metadata: run_metadata: 20 rows where devstage_curation = "Pharyngula" and experiment.platform = "BGISEQ"

20 rows where devstage_curation = "Pharyngula" and experiment.platform = "BGISEQ"

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.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.nofeature_rate.mate1	seqdetective.sparsity.mate1	seqdetective.pos_strand_rate.mate1	seqdetective.readlen.mate1	seqdetective.judgement.mate1	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
48054	48054	SRR7008006	SRX3940581	SRS3171382	SRP140462	PRJNA450341	Primary cilia regulate hematopoietic stem and progenitor cell specification through Notch signaling	PRJNA450341	Other	Hematopoietic stem and progenitor cells HSPCs are capable of producing all mature blood lineages as well as maintaining the self renewal ability throughout life. The hairy like organelle cilia are present in most types of vertebrate cells and play important roles in various biological processes. However it is unclear whether and how cilia regulate HSPC development in vertebrates. Here we show that cilia specific genes involved in primary cilia formation and signaling transduction are required for HSPC development especially at the hemogenic endothelium HE specification step in zebrafish embryos. Blocking primary cilia formation or function by genetic or chemical manipulations impaired HSPC development. Mechanistically we uncover that primary cilia on endothelial cells ECs transduce Notch signal to the earliest HE for proper HSPC specification during embryogenesis. Altogether our findings reveal a pivotal role of endothelial primary cilia in HSPC development and may shed lights into in vitro directed differentiation of HSPCs.			MO26h rep1	MO26h 1	Sample3	strain:zebrafish embryos\|isolate:not applicable\|dev stage:26 hpf\|sex:not applicable\|tissue:trunk region\|collection date:2017 08 11\|geo loc name:China: Beijing\|isolation source:not applicable\|sample type:fsd1morphants 1\|BioSampleModel:Model organism or animal									RNA seq of fsd1 morphants1	MO26h 1	MO26h 1	RNA was isolated from trunk regions of control embryos and fsd1 morphants for cDNA library. The cDNA library for sequenced using BGISEQ 500 platform.			RNA-Seq	TRANSCRIPTOMIC	PCR	SINGLE	BGISEQ	BGISEQ-500	SRP140462	MO26h_1_1.fq.gz	fastq	1193983450.0	23879669.0	MO26h 1 1.fq.gz	0:50	A:313344068;C:282899939;G:291404437;T:306051122;N:283884	50		313344068	282899939	291404437	306051122	283884	SRX3940581	SRS3171382	SRA690964	Institute of Zoology, CHINESE ACADEMY OF SCIENCES\|State Key Laboratory of Membrane Biology	Institute of Zoology, CHINESE ACADEMY OF SCIENCES	1	0.95658	0.07921	0.70307	0.47586	50	B	usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2018-04-16	Pharyngula	Embryo	Trunk	Surface Structure
48055	48055	SRR7008007	SRX3940580	SRS3171381	SRP140462	PRJNA450341	Primary cilia regulate hematopoietic stem and progenitor cell specification through Notch signaling	PRJNA450341	Other	Hematopoietic stem and progenitor cells HSPCs are capable of producing all mature blood lineages as well as maintaining the self renewal ability throughout life. The hairy like organelle cilia are present in most types of vertebrate cells and play important roles in various biological processes. However it is unclear whether and how cilia regulate HSPC development in vertebrates. Here we show that cilia specific genes involved in primary cilia formation and signaling transduction are required for HSPC development especially at the hemogenic endothelium HE specification step in zebrafish embryos. Blocking primary cilia formation or function by genetic or chemical manipulations impaired HSPC development. Mechanistically we uncover that primary cilia on endothelial cells ECs transduce Notch signal to the earliest HE for proper HSPC specification during embryogenesis. Altogether our findings reveal a pivotal role of endothelial primary cilia in HSPC development and may shed lights into in vitro directed differentiation of HSPCs.			MO26h rep2	MO26h 2	Sample4	strain:zebrafish embryos\|isolate:not applicable\|dev stage:26 hpf\|sex:not applicable\|tissue:trunk region\|collection date:2017 08 11\|geo loc name:China: Beijing\|isolation source:not applicable\|sample type:fsd1morphants 2\|BioSampleModel:Model organism or animal									RNA seq of fsd1 morphants2	MO26h 2	MO26h 2	RNA was isolated from trunk regions of control embryos and fsd1 morphants for cDNA library. The cDNA library for sequenced using BGISEQ 500 platform.			RNA-Seq	TRANSCRIPTOMIC	PCR	SINGLE	BGISEQ	BGISEQ-500	SRP140462	MO26h_2_1.fq.gz	fastq	1199524600.0	23990492.0	MO26h 2 1.fq.gz	0:50	A:318726410;C:282721669;G:287606979;T:310182197;N:287345	50		318726410	282721669	287606979	310182197	287345	SRX3940580	SRS3171381	SRA690964	Institute of Zoology, CHINESE ACADEMY OF SCIENCES\|State Key Laboratory of Membrane Biology	Institute of Zoology, CHINESE ACADEMY OF SCIENCES	1	0.9541	0.08695	0.70404	0.47195	50	B	usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2018-04-16	Pharyngula	Embryo	Trunk	Surface Structure
48056	48056	SRR7008008	SRX3940579	SRS3171379	SRP140462	PRJNA450341	Primary cilia regulate hematopoietic stem and progenitor cell specification through Notch signaling	PRJNA450341	Other	Hematopoietic stem and progenitor cells HSPCs are capable of producing all mature blood lineages as well as maintaining the self renewal ability throughout life. The hairy like organelle cilia are present in most types of vertebrate cells and play important roles in various biological processes. However it is unclear whether and how cilia regulate HSPC development in vertebrates. Here we show that cilia specific genes involved in primary cilia formation and signaling transduction are required for HSPC development especially at the hemogenic endothelium HE specification step in zebrafish embryos. Blocking primary cilia formation or function by genetic or chemical manipulations impaired HSPC development. Mechanistically we uncover that primary cilia on endothelial cells ECs transduce Notch signal to the earliest HE for proper HSPC specification during embryogenesis. Altogether our findings reveal a pivotal role of endothelial primary cilia in HSPC development and may shed lights into in vitro directed differentiation of HSPCs.			