metadata: run_metadata: 12 rows where experiment.platform = "ILLUMINA", technology = "strtseq" and tissue_curation

12 rows where experiment.platform = "ILLUMINA", technology = "strtseq" and tissue_curation_coarse = "Cardiovascular System"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.extractprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	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
67022	67022	SRR16973878	SRX13164742	SRS11095945	SRP346708	PRJNA781453	WGBS and RNA seq of Danio rerio in HSPC generation	GSE189072	Other	In this study we interrogated the role of DNA methylation in HSPC generation by taking advantage of dnmt1 knockout/knockdown embryos in zebrafish. First we generated a comprehensive DNA methylation landscape of EHT which revealed gradually hypermethylated regions associated with vasculogenesis. Taking advantage of dnmt1 deficient embryos we showed that the decreased DNA methylation blocked HSPC emergence. Mechanistically we demonstrated that the decreased DNA methylation increased the expression of arterial genes and Notch signaling thus contributing to defects in the EHT in dnmt1 deficient embryos. Herein we identified that DNA methylation as epigenetic regulator participates in the negative modulation of Notch signaling through inhibiting transcription during HSPC generation in zebrafish. Overall design: WGBS and RNA seq of Danio rerio in EC HE and HSPC.	pubmed:35502759	HE mut rep3 RNA	GSM5694252	tissue:hemogenic endothelium cells\|developmental stage:HE\|genotype:dnmt1 mutant\|region:AGM	HE mut rep3 RNA	Basecalls perfomed using CASAVA2.19 WGBS and RNA seq raw sequencing reads were first trimmed for adapter and low quality sequences. Then mapped to GRCz11 using BS Seeker2v2.1.8 and hisat2v2.2.1 with parameters " t Y m 0.04 bt2 end to end" and " known splicesite infile p 30 k 10 dta t" separately. Student's T test was used to perform DMR analysis for WGBS data. Gene expression level was quantified by HTSeqv0.12.4 and differentially expressed genesDEGs were determined by DESeq2v1.30.1 Genome build: GRCz11 Supplementary files format and content: RNA seq raw count matrix Supplementary files format and content: raw count.txt raw counts Supplementary files format and content: EC sib.bed DMRs of EC sibling compared with HE sibling and HSC sibling Supplementary files format and content: HE sib.bed DMRs of HE sibling compared with EC sibling and HSC sibling Supplementary files format and content: HSC sib.bed DMRs of HSC sibling compared with EC sibling and HE sibling Supplementary files format and content: EC HE sib.bed DMRs of EC and HE sibling Supplementary files format and content: HE HSC sib.bed DMRs of HE and HSC sibling Supplementary files format and content: EC sib mut.bed DMRs of EC sibling and EC mutant Supplementary files format and content: HE sib mut.bed DMRs of HE sibling and HE mutant Supplementary files format and content: HSC sib mut.bed DMRs of HSC sibling and HSC mutant	hemogenic endothelium cells	Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3′ biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification	developmental stage:HE\|genotype:dnmt1 mutant\|region:AGM	GSM5694252	GSM5694252: HE mut rep3 RNA; Danio rerio; RNA Seq	GSM5694252	1	Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3′ biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification	GEO Accession:GSM5694252	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP346708	loader:fastq load.py	HE_sib_3_1_RNA.fq.gz HE_sib_3_2_RNA.fq.gz	fastq fastq	8484093900.0	28280313.0	GSM5694252 r1	0:150 1:150	A:2396956113;C:1725799170;G:1832630297;T:2528680586;N:27734	150	150	2396956113	1725799170	1832630297	2528680586	27734	SRX13164742	SRS11095945	SRA1331007	GEO	Institute of Hematology and Blood Diseases Hospital	2	0.93895	0.93325	0.16467	0.16385	0.76595	0.76895	0.47613	0.46536	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	strtseq	China	2021-11-18	Undetermined	Embryo	Endothelium	Cardiovascular System
