2	0.20171	0.89797	0.05294	0.15018	0.98557	0.78865	0.5155	0.57581	150	150	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	China	2019-09-20	Juvenile	Juvenile	Whole Organism	All anatomical structures
54728	54728	SRR10150437	SRX6875872	SRS5411730	SRP222654	PRJNA571187	single cell RNA Seq of juvenile zebrafish	PRJNA571187	Other	single cell RNA Seq of juvenile zebrafish using the 10x Genomics platform with Chromium Single Cell three prime v2 Reagent Kit				whole organism single cell RNA seq of juvenile zebrafish	SC2S3	strain:AB\|age:30 dpf\|sex:not collected\|tissue:whole organism\|genotype:WT\|BioSampleModel:Model organism or animal									single cell RNA Seq of zebrafish: whole organism of juvenile	I4S1	I4S1	A single Juvenile fish at about 30 dpf was anesthetized in tricaine and euthanized on ice. Then it was washed three times with 200 L ice cold HBSS supplemented with 1% BSA and transferred into 200 L Dissociation buffer 1 TrypLE Thermo Fisher Scientific in 1 HBSS [Ca+/Mg+ free] GIBCO. Next the solution was incubated for 20 minutes and mixed occasionally with a pipette. 120 L HBSS and 80 L Digestion cocktail stock 5 mg/mL collagenase Sigma Aldrich 10 mg/mL pronase Sigma Aldrich 10 mg/mL proteinase K Sigma Aldrich were added and the suspension was pipetted until the larva was invisible. The cell suspension was washed with wash buffer twice and pelleted by centrifuging at 600g for 8 minutes at 4 C and resuspended in wash buffer. The cells were filtered through a 35 m strainer and processed using the 10x Genomics platform with Chromium Single Cell 3 v2 Reagent Kit.			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	HiSeq X Ten	SRP222654		S3-I4-Hiseq_S1_L001_R1_001.fastq.gz S3-I4-Hiseq_S1_L001_R2_001.fastq.gz	fastq fastq	7508763300.0	25029211.0	S3 I4 Hiseq S1 L001 R1 001.fastq.gz	0:150 1:150	A:1913388616;C:1347525105;G:1432782100;T:2815014523;N:52956	150	150	1913388616	1347525105	1432782100	2815014523	52956	SRX6875872	SRS5411730	SRA965192	Sun Yat- sen University\|Life Sicence School	Sun Yat- sen University	2	0.07221	0.85601	0.01751	0.14578	0.98569	0.78642	0.49143	0.56028	150	150	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	China	2019-09-20	Juvenile	Juvenile	Whole Organism	All anatomical structures
54729	54729	SRR10150438	SRX6875871	SRS5411730	SRP222654	PRJNA571187	single cell RNA Seq of juvenile zebrafish	PRJNA571187	Other	single cell RNA Seq of juvenile zebrafish using the 10x Genomics platform with Chromium Single Cell three prime v2 Reagent Kit				whole organism single cell RNA seq of juvenile zebrafish	SC2S3	strain:AB\|age:30 dpf\|sex:not collected\|tissue:whole organism\|genotype:WT\|BioSampleModel:Model organism or animal									single cell RNA Seq of zebrafish: whole organism of juvenile	I3S2	I3S2	A single Juvenile fish at about 30 dpf was anesthetized in tricaine and euthanized on ice. Then it was washed three times with 200 L ice cold HBSS supplemented with 1% BSA and transferred into 200 L Dissociation buffer 1 TrypLE Thermo Fisher Scientific in 1 HBSS [Ca+/Mg+ free] GIBCO. Next the solution was incubated for 20 minutes and mixed occasionally with a pipette. 120 L HBSS and 80 L Digestion cocktail stock 5 mg/mL collagenase Sigma Aldrich 10 mg/mL pronase Sigma Aldrich 10 mg/mL proteinase K Sigma Aldrich were added and the suspension was pipetted until the larva was invisible. The cell suspension was washed with wash buffer twice and pelleted by centrifuging at 600g for 8 minutes at 4 C and resuspended in wash buffer. The cells were filtered through a 35 m strainer and processed using the 10x Genomics platform with Chromium Single Cell 3 v2 Reagent Kit.			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	HiSeq X Ten	SRP222654		S3-I3-Hiseq_S2_L001_R1_001.fastq.gz S3-I3-Hiseq_S2_L001_R2_001.fastq.gz	fastq fastq	4273728900.0	14245763.0	S3 I3 Hiseq S2 L001 R1 001.fastq.gz	0:150 1:150	A:1093044190;C:680068409;G:740119940;T:1760292389;N:203972	150	150	1093044190	680068409	740119940	1760292389	203972	SRX6875871	SRS5411730	SRA965192	Sun Yat- sen University\|Life Sicence School	Sun Yat- sen University	2	0.20465	0.90036	0.05289	0.14865	0.98553	0.7877	0.49162	0.55234	150	150	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	China	2019-09-20	Juvenile	Juvenile	Whole Organism	All anatomical structures
54730	54730	SRR10150439	SRX6875870	SRS5411730	SRP222654	PRJNA571187	single cell RNA Seq of juvenile zebrafish	PRJNA571187	Other	single cell RNA Seq of juvenile zebrafish using the 10x Genomics platform with Chromium Single Cell three prime v2 Reagent Kit				whole organism single cell RNA seq of juvenile zebrafish	SC2S3	strain:AB\|age:30 dpf\|sex:not collected\|tissue:whole organism\|genotype:WT\|BioSampleModel:Model organism or animal									single cell RNA Seq of zebrafish: whole organism of juvenile	I3S1	I3S1	A single Juvenile fish at about 30 dpf was anesthetized in tricaine and euthanized on ice. Then it was washed three times with 200 L ice cold HBSS supplemented with 1% BSA and transferred into 200 L Dissociation buffer 1 TrypLE Thermo Fisher Scientific in 1 HBSS [Ca+/Mg+ free] GIBCO. Next the solution was incubated for 20 minutes and mixed occasionally with a pipette. 120 L HBSS and 80 L Digestion cocktail stock 5 mg/mL collagenase Sigma Aldrich 10 mg/mL pronase Sigma Aldrich 10 mg/mL proteinase K Sigma Aldrich were added and the suspension was pipetted until the larva was invisible. The cell suspension was washed with wash buffer twice and pelleted by centrifuging at 600g for 8 minutes at 4 C and resuspended in wash buffer. The cells were filtered through a 35 m strainer and processed using the 10x Genomics platform with Chromium Single Cell 3 v2 Reagent Kit.			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	HiSeq X Ten	SRP222654		S3-I3-Hiseq_S1_L001_R1_001.fastq.gz S3-I3-Hiseq_S1_L001_R2_001.fastq.gz	fastq fastq	9027772200.0	30092574.0	S3 I3 Hiseq S1 L001 R1 001.fastq.gz	0:150 1:150	A:2295058606;C:1618993604;G:1725968569;T:3387689160;N:62261	150	150	2295058606	1618993604	1725968569	3387689160	62261	SRX6875870	SRS5411730	SRA965192	Sun Yat- sen University\|Life Sicence School	Sun Yat- sen University	2	0.07429	0.86204	0.01816	0.14367	0.98638	0.78754	0.51152	0.56418	150	150	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	China	2019-09-20	Juvenile	Juvenile	Whole Organism	All anatomical structures
54731	54731	SRR10150440	SRX6875869	SRS5411730	SRP222654	PRJNA571187	single cell RNA Seq of juvenile zebrafish	PRJNA571187	Other	single cell RNA Seq of juvenile zebrafish using the 10x Genomics platform with Chromium Single Cell three prime v2 Reagent Kit				whole organism single cell RNA seq of juvenile zebrafish	SC2S3	strain:AB\|age:30 dpf\|sex:not collected\|tissue:whole organism\|genotype:WT\|BioSampleModel:Model organism or animal									single cell RNA Seq of zebrafish: whole organism of juvenile	I2S2	I2S2	A single Juvenile fish at about 30 dpf was anesthetized in tricaine and euthanized on ice. Then it was washed three times with 200 L ice cold HBSS supplemented with 1% BSA and transferred into 200 L Dissociation buffer 1 TrypLE Thermo Fisher Scientific in 1 HBSS [Ca+/Mg+ free] GIBCO. Next the solution was incubated for 20 minutes and mixed occasionally with a pipette. 120 L HBSS and 80 L Digestion cocktail stock 5 mg/mL collagenase Sigma Aldrich 10 mg/mL pronase Sigma Aldrich 10 mg/mL proteinase K Sigma Aldrich were added and the suspension was pipetted until the larva was invisible. The cell suspension was washed with wash buffer twice and pelleted by centrifuging at 600g for 8 minutes at 4 C and resuspended in wash buffer. The cells were filtered through a 35 m strainer and processed using the 10x Genomics platform with Chromium Single Cell 3 v2 Reagent Kit.			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	HiSeq X Ten	SRP222654		S3-I2-Hiseq_S2_L001_R1_001.fastq.gz S3-I2-Hiseq_S2_L001_R2_001.fastq.gz	fastq fastq	3198554400.0	10661848.0	S3 I2 Hiseq S2 L001 R1 001.fastq.gz	0:150 1:150	A:818748615;C:508568675;G:554517575;T:1316569216;N:150319	150	150	818748615	508568675	554517575	1316569216	150319	SRX6875869	SRS5411730	SRA965192	Sun Yat- sen University\|Life Sicence School	Sun Yat- sen University	2	0.2074	0.89961	0.05315	0.14953	0.98514	0.78849	0.48568	0.56678	150	150	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	China	2019-09-20	Juvenile	Juvenile	Whole Organism	All anatomical structures
54732	54732	SRR10150441	SRX6875868	SRS5411730	SRP222654	PRJNA571187	single cell RNA Seq of juvenile zebrafish	PRJNA571187	Other	single cell RNA Seq of juvenile zebrafish using the 10x Genomics platform with Chromium Single Cell three prime v2 Reagent Kit				whole organism single cell RNA seq of juvenile zebrafish	SC2S3	strain:AB\|age:30 dpf\|sex:not collected\|tissue:whole organism\|genotype:WT\|BioSampleModel:Model organism or animal									single cell RNA Seq of zebrafish: whole organism of juvenile	I2S1	I2S1	A single Juvenile fish at about 30 dpf was anesthetized in tricaine and euthanized on ice. Then it was washed three times with 200 L ice cold HBSS supplemented with 1% BSA and transferred into 200 L Dissociation buffer 1 TrypLE Thermo Fisher Scientific in 1 HBSS [Ca+/Mg+ free] GIBCO. Next the solution was incubated for 20 minutes and mixed occasionally with a pipette. 120 L HBSS and 80 L Digestion cocktail stock 5 mg/mL collagenase Sigma Aldrich 10 mg/mL pronase Sigma Aldrich 10 mg/mL proteinase K Sigma Aldrich were added and the suspension was pipetted until the larva was invisible. The cell suspension was washed with wash buffer twice and pelleted by centrifuging at 600g for 8 minutes at 4 C and resuspended in wash buffer. The cells were filtered through a 35 m strainer and processed using the 10x Genomics platform with Chromium Single Cell 3 v2 Reagent Kit.			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	HiSeq X Ten	SRP222654		S3-I2-Hiseq_S1_L001_R1_001.fastq.gz S3-I2-Hiseq_S1_L001_R2_001.fastq.gz	fastq fastq	7025021100.0	23416737.0	S3 I2 Hiseq S1 L001 R1 001.fastq.gz	0:150 1:150	A:1791257403;C:1265471598;G:1350119282;T:2618125524;N:47293	150	150	1791257403	1265471598	1350119282	2618125524	47293	SRX6875868	SRS5411730	SRA965192	Sun Yat- sen University\|Life Sicence School	Sun Yat- sen University	2	0.0595	0.8397	0.01378	0.14017	0.98602	0.78618	0.49684	0.57243	150	150	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	China	2019-09-20	Juvenile	Juvenile	Whole Organism	All anatomical structures
54733	54733	SRR10150442	SRX6875867	SRS5411730	SRP222654	PRJNA571187	single cell RNA Seq of juvenile zebrafish	PRJNA571187	Other	single cell RNA Seq of juvenile zebrafish using the 10x Genomics platform with Chromium Single Cell three prime v2 Reagent Kit				whole organism single cell RNA seq of juvenile zebrafish	SC2S3	strain:AB\|age:30 dpf\|sex:not collected\|tissue:whole organism\|genotype:WT\|BioSampleModel:Model organism or animal									single cell RNA Seq of zebrafish: whole organism of juvenile	I1S2	I1S2	A single Juvenile fish at about 30 dpf was anesthetized in tricaine and euthanized on ice. Then it was washed three times with 200 L ice cold HBSS supplemented with 1% BSA and transferred into 200 L Dissociation buffer 1 TrypLE Thermo Fisher Scientific in 1 HBSS [Ca+/Mg+ free] GIBCO. Next the solution was incubated for 20 minutes and mixed occasionally with a pipette. 120 L HBSS and 80 L Digestion cocktail stock 5 mg/mL collagenase Sigma Aldrich 10 mg/mL pronase Sigma Aldrich 10 mg/mL proteinase K Sigma Aldrich were added and the suspension was pipetted until the larva was invisible. The cell suspension was washed with wash buffer twice and pelleted by centrifuging at 600g for 8 minutes at 4 C and resuspended in wash buffer. The cells were filtered through a 35 m strainer and processed using the 10x Genomics platform with Chromium Single Cell 3 v2 Reagent Kit.			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	HiSeq X Ten	SRP222654		S3-I1-Hiseq_S2_L001_R1_001.fastq.gz S3-I1-Hiseq_S2_L001_R2_001.fastq.gz	fastq fastq	3657667800.0	12192226.0	S3 I1 Hiseq S2 L001 R1 001.fastq.gz	0:150 1:150	A:936855915;C:580324428;G:630608753;T:1509707910;N:170794	150	150	936855915	580324428	630608753	1509707910	170794	SRX6875867	SRS5411730	SRA965192	Sun Yat- sen University\|Life Sicence School	Sun Yat- sen University	2	0.20478	0.89817	0.05194	0.15048	0.98543	0.78817	0.49956	0.57664	150	150	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	China	2019-09-20	Juvenile	Juvenile	Whole Organism	All anatomical structures
54734	54734	SRR10150443	SRX6875866	SRS5411730	SRP222654	PRJNA571187	single cell RNA Seq of juvenile zebrafish	PRJNA571187	Other	single cell RNA Seq of juvenile zebrafish using the 10x Genomics platform with Chromium Single Cell three prime v2 Reagent Kit				whole organism single cell RNA seq of juvenile zebrafish	SC2S3	strain:AB\|age:30 dpf\|sex:not collected\|tissue:whole organism\|genotype:WT\|BioSampleModel:Model organism or animal									single cell RNA Seq of zebrafish: whole organism of juvenile	I1S1	I1S1	A single Juvenile fish at about 30 dpf was anesthetized in tricaine and euthanized on ice. Then it was washed three times with 200 L ice cold HBSS supplemented with 1% BSA and transferred into 200 L Dissociation buffer 1 TrypLE Thermo Fisher Scientific in 1 HBSS [Ca+/Mg+ free] GIBCO. Next the solution was incubated for 20 minutes and mixed occasionally with a pipette. 120 L HBSS and 80 L Digestion cocktail stock 5 mg/mL collagenase Sigma Aldrich 10 mg/mL pronase Sigma Aldrich 10 mg/mL proteinase K Sigma Aldrich were added and the suspension was pipetted until the larva was invisible. The cell suspension was washed with wash buffer twice and pelleted by centrifuging at 600g for 8 minutes at 4 C and resuspended in wash buffer. The cells were filtered through a 35 m strainer and processed using the 10x Genomics platform with Chromium Single Cell 3 v2 Reagent Kit.			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	HiSeq X Ten	SRP222654		S3-I1-Hiseq_S1_L001_R1_001.fastq.gz S3-I1-Hiseq_S1_L001_R2_001.fastq.gz	fastq fastq	7809763800.0	26032546.0	S3 I1 Hiseq S1 L001 R1 001.fastq.gz	0:150 1:150	A:1991021603;C:1400155384;G:1489635110;T:2928896892;N:54811	150	150	1991021603	1400155384	1489635110	2928896892	54811	SRX6875866	SRS5411730	SRA965192	Sun Yat- sen University\|Life Sicence School	Sun Yat- sen University	2	0.06891	0.85095	0.01881	0.14251	0.98555	0.78772	0.49154	0.57233	150	150	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	China	2019-09-20	Juvenile	Juvenile	Whole Organism	All anatomical structures
59140	59140	SRR11684023	SRX8244826	SRS6592463	SRP259989	PRJNA630163	Zebrafish juvenile mpeg+ macrophages	GSE149787	Transcriptome Analysis	We used zebrafish lacking functional csf1r or il34 to unravel how and when csf1r is necessary for macrophages. Transcriptomic analysis of mpeg+ macrophages isolated from juvenile fish revealed that csf1r deficient macrophages show a gross macrophage transcriptome but reduced expression of engulfment related genes and increased expression of genes typical for metaphocytes. Overall design: Bulk RNA sequencing of juvenile macrophages obtained from wildtype control il34 / and csf1rDM zebrafish triplicates	parent bioproject:PRJNA630158	pubmed:32367800		33dpf csf1rdm 3	GSM4512715	tissue:whole fish\|developmental stage:33 dpf\|strain:csf1raj4e1/j4e1; csf1rbre01/re01 tgmpeg GFP\|cell type:mpeg GFP+ cells	33dpf csf1rdm 3	Sequencing and base calling was performed on the Illumina hiseq 2500. Resulting base calls were de multiplexed using the Illumina Casava 1.8 software. Subsequently SMARTer adapters were removed using cutadapt followed by the alignment step using STAR version 2.5.4b. Reference genome build GRCz10 danRer10 was used. Abundance estimation was performed using cufflinks v2.2.1 with both the frag bias correct and multi read correct flags set. The raw read counts were measured using HTSeq count version 0.11.0. using the union setting. The ensemble gene database was used. The aligned and filtered data was quantified with the Bioconductor package Genomic Ranges Lawrence et al. Plos Computational Biology 2013. Differential gene expression analysis was performed with Bioconductor package EdgeR Robinson et al. 2010. Genome build: GRCz10 Supplementary files format and content: CPM values [.csv] semicolon delimited files.	whole fish		Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols	HEPES buffered E3 medium 28 degrees celsius 14/10h light/dark cycle until 5 dpf from 5 dpf onwards in regular aquarium. Fed dry food + paramecia from 5 dpf 13 dpf. From 13 dpf onwards brine shrimps paramecia and dry food	developmental stage:33 dpf\|strain:csf1raj4e1/j4e1;csf1rbre01/re01 tgmpeg GFP\|cell type:mpeg GFP+ cells	GSM4512715	GSM4512715: 33dpf csf1rdm 3; Danio rerio; RNA Seq	GSM4512715		1	Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM4512715	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP259989		33dpf_csf1rdm_3_R2.fastq.gz 33dpf_csf1rdm_3_R1.fastq.gz	fastq fastq	4266500984.0	21121292.0	GSM4512715 r1	0:101 1:101	A:1228176589;C:888764172;G:911251380;T:1238297282;N:11561	101	101	1228176589	888764172	911251380	1238297282	11561	SRX8244826	SRS6592463	SRA1072140	GEO	Erasmus MC	2	0.90846	0.8852	0.18604	0.18551	0.77149	0.78056	0.47511	0.46363	101	101	B	B	biological fallback assumption	illumina	hiseq_era	full_length	cdna_unspecified	trueseq	sc	single_cell_plate	smartseq	Netherlands	2020-05-04	Juvenile	Juvenile	Whole Organism	All anatomical structures