WT26h rep1	WT26h 1	Sample1	strain:zebrafish embryos\|isolate:not applicable\|dev stage:26 hpf\|sex:not applicable\|tissue:trunk region\|collection date:2017 08 11\|geo loc name:China: Beijing\|isolation source:not applicable\|sample type:normal embryos 1\|BioSampleModel:Model organism or animal									RNA seq of normal embryos1	WT26h 1	WT26h 1	RNA was isolated from trunk regions of control embryos and fsd1 morphants for cDNA library. The cDNA library for sequenced using BGISEQ 500 platform.			RNA-Seq	TRANSCRIPTOMIC	PCR	SINGLE	BGISEQ	BGISEQ-500	SRP140462	WT26h_1_1.fq.gz	fastq	1200268650.0	24005373.0	WT26h 1 1.fq.gz	0:50	A:315743815;C:284447849;G:295772915;T:303964473;N:339598	50		315743815	284447849	295772915	303964473	339598	SRX3940579	SRS3171379	SRA690964	Institute of Zoology, CHINESE ACADEMY OF SCIENCES\|State Key Laboratory of Membrane Biology	Institute of Zoology, CHINESE ACADEMY OF SCIENCES	1	0.95659	0.07726	0.70425	0.47269	50	B	usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2018-04-16	Pharyngula	Embryo	Trunk	Surface Structure
48057	48057	SRR7008009	SRX3940578	SRS3171380	SRP140462	PRJNA450341	Primary cilia regulate hematopoietic stem and progenitor cell specification through Notch signaling	PRJNA450341	Other	Hematopoietic stem and progenitor cells HSPCs are capable of producing all mature blood lineages as well as maintaining the self renewal ability throughout life. The hairy like organelle cilia are present in most types of vertebrate cells and play important roles in various biological processes. However it is unclear whether and how cilia regulate HSPC development in vertebrates. Here we show that cilia specific genes involved in primary cilia formation and signaling transduction are required for HSPC development especially at the hemogenic endothelium HE specification step in zebrafish embryos. Blocking primary cilia formation or function by genetic or chemical manipulations impaired HSPC development. Mechanistically we uncover that primary cilia on endothelial cells ECs transduce Notch signal to the earliest HE for proper HSPC specification during embryogenesis. Altogether our findings reveal a pivotal role of endothelial primary cilia in HSPC development and may shed lights into in vitro directed differentiation of HSPCs.			WT26h rep2	WT26h 2	Sample2	strain:zebrafish embryos\|isolate:not applicable\|dev stage:26 hpf\|sex:not applicable\|tissue:trunk region\|collection date:2017 08 11\|geo loc name:China: Beijing\|isolation source:not applicable\|sample type:normal embryos 2\|BioSampleModel:Model organism or animal									RNA seq of normal embryos2	WT26h 2	WT26h 2	RNA was isolated from trunk regions of control embryos and fsd1 morphants for cDNA library. The cDNA library for sequenced using BGISEQ 500 platform.			RNA-Seq	TRANSCRIPTOMIC	PCR	SINGLE	BGISEQ	BGISEQ-500	SRP140462	WT26h_2_1.fq.gz	fastq	1199179850.0	23983597.0	WT26h 2 1.fq.gz	0:50	A:316605984;C:281184572;G:292581373;T:308419476;N:388445	50		316605984	281184572	292581373	308419476	388445	SRX3940578	SRS3171380	SRA690964	Institute of Zoology, CHINESE ACADEMY OF SCIENCES\|State Key Laboratory of Membrane Biology	Institute of Zoology, CHINESE ACADEMY OF SCIENCES	1	0.95377	0.08617	0.70508	0.4775	50	B	usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2018-04-16	Pharyngula	Embryo	Trunk	Surface Structure
50717	50717	SRR8257205	SRX5074433	SRS4088243	SRP171045	PRJNA507426	Pioneer and repressive functions of p63 during embryonic ectoderm specification [RNA seq]	GSE123058	Transcriptome Analysis	The transcription factor p63 is a master regulator of ectoderm development essential for epidermal specification. Although previous studies have highlighted the role of p63 triggering the epidermal transcriptomic program its precise mechanism of target gene regulation in the complex context of a developing embryo remains poorly understood. Here we used zebrafish embryos to analyze in vivo how p63 regulates the expression of its target genes during development. We generated tp63 knock out mutants that recapitulate human phenotypes and show down regulated epidermal gene expression. Following p63 binding dynamics during development we found two distinct functions clearly separated in space and time. During early development p63 binds enhancers associated to neural genes where it limits Sox3 binding and reduces the expression of these neural genes. Indeed we show that p63 and Sox3 are co expressed in the neural plate border. Later in development p63 binds enhancers associated to epidermal genes and promotes their expression acting as a pioneer factor as it binds to non accessible chromatin and is required for its opening. Therefore our results suggest that p63 is an important regulator of cell fate decisions during ectoderm specification promoting the epidermal fate and inhibiting the neural program. Overall design: RNA seq assays in tp63 zebrafish mutants	parent bioproject:PRJNA507423	pubmed:31296872		RNAseq in zebrafish wild type embryos at 36hpf replicate 3	GSM3494529	tissue:whole embryo\|developmental stage:36hpf\|genotype:WT	RNAseq in zebrafish wild type embryos at 36hpf replicate 3	Reads were aligned against reference genome using STAR software and reads per gene were counted using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene	whole embryo		RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen	Embryos were cultivated at 28°C in E3 medium until desired developmental stage	developmental stage:36hpf\|genotype:WT	GSM3494529	GSM3494529: RNAseq in zebrafish wild type embryos at 36hpf replicate 3; Danio rerio; RNA Seq	GSM3494529		1	RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen	GEO Accession:GSM3494529	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	BGISEQ	BGISEQ-500	SRP171045	RNAseq_zebra_WT_36hpf_rep3.fq.gz	fastq	2560587500.0	51211750.0	GSM3494529 r1	0:50	A:719232941;C:550474431;G:576590260;T:714289868;N:0	50		719232941	550474431	576590260	714289868	0	SRX5074433	SRS4088243	SRA815839	GEO	CABD/CSIC	1	0.93981	0.10951	0.71388	0.48297	50	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Spain	2018-11-28	Pharyngula	Embryo	Whole Organism	All anatomical structures