67023	67023	SRR16973877	SRX13164741	SRS11095944	SRP346708	PRJNA781453	WGBS and RNA seq of Danio rerio in HSPC generation	GSE189072	Other	In this study we interrogated the role of DNA methylation in HSPC generation by taking advantage of dnmt1 knockout/knockdown embryos in zebrafish. First we generated a comprehensive DNA methylation landscape of EHT which revealed gradually hypermethylated regions associated with vasculogenesis. Taking advantage of dnmt1 deficient embryos we showed that the decreased DNA methylation blocked HSPC emergence. Mechanistically we demonstrated that the decreased DNA methylation increased the expression of arterial genes and Notch signaling thus contributing to defects in the EHT in dnmt1 deficient embryos. Herein we identified that DNA methylation as epigenetic regulator participates in the negative modulation of Notch signaling through inhibiting transcription during HSPC generation in zebrafish. Overall design: WGBS and RNA seq of Danio rerio in EC HE and HSPC.	pubmed:35502759	HE mut rep2 RNA	GSM5694251	tissue:hemogenic endothelium cells\|developmental stage:HE\|genotype:dnmt1 mutant\|region:AGM	HE mut rep2 RNA	Basecalls perfomed using CASAVA2.19 WGBS and RNA seq raw sequencing reads were first trimmed for adapter and low quality sequences. Then mapped to GRCz11 using BS Seeker2v2.1.8 and hisat2v2.2.1 with parameters " t Y m 0.04 bt2 end to end" and " known splicesite infile p 30 k 10 dta t" separately. Student's T test was used to perform DMR analysis for WGBS data. Gene expression level was quantified by HTSeqv0.12.4 and differentially expressed genesDEGs were determined by DESeq2v1.30.1 Genome build: GRCz11 Supplementary files format and content: RNA seq raw count matrix Supplementary files format and content: raw count.txt raw counts Supplementary files format and content: EC sib.bed DMRs of EC sibling compared with HE sibling and HSC sibling Supplementary files format and content: HE sib.bed DMRs of HE sibling compared with EC sibling and HSC sibling Supplementary files format and content: HSC sib.bed DMRs of HSC sibling compared with EC sibling and HE sibling Supplementary files format and content: EC HE sib.bed DMRs of EC and HE sibling Supplementary files format and content: HE HSC sib.bed DMRs of HE and HSC sibling Supplementary files format and content: EC sib mut.bed DMRs of EC sibling and EC mutant Supplementary files format and content: HE sib mut.bed DMRs of HE sibling and HE mutant Supplementary files format and content: HSC sib mut.bed DMRs of HSC sibling and HSC mutant	hemogenic endothelium cells	Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3′ biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification	developmental stage:HE\|genotype:dnmt1 mutant\|region:AGM	GSM5694251	GSM5694251: HE mut rep2 RNA; Danio rerio; RNA Seq	GSM5694251	1	Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3′ biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification	GEO Accession:GSM5694251	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP346708		HE_sib_2_1_RNA.fq.gz HE_sib_2_2_RNA.fq.gz	fastq fastq	3391937700.0	11306459.0	GSM5694251 r1	0:150 1:150	A:981400300;C:664246146;G:716019213;T:1030238113;N:33928	150	150	981400300	664246146	716019213	1030238113	33928	SRX13164741	SRS11095944	SRA1331007	GEO	Institute of Hematology and Blood Diseases Hospital	2	0.88669	0.88216	0.25368	0.25155	0.76361	0.76883	0.54578	0.54556	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	strtseq	China	2021-11-18	Undetermined	Embryo	Endothelium	Cardiovascular System