59141	59141	SRR11684022	SRX8244825	SRS6592462	SRP259989	PRJNA630163	Zebrafish juvenile mpeg+ macrophages	GSE149787	Transcriptome Analysis	We used zebrafish lacking functional csf1r or il34 to unravel how and when csf1r is necessary for macrophages. Transcriptomic analysis of mpeg+ macrophages isolated from juvenile fish revealed that csf1r deficient macrophages show a gross macrophage transcriptome but reduced expression of engulfment related genes and increased expression of genes typical for metaphocytes. Overall design: Bulk RNA sequencing of juvenile macrophages obtained from wildtype control il34 / and csf1rDM zebrafish triplicates	parent bioproject:PRJNA630158	pubmed:32367800		33dpf csf1rdm 2	GSM4512714	tissue:whole fish\|developmental stage:33 dpf\|strain:csf1raj4e1/j4e1; csf1rbre01/re01 tgmpeg GFP\|cell type:mpeg GFP+ cells	33dpf csf1rdm 2	Sequencing and base calling was performed on the Illumina hiseq 2500. Resulting base calls were de multiplexed using the Illumina Casava 1.8 software. Subsequently SMARTer adapters were removed using cutadapt followed by the alignment step using STAR version 2.5.4b. Reference genome build GRCz10 danRer10 was used. Abundance estimation was performed using cufflinks v2.2.1 with both the frag bias correct and multi read correct flags set. The raw read counts were measured using HTSeq count version 0.11.0. using the union setting. The ensemble gene database was used. The aligned and filtered data was quantified with the Bioconductor package Genomic Ranges Lawrence et al. Plos Computational Biology 2013. Differential gene expression analysis was performed with Bioconductor package EdgeR Robinson et al. 2010. Genome build: GRCz10 Supplementary files format and content: CPM values [.csv] semicolon delimited files.	whole fish		Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols	HEPES buffered E3 medium 28 degrees celsius 14/10h light/dark cycle until 5 dpf from 5 dpf onwards in regular aquarium. Fed dry food + paramecia from 5 dpf 13 dpf. From 13 dpf onwards brine shrimps paramecia and dry food	developmental stage:33 dpf\|strain:csf1raj4e1/j4e1;csf1rbre01/re01 tgmpeg GFP\|cell type:mpeg GFP+ cells	GSM4512714	GSM4512714: 33dpf csf1rdm 2; Danio rerio; RNA Seq	GSM4512714		1	Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM4512714	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP259989		33dpf_csf1rdm_2_R2.fastq.gz 33dpf_csf1rdm_2_R1.fastq.gz	fastq fastq	34856013646.0	172554523.0	GSM4512714 r1	0:101 1:101	A:10025368414;C:7294167881;G:7483951837;T:10052430673;N:94841	101	101	10025368414	7294167881	7483951837	10052430673	94841	SRX8244825	SRS6592462	SRA1072140	GEO	Erasmus MC	2	0.90986	0.88677	0.1819	0.18005	0.7601	0.76921	0.48551	0.47188	101	101	B	B	biological fallback assumption	illumina	hiseq_era	full_length	cdna_unspecified	trueseq	sc	single_cell_plate	smartseq	Netherlands	2020-05-04	Juvenile	Juvenile	Whole Organism	All anatomical structures
59142	59142	SRR11684021	SRX8244824	SRS6592461	SRP259989	PRJNA630163	Zebrafish juvenile mpeg+ macrophages	GSE149787	Transcriptome Analysis	We used zebrafish lacking functional csf1r or il34 to unravel how and when csf1r is necessary for macrophages. Transcriptomic analysis of mpeg+ macrophages isolated from juvenile fish revealed that csf1r deficient macrophages show a gross macrophage transcriptome but reduced expression of engulfment related genes and increased expression of genes typical for metaphocytes. Overall design: Bulk RNA sequencing of juvenile macrophages obtained from wildtype control il34 / and csf1rDM zebrafish triplicates	parent bioproject:PRJNA630158	pubmed:32367800		33dpf csf1rdm 1	GSM4512713	tissue:whole fish\|developmental stage:33 dpf\|strain:csf1raj4e1/j4e1; csf1rbre01/re01 tgmpeg GFP\|cell type:mpeg GFP+ cells	33dpf csf1rdm 1	Sequencing and base calling was performed on the Illumina hiseq 2500. Resulting base calls were de multiplexed using the Illumina Casava 1.8 software. Subsequently SMARTer adapters were removed using cutadapt followed by the alignment step using STAR version 2.5.4b. Reference genome build GRCz10 danRer10 was used. Abundance estimation was performed using cufflinks v2.2.1 with both the frag bias correct and multi read correct flags set. The raw read counts were measured using HTSeq count version 0.11.0. using the union setting. The ensemble gene database was used. The aligned and filtered data was quantified with the Bioconductor package Genomic Ranges Lawrence et al. Plos Computational Biology 2013. Differential gene expression analysis was performed with Bioconductor package EdgeR Robinson et al. 2010. Genome build: GRCz10 Supplementary files format and content: CPM values [.csv] semicolon delimited files.	whole fish		Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols	HEPES buffered E3 medium 28 degrees celsius 14/10h light/dark cycle until 5 dpf from 5 dpf onwards in regular aquarium. Fed dry food + paramecia from 5 dpf 13 dpf. From 13 dpf onwards brine shrimps paramecia and dry food	developmental stage:33 dpf\|strain:csf1raj4e1/j4e1;csf1rbre01/re01 tgmpeg GFP\|cell type:mpeg GFP+ cells	GSM4512713	GSM4512713: 33dpf csf1rdm 1; Danio rerio; RNA Seq	GSM4512713		1	Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM4512713	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP259989		33dpf_csf1rdm_1_R1.fastq.gz 33dpf_csf1rdm_1_R2.fastq.gz	fastq fastq	3251371598.0	16095899.0	GSM4512713 r1	0:101 1:101	A:938620484;C:677648040;G:693531098;T:941563341;N:8635	101	101	938620484	677648040	693531098	941563341	8635	SRX8244824	SRS6592461	SRA1072140	GEO	Erasmus MC	2	0.90369	0.88203	0.18089	0.17771	0.78234	0.78847	0.47498	0.47606	101	101	B	B	biological fallback assumption	illumina	hiseq_era	full_length	cdna_unspecified	trueseq	sc	single_cell_plate	smartseq	Netherlands	2020-05-04	Juvenile	Juvenile	Whole Organism	All anatomical structures
59143	59143	SRR11684020	SRX8244823	SRS6592460	SRP259989	PRJNA630163	Zebrafish juvenile mpeg+ macrophages	GSE149787	Transcriptome Analysis	We used zebrafish lacking functional csf1r or il34 to unravel how and when csf1r is necessary for macrophages. Transcriptomic analysis of mpeg+ macrophages isolated from juvenile fish revealed that csf1r deficient macrophages show a gross macrophage transcriptome but reduced expression of engulfment related genes and increased expression of genes typical for metaphocytes. Overall design: Bulk RNA sequencing of juvenile macrophages obtained from wildtype control il34 / and csf1rDM zebrafish triplicates	parent bioproject:PRJNA630158	pubmed:32367800		33dpf control 3	GSM4512712	tissue:whole fish\|developmental stage:33 dpf\|strain:wildtype tgmpeg GFP\|cell type:mpeg GFP+ cells	33dpf control 3	Sequencing and base calling was performed on the Illumina hiseq 2500. Resulting base calls were de multiplexed using the Illumina Casava 1.8 software. Subsequently SMARTer adapters were removed using cutadapt followed by the alignment step using STAR version 2.5.4b. Reference genome build GRCz10 danRer10 was used. Abundance estimation was performed using cufflinks v2.2.1 with both the frag bias correct and multi read correct flags set. The raw read counts were measured using HTSeq count version 0.11.0. using the union setting. The ensemble gene database was used. The aligned and filtered data was quantified with the Bioconductor package Genomic Ranges Lawrence et al. Plos Computational Biology 2013. Differential gene expression analysis was performed with Bioconductor package EdgeR Robinson et al. 2010. Genome build: GRCz10 Supplementary files format and content: CPM values [.csv] semicolon delimited files.	whole fish		Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols	HEPES buffered E3 medium 28 degrees celsius 14/10h light/dark cycle until 5 dpf from 5 dpf onwards in regular aquarium. Fed dry food + paramecia from 5 dpf 13 dpf. From 13 dpf onwards brine shrimps paramecia and dry food	developmental stage:33 dpf\|strain:wildtype tgmpeg GFP\|cell type:mpeg GFP+ cells	GSM4512712	GSM4512712: 33dpf control 3; Danio rerio; RNA Seq	GSM4512712		1	Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM4512712	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP259989		33dpf_control_3_R1.fastq.gz 33dpf_control_3_R2.fastq.gz	fastq fastq	2712847880.0	13429940.0	GSM4512712 r1	0:101 1:101	A:772539767;C:566195541;G:587191020;T:786914116;N:7436	101	101	772539767	566195541	587191020	786914116	7436	SRX8244823	SRS6592460	SRA1072140	GEO	Erasmus MC	2	0.93009	0.89728	0.17089	0.17058	0.74548	0.75722	0.48148	0.47178	101	101	B	B	biological fallback assumption	illumina	hiseq_era	full_length	cdna_unspecified	trueseq	sc	single_cell_plate	smartseq	Netherlands	2020-05-04	Juvenile	Juvenile	Whole Organism	All anatomical structures
59144	59144	SRR11684019	SRX8244822	SRS6592459	SRP259989	PRJNA630163	Zebrafish juvenile mpeg+ macrophages	GSE149787	Transcriptome Analysis	We used zebrafish lacking functional csf1r or il34 to unravel how and when csf1r is necessary for macrophages. Transcriptomic analysis of mpeg+ macrophages isolated from juvenile fish revealed that csf1r deficient macrophages show a gross macrophage transcriptome but reduced expression of engulfment related genes and increased expression of genes typical for metaphocytes. Overall design: Bulk RNA sequencing of juvenile macrophages obtained from wildtype control il34 / and csf1rDM zebrafish triplicates	parent bioproject:PRJNA630158	pubmed:32367800		33dpf control 2	GSM4512711	tissue:whole fish\|developmental stage:33 dpf\|strain:wildtype tgmpeg GFP\|cell type:mpeg GFP+ cells	33dpf control 2	Sequencing and base calling was performed on the Illumina hiseq 2500. Resulting base calls were de multiplexed using the Illumina Casava 1.8 software. Subsequently SMARTer adapters were removed using cutadapt followed by the alignment step using STAR version 2.5.4b. Reference genome build GRCz10 danRer10 was used. Abundance estimation was performed using cufflinks v2.2.1 with both the frag bias correct and multi read correct flags set. The raw read counts were measured using HTSeq count version 0.11.0. using the union setting. The ensemble gene database was used. The aligned and filtered data was quantified with the Bioconductor package Genomic Ranges Lawrence et al. Plos Computational Biology 2013. Differential gene expression analysis was performed with Bioconductor package EdgeR Robinson et al. 2010. Genome build: GRCz10 Supplementary files format and content: CPM values [.csv] semicolon delimited files.	whole fish		Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols	HEPES buffered E3 medium 28 degrees celsius 14/10h light/dark cycle until 5 dpf from 5 dpf onwards in regular aquarium. Fed dry food + paramecia from 5 dpf 13 dpf. From 13 dpf onwards brine shrimps paramecia and dry food	developmental stage:33 dpf\|strain:wildtype tgmpeg GFP\|cell type:mpeg GFP+ cells	GSM4512711	GSM4512711: 33dpf control 2; Danio rerio; RNA Seq	GSM4512711		1	Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM4512711	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP259989		33dpf_control_2_R2.fastq.gz 33dpf_control_2_R1.fastq.gz	fastq fastq	1740822264.0	8617932.0	GSM4512711 r1	0:101 1:101	A:496913292;C:363966331;G:377438086;T:502499900;N:4655	101	101	496913292	363966331	377438086	502499900	4655	SRX8244822	SRS6592459	SRA1072140	GEO	Erasmus MC	2	0.92011	0.89184	0.16484	0.16269	0.7541	0.7655	0.47531	0.46847	101	101	B	B	biological fallback assumption	illumina	hiseq_era	full_length	cdna_unspecified	trueseq	sc	single_cell_plate	smartseq	Netherlands	2020-05-04	Juvenile	Juvenile	Whole Organism	All anatomical structures
59145	59145	SRR11684018	SRX8244821	SRS6592458	SRP259989	PRJNA630163	Zebrafish juvenile mpeg+ macrophages	GSE149787	Transcriptome Analysis	We used zebrafish lacking functional csf1r or il34 to unravel how and when csf1r is necessary for macrophages. Transcriptomic analysis of mpeg+ macrophages isolated from juvenile fish revealed that csf1r deficient macrophages show a gross macrophage transcriptome but reduced expression of engulfment related genes and increased expression of genes typical for metaphocytes. Overall design: Bulk RNA sequencing of juvenile macrophages obtained from wildtype control il34 / and csf1rDM zebrafish triplicates	parent bioproject:PRJNA630158	pubmed:32367800		33dpf control 1	GSM4512710	tissue:whole fish\|developmental stage:33 dpf\|strain:wildtype tgmpeg GFP\|cell type:mpeg GFP+ cells	33dpf control 1	Sequencing and base calling was performed on the Illumina hiseq 2500. Resulting base calls were de multiplexed using the Illumina Casava 1.8 software. Subsequently SMARTer adapters were removed using cutadapt followed by the alignment step using STAR version 2.5.4b. Reference genome build GRCz10 danRer10 was used. Abundance estimation was performed using cufflinks v2.2.1 with both the frag bias correct and multi read correct flags set. The raw read counts were measured using HTSeq count version 0.11.0. using the union setting. The ensemble gene database was used. The aligned and filtered data was quantified with the Bioconductor package Genomic Ranges Lawrence et al. Plos Computational Biology 2013. Differential gene expression analysis was performed with Bioconductor package EdgeR Robinson et al. 2010. Genome build: GRCz10 Supplementary files format and content: CPM values [.csv] semicolon delimited files.	whole fish		Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols	HEPES buffered E3 medium 28 degrees celsius 14/10h light/dark cycle until 5 dpf from 5 dpf onwards in regular aquarium. Fed dry food + paramecia from 5 dpf 13 dpf. From 13 dpf onwards brine shrimps paramecia and dry food	developmental stage:33 dpf\|strain:wildtype tgmpeg GFP\|cell type:mpeg GFP+ cells	GSM4512710	GSM4512710: 33dpf control 1; Danio rerio; RNA Seq	GSM4512710		1	Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM4512710	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP259989		33dpf_control_1_R2.fastq.gz 33dpf_control_1_R1.fastq.gz	fastq fastq	3546165954.0	17555277.0	GSM4512710 r1	0:101 1:101	A:1004040828;C:754797131;G:787411451;T:999907224;N:9320	101	101	1004040828	754797131	787411451	999907224	9320	SRX8244821	SRS6592458	SRA1072140	GEO	Erasmus MC	2	0.93722	0.91292	0.14991	0.14981	0.75191	0.76171	0.47117	0.46955	101	101	B	B	biological fallback assumption	illumina	hiseq_era	full_length	cdna_unspecified	trueseq	sc	single_cell_plate	smartseq	Netherlands	2020-05-04	Juvenile	Juvenile	Whole Organism	All anatomical structures
68196	68196	SRR17658725	SRX13826756	SRS11705914	SRP355720	PRJNA798511	Comparative analysis of transcriptome for heat induced zebrafish during sex differentiation	PRJNA798511	Other	heat treated zebrafish					T60d ZHT	strain:AB\|isolate:35\|breed:zebrafish\|cultivar:TEST\|ecotype:CHINA\|age:60dpf\|sex:not collected\|tissue:whole organism\|BioSampleModel:Model organism or animal									RNAq of zebrafish	T60D	T60D	heat treated zebrafish			RNA-Seq	TRANSCRIPTOMIC	PCR	PAIRED	BGISEQ	BGISEQ-500	SRP355720	loader:fastq load.py			20334742200.0	67782474.0	T60D.7z	0:150 1:150	A:5482201207;C:4682998764;G:4635775004;T:5533378494;N:388731	150	150	5482201207	4682998764	4635775004	5533378494	388731	SRX13826756	SRS11705914	SRA1358616	Hunan University of Science and Technology\|School of Life and Health Sciences	Hunan University of Science and Technology	2	0.94378	0.94515	0.04989	0.04997	0.69848	0.69978	0.50317	0.5041	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2022-12-09	Juvenile	Juvenile	Whole Organism	All anatomical structures
68197	68197	SRR17658726	SRX13826755	SRS11705913	SRP355720	PRJNA798511	Comparative analysis of transcriptome for heat induced zebrafish during sex differentiation	PRJNA798511	Other	heat treated zebrafish					T45d ZHT	strain:AB\|isolate:35\|breed:zebrafish\|cultivar:TEST\|ecotype:CHINA\|age:45dpf\|sex:not collected\|tissue:whole organism\|BioSampleModel:Model organism or animal									RNAq of zebrafish	T45D	T45D	heat treated zebrafish			RNA-Seq	TRANSCRIPTOMIC	PCR	PAIRED	BGISEQ	BGISEQ-500	SRP355720	loader:fastq load.py			20230560300.0	67435201.0	T45D.7z	0:150 1:150	A:5444816209;C:4663007584;G:4631943733;T:5490408754;N:384020	150	150	5444816209	4663007584	4631943733	5490408754	384020	SRX13826755	SRS11705913	SRA1358616	Hunan University of Science and Technology\|School of Life and Health Sciences	Hunan University of Science and Technology	2	0.88041	0.881	0.04485	0.04492	0.72163	0.72236	0.52232	0.52307	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2022-12-09	Juvenile	Juvenile	Whole Organism	All anatomical structures
68198	68198	SRR17658727	SRX13826754	SRS11705912	SRP355720	PRJNA798511	Comparative analysis of transcriptome for heat induced zebrafish during sex differentiation	PRJNA798511	Other	heat treated zebrafish					T35d ZHT	strain:AB\|isolate:35\|breed:zebrafish\|cultivar:TEST\|ecotype:CHINA\|age:35dpf\|sex:not collected\|tissue:whole organism\|BioSampleModel:Model organism or animal									RNAq of zebrafish	T35D	T35D	heat treated zebrafish			RNA-Seq	TRANSCRIPTOMIC	PCR	PAIRED	BGISEQ	BGISEQ-500	SRP355720	loader:fastq load.py			20630503200.0	68768344.0	T35D.7z	0:150 1:150	A:5660657832;C:4654929757;G:4598083304;T:5716350276;N:482031	150	150	5660657832	4654929757	4598083304	5716350276	482031	SRX13826754	SRS11705912	SRA1358616	Hunan University of Science and Technology\|School of Life and Health Sciences	Hunan University of Science and Technology	2	0.9134	0.91476	0.06961	0.06972	0.69035	0.69215	0.52155	0.5154	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2022-12-09	Juvenile	Juvenile	Whole Organism	All anatomical structures