50718	50718	SRR8257204	SRX5074432	SRS4088242	SRP171045	PRJNA507426	Pioneer and repressive functions of p63 during embryonic ectoderm specification [RNA seq]	GSE123058	Transcriptome Analysis	The transcription factor p63 is a master regulator of ectoderm development essential for epidermal specification. Although previous studies have highlighted the role of p63 triggering the epidermal transcriptomic program its precise mechanism of target gene regulation in the complex context of a developing embryo remains poorly understood. Here we used zebrafish embryos to analyze in vivo how p63 regulates the expression of its target genes during development. We generated tp63 knock out mutants that recapitulate human phenotypes and show down regulated epidermal gene expression. Following p63 binding dynamics during development we found two distinct functions clearly separated in space and time. During early development p63 binds enhancers associated to neural genes where it limits Sox3 binding and reduces the expression of these neural genes. Indeed we show that p63 and Sox3 are co expressed in the neural plate border. Later in development p63 binds enhancers associated to epidermal genes and promotes their expression acting as a pioneer factor as it binds to non accessible chromatin and is required for its opening. Therefore our results suggest that p63 is an important regulator of cell fate decisions during ectoderm specification promoting the epidermal fate and inhibiting the neural program. Overall design: RNA seq assays in tp63 zebrafish mutants	parent bioproject:PRJNA507423	pubmed:31296872		RNAseq in zebrafish wild type embryos at 36hpf replicate 2	GSM3494528	tissue:whole embryo\|developmental stage:36hpf\|genotype:WT	RNAseq in zebrafish wild type embryos at 36hpf replicate 2	Reads were aligned against reference genome using STAR software and reads per gene were counted using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene	whole embryo		RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen	Embryos were cultivated at 28°C in E3 medium until desired developmental stage	developmental stage:36hpf\|genotype:WT	GSM3494528	GSM3494528: RNAseq in zebrafish wild type embryos at 36hpf replicate 2; Danio rerio; RNA Seq	GSM3494528		1	RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen	GEO Accession:GSM3494528	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	BGISEQ	BGISEQ-500	SRP171045	RNAseq_zebra_WT_36hpf_rep2.fq.gz	fastq	2775840750.0	55516815.0	GSM3494528 r1	0:50	A:783053027;C:587947172;G:603351259;T:801489292;N:0	50		783053027	587947172	603351259	801489292	0	SRX5074432	SRS4088242	SRA815839	GEO	CABD/CSIC	1	0.93386	0.11853	0.7007	0.48856	50	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Spain	2018-11-28	Pharyngula	Embryo	Whole Organism	All anatomical structures
50719	50719	SRR8257203	SRX5074431	SRS4088241	SRP171045	PRJNA507426	Pioneer and repressive functions of p63 during embryonic ectoderm specification [RNA seq]	GSE123058	Transcriptome Analysis	The transcription factor p63 is a master regulator of ectoderm development essential for epidermal specification. Although previous studies have highlighted the role of p63 triggering the epidermal transcriptomic program its precise mechanism of target gene regulation in the complex context of a developing embryo remains poorly understood. Here we used zebrafish embryos to analyze in vivo how p63 regulates the expression of its target genes during development. We generated tp63 knock out mutants that recapitulate human phenotypes and show down regulated epidermal gene expression. Following p63 binding dynamics during development we found two distinct functions clearly separated in space and time. During early development p63 binds enhancers associated to neural genes where it limits Sox3 binding and reduces the expression of these neural genes. Indeed we show that p63 and Sox3 are co expressed in the neural plate border. Later in development p63 binds enhancers associated to epidermal genes and promotes their expression acting as a pioneer factor as it binds to non accessible chromatin and is required for its opening. Therefore our results suggest that p63 is an important regulator of cell fate decisions during ectoderm specification promoting the epidermal fate and inhibiting the neural program. Overall design: RNA seq assays in tp63 zebrafish mutants	parent bioproject:PRJNA507423	pubmed:31296872		RNAseq in zebrafish wild type embryos at 36hpf replicate 1	GSM3494527	tissue:whole embryo\|developmental stage:36hpf\|genotype:WT	RNAseq in zebrafish wild type embryos at 36hpf replicate 1	Reads were aligned against reference genome using STAR software and reads per gene were counted using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene	whole embryo		RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen	Embryos were cultivated at 28°C in E3 medium until desired developmental stage	developmental stage:36hpf\|genotype:WT	GSM3494527	GSM3494527: RNAseq in zebrafish wild type embryos at 36hpf replicate 1; Danio rerio; RNA Seq	GSM3494527		1	RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen	GEO Accession:GSM3494527	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	BGISEQ	BGISEQ-500	SRP171045	RNAseq_zebra_WT_36hpf_rep1.fq.gz	fastq	2638769750.0	52775395.0	GSM3494527 r1	0:50	A:749627286;C:556213831;G:574654547;T:758274086;N:0	50		749627286	556213831	574654547	758274086	0	SRX5074431	SRS4088241	SRA815839	GEO	CABD/CSIC	1	0.92992	0.12022	0.72174	0.49097	50	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Spain	2018-11-28	Pharyngula	Embryo	Whole Organism	All anatomical structures