67024	67024	SRR16973876	SRX13164740	SRS11095942	SRP346708	PRJNA781453	WGBS and RNA seq of Danio rerio in HSPC generation	GSE189072	Other	In this study we interrogated the role of DNA methylation in HSPC generation by taking advantage of dnmt1 knockout/knockdown embryos in zebrafish. First we generated a comprehensive DNA methylation landscape of EHT which revealed gradually hypermethylated regions associated with vasculogenesis. Taking advantage of dnmt1 deficient embryos we showed that the decreased DNA methylation blocked HSPC emergence. Mechanistically we demonstrated that the decreased DNA methylation increased the expression of arterial genes and Notch signaling thus contributing to defects in the EHT in dnmt1 deficient embryos. Herein we identified that DNA methylation as epigenetic regulator participates in the negative modulation of Notch signaling through inhibiting transcription during HSPC generation in zebrafish. Overall design: WGBS and RNA seq of Danio rerio in EC HE and HSPC.	pubmed:35502759	HE mut rep1 RNA	GSM5694250	tissue:hemogenic endothelium cells\|developmental stage:HE\|genotype:dnmt1 mutant\|region:AGM	HE mut rep1 RNA	Basecalls perfomed using CASAVA2.19 WGBS and RNA seq raw sequencing reads were first trimmed for adapter and low quality sequences. Then mapped to GRCz11 using BS Seeker2v2.1.8 and hisat2v2.2.1 with parameters " t Y m 0.04 bt2 end to end" and " known splicesite infile p 30 k 10 dta t" separately. Student's T test was used to perform DMR analysis for WGBS data. Gene expression level was quantified by HTSeqv0.12.4 and differentially expressed genesDEGs were determined by DESeq2v1.30.1 Genome build: GRCz11 Supplementary files format and content: RNA seq raw count matrix Supplementary files format and content: raw count.txt raw counts Supplementary files format and content: EC sib.bed DMRs of EC sibling compared with HE sibling and HSC sibling Supplementary files format and content: HE sib.bed DMRs of HE sibling compared with EC sibling and HSC sibling Supplementary files format and content: HSC sib.bed DMRs of HSC sibling compared with EC sibling and HE sibling Supplementary files format and content: EC HE sib.bed DMRs of EC and HE sibling Supplementary files format and content: HE HSC sib.bed DMRs of HE and HSC sibling Supplementary files format and content: EC sib mut.bed DMRs of EC sibling and EC mutant Supplementary files format and content: HE sib mut.bed DMRs of HE sibling and HE mutant Supplementary files format and content: HSC sib mut.bed DMRs of HSC sibling and HSC mutant	hemogenic endothelium cells	Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3′ biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification	developmental stage:HE\|genotype:dnmt1 mutant\|region:AGM	GSM5694250	GSM5694250: HE mut rep1 RNA; Danio rerio; RNA Seq	GSM5694250	1	Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3′ biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification	GEO Accession:GSM5694250	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP346708		HE_sib_1_1_RNA.fq.gz HE_sib_1_2_RNA.fq.gz	fastq fastq	3246930300.0	10823101.0	GSM5694250 r1	0:150 1:150	A:938425919;C:639911754;G:671817291;T:996741337;N:33999	150	150	938425919	639911754	671817291	996741337	33999	SRX13164740	SRS11095942	SRA1331007	GEO	Institute of Hematology and Blood Diseases Hospital	2	0.93431	0.92139	0.18855	0.18424	0.78886	0.79308	0.52892	0.52798	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	strtseq	China	2021-11-18	Undetermined	Embryo	Endothelium	Cardiovascular System
67025	67025	SRR16973875	SRX13164739	SRS11095943	SRP346708	PRJNA781453	WGBS and RNA seq of Danio rerio in HSPC generation	GSE189072	Other	In this study we interrogated the role of DNA methylation in HSPC generation by taking advantage of dnmt1 knockout/knockdown embryos in zebrafish. First we generated a comprehensive DNA methylation landscape of EHT which revealed gradually hypermethylated regions associated with vasculogenesis. Taking advantage of dnmt1 deficient embryos we showed that the decreased DNA methylation blocked HSPC emergence. Mechanistically we demonstrated that the decreased DNA methylation increased the expression of arterial genes and Notch signaling thus contributing to defects in the EHT in dnmt1 deficient embryos. Herein we identified that DNA methylation as epigenetic regulator participates in the negative modulation of Notch signaling through inhibiting transcription during HSPC generation in zebrafish. Overall design: WGBS and RNA seq of Danio rerio in EC HE and HSPC.	pubmed:35502759	