68199	68199	SRR17658728	SRX13826753	SRS11705911	SRP355720	PRJNA798511	Comparative analysis of transcriptome for heat induced zebrafish during sex differentiation	PRJNA798511	Other	heat treated zebrafish					C60d ZHT	strain:AB\|isolate:28\|breed:zebrafish\|cultivar:WT\|ecotype:CHINA\|age:60dpf\|sex:not collected\|tissue:whole organism\|BioSampleModel:Model organism or animal									RNAq of zebrafish	C60D	C60D	WT zebrafish			RNA-Seq	TRANSCRIPTOMIC	PCR	PAIRED	BGISEQ	BGISEQ-500	SRP355720	loader:fastq load.py			10921407600.0	44923977.0	C60D.7z		A:2992232295;C:2470688717;G:2440861228;T:3017432565;N:192795			2992232295	2470688717	2440861228	3017432565	192795	SRX13826753	SRS11705911	SRA1358616	Hunan University of Science and Technology\|School of Life and Health Sciences	Hunan University of Science and Technology	2	0.93932	0.94095	0.06489	0.06559	0.77871	0.77759	0.56384	0.56447	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2022-12-09	Juvenile	Juvenile	Whole Organism	All anatomical structures
68200	68200	SRR17658729	SRX13826752	SRS11705910	SRP355720	PRJNA798511	Comparative analysis of transcriptome for heat induced zebrafish during sex differentiation	PRJNA798511	Other	heat treated zebrafish					C45d ZHT	strain:AB\|isolate:28\|breed:zebrafish\|cultivar:WT\|ecotype:CHINA\|age:45dpf\|sex:not collected\|tissue:whole organism\|BioSampleModel:Model organism or animal									RNAq of zebrafish	C45D	C45D	WT zebrafish			RNA-Seq	TRANSCRIPTOMIC	PCR	PAIRED	BGISEQ	BGISEQ-500	SRP355720	loader:fastq load.py			20413229700.0	68044099.0	C45D.7z	0:150 1:150	A:5619395833;C:4581611789;G:4543973618;T:5667873613;N:374847	150	150	5619395833	4581611789	4543973618	5667873613	374847	SRX13826752	SRS11705910	SRA1358616	Hunan University of Science and Technology\|School of Life and Health Sciences	Hunan University of Science and Technology	2	0.86848	0.87064	0.0719	0.07252	0.69879	0.69834	0.52279	0.51074	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2022-12-09	Juvenile	Juvenile	Whole Organism	All anatomical structures
68201	68201	SRR17658730	SRX13826751	SRS11705909	SRP355720	PRJNA798511	Comparative analysis of transcriptome for heat induced zebrafish during sex differentiation	PRJNA798511	Other	heat treated zebrafish					C35d ZHT	strain:AB\|isolate:28\|breed:zebrafish\|cultivar:WT\|ecotype:CHINA\|age:35dpf\|sex:not collected\|tissue:whole organism\|BioSampleModel:Model organism or animal									RNAq of zebrafish	C35D	C35D	WT zebrafish			RNA-Seq	TRANSCRIPTOMIC	PCR	PAIRED	BGISEQ	BGISEQ-500	SRP355720	loader:fastq load.py			20469803700.0	68232679.0	C35D.7z	0:150 1:150	A:5556774511;C:4678377106;G:4627472920;T:5606765895;N:413268	150	150	5556774511	4678377106	4627472920	5606765895	413268	SRX13826751	SRS11705909	SRA1358616	Hunan University of Science and Technology\|School of Life and Health Sciences	Hunan University of Science and Technology	2	0.93663	0.93871	0.06853	0.06895	0.6982	0.69901	0.51209	0.51148	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2022-12-09	Juvenile	Juvenile	Whole Organism	All anatomical structures
69610	69610	SRR18959644	SRX15036823	SRS12783659	SRP372606	PRJNA832865	Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation	GSE201748	Transcriptome Analysis	The influence of environmental factors especially temperature on sex ratio is of great significance to elucidate the mechanism of sex determination. However the molecular mechanisms by which temperature affects sex determination remains unclear although a few candidate genes have been found to play a role in the process. In this study we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171 1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35 45 dpf and 60 dpf dpf respectively revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway cell cycle oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation		pubmed:35641933		T60d 3	GSM6070558	source name:Whole fish\|tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:60dpf\|treatment:heat shock	T60d 3	The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base‘N’ base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11 then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value ≤ 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value≤ 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample	Whole fish	The control group was kept at 28℃ whereas the thermal treatment group was exposed to 35℃for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment fish were returned at 28℃ until the fish reached to sexual maturity 90 dpf.	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …	The AB strain were maintained in a glass aquarium with a circulating water system at 28±0.5℃ with photoperiods of 14L 10D and the number of fish in each 5 liter tank was 50 55.	tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:60dpf\|treatment:heat shock	GSM6070558	GSM6070558: T60d 3; Danio rerio; RNA Seq	GSM6070558 r1	GSM6070558	1	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP372606		T60d_3_1.fq.gz T60d_3_2.fq.gz	fastq fastq	6668586300.0	44457242.0	GSM6070558 r1	0:150 1:150	A:1798105768;C:1533776293;G:1519933345;T:1816635529;N:135365	150	150	1798105768	1533776293	1519933345	1816635529	135365	SRX15036823	SRS12783659	SRA1411536	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	1	0.94696		0.03818		0.72754		0.44424		150		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-04-27	Juvenile	Juvenile	Whole Organism	All anatomical structures
69611	69611	SRR18959645	SRX15036822	SRS12783660	SRP372606	PRJNA832865	Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation	GSE201748	Transcriptome Analysis	The influence of environmental factors especially temperature on sex ratio is of great significance to elucidate the mechanism of sex determination. However the molecular mechanisms by which temperature affects sex determination remains unclear although a few candidate genes have been found to play a role in the process. In this study we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171 1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35 45 dpf and 60 dpf dpf respectively revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway cell cycle oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation		pubmed:35641933		T60d 2	GSM6070557	source name:Whole fish\|tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:60dpf\|treatment:heat shock	T60d 2	The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base‘N’ base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11 then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value ≤ 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value≤ 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample	Whole fish	The control group was kept at 28℃ whereas the thermal treatment group was exposed to 35℃for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment fish were returned at 28℃ until the fish reached to sexual maturity 90 dpf.	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …	The AB strain were maintained in a glass aquarium with a circulating water system at 28±0.5℃ with photoperiods of 14L 10D and the number of fish in each 5 liter tank was 50 55.	tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:60dpf\|treatment:heat shock	GSM6070557	GSM6070557: T60d 2; Danio rerio; RNA Seq	GSM6070557 r1	GSM6070557	1	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP372606		T60d_2_1.fq.gz T60d_2_2.fq.gz	fastq fastq	6790474800.0	45269832.0	GSM6070557 r1	0:150 1:150	A:1792022273;C:1601949824;G:1583360851;T:1813022005;N:119847	150	150	1792022273	1601949824	1583360851	1813022005	119847	SRX15036822	SRS12783660	SRA1411536	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	1	0.9518		0.03662		0.72892		0.50564		150		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-04-27	Juvenile	Juvenile	Whole Organism	All anatomical structures
69612	69612	SRR18959646	SRX15036821	SRS12783661	SRP372606	PRJNA832865	Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation	GSE201748	Transcriptome Analysis	The influence of environmental factors especially temperature on sex ratio is of great significance to elucidate the mechanism of sex determination. However the molecular mechanisms by which temperature affects sex determination remains unclear although a few candidate genes have been found to play a role in the process. In this study we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171 1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35 45 dpf and 60 dpf dpf respectively revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway cell cycle oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation		pubmed:35641933		T60d 1	GSM6070556	source name:Whole fish\|tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:60dpf\|treatment:heat shock	T60d 1	The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base‘N’ base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11 then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value ≤ 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value≤ 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample	Whole fish	The control group was kept at 28℃ whereas the thermal treatment group was exposed to 35℃for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment fish were returned at 28℃ until the fish reached to sexual maturity 90 dpf.	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …	The AB strain were maintained in a glass aquarium with a circulating water system at 28±0.5℃ with photoperiods of 14L 10D and the number of fish in each 5 liter tank was 50 55.	tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:60dpf\|treatment:heat shock	GSM6070556	GSM6070556: T60d 1; Danio rerio; RNA Seq	GSM6070556 r1	GSM6070556	1	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP372606		T60d_1_1.fq.gz T60d_1_2.fq.gz	fastq fastq	6875681100.0	45837874.0	GSM6070556 r1	0:150 1:150	A:1892073166;C:1547272647;G:1532480808;T:1903720960;N:133519	150	150	1892073166	1547272647	1532480808	1903720960	133519	SRX15036821	SRS12783661	SRA1411536	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	1	0.93516		0.0737		0.70394		0.55661		150		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-04-27	Juvenile	Juvenile	Whole Organism	All anatomical structures
69613	69613	SRR18959647	SRX15036820	SRS12783658	SRP372606	PRJNA832865	Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation	GSE201748	Transcriptome Analysis	The influence of environmental factors especially temperature on sex ratio is of great significance to elucidate the mechanism of sex determination. However the molecular mechanisms by which temperature affects sex determination remains unclear although a few candidate genes have been found to play a role in the process. In this study we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171 1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35 45 dpf and 60 dpf dpf respectively revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway cell cycle oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation		pubmed:35641933		T45d 3	GSM6070555	source name:Whole fish\|tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:45dpf\|treatment:heat shock	T45d 3	The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base‘N’ base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11 then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value ≤ 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value≤ 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample	Whole fish	The control group was kept at 28℃ whereas the thermal treatment group was exposed to 35℃for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment fish were returned at 28℃ until the fish reached to sexual maturity 90 dpf.	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …	The AB strain were maintained in a glass aquarium with a circulating water system at 28±0.5℃ with photoperiods of 14L 10D and the number of fish in each 5 liter tank was 50 55.	tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:45dpf\|treatment:heat shock	GSM6070555	GSM6070555: T45d 3; Danio rerio; RNA Seq	GSM6070555 r1	GSM6070555	1	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP372606		T45d_3_1.fq.gz T45d_3_2.fq.gz	fastq fastq	6677602800.0	44517352.0	GSM6070555 r1	0:150 1:150	A:1776927020;C:1564627916;G:1551750199;T:1784113081;N:184584	150	150	1776927020	1564627916	1551750199	1784113081	184584	SRX15036820	SRS12783658	SRA1411536	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	1	0.95333		0.04626		0.79788		0.53869		150		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-04-27	Juvenile	Juvenile	Whole Organism	All anatomical structures
69614	69614	SRR18959648	SRX15036819	SRS12783657	SRP372606	PRJNA832865	Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation	GSE201748	Transcriptome Analysis	The influence of environmental factors especially temperature on sex ratio is of great significance to elucidate the mechanism of sex determination. However the molecular mechanisms by which temperature affects sex determination remains unclear although a few candidate genes have been found to play a role in the process. In this study we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171 1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35 45 dpf and 60 dpf dpf respectively revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway cell cycle oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation		pubmed:35641933		T45d 2	GSM6070554	source name:Whole fish\|tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:45dpf\|treatment:heat shock	T45d 2	The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base‘N’ base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11 then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value ≤ 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value≤ 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample	Whole fish	The control group was kept at 28℃ whereas the thermal treatment group was exposed to 35℃for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment fish were returned at 28℃ until the fish reached to sexual maturity 90 dpf.	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …	The AB strain were maintained in a glass aquarium with a circulating water system at 28±0.5℃ with photoperiods of 14L 10D and the number of fish in each 5 liter tank was 50 55.	tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:45dpf\|treatment:heat shock	GSM6070554	GSM6070554: T45d 2; Danio rerio; RNA Seq	GSM6070554 r1	GSM6070554	1	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP372606		T45d_2_1.fq.gz T45d_2_2.fq.gz	fastq fastq	6866885100.0	45779234.0	GSM6070554 r1	0:150 1:150	A:1855996561;C:1572989256;G:1559095064;T:1878636946;N:167273	150	150	1855996561	1572989256	1559095064	1878636946	167273	SRX15036819	SRS12783657	SRA1411536	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	1	0.85691		0.0428		0.70059		0.48517		150		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-04-27	Juvenile	Juvenile	Whole Organism	All anatomical structures
69615	69615	SRR18959649	SRX15036818	SRS12783655	SRP372606	PRJNA832865	Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation	GSE201748	Transcriptome Analysis	The influence of environmental factors especially temperature on sex ratio is of great significance to elucidate the mechanism of sex determination. However the molecular mechanisms by which temperature affects sex determination remains unclear although a few candidate genes have been found to play a role in the process. In this study we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171 1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35 45 dpf and 60 dpf dpf respectively revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway cell cycle oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation		pubmed:35641933		T45d 1	GSM6070553	source name:Whole fish\|tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:45dpf\|treatment:heat shock	T45d 1	The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base‘N’ base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11 then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value ≤ 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value≤ 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample	Whole fish	The control group was kept at 28℃ whereas the thermal treatment group was exposed to 35℃for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment fish were returned at 28℃ until the fish reached to sexual maturity 90 dpf.	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …	The AB strain were maintained in a glass aquarium with a circulating water system at 28±0.5℃ with photoperiods of 14L 10D and the number of fish in each 5 liter tank was 50 55.	tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:45dpf\|treatment:heat shock	GSM6070553	GSM6070553: T45d 1; Danio rerio; RNA Seq	GSM6070553 r1	GSM6070553	1	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP372606		T45d_1_1.fq.gz T45d_1_2.fq.gz	fastq fastq	6686072400.0	44573816.0	GSM6070553 r1	0:150 1:150	A:1811892628;C:1525390412;G:1521098470;T:1827658727;N:32163	150	150	1811892628	1525390412	1521098470	1827658727	32163	SRX15036818	SRS12783655	SRA1411536	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	1	0.83063		0.04482		0.75227		0.53268		150		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-04-27	Juvenile	Juvenile	Whole Organism	All anatomical structures