50720	50720	SRR8257202	SRX5074430	SRS4088240	SRP171045	PRJNA507426	Pioneer and repressive functions of p63 during embryonic ectoderm specification [RNA seq]	GSE123058	Transcriptome Analysis	The transcription factor p63 is a master regulator of ectoderm development essential for epidermal specification. Although previous studies have highlighted the role of p63 triggering the epidermal transcriptomic program its precise mechanism of target gene regulation in the complex context of a developing embryo remains poorly understood. Here we used zebrafish embryos to analyze in vivo how p63 regulates the expression of its target genes during development. We generated tp63 knock out mutants that recapitulate human phenotypes and show down regulated epidermal gene expression. Following p63 binding dynamics during development we found two distinct functions clearly separated in space and time. During early development p63 binds enhancers associated to neural genes where it limits Sox3 binding and reduces the expression of these neural genes. Indeed we show that p63 and Sox3 are co expressed in the neural plate border. Later in development p63 binds enhancers associated to epidermal genes and promotes their expression acting as a pioneer factor as it binds to non accessible chromatin and is required for its opening. Therefore our results suggest that p63 is an important regulator of cell fate decisions during ectoderm specification promoting the epidermal fate and inhibiting the neural program. Overall design: RNA seq assays in tp63 zebrafish mutants	parent bioproject:PRJNA507423	pubmed:31296872		RNAseq in zebrafish tp63 mutant embryos at 36hpf replicate 3	GSM3494526	tissue:whole embryo\|developmental stage:36hpf\|genotype:tp63 /	RNAseq in zebrafish tp63 mutant embryos at 36hpf replicate 3	Reads were aligned against reference genome using STAR software and reads per gene were counted using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene	whole embryo		RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen	Embryos were cultivated at 28°C in E3 medium until desired developmental stage	developmental stage:36hpf\|genotype:tp63 /	GSM3494526	GSM3494526: RNAseq in zebrafish tp63 mutant embryos at 36hpf replicate 3; Danio rerio; RNA Seq	GSM3494526		1	RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen	GEO Accession:GSM3494526	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	BGISEQ	BGISEQ-500	SRP171045	RNAseq_zebra_p63mut_36hpf_rep3.fq.gz	fastq	2651169450.0	53023389.0	GSM3494526 r1	0:50	A:752539060;C:560162268;G:581624300;T:756843822;N:0	50		752539060	560162268	581624300	756843822	0	SRX5074430	SRS4088240	SRA815839	GEO	CABD/CSIC	1	0.94022	0.12949	0.70019	0.50336	50	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Spain	2018-11-28	Pharyngula	Embryo	Whole Organism	All anatomical structures
50721	50721	SRR8257201	SRX5074429	SRS4088239	SRP171045	PRJNA507426	Pioneer and repressive functions of p63 during embryonic ectoderm specification [RNA seq]	GSE123058	Transcriptome Analysis	The transcription factor p63 is a master regulator of ectoderm development essential for epidermal specification. Although previous studies have highlighted the role of p63 triggering the epidermal transcriptomic program its precise mechanism of target gene regulation in the complex context of a developing embryo remains poorly understood. Here we used zebrafish embryos to analyze in vivo how p63 regulates the expression of its target genes during development. We generated tp63 knock out mutants that recapitulate human phenotypes and show down regulated epidermal gene expression. Following p63 binding dynamics during development we found two distinct functions clearly separated in space and time. During early development p63 binds enhancers associated to neural genes where it limits Sox3 binding and reduces the expression of these neural genes. Indeed we show that p63 and Sox3 are co expressed in the neural plate border. Later in development p63 binds enhancers associated to epidermal genes and promotes their expression acting as a pioneer factor as it binds to non accessible chromatin and is required for its opening. Therefore our results suggest that p63 is an important regulator of cell fate decisions during ectoderm specification promoting the epidermal fate and inhibiting the neural program. Overall design: RNA seq assays in tp63 zebrafish mutants	parent bioproject:PRJNA507423	pubmed:31296872		RNAseq in zebrafish tp63 mutant embryos at 36hpf replicate 2	GSM3494525	tissue:whole embryo\|developmental stage:36hpf\|genotype:tp63 /	RNAseq in zebrafish tp63 mutant embryos at 36hpf replicate 2	Reads were aligned against reference genome using STAR software and reads per gene were counted using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene	whole embryo		RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen	Embryos were cultivated at 28°C in E3 medium until desired developmental stage	developmental stage:36hpf\|genotype:tp63 /	GSM3494525	GSM3494525: RNAseq in zebrafish tp63 mutant embryos at 36hpf replicate 2; Danio rerio; RNA Seq	GSM3494525		1	RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen	GEO Accession:GSM3494525	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	BGISEQ	BGISEQ-500	SRP171045	RNAseq_zebra_p63mut_36hpf_rep2.fq.gz	fastq	2821501700.0	56430034.0	GSM3494525 r1	0:50	A:795357588;C:599294949;G:620563224;T:806285939;N:0	50		795357588	599294949	620563224	806285939	0	SRX5074429	SRS4088239	SRA815839	GEO	CABD/CSIC	1	0.93671	0.12314	0.6957	0.48362	50	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Spain	2018-11-28	Pharyngula	Embryo	Whole Organism	All anatomical structures