HE sib rep3 RNA	GSM5694249	tissue:hemogenic endothelium cells\|developmental stage:HE\|genotype:sibling\|region:AGM	HE sib rep3 RNA	Basecalls perfomed using CASAVA2.19 WGBS and RNA seq raw sequencing reads were first trimmed for adapter and low quality sequences. Then mapped to GRCz11 using BS Seeker2v2.1.8 and hisat2v2.2.1 with parameters " t Y m 0.04 bt2 end to end" and " known splicesite infile p 30 k 10 dta t" separately. Student's T test was used to perform DMR analysis for WGBS data. Gene expression level was quantified by HTSeqv0.12.4 and differentially expressed genesDEGs were determined by DESeq2v1.30.1 Genome build: GRCz11 Supplementary files format and content: RNA seq raw count matrix Supplementary files format and content: raw count.txt raw counts Supplementary files format and content: EC sib.bed DMRs of EC sibling compared with HE sibling and HSC sibling Supplementary files format and content: HE sib.bed DMRs of HE sibling compared with EC sibling and HSC sibling Supplementary files format and content: HSC sib.bed DMRs of HSC sibling compared with EC sibling and HE sibling Supplementary files format and content: EC HE sib.bed DMRs of EC and HE sibling Supplementary files format and content: HE HSC sib.bed DMRs of HE and HSC sibling Supplementary files format and content: EC sib mut.bed DMRs of EC sibling and EC mutant Supplementary files format and content: HE sib mut.bed DMRs of HE sibling and HE mutant Supplementary files format and content: HSC sib mut.bed DMRs of HSC sibling and HSC mutant	hemogenic endothelium cells	Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3′ biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification	developmental stage:HE\|genotype:sibling\|region:AGM	GSM5694249	GSM5694249: HE sib rep3 RNA; Danio rerio; RNA Seq	GSM5694249	1	Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3′ biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification	GEO Accession:GSM5694249	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP346708	loader:fastq load.py	HE_mut_3_1_RNA.fq.gz HE_mut_3_2_RNA.fq.gz	fastq fastq	7531062600.0	25103542.0	GSM5694249 r1	0:150 1:150	A:2130133337;C:1522023953;G:1620977746;T:2257902956;N:24608	150	150	2130133337	1522023953	1620977746	2257902956	24608	SRX13164739	SRS11095943	SRA1331007	GEO	Institute of Hematology and Blood Diseases Hospital	2	0.93514	0.92906	0.1645	0.16366	0.76706	0.77086	0.4871	0.48732	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	strtseq	China	2021-11-18	Undetermined	Embryo	Endothelium	Cardiovascular System
67026	67026	SRR16973874	SRX13164738	SRS11095941	SRP346708	PRJNA781453	WGBS and RNA seq of Danio rerio in HSPC generation	GSE189072	Other	In this study we interrogated the role of DNA methylation in HSPC generation by taking advantage of dnmt1 knockout/knockdown embryos in zebrafish. First we generated a comprehensive DNA methylation landscape of EHT which revealed gradually hypermethylated regions associated with vasculogenesis. Taking advantage of dnmt1 deficient embryos we showed that the decreased DNA methylation blocked HSPC emergence. Mechanistically we demonstrated that the decreased DNA methylation increased the expression of arterial genes and Notch signaling thus contributing to defects in the EHT in dnmt1 deficient embryos. Herein we identified that DNA methylation as epigenetic regulator participates in the negative modulation of Notch signaling through inhibiting transcription during HSPC generation in zebrafish. Overall design: WGBS and RNA seq of Danio rerio in EC HE and HSPC.	pubmed:35502759	HE sib rep2 RNA	GSM5694248	tissue:hemogenic endothelium cells\|developmental stage:HE\|genotype:sibling\|region:AGM	HE sib rep2 RNA	Basecalls perfomed using CASAVA2.19 WGBS and RNA seq raw sequencing reads were first trimmed for adapter and low quality sequences. Then mapped to GRCz11 using BS Seeker2v2.1.8 and hisat2v2.2.1 with parameters " t Y m 0.04 bt2 end to end" and " known splicesite infile p 30 k 10 dta t" separately. Student's T test was used to perform