69616	69616	SRR18959650	SRX15036817	SRS12783656	SRP372606	PRJNA832865	Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation	GSE201748	Transcriptome Analysis	The influence of environmental factors especially temperature on sex ratio is of great significance to elucidate the mechanism of sex determination. However the molecular mechanisms by which temperature affects sex determination remains unclear although a few candidate genes have been found to play a role in the process. In this study we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171 1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35 45 dpf and 60 dpf dpf respectively revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway cell cycle oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation		pubmed:35641933		T35d 3	GSM6070552	source name:Whole fish\|tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:35dpf\|treatment:heat shock	T35d 3	The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base‘N’ base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11 then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value ≤ 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value≤ 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample	Whole fish	The control group was kept at 28℃ whereas the thermal treatment group was exposed to 35℃for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment fish were returned at 28℃ until the fish reached to sexual maturity 90 dpf.	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …	The AB strain were maintained in a glass aquarium with a circulating water system at 28±0.5℃ with photoperiods of 14L 10D and the number of fish in each 5 liter tank was 50 55.	tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:35dpf\|treatment:heat shock	GSM6070552	GSM6070552: T35d 3; Danio rerio; RNA Seq	GSM6070552 r1	GSM6070552	1	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP372606		T35d_3_1.fq.gz T35d_3_2.fq.gz	fastq fastq	6886247700.0	45908318.0	GSM6070552 r1	0:150 1:150	A:1822190170;C:1616493163;G:1597658988;T:1849741504;N:163875	150	150	1822190170	1616493163	1597658988	1849741504	163875	SRX15036817	SRS12783656	SRA1411536	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	1	0.94299		0.03719		0.71165		0.49413		150		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-04-27	Juvenile	Juvenile	Whole Organism	All anatomical structures
69617	69617	SRR18959651	SRX15036816	SRS12783654	SRP372606	PRJNA832865	Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation	GSE201748	Transcriptome Analysis	The influence of environmental factors especially temperature on sex ratio is of great significance to elucidate the mechanism of sex determination. However the molecular mechanisms by which temperature affects sex determination remains unclear although a few candidate genes have been found to play a role in the process. In this study we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171 1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35 45 dpf and 60 dpf dpf respectively revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway cell cycle oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation		pubmed:35641933		T35d 2	GSM6070551	source name:Whole fish\|tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:35dpf\|treatment:heat shock	T35d 2	The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base‘N’ base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11 then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value ≤ 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value≤ 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample	Whole fish	The control group was kept at 28℃ whereas the thermal treatment group was exposed to 35℃for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment fish were returned at 28℃ until the fish reached to sexual maturity 90 dpf.	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …	The AB strain were maintained in a glass aquarium with a circulating water system at 28±0.5℃ with photoperiods of 14L 10D and the number of fish in each 5 liter tank was 50 55.	tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:35dpf\|treatment:heat shock	GSM6070551	GSM6070551: T35d 2; Danio rerio; RNA Seq	GSM6070551 r1	GSM6070551	1	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP372606		T35d_2_1.fq.gz T35d_2_2.fq.gz	fastq fastq	6851241900.0	45674946.0	GSM6070551 r1	0:150 1:150	A:1925245234;C:1503184374;G:1483632128;T:1939009289;N:170875	150	150	1925245234	1503184374	1483632128	1939009289	170875	SRX15036816	SRS12783654	SRA1411536	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	1	0.86703		0.08277		0.70619		0.47871		150		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-04-27	Juvenile	Juvenile	Whole Organism	All anatomical structures
69618	69618	SRR18959652	SRX15036815	SRS12783653	SRP372606	PRJNA832865	Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation	GSE201748	Transcriptome Analysis	The influence of environmental factors especially temperature on sex ratio is of great significance to elucidate the mechanism of sex determination. However the molecular mechanisms by which temperature affects sex determination remains unclear although a few candidate genes have been found to play a role in the process. In this study we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171 1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35 45 dpf and 60 dpf dpf respectively revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway cell cycle oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation		pubmed:35641933		T35d 1	GSM6070550	source name:Whole fish\|tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:35dpf\|treatment:heat shock	T35d 1	The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base‘N’ base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11 then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value ≤ 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value≤ 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample	Whole fish	The control group was kept at 28℃ whereas the thermal treatment group was exposed to 35℃for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment fish were returned at 28℃ until the fish reached to sexual maturity 90 dpf.	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …	The AB strain were maintained in a glass aquarium with a circulating water system at 28±0.5℃ with photoperiods of 14L 10D and the number of fish in each 5 liter tank was 50 55.	tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:35dpf\|treatment:heat shock	GSM6070550	GSM6070550: T35d 1; Danio rerio; RNA Seq	GSM6070550 r1	GSM6070550	1	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP372606		T35d_1_1.fq.gz T35d_1_2.fq.gz	fastq fastq	6893013600.0	45953424.0	GSM6070550 r1	0:150 1:150	A:1913222428;C:1535252220;G:1516792188;T:1927599483;N:147281	150	150	1913222428	1535252220	1516792188	1927599483	147281	SRX15036815	SRS12783653	SRA1411536	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	1	0.93126		0.08861		0.70711		0.53182		150		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-04-27	Juvenile	Juvenile	Whole Organism	All anatomical structures
69619	69619	SRR18959653	SRX15036814	SRS12783652	SRP372606	PRJNA832865	Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation	GSE201748	Transcriptome Analysis	The influence of environmental factors especially temperature on sex ratio is of great significance to elucidate the mechanism of sex determination. However the molecular mechanisms by which temperature affects sex determination remains unclear although a few candidate genes have been found to play a role in the process. In this study we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171 1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35 45 dpf and 60 dpf dpf respectively revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway cell cycle oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation		pubmed:35641933		C60d 3	GSM6070549	source name:Whole fish\|tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:60dpf\|treatment:control	C60d 3	The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base‘N’ base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11 then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value ≤ 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value≤ 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample	Whole fish	The control group was kept at 28℃ whereas the thermal treatment group was exposed to 35℃for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment fish were returned at 28℃ until the fish reached to sexual maturity 90 dpf.	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …	The AB strain were maintained in a glass aquarium with a circulating water system at 28±0.5℃ with photoperiods of 14L 10D and the number of fish in each 5 liter tank was 50 55.	tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:60dpf\|treatment:control	GSM6070549	GSM6070549: C60d 3; Danio rerio; RNA Seq	GSM6070549 r1	GSM6070549	1	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP372606		C60d_3_1.fq.gz C60d_3_2.fq.gz	fastq fastq	6732458700.0	44883058.0	GSM6070549 r1	0:150 1:150	A:1840891044;C:1527037740;G:1515664962;T:1848770869;N:94085	150	150	1840891044	1527037740	1515664962	1848770869	94085	SRX15036814	SRS12783652	SRA1411536	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	1	0.94478		0.05996		0.73661		0.56885		150		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-04-27	Juvenile	Juvenile	Whole Organism	All anatomical structures
69620	69620	SRR18959654	SRX15036813	SRS12783651	SRP372606	PRJNA832865	Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation	GSE201748	Transcriptome Analysis	The influence of environmental factors especially temperature on sex ratio is of great significance to elucidate the mechanism of sex determination. However the molecular mechanisms by which temperature affects sex determination remains unclear although a few candidate genes have been found to play a role in the process. In this study we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171 1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35 45 dpf and 60 dpf dpf respectively revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway cell cycle oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation		pubmed:35641933		C60d 2	GSM6070548	source name:Whole fish\|tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:60dpf\|treatment:control	C60d 2	The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base‘N’ base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11 then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value ≤ 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value≤ 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample	Whole fish	The control group was kept at 28℃ whereas the thermal treatment group was exposed to 35℃for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment fish were returned at 28℃ until the fish reached to sexual maturity 90 dpf.	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …	The AB strain were maintained in a glass aquarium with a circulating water system at 28±0.5℃ with photoperiods of 14L 10D and the number of fish in each 5 liter tank was 50 55.	tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:60dpf\|treatment:control	GSM6070548	GSM6070548: C60d 2; Danio rerio; RNA Seq	GSM6070548 r1	GSM6070548	1	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP372606		C60d_2_1.fq.gz C60d_2_2.fq.gz	fastq fastq	6920478600.0	46136524.0	GSM6070548 r1	0:150 1:150	A:1860288879;C:1602876302;G:1589399217;T:1867783032;N:131170	150	150	1860288879	1602876302	1589399217	1867783032	131170	SRX15036813	SRS12783651	SRA1411536	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	1	0.95235		0.05236		0.74836		0.55427		150		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-04-27	Juvenile	Juvenile	Whole Organism	All anatomical structures
69621	69621	SRR18959655	SRX15036812	SRS12783650	SRP372606	PRJNA832865	Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation	GSE201748	Transcriptome Analysis	The influence of environmental factors especially temperature on sex ratio is of great significance to elucidate the mechanism of sex determination. However the molecular mechanisms by which temperature affects sex determination remains unclear although a few candidate genes have been found to play a role in the process. In this study we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171 1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35 45 dpf and 60 dpf dpf respectively revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway cell cycle oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation		pubmed:35641933		C60d 1	GSM6070547	source name:Whole fish\|tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:60dpf\|treatment:control	C60d 1	The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base‘N’ base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11 then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value ≤ 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value≤ 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample	Whole fish	The control group was kept at 28℃ whereas the thermal treatment group was exposed to 35℃for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment fish were returned at 28℃ until the fish reached to sexual maturity 90 dpf.	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …	The AB strain were maintained in a glass aquarium with a circulating water system at 28±0.5℃ with photoperiods of 14L 10D and the number of fish in each 5 liter tank was 50 55.	tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:60dpf\|treatment:control	GSM6070547	GSM6070547: C60d 1; Danio rerio; RNA Seq	GSM6070547 r1	GSM6070547	1	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP372606		C60d_1_1.fq.gz C60d_1_2.fq.gz	fastq fastq	6744639300.0	44964262.0	GSM6070547 r1	0:150 1:150	A:1855599360;C:1516548729;G:1501772747;T:1870587619;N:130845	150	150	1855599360	1516548729	1501772747	1870587619	130845	SRX15036812	SRS12783650	SRA1411536	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	1	0.93949		0.06857		0.73805		0.54443		150		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-04-27	Juvenile	Juvenile	Whole Organism	All anatomical structures
69622	69622	SRR18959656	SRX15036811	SRS12783649	SRP372606	PRJNA832865	Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation	GSE201748	Transcriptome Analysis	The influence of environmental factors especially temperature on sex ratio is of great significance to elucidate the mechanism of sex determination. However the molecular mechanisms by which temperature affects sex determination remains unclear although a few candidate genes have been found to play a role in the process. In this study we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171 1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35 45 dpf and 60 dpf dpf respectively revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway cell cycle oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation		pubmed:35641933		C45d 3	GSM6070546	source name:Whole fish\|tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:45dpf\|treatment:control	C45d 3	The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base‘N’ base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11 then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value ≤ 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value≤ 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample	Whole fish	The control group was kept at 28℃ whereas the thermal treatment group was exposed to 35℃for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment fish were returned at 28℃ until the fish reached to sexual maturity 90 dpf.	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …	The AB strain were maintained in a glass aquarium with a circulating water system at 28±0.5℃ with photoperiods of 14L 10D and the number of fish in each 5 liter tank was 50 55.	tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:45dpf\|treatment:control	GSM6070546	GSM6070546: C45d 3; Danio rerio; RNA Seq	GSM6070546 r1	GSM6070546	1	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP372606		C45d_3_1.fq.gz C45d_3_2.fq.gz	fastq fastq	6743568300.0	44957122.0	GSM6070546 r1	0:150 1:150	A:1852733188;C:1516814321;G:1505754587;T:1868137549;N:128655	150	150	1852733188	1516814321	1505754587	1868137549	128655	SRX15036811	SRS12783649	SRA1411536	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	1	0.87046		0.07264		0.69996		0.51275		150		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-04-27	Juvenile	Juvenile	Whole Organism	All anatomical structures
69623	69623	SRR18959657	SRX15036810	SRS12783648	SRP372606	PRJNA832865	Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation	GSE201748	Transcriptome Analysis	The influence of environmental factors especially temperature on sex ratio is of great significance to elucidate the mechanism of sex determination. However the molecular mechanisms by which temperature affects sex determination remains unclear although a few candidate genes have been found to play a role in the process. In this study we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171 1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35 45 dpf and 60 dpf dpf respectively revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway cell cycle oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation		pubmed:35641933		C45d 2	GSM6070545	source name:Whole fish\|tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:45dpf\|treatment:control	C45d 2	The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base‘N’ base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11 then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value ≤ 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value≤ 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample	Whole fish	The control group was kept at 28℃ whereas the thermal treatment group was exposed to 35℃for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment fish were returned at 28℃ until the fish reached to sexual maturity 90 dpf.	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …	The AB strain were maintained in a glass aquarium with a circulating water system at 28±0.5℃ with photoperiods of 14L 10D and the number of fish in each 5 liter tank was 50 55.	tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:45dpf\|treatment:control	GSM6070545	GSM6070545: C45d 2; Danio rerio; RNA Seq	GSM6070545 r1	GSM6070545	1	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP372606		C45d_2_1.fq.gz C45d_2_2.fq.gz	fastq fastq	6742016100.0	44946774.0	GSM6070545 r1	0:150 1:150	A:1859613225;C:1508260261;G:1496299109;T:1877718155;N:125350	150	150	1859613225	1508260261	1496299109	1877718155	125350	SRX15036810	SRS12783648	SRA1411536	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	1	0.84381		0.07253		0.68769		0.51224		150		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-04-27	Juvenile	Juvenile	Whole Organism	All anatomical structures