50722	50722	SRR8257200	SRX5074428	SRS4088238	SRP171045	PRJNA507426	Pioneer and repressive functions of p63 during embryonic ectoderm specification [RNA seq]	GSE123058	Transcriptome Analysis	The transcription factor p63 is a master regulator of ectoderm development essential for epidermal specification. Although previous studies have highlighted the role of p63 triggering the epidermal transcriptomic program its precise mechanism of target gene regulation in the complex context of a developing embryo remains poorly understood. Here we used zebrafish embryos to analyze in vivo how p63 regulates the expression of its target genes during development. We generated tp63 knock out mutants that recapitulate human phenotypes and show down regulated epidermal gene expression. Following p63 binding dynamics during development we found two distinct functions clearly separated in space and time. During early development p63 binds enhancers associated to neural genes where it limits Sox3 binding and reduces the expression of these neural genes. Indeed we show that p63 and Sox3 are co expressed in the neural plate border. Later in development p63 binds enhancers associated to epidermal genes and promotes their expression acting as a pioneer factor as it binds to non accessible chromatin and is required for its opening. Therefore our results suggest that p63 is an important regulator of cell fate decisions during ectoderm specification promoting the epidermal fate and inhibiting the neural program. Overall design: RNA seq assays in tp63 zebrafish mutants	parent bioproject:PRJNA507423	pubmed:31296872		RNAseq in zebrafish tp63 mutant embryos at 36hpf replicate 1	GSM3494524	tissue:whole embryo\|developmental stage:36hpf\|genotype:tp63 /	RNAseq in zebrafish tp63 mutant embryos at 36hpf replicate 1	Reads were aligned against reference genome using STAR software and reads per gene were counted using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene	whole embryo		RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen	Embryos were cultivated at 28°C in E3 medium until desired developmental stage	developmental stage:36hpf\|genotype:tp63 /	GSM3494524	GSM3494524: RNAseq in zebrafish tp63 mutant embryos at 36hpf replicate 1; Danio rerio; RNA Seq	GSM3494524		1	RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen	GEO Accession:GSM3494524	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	BGISEQ	BGISEQ-500	SRP171045	RNAseq_zebra_p63mut_36hpf_rep1.fq.gz	fastq	2592494100.0	51849882.0	GSM3494524 r1	0:50	A:730978948;C:550803197;G:572081489;T:738630466;N:0	50		730978948	550803197	572081489	738630466	0	SRX5074428	SRS4088238	SRA815839	GEO	CABD/CSIC	1	0.94035	0.11571	0.70796	0.49468	50	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Spain	2018-11-28	Pharyngula	Embryo	Whole Organism	All anatomical structures
60613	60613	SRR12435888	SRX8931583	SRS7187991	SRP277167	PRJNA656771	CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression [RNA seq]	GSE156094	Transcriptome Analysis	CTCF is an 11 zinc finger DNA binding protein that acts as a transcriptional repressor and insulator as well as an architectural protein required for 3D genome folding. CTCF mediates long range chromatin looping and is enriched at the boundaries of topologically associating domains TADs which are sub megabase chromatin structures composed of genomic regions with high contact frequency. Although CTCF is essential for cycling cells and developing embryos its in vitro removal has only modest effects over gene expression challenging the generally accepted idea that TADs facilitate enhancer promoter interactions within gene regulatory landscapes. However the effects of an altered CTCF mediated chromatin structure on gene regulation in vivo are poorly understood. Here we have generated a ctcf knockout mutant in zebrafish that allows us to monitor the effect of CTCF loss of function during embryo patterning and organogenesis. CTCF absence leads to a loss of chromatin structure in zebrafish embryos and affects the expression of thousands of genes among them many developmental genes. In addition we show that chromatin accessibility both at CTCF sites and at developmental cis regulatory elements CREs is severely compromised in ctcf mutants. Probing chromatin interactions from developmental genes at high resolution we further demonstrate that promoters fail to fully establish long range contacts with their associated regulatory landscapes leading to altered gene expression patterns during development. Therefore our results demonstrate that CTCF and TADs are essential to finetune gene expression during embryonic development providing the structural basis for the establishment of developmental gene regulatory landscapes. Overall design: RNA seq assays in wild type and ctcf zebrafish mutants at developmental stages 24 hpf and 48 hpf with and without xxx of tp53 morpholino	parent bioproject:PRJNA656767	pubmed:34518536		RNA seq in zebrafish wild type embryos at 24hpf replicate 2	GSM4724530	tissue:whole embryo\|developmental stage:24 hpf\|genotype:WT	RNA seq in zebrafish wild type embryos at 24hpf replicate 2	Reads were aligned against reference genome using STAR software Read counts per gene were calculated using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene	whole embryo	Injection of tp53 morpholino was performed at 1 cell stage	RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen	Embryos were grown at 28°C in E3 medium until desired developmental stage	developmental stage:24 hpf\|genotype:WT	GSM4724530	GSM4724530: RNA seq in zebrafish wild type embryos at 24hpf replicate 2; Danio rerio; RNA Seq	GSM4724530		1	RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen	GEO Accession:GSM4724530	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	BGISEQ	BGISEQ-500	SRP277167	RNAseq_24h_wt_rep2_1.fq.gz	fastq	2241073250.0	44821465.0	GSM4724530 r1	0:50	A:593435654;C:517470954;G:544866646;T:585299996;N:0	50		593435654	517470954	544866646	585299996	0	SRX8931583	SRS7187991	SRA1111981	GEO	CABD, Universidad Pablo de Olavide-CSIC	1	0.9534	0.07821	0.70331	0.47463	50	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Spain	2020-08-12	Pharyngula	Embryo	Whole Organism	All anatomical structures