DMR analysis for WGBS data. Gene expression level was quantified by HTSeqv0.12.4 and differentially expressed genesDEGs were determined by DESeq2v1.30.1 Genome build: GRCz11 Supplementary files format and content: RNA seq raw count matrix Supplementary files format and content: raw count.txt raw counts Supplementary files format and content: EC sib.bed DMRs of EC sibling compared with HE sibling and HSC sibling Supplementary files format and content: HE sib.bed DMRs of HE sibling compared with EC sibling and HSC sibling Supplementary files format and content: HSC sib.bed DMRs of HSC sibling compared with EC sibling and HE sibling Supplementary files format and content: EC HE sib.bed DMRs of EC and HE sibling Supplementary files format and content: HE HSC sib.bed DMRs of HE and HSC sibling Supplementary files format and content: EC sib mut.bed DMRs of EC sibling and EC mutant Supplementary files format and content: HE sib mut.bed DMRs of HE sibling and HE mutant Supplementary files format and content: HSC sib mut.bed DMRs of HSC sibling and HSC mutant	hemogenic endothelium cells	Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3′ biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification	developmental stage:HE\|genotype:sibling\|region:AGM	GSM5694248	GSM5694248: HE sib rep2 RNA; Danio rerio; RNA Seq	GSM5694248	1	Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3′ biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification	GEO Accession:GSM5694248	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP346708		HE_mut_2_1_RNA.fq.gz HE_mut_2_2_RNA.fq.gz	fastq fastq	3480792300.0	11602641.0	GSM5694248 r1	0:150 1:150	A:992011776;C:688862509;G:749973391;T:1049913481;N:31143	150	150	992011776	688862509	749973391	1049913481	31143	SRX13164738	SRS11095941	SRA1331007	GEO	Institute of Hematology and Blood Diseases Hospital	2	0.92794	0.92305	0.17775	0.17805	0.77159	0.77705	0.51315	0.52162	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	strtseq	China	2021-11-18	Undetermined	Embryo	Endothelium	Cardiovascular System
67027	67027	SRR16973873	SRX13164737	SRS11095940	SRP346708	PRJNA781453	WGBS and RNA seq of Danio rerio in HSPC generation	GSE189072	Other	In this study we interrogated the role of DNA methylation in HSPC generation by taking advantage of dnmt1 knockout/knockdown embryos in zebrafish. First we generated a comprehensive DNA methylation landscape of EHT which revealed gradually hypermethylated regions associated with vasculogenesis. Taking advantage of dnmt1 deficient embryos we showed that the decreased DNA methylation blocked HSPC emergence. Mechanistically we demonstrated that the decreased DNA methylation increased the expression of arterial genes and Notch signaling thus contributing to defects in the EHT in dnmt1 deficient embryos. Herein we identified that DNA methylation as epigenetic regulator participates in the negative modulation of Notch signaling through inhibiting transcription during HSPC generation in zebrafish. Overall design: WGBS and RNA seq of Danio rerio in EC HE and HSPC.	pubmed:35502759	HE sib rep1 RNA	GSM5694247	tissue:hemogenic endothelium cells\|developmental stage:HE\|genotype:sibling\|region:AGM	HE sib rep1 RNA	Basecalls perfomed using CASAVA2.19 WGBS and RNA seq raw sequencing reads were first trimmed for adapter and low quality sequences. Then mapped to GRCz11 using BS Seeker2v2.1.8 and hisat2v2.2.1 with parameters " t Y m 0.04 bt2 end to end" and " known splicesite infile p 30 k 10 dta t" separately. Student's T test was used to perform DMR analysis for WGBS data. Gene expression level was quantified by HTSeqv0.12.4 and differentially expressed genesDEGs were determined by DESeq2v1.30.1 Genome build: GRCz11 Supplementary files format and content: RNA seq raw count matrix Supplementary files format and content: raw count.txt raw counts Supplementary files format and content: EC sib.bed DMRs of EC sibling compared with HE sibling and HSC sibling Supplementary files format and content: HE sib.bed DMRs of HE sibling compared