69624	69624	SRR18959658	SRX15036809	SRS12783647	SRP372606	PRJNA832865	Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation	GSE201748	Transcriptome Analysis	The influence of environmental factors especially temperature on sex ratio is of great significance to elucidate the mechanism of sex determination. However the molecular mechanisms by which temperature affects sex determination remains unclear although a few candidate genes have been found to play a role in the process. In this study we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171 1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35 45 dpf and 60 dpf dpf respectively revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway cell cycle oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation		pubmed:35641933		C45d 1	GSM6070544	source name:Whole fish\|tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:45dpf\|treatment:control	C45d 1	The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base‘N’ base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11 then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value ≤ 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value≤ 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample	Whole fish	The control group was kept at 28℃ whereas the thermal treatment group was exposed to 35℃for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment fish were returned at 28℃ until the fish reached to sexual maturity 90 dpf.	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …	The AB strain were maintained in a glass aquarium with a circulating water system at 28±0.5℃ with photoperiods of 14L 10D and the number of fish in each 5 liter tank was 50 55.	tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:45dpf\|treatment:control	GSM6070544	GSM6070544: C45d 1; Danio rerio; RNA Seq	GSM6070544 r1	GSM6070544	1	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP372606		C45d_1_1.fq.gz C45d_1_2.fq.gz	fastq fastq	6927645300.0	46184302.0	GSM6070544 r1	0:150 1:150	A:1907049420;C:1556537207;G:1541919922;T:1922017909;N:120842	150	150	1907049420	1556537207	1541919922	1922017909	120842	SRX15036809	SRS12783647	SRA1411536	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	1	0.89529		0.07244		0.71703		0.53737		150		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-04-27	Juvenile	Juvenile	Whole Organism	All anatomical structures
69625	69625	SRR18959659	SRX15036808	SRS12783646	SRP372606	PRJNA832865	Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation	GSE201748	Transcriptome Analysis	The influence of environmental factors especially temperature on sex ratio is of great significance to elucidate the mechanism of sex determination. However the molecular mechanisms by which temperature affects sex determination remains unclear although a few candidate genes have been found to play a role in the process. In this study we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171 1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35 45 dpf and 60 dpf dpf respectively revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway cell cycle oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation		pubmed:35641933		C35d 3	GSM6070543	source name:Whole fish\|tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:35dpf\|treatment:control	C35d 3	The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base‘N’ base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11 then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value ≤ 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value≤ 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample	Whole fish	The control group was kept at 28℃ whereas the thermal treatment group was exposed to 35℃for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment fish were returned at 28℃ until the fish reached to sexual maturity 90 dpf.	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …	The AB strain were maintained in a glass aquarium with a circulating water system at 28±0.5℃ with photoperiods of 14L 10D and the number of fish in each 5 liter tank was 50 55.	tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:35dpf\|treatment:control	GSM6070543	GSM6070543: C35d 3; Danio rerio; RNA Seq	GSM6070543 r1	GSM6070543	1	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP372606		C35d_3_1.fq.gz C35d_3_2.fq.gz	fastq fastq	6874832400.0	45832216.0	GSM6070543 r1	0:150 1:150	A:1849406781;C:1586828671;G:1570455371;T:1867999362;N:142215	150	150	1849406781	1586828671	1570455371	1867999362	142215	SRX15036808	SRS12783646	SRA1411536	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	1	0.94372		0.06412		0.71043		0.5035		150		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-04-27	Juvenile	Juvenile	Whole Organism	All anatomical structures
69626	69626	SRR18959660	SRX15036807	SRS12783645	SRP372606	PRJNA832865	Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation	GSE201748	Transcriptome Analysis	The influence of environmental factors especially temperature on sex ratio is of great significance to elucidate the mechanism of sex determination. However the molecular mechanisms by which temperature affects sex determination remains unclear although a few candidate genes have been found to play a role in the process. In this study we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171 1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35 45 dpf and 60 dpf dpf respectively revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway cell cycle oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation		pubmed:35641933		C35d 2	GSM6070542	source name:Whole fish\|tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:35dpf\|treatment:control	C35d 2	The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base‘N’ base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11 then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value ≤ 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value≤ 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample	Whole fish	The control group was kept at 28℃ whereas the thermal treatment group was exposed to 35℃for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment fish were returned at 28℃ until the fish reached to sexual maturity 90 dpf.	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …	The AB strain were maintained in a glass aquarium with a circulating water system at 28±0.5℃ with photoperiods of 14L 10D and the number of fish in each 5 liter tank was 50 55.	tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:35dpf\|treatment:control	GSM6070542	GSM6070542: C35d 2; Danio rerio; RNA Seq	GSM6070542 r1	GSM6070542	1	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP372606		C35d_2_1.fq.gz C35d_2_2.fq.gz	fastq fastq	6709504200.0	44730028.0	GSM6070542 r1	0:150 1:150	A:1832012065;C:1521825928;G:1505192413;T:1850347840;N:125954	150	150	1832012065	1521825928	1505192413	1850347840	125954	SRX15036807	SRS12783645	SRA1411536	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	1	0.9254		0.07577		0.67537		0.51805		150		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-04-27	Juvenile	Juvenile	Whole Organism	All anatomical structures
69627	69627	SRR18959661	SRX15036806	SRS12783644	SRP372606	PRJNA832865	Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation	GSE201748	Transcriptome Analysis	The influence of environmental factors especially temperature on sex ratio is of great significance to elucidate the mechanism of sex determination. However the molecular mechanisms by which temperature affects sex determination remains unclear although a few candidate genes have been found to play a role in the process. In this study we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171 1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35 45 dpf and 60 dpf dpf respectively revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway cell cycle oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation		pubmed:35641933		C35d 1	GSM6070541	source name:Whole fish\|tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:35dpf\|treatment:control	C35d 1	The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base‘N’ base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11 then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value ≤ 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value≤ 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample	Whole fish	The control group was kept at 28℃ whereas the thermal treatment group was exposed to 35℃for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment fish were returned at 28℃ until the fish reached to sexual maturity 90 dpf.	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …	The AB strain were maintained in a glass aquarium with a circulating water system at 28±0.5℃ with photoperiods of 14L 10D and the number of fish in each 5 liter tank was 50 55.	tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:35dpf\|treatment:control	GSM6070541	GSM6070541: C35d 1; Danio rerio; RNA Seq	GSM6070541 r1	GSM6070541	1	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP372606		C35d_1_1.fq.gz C35d_1_2.fq.gz	fastq fastq	6885467100.0	45903114.0	GSM6070541 r1	0:150 1:150	A:1875355665;C:1569722507;G:1551825136;T:1888418693;N:145099	150	150	1875355665	1569722507	1551825136	1888418693	145099	SRX15036806	SRS12783644	SRA1411536	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	1	0.9444		0.06579		0.73312		0.53564		150		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-04-27	Juvenile	Juvenile	Whole Organism	All anatomical structures
70056	70056	SRR19392694	SRX15447454	SRS13169844	SRP376956	PRJNA842165	Danio rerio Raw sequence reads	PRJNA842165	Whole Genome Sequencing	the RNA seq of 45dpf whole fish					whole zebrafish	breed:AB\|age:45days\|sex:pooled male and female\|tissue:whole fish\|BioSampleModel:Model organism or animal									RNAseq of zebrafish	mut 3 45dpf	mut 3 45dpf	RNAseq of whole fish			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP376956		6Hmut_3_R1.fastq.gz 6Hmut_3_R2.fastq.gz	fastq fastq	6560549850.0	21723675.0	6Hmut 3 R1.fastq.gz	0:151 1:151	A:1737437159;C:1534810355;G:1561501860;T:1726789854;N:10622	151	151	1737437159	1534810355	1561501860	1726789854	10622	SRX15447454	SRS13169844	SRA1426081	Huazhong Agricultural university\|Huazhong Agricultural university	Huazhong Agricultural university	2	0.93435	0.93393	0.06267	0.06345	0.65776	0.65871	0.49762	0.49344	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-05-25	Juvenile	Juvenile	Whole Organism	All anatomical structures
70057	70057	SRR19392695	SRX15447453	SRS13169844	SRP376956	PRJNA842165	Danio rerio Raw sequence reads	PRJNA842165	Whole Genome Sequencing	the RNA seq of 45dpf whole fish					whole zebrafish	breed:AB\|age:45days\|sex:pooled male and female\|tissue:whole fish\|BioSampleModel:Model organism or animal									RNAseq of zebrafish	mut 2 45dpf	mut 2 45dpf	RNAseq of whole fish			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP376956		6Hmut_2_R1.fastq.gz 6Hmut_2_R2.fastq.gz	fastq fastq	6478614532.0	21452366.0	6Hmut 2 R1.fastq.gz	0:151 1:151	A:1722746415;C:1511301958;G:1537581513;T:1706974238;N:10408	151	151	1722746415	1511301958	1537581513	1706974238	10408	SRX15447453	SRS13169844	SRA1426081	Huazhong Agricultural university\|Huazhong Agricultural university	Huazhong Agricultural university	2	0.94033	0.93884	0.0793	0.07897	0.66979	0.67063	0.51091	0.50721	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-05-25	Juvenile	Juvenile	Whole Organism	All anatomical structures
70058	70058	SRR19392696	SRX15447452	SRS13169844	SRP376956	PRJNA842165	Danio rerio Raw sequence reads	PRJNA842165	Whole Genome Sequencing	the RNA seq of 45dpf whole fish					whole zebrafish	breed:AB\|age:45days\|sex:pooled male and female\|tissue:whole fish\|BioSampleModel:Model organism or animal									RNAseq of zebrafish	mut 1 45dpf	mut 1 45dpf	RNAseq of whole fish			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP376956		6Hmut_1_R1.fastq.gz 6Hmut_1_R2.fastq.gz	fastq fastq	7131696780.0	23614890.0	6Hmut 1 R1.fastq.gz	0:151 1:151	A:1896556650;C:1662708805;G:1692110221;T:1880309012;N:12092	151	151	1896556650	1662708805	1692110221	1880309012	12092	SRX15447452	SRS13169844	SRA1426081	Huazhong Agricultural university\|Huazhong Agricultural university	Huazhong Agricultural university	2	0.93784	0.93841	0.07685	0.07715	0.65969	0.65999	0.50615	0.51174	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-05-25	Juvenile	Juvenile	Whole Organism	All anatomical structures
70059	70059	SRR19392697	SRX15447451	SRS13169844	SRP376956	PRJNA842165	Danio rerio Raw sequence reads	PRJNA842165	Whole Genome Sequencing	the RNA seq of 45dpf whole fish					whole zebrafish	breed:AB\|age:45days\|sex:pooled male and female\|tissue:whole fish\|BioSampleModel:Model organism or animal									RNAseq of zebrafish	wt 3 45dpf	wt 3 45dpf	RNAseq of whole fish			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP376956		wt_3_R1.fastq.gz wt_3_R2.fastq.gz	fastq fastq	6772530000.0	22575100.0	wt 3 R1.fastq.gz	0:150 1:150	A:1761127291;C:1612285256;G:1643602723;T:1755489964;N:24766	150	150	1761127291	1612285256	1643602723	1755489964	24766	SRX15447451	SRS13169844	SRA1426081	Huazhong Agricultural university\|Huazhong Agricultural university	Huazhong Agricultural university	2	0.94155	0.94016	0.04781	0.04747	0.67054	0.67227	0.49488	0.49322	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-05-25	Juvenile	Juvenile	Whole Organism	All anatomical structures
70060	70060	SRR19392698	SRX15447450	SRS13169844	SRP376956	PRJNA842165	Danio rerio Raw sequence reads	PRJNA842165	Whole Genome Sequencing	the RNA seq of 45dpf whole fish					whole zebrafish	breed:AB\|age:45days\|sex:pooled male and female\|tissue:whole fish\|BioSampleModel:Model organism or animal									RNAseq of zebrafish	wt 2 45dpf	wt 2 45dpf	RNAseq of whole fish			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP376956		wt_2_R1.fastq.gz wt_2_R2.fastq.gz	fastq fastq	7643857500.0	25479525.0	wt 2 R1.fastq.gz	0:150 1:150	A:1983773833;C:1824285264;G:1856615811;T:1979155020;N:27572	150	150	1983773833	1824285264	1856615811	1979155020	27572	SRX15447450	SRS13169844	SRA1426081	Huazhong Agricultural university\|Huazhong Agricultural university	Huazhong Agricultural university	2	0.93966	0.93936	0.04464	0.04509	0.66947	0.67006	0.47294	0.48847	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-05-25	Juvenile	Juvenile	Whole Organism	All anatomical structures
70061	70061	SRR19392699	SRX15447449	SRS13169844	SRP376956	PRJNA842165	Danio rerio Raw sequence reads	PRJNA842165	Whole Genome Sequencing	the RNA seq of 45dpf whole fish					whole zebrafish	breed:AB\|age:45days\|sex:pooled male and female\|tissue:whole fish\|BioSampleModel:Model organism or animal									RNAseq of zebrafish	wt 1 45dpf	wt 1 45dpf	RNAseq of whole fish			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP376956		wt_1_R1.fastq.gz wt_1_R2.fastq.gz	fastq fastq	7810923300.0	26036411.0	wt 1 R1.fastq.gz	0:150 1:150	A:2023252187;C:1867703140;G:1901935578;T:2018003438;N:28957	150	150	2023252187	1867703140	1901935578	2018003438	28957	SRX15447449	SRS13169844	SRA1426081	Huazhong Agricultural university\|Huazhong Agricultural university	Huazhong Agricultural university	2	0.94254	0.94222	0.04298	0.04298	0.66884	0.67073	0.47763	0.48746	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-05-25	Juvenile	Juvenile	Whole Organism	All anatomical structures
72671	72671	SRR23060055	SRX19013379	SRS16433016	SRP417129	PRJNA922890	Danio rerio Raw sequence reads	PRJNA922890	Whole Genome Sequencing	normal reference transcriptome of zebrafish					BPA225 3	strain:not collected\|isolate:not collected\|breed:not collected\|cultivar:not collected\|ecotype:not collected\|age:not collected\|dev stage:not collected\|sex:not collected\|tissue:Juvenile whole fish\|replicate:replicate = biological replicate 9\|BioSampleModel:Model organism or animal									RNA seq of Danio rerio	Z908	Z908	normal RNA seq of zebrafish			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP417129		BPA225_3_Clean_Data1.fq.gz BPA225_3_Clean_Data2.fq.gz	fastq fastq	5922430705.0	21094865.0	BPA225 3 Clean Data1.fq.gz										SRX19013379	SRS16433016	SRA1573339	yangzhou university\|College of Animal Science and Technology	yangzhou university	2	0.94064	0.94209	0.10366	0.10189	0.70092	0.6997	0.46735	0.4612	141	141	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2023-01-12	Juvenile	Juvenile	Whole Organism	All anatomical structures