60614	60614	SRR12435887	SRX8931582	SRS7187990	SRP277167	PRJNA656771	CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression [RNA seq]	GSE156094	Transcriptome Analysis	CTCF is an 11 zinc finger DNA binding protein that acts as a transcriptional repressor and insulator as well as an architectural protein required for 3D genome folding. CTCF mediates long range chromatin looping and is enriched at the boundaries of topologically associating domains TADs which are sub megabase chromatin structures composed of genomic regions with high contact frequency. Although CTCF is essential for cycling cells and developing embryos its in vitro removal has only modest effects over gene expression challenging the generally accepted idea that TADs facilitate enhancer promoter interactions within gene regulatory landscapes. However the effects of an altered CTCF mediated chromatin structure on gene regulation in vivo are poorly understood. Here we have generated a ctcf knockout mutant in zebrafish that allows us to monitor the effect of CTCF loss of function during embryo patterning and organogenesis. CTCF absence leads to a loss of chromatin structure in zebrafish embryos and affects the expression of thousands of genes among them many developmental genes. In addition we show that chromatin accessibility both at CTCF sites and at developmental cis regulatory elements CREs is severely compromised in ctcf mutants. Probing chromatin interactions from developmental genes at high resolution we further demonstrate that promoters fail to fully establish long range contacts with their associated regulatory landscapes leading to altered gene expression patterns during development. Therefore our results demonstrate that CTCF and TADs are essential to finetune gene expression during embryonic development providing the structural basis for the establishment of developmental gene regulatory landscapes. Overall design: RNA seq assays in wild type and ctcf zebrafish mutants at developmental stages 24 hpf and 48 hpf with and without xxx of tp53 morpholino	parent bioproject:PRJNA656767	pubmed:34518536		RNA seq in zebrafish wild type embryos at 24hpf replicate 1	GSM4724529	tissue:whole embryo\|developmental stage:24 hpf\|genotype:WT	RNA seq in zebrafish wild type embryos at 24hpf replicate 1	Reads were aligned against reference genome using STAR software Read counts per gene were calculated using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene	whole embryo	Injection of tp53 morpholino was performed at 1 cell stage	RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen	Embryos were grown at 28°C in E3 medium until desired developmental stage	developmental stage:24 hpf\|genotype:WT	GSM4724529	GSM4724529: RNA seq in zebrafish wild type embryos at 24hpf replicate 1; Danio rerio; RNA Seq	GSM4724529		1	RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen	GEO Accession:GSM4724529	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	BGISEQ	BGISEQ-500	SRP277167	RNAseq_24h_wt_rep1_1.fq.gz	fastq	1206103900.0	24122078.0	GSM4724529 r1	0:50	A:329983157;C:268788282;G:289794374;T:316858580;N:679507	50		329983157	268788282	289794374	316858580	679507	SRX8931582	SRS7187990	SRA1111981	GEO	CABD, Universidad Pablo de Olavide-CSIC	1	0.94221	0.09615	0.69077	0.47405	50	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Spain	2020-08-12	Pharyngula	Embryo	Whole Organism	All anatomical structures
60615	60615	SRR12435886	SRX8931581	SRS7187989	SRP277167	PRJNA656771	CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression [RNA seq]	GSE156094	Transcriptome Analysis	CTCF is an 11 zinc finger DNA binding protein that acts as a transcriptional repressor and insulator as well as an architectural protein required for 3D genome folding. CTCF mediates long range chromatin looping and is enriched at the boundaries of topologically associating domains TADs which are sub megabase chromatin structures composed of genomic regions with high contact frequency. Although CTCF is essential for cycling cells and developing embryos its in vitro removal has only modest effects over gene expression challenging the generally accepted idea that TADs facilitate enhancer promoter interactions within gene regulatory landscapes. However the effects of an altered CTCF mediated chromatin structure on gene regulation in vivo are poorly understood. Here we have generated a ctcf knockout mutant in zebrafish that allows us to monitor the effect of CTCF loss of function during embryo patterning and organogenesis. CTCF absence leads to a loss of chromatin structure in zebrafish embryos and affects the expression of thousands of genes among them many developmental genes. In addition we show that chromatin accessibility both at CTCF sites and at developmental cis regulatory elements CREs is severely compromised in ctcf mutants. Probing chromatin interactions from developmental genes at high resolution we further demonstrate that promoters fail to fully establish long range contacts with their associated regulatory landscapes leading to altered gene expression patterns during development. Therefore our results demonstrate that CTCF and TADs are essential to finetune gene expression during embryonic development providing the structural basis for the establishment of developmental gene regulatory landscapes. Overall design: RNA seq assays in wild type and ctcf zebrafish mutants at developmental stages 24 hpf and 48 hpf with and without xxx of tp53 morpholino	parent bioproject:PRJNA656767	pubmed:34518536		RNA seq in zebrafish ctcf mutant embryos at 24hpf replicate 2	GSM4724528	tissue:whole embryo\|developmental stage:24 hpf\|genotype:ctcf /	RNA seq in zebrafish ctcf mutant embryos at 24hpf replicate 2	Reads were aligned against reference genome using STAR software Read counts per gene were calculated using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene	whole embryo	Injection of tp53 morpholino was performed at 1 cell stage	RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen	Embryos were grown at 28°C in E3 medium until desired developmental stage	developmental stage:24 hpf\|genotype:ctcf /	GSM4724528	GSM4724528: RNA seq in zebrafish ctcf mutant embryos at 24hpf replicate 2; Danio rerio; RNA Seq	GSM4724528		1	RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen	GEO Accession:GSM4724528	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	BGISEQ	BGISEQ-500	SRP277167	RNAseq_24h_ctcf_rep2_1.fq.gz	fastq	2823674750.0	56473495.0	GSM4724528 r1	0:50	A:743759446;C:653943934;G:679405104;T:746566266;N:0	50		743759446	653943934	679405104	746566266	0	SRX8931581	SRS7187989	SRA1111981	GEO	CABD, Universidad Pablo de Olavide-CSIC	1	0.95027	0.08763	0.6984	0.487	50	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Spain	2020-08-12	Pharyngula	Embryo	Whole Organism	All anatomical structures