with EC sibling and HSC sibling Supplementary files format and content: HSC sib.bed DMRs of HSC sibling compared with EC sibling and HE sibling Supplementary files format and content: EC HE sib.bed DMRs of EC and HE sibling Supplementary files format and content: HE HSC sib.bed DMRs of HE and HSC sibling Supplementary files format and content: EC sib mut.bed DMRs of EC sibling and EC mutant Supplementary files format and content: HE sib mut.bed DMRs of HE sibling and HE mutant Supplementary files format and content: HSC sib mut.bed DMRs of HSC sibling and HSC mutant	hemogenic endothelium cells	Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3′ biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification	developmental stage:HE\|genotype:sibling\|region:AGM	GSM5694247	GSM5694247: HE sib rep1 RNA; Danio rerio; RNA Seq	GSM5694247	1	Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3′ biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification	GEO Accession:GSM5694247	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP346708		HE_mut_1_1_RNA.fq.gz HE_mut_1_2_RNA.fq.gz	fastq fastq	4147333500.0	13824445.0	GSM5694247 r1	0:150 1:150	A:1182622375;C:805503602;G:885424962;T:1273741037;N:41524	150	150	1182622375	805503602	885424962	1273741037	41524	SRX13164737	SRS11095940	SRA1331007	GEO	Institute of Hematology and Blood Diseases Hospital	2	0.92289	0.91984	0.22715	0.22596	0.77926	0.78644	0.54161	0.53476	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	strtseq	China	2021-11-18	Undetermined	Embryo	Endothelium	Cardiovascular System
67028	67028	SRR16973872	SRX13164736	SRS11095939	SRP346708	PRJNA781453	WGBS and RNA seq of Danio rerio in HSPC generation	GSE189072	Other	In this study we interrogated the role of DNA methylation in HSPC generation by taking advantage of dnmt1 knockout/knockdown embryos in zebrafish. First we generated a comprehensive DNA methylation landscape of EHT which revealed gradually hypermethylated regions associated with vasculogenesis. Taking advantage of dnmt1 deficient embryos we showed that the decreased DNA methylation blocked HSPC emergence. Mechanistically we demonstrated that the decreased DNA methylation increased the expression of arterial genes and Notch signaling thus contributing to defects in the EHT in dnmt1 deficient embryos. Herein we identified that DNA methylation as epigenetic regulator participates in the negative modulation of Notch signaling through inhibiting transcription during HSPC generation in zebrafish. Overall design: WGBS and RNA seq of Danio rerio in EC HE and HSPC.	pubmed:35502759	EC mut rep3 RNA	GSM5694246	tissue:endothelial cells\|developmental stage:EC\|genotype:dnmt1 mutant\|region:AGM	EC mut rep3 RNA	Basecalls perfomed using CASAVA2.19 WGBS and RNA seq raw sequencing reads were first trimmed for adapter and low quality sequences. Then mapped to GRCz11 using BS Seeker2v2.1.8 and hisat2v2.2.1 with parameters " t Y m 0.04 bt2 end to end" and " known splicesite infile p 30 k 10 dta t" separately. Student's T test was used to perform DMR analysis for WGBS data. Gene expression level was quantified by HTSeqv0.12.4 and differentially expressed genesDEGs were determined by DESeq2v1.30.1 Genome build: GRCz11 Supplementary files format and content: RNA seq raw count matrix Supplementary files format and content: raw count.txt raw counts Supplementary files format and content: EC sib.bed DMRs of EC sibling compared with HE sibling and HSC sibling Supplementary files format and content: HE sib.bed DMRs of HE sibling compared with EC sibling and HSC sibling Supplementary files format and content: HSC sib.bed DMRs of HSC sibling compared with EC sibling and HE sibling Supplementary files format and content: EC HE sib.bed DMRs of EC and HE sibling Supplementary files format and content: HE HSC sib.bed DMRs of HE and HSC sibling Supplementary files format and content: EC sib mut.bed DMRs of EC sibling and EC mutant Supplementary files format and content: HE sib mut.bed DMRs of HE sibling and HE mutant Supplementary