72672	72672	SRR23060056	SRX19013378	SRS16433015	SRP417129	PRJNA922890	Danio rerio Raw sequence reads	PRJNA922890	Whole Genome Sequencing	normal reference transcriptome of zebrafish					BPA225 2	strain:not collected\|isolate:not collected\|breed:not collected\|cultivar:not collected\|ecotype:not collected\|age:not collected\|dev stage:not collected\|sex:not collected\|tissue:Juvenile whole fish\|replicate:replicate = biological replicate 8\|BioSampleModel:Model organism or animal									RNA seq of Danio rerio	Z907	Z907	normal RNA seq of zebrafish			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP417129		BPA225_2_Clean_Data1.fq.gz BPA225_2_Clean_Data2.fq.gz	fastq fastq	5509331897.0	19639714.0	BPA225 2 Clean Data1.fq.gz										SRX19013378	SRS16433015	SRA1573339	yangzhou university\|College of Animal Science and Technology	yangzhou university	2	0.9374	0.93862	0.11618	0.11425	0.69972	0.69952	0.46205	0.46585	141	141	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2023-01-12	Juvenile	Juvenile	Whole Organism	All anatomical structures
72673	72673	SRR23060057	SRX19013377	SRS16433014	SRP417129	PRJNA922890	Danio rerio Raw sequence reads	PRJNA922890	Whole Genome Sequencing	normal reference transcriptome of zebrafish					BPA225 1	strain:not collected\|isolate:not collected\|breed:not collected\|cultivar:not collected\|ecotype:not collected\|age:not collected\|dev stage:not collected\|sex:not collected\|tissue:Juvenile whole fish\|replicate:replicate = biological replicate 7\|BioSampleModel:Model organism or animal									RNA seq of Danio rerio	Z906	Z906	normal RNA seq of zebrafish			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP417129		BPA225_1_Clean_Data1.fq.gz BPA225_1_Clean_Data2.fq.gz	fastq fastq	6015141019.0	21413611.0	BPA225 1 Clean Data1.fq.gz	0:140.46 1:140.44	A:1623319583;C:1384519528;G:1394796849;T:1612405771;N:99288	140	140	1623319583	1384519528	1394796849	1612405771	99288	SRX19013377	SRS16433014	SRA1573339	yangzhou university\|College of Animal Science and Technology	yangzhou university	2	0.9392	0.94002	0.10822	0.10578	0.69146	0.69063	0.46651	0.4618	141	141	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2023-01-12	Juvenile	Juvenile	Whole Organism	All anatomical structures
72674	72674	SRR23060058	SRX19013376	SRS16433013	SRP417129	PRJNA922890	Danio rerio Raw sequence reads	PRJNA922890	Whole Genome Sequencing	normal reference transcriptome of zebrafish					BPA15 3	strain:not collected\|isolate:not collected\|breed:not collected\|cultivar:not collected\|ecotype:not collected\|age:not collected\|dev stage:not collected\|sex:not collected\|tissue:Juvenile whole fish\|replicate:replicate = biological replicate 6\|BioSampleModel:Model organism or animal									RNA seq of Danio rerio	Z905	Z905	normal RNA seq of zebrafish			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP417129		BPA15_3_Clean_Data1.fq.gz BPA15_3_Clean_Data2.fq.gz	fastq fastq	5412693513.0	19255194.0	BPA15 3 Clean Data1.fq.gz										SRX19013376	SRS16433013	SRA1573339	yangzhou university\|College of Animal Science and Technology	yangzhou university	2	0.939	0.93943	0.11111	0.10838	0.69798	0.69777	0.46519	0.46877	141	141	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2023-01-12	Juvenile	Juvenile	Whole Organism	All anatomical structures
72675	72675	SRR23060059	SRX19013375	SRS16433012	SRP417129	PRJNA922890	Danio rerio Raw sequence reads	PRJNA922890	Whole Genome Sequencing	normal reference transcriptome of zebrafish					BPA15 2	strain:not collected\|isolate:not collected\|breed:not collected\|cultivar:not collected\|ecotype:not collected\|age:not collected\|dev stage:not collected\|sex:not collected\|tissue:Juvenile whole fish\|replicate:replicate = biological replicate 5\|BioSampleModel:Model organism or animal									RNA seq of Danio rerio	Z904	Z904	normal RNA seq of zebrafish			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP417129		BPA15_2_Clean_Data1.fq.gz BPA15_2_Clean_Data2.fq.gz	fastq fastq	5836868617.0	20778949.0	BPA15 2 Clean Data1.fq.gz	0:140.46 1:140.45	A:1603966024;C:1315242512;G:1325577058;T:1591978988;N:104035	140	140	1603966024	1315242512	1325577058	1591978988	104035	SRX19013375	SRS16433012	SRA1573339	yangzhou university\|College of Animal Science and Technology	yangzhou university	2	0.93522	0.93486	0.12945	0.12692	0.69735	0.69702	0.47307	0.47198	141	141	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2023-01-12	Juvenile	Juvenile	Whole Organism	All anatomical structures
72676	72676	SRR23060060	SRX19013374	SRS16433010	SRP417129	PRJNA922890	Danio rerio Raw sequence reads	PRJNA922890	Whole Genome Sequencing	normal reference transcriptome of zebrafish					BPA15 1	strain:not collected\|isolate:not collected\|breed:not collected\|cultivar:not collected\|ecotype:not collected\|age:not collected\|dev stage:not collected\|sex:not collected\|tissue:Juvenile whole fish\|replicate:replicate = biological replicate 4\|BioSampleModel:Model organism or animal									RNA seq of Danio rerio	Z903	Z903	normal RNA seq of zebrafish			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP417129		BPA15_1_Clean_Data1.fq.gz BPA15_1_Clean_Data2.fq.gz	fastq fastq	5565976271.0	19806071.0	BPA15 1 Clean Data1.fq.gz	0:140.52 1:140.51	A:1513411045;C:1269789679;G:1278952098;T:1503723540;N:99909	140	140	1513411045	1269789679	1278952098	1503723540	99909	SRX19013374	SRS16433010	SRA1573339	yangzhou university\|College of Animal Science and Technology	yangzhou university	2	0.93415	0.93473	0.12035	0.11811	0.69315	0.69254	0.47054	0.47231	105	105	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2023-01-12	Juvenile	Juvenile	Whole Organism	All anatomical structures
72677	72677	SRR23060061	SRX19013373	SRS16433009	SRP417129	PRJNA922890	Danio rerio Raw sequence reads	PRJNA922890	Whole Genome Sequencing	normal reference transcriptome of zebrafish					Control 3	strain:not collected\|isolate:not collected\|breed:not collected\|cultivar:not collected\|ecotype:not collected\|age:not collected\|dev stage:not collected\|sex:not collected\|tissue:Juvenile whole fish\|replicate:replicate = biological replicate 3\|BioSampleModel:Model organism or animal									RNA seq of Danio rerio	Z902	Z902	normal RNA seq of zebrafish			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP417129		Control_3_Clean_Data1.fq.gz Control_3_Clean_Data2.fq.gz	fastq fastq	4866202369.0	17323282.0	Control 3 Clean Data1.fq.gz										SRX19013373	SRS16433009	SRA1573339	yangzhou university\|College of Animal Science and Technology	yangzhou university	2	0.91765	0.91705	0.17214	0.16747	0.69765	0.69739	0.48756	0.49157	141	141	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2023-01-12	Juvenile	Juvenile	Whole Organism	All anatomical structures
72678	72678	SRR23060062	SRX19013372	SRS16433011	SRP417129	PRJNA922890	Danio rerio Raw sequence reads	PRJNA922890	Whole Genome Sequencing	normal reference transcriptome of zebrafish					Control 2	strain:not collected\|isolate:not collected\|breed:not collected\|cultivar:not collected\|ecotype:not collected\|age:not collected\|dev stage:not collected\|sex:not collected\|tissue:Juvenile whole fish\|replicate:replicate = biological replicate 2\|BioSampleModel:Model organism or animal									RNA seq of Danio rerio	Z901	Z901	normal RNA seq of zebrafish			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP417129		Control_2_Clean_Data1.fq.gz Control_2_Clean_Data2.fq.gz	fastq fastq	5265679291.0	18766450.0	Control 2 Clean Data1.fq.gz										SRX19013372	SRS16433011	SRA1573339	yangzhou university\|College of Animal Science and Technology	yangzhou university	2	0.92738	0.92679	0.17397	0.17035	0.69948	0.69891	0.48006	0.48572	141	141	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2023-01-12	Juvenile	Juvenile	Whole Organism	All anatomical structures
72679	72679	SRR23060063	SRX19013371	SRS16433008	SRP417129	PRJNA922890	Danio rerio Raw sequence reads	PRJNA922890	Whole Genome Sequencing	normal reference transcriptome of zebrafish					Control 1	strain:not collected\|isolate:not collected\|breed:not collected\|cultivar:not collected\|ecotype:not collected\|age:not collected\|dev stage:not collected\|sex:not collected\|tissue:Juvenile whole fish\|replicate:replicate = biological replicate 1\|BioSampleModel:Model organism or animal									RNA seq of Danio rerio	Z900	Z900	normal RNA seq of zebrafish			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP417129		Control_1_Clean_Data1.fq.gz Control_1_Clean_Data2.fq.gz	fastq fastq	5769401401.0	20486114.0	Control 1 Clean Data1.fq.gz	0:140.82 1:140.80	A:1567930643;C:1316937376;G:1327529593;T:1556929210;N:74579	140	140	1567930643	1316937376	1327529593	1556929210	74579	SRX19013371	SRS16433008	SRA1573339	yangzhou university\|College of Animal Science and Technology	yangzhou university	2	0.94089	0.94089	0.11671	0.11386	0.69923	0.6994	0.46151	0.46472	141	141	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2023-01-12	Juvenile	Juvenile	Whole Organism	All anatomical structures
72748	72748	SRR23110580	SRX19061956	SRS16477631	SRP418118	PRJNA925134	BMP dependent cellular dynamics during cranial suture establishment in zebrafish	GSE223147	Transcriptome Analysis	Cranial sutures separate neighboring skull bones and contain skeletal stem cells that drive bone growth. A key question is how osteogenic activity is controlled to promote bone growth while preventing aberrant bone fusions during skull expansion. Here we integrate single cell transcriptomics in vivo expression validation photoconversion based lineage tracing and a zebrafish craniosynostosis model to uncover key developmental transitions regulating bone formation during skull expansion. In addition to conservation of meninges and osteoblast lineage cells between zebrafish and mouse single cell transcriptomic analysis of the zebrafish skull reveals distinct subpopulations of suture mesenchyme that undergo transcriptomic changes during suture establishment. While lineage tracing with an osteoblast specific nlsEOS reporter shows that bone formation largely occurs at suture edges a subset of mesenchyme cells in the mid suture region upregulate a suite of genes including BMP antagonists e.g. grem1a and pro angiogenic factors. Further lineage tracing with grem1a:nlsEOS reveals that this mid suture subpopulation is largely non osteogenic. In twist1b; tcf12 mutant zebrafish a model for the coronal synostosis of Saethre Chotzen Syndrome reduction of grem1a+ mid suture cells correlates with misregulated bone formation and reduced blood vessels at the coronal suture. In addition combinatorial mutation of BMP antagonists enriched in the mid suture subpopulation results in increased BMP signaling in the suture misregulated bone formation and abnormal suture morphology. These data support roles of a subset of mid suture mesenchyme in locally promoting BMP antagonism that ensures proper suture morphology. Overall design: Dissected calvaria of zebrafish were dissociated from juvenvile and adult zebrafish and live cells were identified by sorting for the absence of fluoresence sp7:GFP or ecad:YFP and the absence of DAPI using Fluorescence activated cell sorting FACS. Sorted cells were processed using 10X Genomics		pubmed:39138165		9 11 mm Juvenile Calvaria sp7GFPdepleted DAPI neg	GSM6940303	source name:calvaria\|cell type:various\|tissue:calvaria\|age:juvenile 9 11 mm\|strain:tubingen\|geo loc name:missing\|collection date:missing	9 11 mm Juvenile Calvaria sp7GFPdepleted DAPI neg	Data analysis was performed with Seurat version 4.1.1 and datasets were filtered by nFeature RNA > 200 nFeature RNA < 2500 and percent.mt < 25. Filtered cells were normalized with SCTransform and datasets were integrated based on the tutorial “Integration and Label Transfer” from Seurat https://satijalab.org/seurat/archive/v3.0/integration.html. The data were processed using the FindNeighbors and FindClusters functions and data were visualized with UMAP 30 principal components. The osteogenic subset of the integrated Seurat object was converted into a Monocle cell dataset and Monocle was performed following the Monocle3 recommended parameters https://cole trapnell lab.github.io/monocle3/docs/trajectories/#learn graph. Assembly: GRCz11 Supplementary files format and content: Tab separated values files matrix files and rds files	calvaria		We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset fish away from brain tissue in Ringer’s solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies 15090 046 1 mM EDTA and 400 mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4 °C rinsed in suspension media 1% FBS 0.8 mM CaCl2 Sigma Aldrich St. Louis MO in phenol red free Leibovitz’s L15 medium Life Technologies and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3′ Library and Gel Bead Kit v.2 according to the manufacturer’s instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.	The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5°C. For adults in the institute vivarium according to Protocol 20771.	cell type:various\|tissue:calvaria\|age:juvenile 9 11 mm\|strain:tubingen	GSM6940303	GSM6940303: 9 11 mm Juvenile Calvaria sp7GFPdepleted DAPI neg; Danio rerio; RNA Seq	GSM6940303 r1	GSM6940303	1	We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset fish away from brain tissue in Ringer's solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies 15090 046 1 mM EDTA and 400 mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4 °C rinsed in suspension media 1% FBS 0.8 mM CaCl2 Sigma Aldrich St. Louis MO in phenol red free Leibovitz's L15 medium Life Technologies and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3′ Library and Gel Bead Kit v.2 according to the manufacturer's instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 3000	SRP418118		9-11_mm_Juvenile_Calvaria_sp7GFPdepleted_DAPI_neg-1_S21_L001_R1_001.fastq.gz 9-11_mm_Juvenile_Calvaria_sp7GFPdepleted_DAPI_neg-1_S21_L001_R2_001.fastq.gz	fastq fastq	26193525700.0	177672099.0	GSM6940303 r1	0:27 1:120.43	A:7719827835;C:5410495858;G:5661676554;T:7386218620;N:15306833	27	120	7719827835	5410495858	5661676554	7386218620	15306833	SRX19061956	SRS16477631	SRA1576283	Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles	Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles	2	0.00368	0.88598	0.00112	0.18215	0.99168	0.77757	0.47975	0.51393	27	120	T	B	sc-like readlen	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-01-18	Juvenile	Juvenile	Embryo Imprecise	All anatomical structures
72749	72749	SRR23110581	SRX19061956	SRS16477631	SRP418118	PRJNA925134	BMP dependent cellular dynamics during cranial suture establishment in zebrafish	GSE223147	Transcriptome Analysis	Cranial sutures separate neighboring skull bones and contain skeletal stem cells that drive bone growth. A key question is how osteogenic activity is controlled to promote bone growth while preventing aberrant bone fusions during skull expansion. Here we integrate single cell transcriptomics in vivo expression validation photoconversion based lineage tracing and a zebrafish craniosynostosis model to uncover key developmental transitions regulating bone formation during skull expansion. In addition to conservation of meninges and osteoblast lineage cells between zebrafish and mouse single cell transcriptomic analysis of the zebrafish skull reveals distinct subpopulations of suture mesenchyme that undergo transcriptomic changes during suture establishment. While lineage tracing with an osteoblast specific nlsEOS reporter shows that bone formation largely occurs at suture edges a subset of mesenchyme cells in the mid suture region upregulate a suite of genes including BMP antagonists e.g. grem1a and pro angiogenic factors. Further lineage tracing with grem1a:nlsEOS reveals that this mid suture subpopulation is largely non osteogenic. In twist1b; tcf12 mutant zebrafish a model for the coronal synostosis of Saethre Chotzen Syndrome reduction of grem1a+ mid suture cells correlates with misregulated bone formation and reduced blood vessels at the coronal suture. In addition combinatorial mutation of BMP antagonists enriched in the mid suture subpopulation results in increased BMP signaling in the suture misregulated bone formation and abnormal suture morphology. These data support roles of a subset of mid suture mesenchyme in locally promoting BMP antagonism that ensures proper suture morphology. Overall design: Dissected calvaria of zebrafish were dissociated from juvenvile and adult zebrafish and live cells were identified by sorting for the absence of fluoresence sp7:GFP or ecad:YFP and the absence of DAPI using Fluorescence activated cell sorting FACS. Sorted cells were processed using 10X Genomics		pubmed:39138165		9 11 mm Juvenile Calvaria sp7GFPdepleted DAPI neg	GSM6940303	source name:calvaria\|cell type:various\|tissue:calvaria\|age:juvenile 9 11 mm\|strain:tubingen\|geo loc name:missing\|collection date:missing	9 11 mm Juvenile Calvaria sp7GFPdepleted DAPI neg	Data analysis was performed with Seurat version 4.1.1 and datasets were filtered by nFeature RNA > 200 nFeature RNA < 2500 and percent.mt < 25. Filtered cells were normalized with SCTransform and datasets were integrated based on the tutorial “Integration and Label Transfer” from Seurat https://satijalab.org/seurat/archive/v3.0/integration.html. The data were processed using the FindNeighbors and FindClusters functions and data were visualized with UMAP 30 principal components. The osteogenic subset of the integrated Seurat object was converted into a Monocle cell dataset and Monocle was performed following the Monocle3 recommended parameters https://cole trapnell lab.github.io/monocle3/docs/trajectories/#learn graph. Assembly: GRCz11 Supplementary files format and content: Tab separated values files matrix files and rds files	calvaria		We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset fish away from brain tissue in Ringer’s solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies 15090 046 1 mM EDTA and 400 mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4 °C rinsed in suspension media 1% FBS 0.8 mM CaCl2 Sigma Aldrich St. Louis MO in phenol red free Leibovitz’s L15 medium Life Technologies and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3′ Library and Gel Bead Kit v.2 according to the manufacturer’s instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.	The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5°C. For adults in the institute vivarium according to Protocol 20771.	cell type:various\|tissue:calvaria\|age:juvenile 9 11 mm\|strain:tubingen	GSM6940303	GSM6940303: 9 11 mm Juvenile Calvaria sp7GFPdepleted DAPI neg; Danio rerio; RNA Seq	GSM6940303 r1	GSM6940303	1	We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset fish away from brain tissue in Ringer's solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies 15090 046 1 mM EDTA and 400 mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4 °C rinsed in suspension media 1% FBS 0.8 mM CaCl2 Sigma Aldrich St. Louis MO in phenol red free Leibovitz's L15 medium Life Technologies and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3′ Library and Gel Bead Kit v.2 according to the manufacturer's instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 3000	SRP418118		9-11_mm_Juvenile_Calvaria_sp7GFPdepleted_DAPI_neg-2_S22_L001_R1_001.fastq.gz 9-11_mm_Juvenile_Calvaria_sp7GFPdepleted_DAPI_neg-2_S22_L001_R2_001.fastq.gz	fastq fastq	20405308570.0	138407397.0	GSM6940303 r2	0:27 1:120.43	A:6066761212;C:4188427284;G:4382899879;T:5755324838;N:11895357	27	120	6066761212	4188427284	4382899879	5755324838	11895357	SRX19061956	SRS16477631	SRA1576283	Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles	Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles	2	0.00368	0.88942	0.00119	0.18885	0.99184	0.78693	0.44927	0.51797	27	121	T	B	sc-like readlen	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-01-18	Juvenile	Juvenile	Embryo Imprecise	All anatomical structures