60616	60616	SRR12435885	SRX8931580	SRS7187988	SRP277167	PRJNA656771	CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression [RNA seq]	GSE156094	Transcriptome Analysis	CTCF is an 11 zinc finger DNA binding protein that acts as a transcriptional repressor and insulator as well as an architectural protein required for 3D genome folding. CTCF mediates long range chromatin looping and is enriched at the boundaries of topologically associating domains TADs which are sub megabase chromatin structures composed of genomic regions with high contact frequency. Although CTCF is essential for cycling cells and developing embryos its in vitro removal has only modest effects over gene expression challenging the generally accepted idea that TADs facilitate enhancer promoter interactions within gene regulatory landscapes. However the effects of an altered CTCF mediated chromatin structure on gene regulation in vivo are poorly understood. Here we have generated a ctcf knockout mutant in zebrafish that allows us to monitor the effect of CTCF loss of function during embryo patterning and organogenesis. CTCF absence leads to a loss of chromatin structure in zebrafish embryos and affects the expression of thousands of genes among them many developmental genes. In addition we show that chromatin accessibility both at CTCF sites and at developmental cis regulatory elements CREs is severely compromised in ctcf mutants. Probing chromatin interactions from developmental genes at high resolution we further demonstrate that promoters fail to fully establish long range contacts with their associated regulatory landscapes leading to altered gene expression patterns during development. Therefore our results demonstrate that CTCF and TADs are essential to finetune gene expression during embryonic development providing the structural basis for the establishment of developmental gene regulatory landscapes. Overall design: RNA seq assays in wild type and ctcf zebrafish mutants at developmental stages 24 hpf and 48 hpf with and without xxx of tp53 morpholino	parent bioproject:PRJNA656767	pubmed:34518536		RNA seq in zebrafish ctcf mutant embryos at 24hpf replicate 1	GSM4724527	tissue:whole embryo\|developmental stage:24 hpf\|genotype:ctcf /	RNA seq in zebrafish ctcf mutant embryos at 24hpf replicate 1	Reads were aligned against reference genome using STAR software Read counts per gene were calculated using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene	whole embryo	Injection of tp53 morpholino was performed at 1 cell stage	RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen	Embryos were grown at 28°C in E3 medium until desired developmental stage	developmental stage:24 hpf\|genotype:ctcf /	GSM4724527	GSM4724527: RNA seq in zebrafish ctcf mutant embryos at 24hpf replicate 1; Danio rerio; RNA Seq	GSM4724527		1	RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen	GEO Accession:GSM4724527	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	BGISEQ	BGISEQ-500	SRP277167	RNAseq_24h_ctcf_rep1_1.fq.gz	fastq	2408631250.0	48172625.0	GSM4724527 r1	0:50	A:623761639;C:570722378;G:584932664;T:629214569;N:0	50		623761639	570722378	584932664	629214569	0	SRX8931580	SRS7187988	SRA1111981	GEO	CABD, Universidad Pablo de Olavide-CSIC	1	0.95366	0.07765	0.70023	0.47375	50	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Spain	2020-08-12	Pharyngula	Embryo	Whole Organism	All anatomical structures
71549	71549	SRR21700247	SRX17697774	SRS15228561	SRP399479	PRJNA884084	RNA Seq data of gmfg morphants and their control siblings	PRJNA884084	Other	To more specifically explore the underlying mechanism by which gmfg regulates HSPC initiation we performed RNA sequencing RNA Seq with the dissected trunk and tail from 26 hpf gmfg morphants and their control siblings.				biological replicate 3	gmfg atgMO 3	strain:not applicable\|isolate:not applicable\|dev stage:26 hpf\|sex:not applicable\|tissue:the dissected trunk and tail\|collection date:2021 02 26\|geo loc name:China:Shenzhen Guangdong\|sample type:mo3\|BioSampleModel:Model organism or animal									RNA seq of Danio rerio	MO3 20210214	MO3 20210214	RNA seq of Danio rerio in different conditions			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	SINGLE	BGISEQ	BGISEQ-500	SRP399479	MO_3_1.fq.gz	fastq	1194263900.0	23885278.0	MO 3 1.fq.gz	0:50 1:0	A:315714579;C:274130504;G:282488713;T:321930104;N:0	50	0	315714579	274130504	282488713	321930104	0	SRX17697774	SRS15228561	SRA1506658	the First Affiliated Hospital, School of Medicine, Zhejiang University\|BoneMarrow Transplantation Center	the First Affiliated Hospital, School of Medicine, Zhejiang University	1	0.9415	0.07261	0.70701	0.47029	50	B	usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2022-09-25	Pharyngula	Embryo	Multi-tissue	Multi-system
71550	71550	SRR21700248	SRX17697773	SRS15228560	SRP399479	PRJNA884084	RNA Seq data of gmfg morphants and their control siblings	PRJNA884084	Other	To more specifically explore the underlying mechanism by which gmfg regulates HSPC initiation we performed RNA sequencing RNA Seq with the dissected trunk and tail from 26 hpf gmfg morphants and their control siblings.				biological replicate 2	gmfg atgMO 2	strain:not applicable\|isolate:not applicable\|dev stage:26 hpf\|sex:not applicable\|tissue:the dissected trunk and tail\|collection date:2021 02 26\|geo loc name:China:Shenzhen Guangdong\|sample type:mo2\|BioSampleModel:Model organism or animal									RNA seq of Danio rerio	MO2 20210213	MO2 20210213	RNA seq of Danio rerio in different conditions			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	SINGLE	BGISEQ	BGISEQ-500	SRP399479	MO_2_1.fq.gz	fastq	1193697300.0	23873946.0	MO 2 1.fq.gz	0:50 1:0	A:316188077;C:272941933;G:282559962;T:322007328;N:0	50	0	316188077	272941933	282559962	322007328	0	SRX17697773	SRS15228560	SRA1506658	the First Affiliated Hospital, School of Medicine, Zhejiang University\|BoneMarrow Transplantation Center	the First Affiliated Hospital, School of Medicine, Zhejiang University	1	0.94144	0.07426	0.70715	0.47856	50	B	usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2022-09-25	Pharyngula	Embryo	Multi-tissue	Multi-system