files format and content: HSC sib mut.bed DMRs of HSC sibling and HSC mutant	endothelial cells	Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3′ biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification	developmental stage:EC\|genotype:dnmt1 mutant\|region:AGM	GSM5694246	GSM5694246: EC mut rep3 RNA; Danio rerio; RNA Seq	GSM5694246	1	Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3′ biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification	GEO Accession:GSM5694246	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP346708	loader:fastq load.py	EC_sib_3_1_RNA.fq.gz EC_sib_3_2_RNA.fq.gz	fastq fastq	5197238700.0	17324129.0	GSM5694246 r1	0:150 1:150	A:1518447950;C:1011812171;G:1095102019;T:1571846375;N:30185	150	150	1518447950	1011812171	1095102019	1571846375	30185	SRX13164736	SRS11095939	SRA1331007	GEO	Institute of Hematology and Blood Diseases Hospital	2	0.91741	0.90997	0.30958	0.30583	0.78573	0.79243	0.44787	0.56503	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	strtseq	China	2021-11-18	Undetermined	Embryo	Endothelium	Cardiovascular System
67029	67029	SRR16973871	SRX13164735	SRS11095938	SRP346708	PRJNA781453	WGBS and RNA seq of Danio rerio in HSPC generation	GSE189072	Other	In this study we interrogated the role of DNA methylation in HSPC generation by taking advantage of dnmt1 knockout/knockdown embryos in zebrafish. First we generated a comprehensive DNA methylation landscape of EHT which revealed gradually hypermethylated regions associated with vasculogenesis. Taking advantage of dnmt1 deficient embryos we showed that the decreased DNA methylation blocked HSPC emergence. Mechanistically we demonstrated that the decreased DNA methylation increased the expression of arterial genes and Notch signaling thus contributing to defects in the EHT in dnmt1 deficient embryos. Herein we identified that DNA methylation as epigenetic regulator participates in the negative modulation of Notch signaling through inhibiting transcription during HSPC generation in zebrafish. Overall design: WGBS and RNA seq of Danio rerio in EC HE and HSPC.	pubmed:35502759	EC mut rep2 RNA	GSM5694245	tissue:endothelial cells\|developmental stage:EC\|genotype:dnmt1 mutant\|region:AGM	EC mut rep2 RNA	Basecalls perfomed using CASAVA2.19 WGBS and RNA seq raw sequencing reads were first trimmed for adapter and low quality sequences. Then mapped to GRCz11 using BS Seeker2v2.1.8 and hisat2v2.2.1 with parameters " t Y m 0.04 bt2 end to end" and " known splicesite infile p 30 k 10 dta t" separately. Student's T test was used to perform DMR analysis for WGBS data. Gene expression level was quantified by HTSeqv0.12.4 and differentially expressed genesDEGs were determined by DESeq2v1.30.1 Genome build: GRCz11 Supplementary files format and content: RNA seq raw count matrix Supplementary files format and content: raw count.txt raw counts Supplementary files format and content: EC sib.bed DMRs of EC sibling compared with HE sibling and HSC sibling Supplementary files format and content: HE sib.bed DMRs of HE sibling compared with EC sibling and HSC sibling Supplementary files format and content: HSC sib.bed DMRs of HSC sibling compared with EC sibling and HE sibling Supplementary files format and content: EC HE sib.bed DMRs of EC and HE sibling Supplementary files format and content: HE HSC sib.bed DMRs of HE and HSC sibling Supplementary files format and content: EC sib mut.bed DMRs of EC sibling and EC mutant Supplementary files format and content: HE sib mut.bed DMRs of HE sibling and HE mutant Supplementary files format and content: HSC sib mut.bed DMRs of HSC sibling and HSC mutant	endothelial cells	Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3′ biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification	developmental stage:EC\|genotype:dnmt1 mutant\|region:AGM	GSM5694245	GSM5694245: EC mut rep2 RNA; Danio rerio; RNA Seq	GSM5694245	1	Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3′ biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification	GEO Accession:GSM5694245	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP346708		EC_sib_2_1_RNA.fq.gz EC_sib_2_2_RNA.fq.gz	fastq fastq	3166511400.0	10555038.0	GSM5694245 r1	0:150 1:150	A:953416270;C:589683319;G:624608777;T:998770674;N:32360	150	150	953416270	589683319	624608777	998770674	32360	SRX13164735	SRS11095938	SRA1331007	GEO	Institute of Hematology and Blood Diseases Hospital	2	0.90602	0.89266	0.283	0.28004	0.78804	0.79259	0.46429	0.58332	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	strtseq	China	2021-11-18	Undetermined	Embryo	Endothelium	Cardiovascular System