72750	72750	SRR23110582	SRX19061956	SRS16477631	SRP418118	PRJNA925134	BMP dependent cellular dynamics during cranial suture establishment in zebrafish	GSE223147	Transcriptome Analysis	Cranial sutures separate neighboring skull bones and contain skeletal stem cells that drive bone growth. A key question is how osteogenic activity is controlled to promote bone growth while preventing aberrant bone fusions during skull expansion. Here we integrate single cell transcriptomics in vivo expression validation photoconversion based lineage tracing and a zebrafish craniosynostosis model to uncover key developmental transitions regulating bone formation during skull expansion. In addition to conservation of meninges and osteoblast lineage cells between zebrafish and mouse single cell transcriptomic analysis of the zebrafish skull reveals distinct subpopulations of suture mesenchyme that undergo transcriptomic changes during suture establishment. While lineage tracing with an osteoblast specific nlsEOS reporter shows that bone formation largely occurs at suture edges a subset of mesenchyme cells in the mid suture region upregulate a suite of genes including BMP antagonists e.g. grem1a and pro angiogenic factors. Further lineage tracing with grem1a:nlsEOS reveals that this mid suture subpopulation is largely non osteogenic. In twist1b; tcf12 mutant zebrafish a model for the coronal synostosis of Saethre Chotzen Syndrome reduction of grem1a+ mid suture cells correlates with misregulated bone formation and reduced blood vessels at the coronal suture. In addition combinatorial mutation of BMP antagonists enriched in the mid suture subpopulation results in increased BMP signaling in the suture misregulated bone formation and abnormal suture morphology. These data support roles of a subset of mid suture mesenchyme in locally promoting BMP antagonism that ensures proper suture morphology. Overall design: Dissected calvaria of zebrafish were dissociated from juvenvile and adult zebrafish and live cells were identified by sorting for the absence of fluoresence sp7:GFP or ecad:YFP and the absence of DAPI using Fluorescence activated cell sorting FACS. Sorted cells were processed using 10X Genomics		pubmed:39138165		9 11 mm Juvenile Calvaria sp7GFPdepleted DAPI neg	GSM6940303	source name:calvaria\|cell type:various\|tissue:calvaria\|age:juvenile 9 11 mm\|strain:tubingen\|geo loc name:missing\|collection date:missing	9 11 mm Juvenile Calvaria sp7GFPdepleted DAPI neg	Data analysis was performed with Seurat version 4.1.1 and datasets were filtered by nFeature RNA > 200 nFeature RNA < 2500 and percent.mt < 25. Filtered cells were normalized with SCTransform and datasets were integrated based on the tutorial “Integration and Label Transfer” from Seurat https://satijalab.org/seurat/archive/v3.0/integration.html. The data were processed using the FindNeighbors and FindClusters functions and data were visualized with UMAP 30 principal components. The osteogenic subset of the integrated Seurat object was converted into a Monocle cell dataset and Monocle was performed following the Monocle3 recommended parameters https://cole trapnell lab.github.io/monocle3/docs/trajectories/#learn graph. Assembly: GRCz11 Supplementary files format and content: Tab separated values files matrix files and rds files	calvaria		We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset fish away from brain tissue in Ringer’s solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies 15090 046 1 mM EDTA and 400 mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4 °C rinsed in suspension media 1% FBS 0.8 mM CaCl2 Sigma Aldrich St. Louis MO in phenol red free Leibovitz’s L15 medium Life Technologies and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3′ Library and Gel Bead Kit v.2 according to the manufacturer’s instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.	The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5°C. For adults in the institute vivarium according to Protocol 20771.	cell type:various\|tissue:calvaria\|age:juvenile 9 11 mm\|strain:tubingen	GSM6940303	GSM6940303: 9 11 mm Juvenile Calvaria sp7GFPdepleted DAPI neg; Danio rerio; RNA Seq	GSM6940303 r1	GSM6940303	1	We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset fish away from brain tissue in Ringer's solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies 15090 046 1 mM EDTA and 400 mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4 °C rinsed in suspension media 1% FBS 0.8 mM CaCl2 Sigma Aldrich St. Louis MO in phenol red free Leibovitz's L15 medium Life Technologies and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3′ Library and Gel Bead Kit v.2 according to the manufacturer's instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 3000	SRP418118		9-11_mm_Juvenile_Calvaria_sp7GFPdepleted_DAPI_neg-3_S23_L001_R1_001.fastq.gz 9-11_mm_Juvenile_Calvaria_sp7GFPdepleted_DAPI_neg-3_S23_L001_R2_001.fastq.gz	fastq fastq	12307572438.0	83482484.0	GSM6940303 r3	0:27 1:120.43	A:3633520237;C:2534467756;G:2656045405;T:3476373726;N:7165314	27	120	3633520237	2534467756	2656045405	3476373726	7165314	SRX19061956	SRS16477631	SRA1576283	Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles	Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles	2	0.0038	0.8858	0.00113	0.18267	0.99101	0.77699	0.46833	0.52027	27	121	T	B	sc-like readlen	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-01-18	Juvenile	Juvenile	Embryo Imprecise	All anatomical structures
72751	72751	SRR23110583	SRX19061956	SRS16477631	SRP418118	PRJNA925134	BMP dependent cellular dynamics during cranial suture establishment in zebrafish	GSE223147	Transcriptome Analysis	Cranial sutures separate neighboring skull bones and contain skeletal stem cells that drive bone growth. A key question is how osteogenic activity is controlled to promote bone growth while preventing aberrant bone fusions during skull expansion. Here we integrate single cell transcriptomics in vivo expression validation photoconversion based lineage tracing and a zebrafish craniosynostosis model to uncover key developmental transitions regulating bone formation during skull expansion. In addition to conservation of meninges and osteoblast lineage cells between zebrafish and mouse single cell transcriptomic analysis of the zebrafish skull reveals distinct subpopulations of suture mesenchyme that undergo transcriptomic changes during suture establishment. While lineage tracing with an osteoblast specific nlsEOS reporter shows that bone formation largely occurs at suture edges a subset of mesenchyme cells in the mid suture region upregulate a suite of genes including BMP antagonists e.g. grem1a and pro angiogenic factors. Further lineage tracing with grem1a:nlsEOS reveals that this mid suture subpopulation is largely non osteogenic. In twist1b; tcf12 mutant zebrafish a model for the coronal synostosis of Saethre Chotzen Syndrome reduction of grem1a+ mid suture cells correlates with misregulated bone formation and reduced blood vessels at the coronal suture. In addition combinatorial mutation of BMP antagonists enriched in the mid suture subpopulation results in increased BMP signaling in the suture misregulated bone formation and abnormal suture morphology. These data support roles of a subset of mid suture mesenchyme in locally promoting BMP antagonism that ensures proper suture morphology. Overall design: Dissected calvaria of zebrafish were dissociated from juvenvile and adult zebrafish and live cells were identified by sorting for the absence of fluoresence sp7:GFP or ecad:YFP and the absence of DAPI using Fluorescence activated cell sorting FACS. Sorted cells were processed using 10X Genomics		pubmed:39138165		9 11 mm Juvenile Calvaria sp7GFPdepleted DAPI neg	GSM6940303	source name:calvaria\|cell type:various\|tissue:calvaria\|age:juvenile 9 11 mm\|strain:tubingen\|geo loc name:missing\|collection date:missing	9 11 mm Juvenile Calvaria sp7GFPdepleted DAPI neg	Data analysis was performed with Seurat version 4.1.1 and datasets were filtered by nFeature RNA > 200 nFeature RNA < 2500 and percent.mt < 25. Filtered cells were normalized with SCTransform and datasets were integrated based on the tutorial “Integration and Label Transfer” from Seurat https://satijalab.org/seurat/archive/v3.0/integration.html. The data were processed using the FindNeighbors and FindClusters functions and data were visualized with UMAP 30 principal components. The osteogenic subset of the integrated Seurat object was converted into a Monocle cell dataset and Monocle was performed following the Monocle3 recommended parameters https://cole trapnell lab.github.io/monocle3/docs/trajectories/#learn graph. Assembly: GRCz11 Supplementary files format and content: Tab separated values files matrix files and rds files	calvaria		We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset fish away from brain tissue in Ringer’s solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies 15090 046 1 mM EDTA and 400 mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4 °C rinsed in suspension media 1% FBS 0.8 mM CaCl2 Sigma Aldrich St. Louis MO in phenol red free Leibovitz’s L15 medium Life Technologies and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3′ Library and Gel Bead Kit v.2 according to the manufacturer’s instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.	The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5°C. For adults in the institute vivarium according to Protocol 20771.	cell type:various\|tissue:calvaria\|age:juvenile 9 11 mm\|strain:tubingen	GSM6940303	GSM6940303: 9 11 mm Juvenile Calvaria sp7GFPdepleted DAPI neg; Danio rerio; RNA Seq	GSM6940303 r1	GSM6940303	1	We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset fish away from brain tissue in Ringer's solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies 15090 046 1 mM EDTA and 400 mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4 °C rinsed in suspension media 1% FBS 0.8 mM CaCl2 Sigma Aldrich St. Louis MO in phenol red free Leibovitz's L15 medium Life Technologies and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3′ Library and Gel Bead Kit v.2 according to the manufacturer's instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 3000	SRP418118		9-11_mm_Juvenile_Calvaria_sp7GFPdepleted_DAPI_neg-4_S24_L001_R1_001.fastq.gz 9-11_mm_Juvenile_Calvaria_sp7GFPdepleted_DAPI_neg-4_S24_L001_R2_001.fastq.gz	fastq fastq	18938094183.0	128455057.0	GSM6940303 r4	0:27 1:120.43	A:5600343426;C:3891577388;G:4069279675;T:5365803260;N:11090434	27	120	5600343426	3891577388	4069279675	5365803260	11090434	SRX19061956	SRS16477631	SRA1576283	Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles	Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles	2	0.00359	0.88634	0.00128	0.18783	0.99212	0.77893	0.48997	0.50684	27	120	T	B	sc-like readlen	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-01-18	Juvenile	Juvenile	Embryo Imprecise	All anatomical structures
72752	72752	SRR23110584	SRX19061955	SRS16477630	SRP418118	PRJNA925134	BMP dependent cellular dynamics during cranial suture establishment in zebrafish	GSE223147	Transcriptome Analysis	Cranial sutures separate neighboring skull bones and contain skeletal stem cells that drive bone growth. A key question is how osteogenic activity is controlled to promote bone growth while preventing aberrant bone fusions during skull expansion. Here we integrate single cell transcriptomics in vivo expression validation photoconversion based lineage tracing and a zebrafish craniosynostosis model to uncover key developmental transitions regulating bone formation during skull expansion. In addition to conservation of meninges and osteoblast lineage cells between zebrafish and mouse single cell transcriptomic analysis of the zebrafish skull reveals distinct subpopulations of suture mesenchyme that undergo transcriptomic changes during suture establishment. While lineage tracing with an osteoblast specific nlsEOS reporter shows that bone formation largely occurs at suture edges a subset of mesenchyme cells in the mid suture region upregulate a suite of genes including BMP antagonists e.g. grem1a and pro angiogenic factors. Further lineage tracing with grem1a:nlsEOS reveals that this mid suture subpopulation is largely non osteogenic. In twist1b; tcf12 mutant zebrafish a model for the coronal synostosis of Saethre Chotzen Syndrome reduction of grem1a+ mid suture cells correlates with misregulated bone formation and reduced blood vessels at the coronal suture. In addition combinatorial mutation of BMP antagonists enriched in the mid suture subpopulation results in increased BMP signaling in the suture misregulated bone formation and abnormal suture morphology. These data support roles of a subset of mid suture mesenchyme in locally promoting BMP antagonism that ensures proper suture morphology. Overall design: Dissected calvaria of zebrafish were dissociated from juvenvile and adult zebrafish and live cells were identified by sorting for the absence of fluoresence sp7:GFP or ecad:YFP and the absence of DAPI using Fluorescence activated cell sorting FACS. Sorted cells were processed using 10X Genomics		pubmed:39138165		9 11 mm Juvenile Calvaria ecadYFPdepleted DAPI neg	GSM6940302	source name:calvaria\|cell type:various\|tissue:calvaria\|age:juvenile 9 11 mm\|strain:tubingen\|geo loc name:missing\|collection date:missing	9 11 mm Juvenile Calvaria ecadYFPdepleted DAPI neg	Data analysis was performed with Seurat version 4.1.1 and datasets were filtered by nFeature RNA > 200 nFeature RNA < 2500 and percent.mt < 25. Filtered cells were normalized with SCTransform and datasets were integrated based on the tutorial “Integration and Label Transfer” from Seurat https://satijalab.org/seurat/archive/v3.0/integration.html. The data were processed using the FindNeighbors and FindClusters functions and data were visualized with UMAP 30 principal components. The osteogenic subset of the integrated Seurat object was converted into a Monocle cell dataset and Monocle was performed following the Monocle3 recommended parameters https://cole trapnell lab.github.io/monocle3/docs/trajectories/#learn graph. Assembly: GRCz11 Supplementary files format and content: Tab separated values files matrix files and rds files	calvaria		We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset fish away from brain tissue in Ringer’s solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies 15090 046 1 mM EDTA and 400 mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4 °C rinsed in suspension media 1% FBS 0.8 mM CaCl2 Sigma Aldrich St. Louis MO in phenol red free Leibovitz’s L15 medium Life Technologies and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3′ Library and Gel Bead Kit v.2 according to the manufacturer’s instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.	The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5°C. For adults in the institute vivarium according to Protocol 20771.	cell type:various\|tissue:calvaria\|age:juvenile 9 11 mm\|strain:tubingen	GSM6940302	GSM6940302: 9 11 mm Juvenile Calvaria ecadYFPdepleted DAPI neg; Danio rerio; RNA Seq	GSM6940302 r1	GSM6940302	1	We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset fish away from brain tissue in Ringer's solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies 15090 046 1 mM EDTA and 400 mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4 °C rinsed in suspension media 1% FBS 0.8 mM CaCl2 Sigma Aldrich St. Louis MO in phenol red free Leibovitz's L15 medium Life Technologies and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3′ Library and Gel Bead Kit v.2 according to the manufacturer's instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP418118		9-11_mm_Juvenile_Calvaria_ecadYFPdepleted_DAPI_neg-1_S1_L001_R1_001.fastq.gz 9-11_mm_Juvenile_Calvaria_ecadYFPdepleted_DAPI_neg-1_S1_L001_R2_001.fastq.gz	fastq fastq	11012858533.0	74696398.0	GSM6940302 r1	0:27 1:120.43	A:3253931864;C:2230032555;G:2516883171;T:3003935990;N:8074953	27	120	3253931864	2230032555	2516883171	3003935990	8074953	SRX19061955	SRS16477630	SRA1576283	Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles	Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles	2	0.00603	0.89151	0.00212	0.18091	0.98849	0.79634	0.5277	0.52269	27	120	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-01-18	Juvenile	Juvenile	Embryo Imprecise	All anatomical structures