71551	71551	SRR21700249	SRX17697772	SRS15228559	SRP399479	PRJNA884084	RNA Seq data of gmfg morphants and their control siblings	PRJNA884084	Other	To more specifically explore the underlying mechanism by which gmfg regulates HSPC initiation we performed RNA sequencing RNA Seq with the dissected trunk and tail from 26 hpf gmfg morphants and their control siblings.				biological replicate 1	gmfg atgMO 1	strain:not applicable\|isolate:not applicable\|dev stage:26 hpf\|sex:not applicable\|tissue:the dissected trunk and tail\|collection date:2021 02 26\|geo loc name:China:Shenzhen Guangdong\|sample type:mo1\|BioSampleModel:Model organism or animal									RNA seq of Danio rerio	MO1 20210212	MO1 20210212	RNA seq of Danio rerio in different conditions			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	SINGLE	BGISEQ	BGISEQ-500	SRP399479	MO_1_1.fq.gz	fastq	1194311300.0	23886226.0	MO 1 1.fq.gz	0:50 1:0	A:317344841;C:272348188;G:281111904;T:323506367;N:0	50	0	317344841	272348188	281111904	323506367	0	SRX17697772	SRS15228559	SRA1506658	the First Affiliated Hospital, School of Medicine, Zhejiang University\|BoneMarrow Transplantation Center	the First Affiliated Hospital, School of Medicine, Zhejiang University	1	0.94366	0.07701	0.70274	0.47929	50	B	usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2022-09-25	Pharyngula	Embryo	Multi-tissue	Multi-system
71552	71552	SRR21700250	SRX17697771	SRS15228558	SRP399479	PRJNA884084	RNA Seq data of gmfg morphants and their control siblings	PRJNA884084	Other	To more specifically explore the underlying mechanism by which gmfg regulates HSPC initiation we performed RNA sequencing RNA Seq with the dissected trunk and tail from 26 hpf gmfg morphants and their control siblings.				biological replicate 3	ctl 3	strain:not applicable\|isolate:not applicable\|dev stage:26 hpf\|sex:not applicable\|tissue:the dissected trunk and tail\|collection date:2021 02 26\|geo loc name:China:Shenzhen Guangdong\|sample type:ctl3\|BioSampleModel:Model organism or animal									RNA seq of Danio rerio	ctl3 20210211	ctl3 20210211	RNA seq of Danio rerio in different conditions			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	SINGLE	BGISEQ	BGISEQ-500	SRP399479	ctl_3_1.fq.gz	fastq	1190502850.0	23810057.0	ctl 3 1.fq.gz	0:50 1:0	A:314168919;C:272277792;G:283249731;T:320806408;N:0	50	0	314168919	272277792	283249731	320806408	0	SRX17697771	SRS15228558	SRA1506658	the First Affiliated Hospital, School of Medicine, Zhejiang University\|BoneMarrow Transplantation Center	the First Affiliated Hospital, School of Medicine, Zhejiang University	1	0.94354	0.08493	0.70228	0.48147	50	B	usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2022-09-25	Pharyngula	Embryo	Multi-tissue	Multi-system
71553	71553	SRR21700251	SRX17697770	SRS15228557	SRP399479	PRJNA884084	RNA Seq data of gmfg morphants and their control siblings	PRJNA884084	Other	To more specifically explore the underlying mechanism by which gmfg regulates HSPC initiation we performed RNA sequencing RNA Seq with the dissected trunk and tail from 26 hpf gmfg morphants and their control siblings.				biological replicate 2	ctl 2	strain:not applicable\|isolate:not applicable\|dev stage:26 hpf\|sex:not applicable\|tissue:the dissected trunk and tail\|collection date:2021 02 26\|geo loc name:China:Shenzhen Guangdong\|sample type:ctl2\|BioSampleModel:Model organism or animal									RNA seq of Danio rerio	ctl2 20210210	ctl2 20210210	RNA seq of Danio rerio in different conditions			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	SINGLE	BGISEQ	BGISEQ-500	SRP399479	ctl_2_1.fq.gz	fastq	1193941900.0	23878838.0	ctl 2 1.fq.gz	0:50 1:0	A:315521033;C:273947671;G:281554279;T:322918917;N:0	50	0	315521033	273947671	281554279	322918917	0	SRX17697770	SRS15228557	SRA1506658	the First Affiliated Hospital, School of Medicine, Zhejiang University\|BoneMarrow Transplantation Center	the First Affiliated Hospital, School of Medicine, Zhejiang University	1	0.94073	0.08514	0.70281	0.4767	50	B	usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2022-09-25	Pharyngula	Embryo	Multi-tissue	Multi-system
71554	71554	SRR21700252	SRX17697769	SRS15228556	SRP399479	PRJNA884084	RNA Seq data of gmfg morphants and their control siblings	PRJNA884084	Other	To more specifically explore the underlying mechanism by which gmfg regulates HSPC initiation we performed RNA sequencing RNA Seq with the dissected trunk and tail from 26 hpf gmfg morphants and their control siblings.				biological replicate 1	ctl 1	strain:not applicable\|isolate:not applicable\|dev stage:26 hpf\|sex:not applicable\|tissue:the dissected trunk and tail\|collection date:2021 02 26\|geo loc name:China:Shenzhen Guangdong\|sample type:ctl1\|BioSampleModel:Model organism or animal									RNA seq of Danio rerio	ctl1 20210209	ctl1 20210209	RNA seq of Danio rerio in different conditions			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	SINGLE	BGISEQ	BGISEQ-500	SRP399479	ctl_1_1.fq.gz	fastq	1194196300.0	23883926.0	ctl 1 1.fq.gz	0:50 1:0	A:315050496;C:273915045;G:282252071;T:322978688;N:0	50	0	315050496	273915045	282252071	322978688	0	SRX17697769	SRS15228556	SRA1506658	the First Affiliated Hospital, School of Medicine, Zhejiang University\|BoneMarrow Transplantation Center	the First Affiliated Hospital, School of Medicine, Zhejiang University	1	0.94272	0.08675	0.70234	0.47397	50	B	usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2022-09-25	Pharyngula	Embryo	Multi-tissue	Multi-system

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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");;