72753	72753	SRR23110585	SRX19061955	SRS16477630	SRP418118	PRJNA925134	BMP dependent cellular dynamics during cranial suture establishment in zebrafish	GSE223147	Transcriptome Analysis	Cranial sutures separate neighboring skull bones and contain skeletal stem cells that drive bone growth. A key question is how osteogenic activity is controlled to promote bone growth while preventing aberrant bone fusions during skull expansion. Here we integrate single cell transcriptomics in vivo expression validation photoconversion based lineage tracing and a zebrafish craniosynostosis model to uncover key developmental transitions regulating bone formation during skull expansion. In addition to conservation of meninges and osteoblast lineage cells between zebrafish and mouse single cell transcriptomic analysis of the zebrafish skull reveals distinct subpopulations of suture mesenchyme that undergo transcriptomic changes during suture establishment. While lineage tracing with an osteoblast specific nlsEOS reporter shows that bone formation largely occurs at suture edges a subset of mesenchyme cells in the mid suture region upregulate a suite of genes including BMP antagonists e.g. grem1a and pro angiogenic factors. Further lineage tracing with grem1a:nlsEOS reveals that this mid suture subpopulation is largely non osteogenic. In twist1b; tcf12 mutant zebrafish a model for the coronal synostosis of Saethre Chotzen Syndrome reduction of grem1a+ mid suture cells correlates with misregulated bone formation and reduced blood vessels at the coronal suture. In addition combinatorial mutation of BMP antagonists enriched in the mid suture subpopulation results in increased BMP signaling in the suture misregulated bone formation and abnormal suture morphology. These data support roles of a subset of mid suture mesenchyme in locally promoting BMP antagonism that ensures proper suture morphology. Overall design: Dissected calvaria of zebrafish were dissociated from juvenvile and adult zebrafish and live cells were identified by sorting for the absence of fluoresence sp7:GFP or ecad:YFP and the absence of DAPI using Fluorescence activated cell sorting FACS. Sorted cells were processed using 10X Genomics		pubmed:39138165		9 11 mm Juvenile Calvaria ecadYFPdepleted DAPI neg	GSM6940302	source name:calvaria\|cell type:various\|tissue:calvaria\|age:juvenile 9 11 mm\|strain:tubingen\|geo loc name:missing\|collection date:missing	9 11 mm Juvenile Calvaria ecadYFPdepleted DAPI neg	Data analysis was performed with Seurat version 4.1.1 and datasets were filtered by nFeature RNA > 200 nFeature RNA < 2500 and percent.mt < 25. Filtered cells were normalized with SCTransform and datasets were integrated based on the tutorial “Integration and Label Transfer” from Seurat https://satijalab.org/seurat/archive/v3.0/integration.html. The data were processed using the FindNeighbors and FindClusters functions and data were visualized with UMAP 30 principal components. The osteogenic subset of the integrated Seurat object was converted into a Monocle cell dataset and Monocle was performed following the Monocle3 recommended parameters https://cole trapnell lab.github.io/monocle3/docs/trajectories/#learn graph. Assembly: GRCz11 Supplementary files format and content: Tab separated values files matrix files and rds files	calvaria		We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset fish away from brain tissue in Ringer’s solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies 15090 046 1 mM EDTA and 400 mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4 °C rinsed in suspension media 1% FBS 0.8 mM CaCl2 Sigma Aldrich St. Louis MO in phenol red free Leibovitz’s L15 medium Life Technologies and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3′ Library and Gel Bead Kit v.2 according to the manufacturer’s instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.	The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5°C. For adults in the institute vivarium according to Protocol 20771.	cell type:various\|tissue:calvaria\|age:juvenile 9 11 mm\|strain:tubingen	GSM6940302	GSM6940302: 9 11 mm Juvenile Calvaria ecadYFPdepleted DAPI neg; Danio rerio; RNA Seq	GSM6940302 r1	GSM6940302	1	We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset fish away from brain tissue in Ringer's solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies 15090 046 1 mM EDTA and 400 mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4 °C rinsed in suspension media 1% FBS 0.8 mM CaCl2 Sigma Aldrich St. Louis MO in phenol red free Leibovitz's L15 medium Life Technologies and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3′ Library and Gel Bead Kit v.2 according to the manufacturer's instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP418118		9-11_mm_Juvenile_Calvaria_ecadYFPdepleted_DAPI_neg-2_S2_L001_R1_001.fastq.gz 9-11_mm_Juvenile_Calvaria_ecadYFPdepleted_DAPI_neg-2_S2_L001_R2_001.fastq.gz	fastq fastq	10212715196.0	69269302.0	GSM6940302 r2	0:27 1:120.43	A:3014265330;C:2070878830;G:2341755898;T:2778343711;N:7471427	27	120	3014265330	2070878830	2341755898	2778343711	7471427	SRX19061955	SRS16477630	SRA1576283	Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles	Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles	2	0.00554	0.89174	0.00191	0.1793	0.98884	0.79732	0.51857	0.52305	27	121	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-01-18	Juvenile	Juvenile	Embryo Imprecise	All anatomical structures
72754	72754	SRR23110586	SRX19061955	SRS16477630	SRP418118	PRJNA925134	BMP dependent cellular dynamics during cranial suture establishment in zebrafish	GSE223147	Transcriptome Analysis	Cranial sutures separate neighboring skull bones and contain skeletal stem cells that drive bone growth. A key question is how osteogenic activity is controlled to promote bone growth while preventing aberrant bone fusions during skull expansion. Here we integrate single cell transcriptomics in vivo expression validation photoconversion based lineage tracing and a zebrafish craniosynostosis model to uncover key developmental transitions regulating bone formation during skull expansion. In addition to conservation of meninges and osteoblast lineage cells between zebrafish and mouse single cell transcriptomic analysis of the zebrafish skull reveals distinct subpopulations of suture mesenchyme that undergo transcriptomic changes during suture establishment. While lineage tracing with an osteoblast specific nlsEOS reporter shows that bone formation largely occurs at suture edges a subset of mesenchyme cells in the mid suture region upregulate a suite of genes including BMP antagonists e.g. grem1a and pro angiogenic factors. Further lineage tracing with grem1a:nlsEOS reveals that this mid suture subpopulation is largely non osteogenic. In twist1b; tcf12 mutant zebrafish a model for the coronal synostosis of Saethre Chotzen Syndrome reduction of grem1a+ mid suture cells correlates with misregulated bone formation and reduced blood vessels at the coronal suture. In addition combinatorial mutation of BMP antagonists enriched in the mid suture subpopulation results in increased BMP signaling in the suture misregulated bone formation and abnormal suture morphology. These data support roles of a subset of mid suture mesenchyme in locally promoting BMP antagonism that ensures proper suture morphology. Overall design: Dissected calvaria of zebrafish were dissociated from juvenvile and adult zebrafish and live cells were identified by sorting for the absence of fluoresence sp7:GFP or ecad:YFP and the absence of DAPI using Fluorescence activated cell sorting FACS. Sorted cells were processed using 10X Genomics		pubmed:39138165		9 11 mm Juvenile Calvaria ecadYFPdepleted DAPI neg	GSM6940302	source name:calvaria\|cell type:various\|tissue:calvaria\|age:juvenile 9 11 mm\|strain:tubingen\|geo loc name:missing\|collection date:missing	9 11 mm Juvenile Calvaria ecadYFPdepleted DAPI neg	Data analysis was performed with Seurat version 4.1.1 and datasets were filtered by nFeature RNA > 200 nFeature RNA < 2500 and percent.mt < 25. Filtered cells were normalized with SCTransform and datasets were integrated based on the tutorial “Integration and Label Transfer” from Seurat https://satijalab.org/seurat/archive/v3.0/integration.html. The data were processed using the FindNeighbors and FindClusters functions and data were visualized with UMAP 30 principal components. The osteogenic subset of the integrated Seurat object was converted into a Monocle cell dataset and Monocle was performed following the Monocle3 recommended parameters https://cole trapnell lab.github.io/monocle3/docs/trajectories/#learn graph. Assembly: GRCz11 Supplementary files format and content: Tab separated values files matrix files and rds files	calvaria		We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset fish away from brain tissue in Ringer’s solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies 15090 046 1 mM EDTA and 400 mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4 °C rinsed in suspension media 1% FBS 0.8 mM CaCl2 Sigma Aldrich St. Louis MO in phenol red free Leibovitz’s L15 medium Life Technologies and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3′ Library and Gel Bead Kit v.2 according to the manufacturer’s instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.	The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5°C. For adults in the institute vivarium according to Protocol 20771.	cell type:various\|tissue:calvaria\|age:juvenile 9 11 mm\|strain:tubingen	GSM6940302	GSM6940302: 9 11 mm Juvenile Calvaria ecadYFPdepleted DAPI neg; Danio rerio; RNA Seq	GSM6940302 r1	GSM6940302	1	We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset fish away from brain tissue in Ringer's solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies 15090 046 1 mM EDTA and 400 mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4 °C rinsed in suspension media 1% FBS 0.8 mM CaCl2 Sigma Aldrich St. Louis MO in phenol red free Leibovitz's L15 medium Life Technologies and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3′ Library and Gel Bead Kit v.2 according to the manufacturer's instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP418118		9-11_mm_Juvenile_Calvaria_ecadYFPdepleted_DAPI_neg-3_S3_L001_R1_001.fastq.gz 9-11_mm_Juvenile_Calvaria_ecadYFPdepleted_DAPI_neg-3_S3_L001_R2_001.fastq.gz	fastq fastq	7996112551.0	54234020.0	GSM6940302 r3	0:27 1:120.44	A:2359724282;C:1611743954;G:1830950721;T:2187871443;N:5822151	27	120	2359724282	1611743954	1830950721	2187871443	5822151	SRX19061955	SRS16477630	SRA1576283	Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles	Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles	2	0.00614	0.88908	0.00216	0.1836	0.98821	0.79547	0.52232	0.51954	27	121	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-01-18	Juvenile	Juvenile	Embryo Imprecise	All anatomical structures
72755	72755	SRR23110587	SRX19061955	SRS16477630	SRP418118	PRJNA925134	BMP dependent cellular dynamics during cranial suture establishment in zebrafish	GSE223147	Transcriptome Analysis	Cranial sutures separate neighboring skull bones and contain skeletal stem cells that drive bone growth. A key question is how osteogenic activity is controlled to promote bone growth while preventing aberrant bone fusions during skull expansion. Here we integrate single cell transcriptomics in vivo expression validation photoconversion based lineage tracing and a zebrafish craniosynostosis model to uncover key developmental transitions regulating bone formation during skull expansion. In addition to conservation of meninges and osteoblast lineage cells between zebrafish and mouse single cell transcriptomic analysis of the zebrafish skull reveals distinct subpopulations of suture mesenchyme that undergo transcriptomic changes during suture establishment. While lineage tracing with an osteoblast specific nlsEOS reporter shows that bone formation largely occurs at suture edges a subset of mesenchyme cells in the mid suture region upregulate a suite of genes including BMP antagonists e.g. grem1a and pro angiogenic factors. Further lineage tracing with grem1a:nlsEOS reveals that this mid suture subpopulation is largely non osteogenic. In twist1b; tcf12 mutant zebrafish a model for the coronal synostosis of Saethre Chotzen Syndrome reduction of grem1a+ mid suture cells correlates with misregulated bone formation and reduced blood vessels at the coronal suture. In addition combinatorial mutation of BMP antagonists enriched in the mid suture subpopulation results in increased BMP signaling in the suture misregulated bone formation and abnormal suture morphology. These data support roles of a subset of mid suture mesenchyme in locally promoting BMP antagonism that ensures proper suture morphology. Overall design: Dissected calvaria of zebrafish were dissociated from juvenvile and adult zebrafish and live cells were identified by sorting for the absence of fluoresence sp7:GFP or ecad:YFP and the absence of DAPI using Fluorescence activated cell sorting FACS. Sorted cells were processed using 10X Genomics		pubmed:39138165		9 11 mm Juvenile Calvaria ecadYFPdepleted DAPI neg	GSM6940302	source name:calvaria\|cell type:various\|tissue:calvaria\|age:juvenile 9 11 mm\|strain:tubingen\|geo loc name:missing\|collection date:missing	9 11 mm Juvenile Calvaria ecadYFPdepleted DAPI neg	Data analysis was performed with Seurat version 4.1.1 and datasets were filtered by nFeature RNA > 200 nFeature RNA < 2500 and percent.mt < 25. Filtered cells were normalized with SCTransform and datasets were integrated based on the tutorial “Integration and Label Transfer” from Seurat https://satijalab.org/seurat/archive/v3.0/integration.html. The data were processed using the FindNeighbors and FindClusters functions and data were visualized with UMAP 30 principal components. The osteogenic subset of the integrated Seurat object was converted into a Monocle cell dataset and Monocle was performed following the Monocle3 recommended parameters https://cole trapnell lab.github.io/monocle3/docs/trajectories/#learn graph. Assembly: GRCz11 Supplementary files format and content: Tab separated values files matrix files and rds files	calvaria		We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset fish away from brain tissue in Ringer’s solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies 15090 046 1 mM EDTA and 400 mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4 °C rinsed in suspension media 1% FBS 0.8 mM CaCl2 Sigma Aldrich St. Louis MO in phenol red free Leibovitz’s L15 medium Life Technologies and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3′ Library and Gel Bead Kit v.2 according to the manufacturer’s instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.	The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5°C. For adults in the institute vivarium according to Protocol 20771.	cell type:various\|tissue:calvaria\|age:juvenile 9 11 mm\|strain:tubingen	GSM6940302	GSM6940302: 9 11 mm Juvenile Calvaria ecadYFPdepleted DAPI neg; Danio rerio; RNA Seq	GSM6940302 r1	GSM6940302	1	We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset fish away from brain tissue in Ringer's solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies 15090 046 1 mM EDTA and 400 mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4 °C rinsed in suspension media 1% FBS 0.8 mM CaCl2 Sigma Aldrich St. Louis MO in phenol red free Leibovitz's L15 medium Life Technologies and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3′ Library and Gel Bead Kit v.2 according to the manufacturer's instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP418118		9-11_mm_Juvenile_Calvaria_ecadYFPdepleted_DAPI_neg-4_S4_L001_R1_001.fastq.gz 9-11_mm_Juvenile_Calvaria_ecadYFPdepleted_DAPI_neg-4_S4_L001_R2_001.fastq.gz	fastq fastq	11056657034.0	74991022.0	GSM6940302 r4	0:27 1:120.44	A:3246337136;C:2242556246;G:2556848463;T:3002783409;N:8131780	27	120	3246337136	2242556246	2556848463	3002783409	8131780	SRX19061955	SRS16477630	SRA1576283	Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles	Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles	2	0.00621	0.8906	0.00194	0.17648	0.98762	0.80133	0.48802	0.52225	27	121	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-01-18	Juvenile	Juvenile	Embryo Imprecise	All anatomical structures

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;