67030	67030	SRR16973870	SRX13164734	SRS11095937	SRP346708	PRJNA781453	WGBS and RNA seq of Danio rerio in HSPC generation	GSE189072	Other	In this study we interrogated the role of DNA methylation in HSPC generation by taking advantage of dnmt1 knockout/knockdown embryos in zebrafish. First we generated a comprehensive DNA methylation landscape of EHT which revealed gradually hypermethylated regions associated with vasculogenesis. Taking advantage of dnmt1 deficient embryos we showed that the decreased DNA methylation blocked HSPC emergence. Mechanistically we demonstrated that the decreased DNA methylation increased the expression of arterial genes and Notch signaling thus contributing to defects in the EHT in dnmt1 deficient embryos. Herein we identified that DNA methylation as epigenetic regulator participates in the negative modulation of Notch signaling through inhibiting transcription during HSPC generation in zebrafish. Overall design: WGBS and RNA seq of Danio rerio in EC HE and HSPC.	pubmed:35502759	EC mut rep1 RNA	GSM5694244	tissue:endothelial cells\|developmental stage:EC\|genotype:dnmt1 mutant\|region:AGM	EC mut rep1 RNA	Basecalls perfomed using CASAVA2.19 WGBS and RNA seq raw sequencing reads were first trimmed for adapter and low quality sequences. Then mapped to GRCz11 using BS Seeker2v2.1.8 and hisat2v2.2.1 with parameters " t Y m 0.04 bt2 end to end" and " known splicesite infile p 30 k 10 dta t" separately. Student's T test was used to perform DMR analysis for WGBS data. Gene expression level was quantified by HTSeqv0.12.4 and differentially expressed genesDEGs were determined by DESeq2v1.30.1 Genome build: GRCz11 Supplementary files format and content: RNA seq raw count matrix Supplementary files format and content: raw count.txt raw counts Supplementary files format and content: EC sib.bed DMRs of EC sibling compared with HE sibling and HSC sibling Supplementary files format and content: HE sib.bed DMRs of HE sibling compared with EC sibling and HSC sibling Supplementary files format and content: HSC sib.bed DMRs of HSC sibling compared with EC sibling and HE sibling Supplementary files format and content: EC HE sib.bed DMRs of EC and HE sibling Supplementary files format and content: HE HSC sib.bed DMRs of HE and HSC sibling Supplementary files format and content: EC sib mut.bed DMRs of EC sibling and EC mutant Supplementary files format and content: HE sib mut.bed DMRs of HE sibling and HE mutant Supplementary files format and content: HSC sib mut.bed DMRs of HSC sibling and HSC mutant	endothelial cells	Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3′ biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification	developmental stage:EC\|genotype:dnmt1 mutant\|region:AGM	GSM5694244	GSM5694244: EC mut rep1 RNA; Danio rerio; RNA Seq	GSM5694244	1	Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3′ biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification	GEO Accession:GSM5694244	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP346708		EC_sib_1_1_RNA.fq.gz EC_sib_1_2_RNA.fq.gz	fastq fastq	3962208600.0	13207362.0	GSM5694244 r1	0:150 1:150	A:1157734424;C:769637879;G:815215301;T:1219572479;N:48517	150	150	1157734424	769637879	815215301	1219572479	48517	SRX13164734	SRS11095937	SRA1331007	GEO	Institute of Hematology and Blood Diseases Hospital	2	0.9138	0.90509	0.21931	0.21725	0.77479	0.77741	0.5314	0.53073	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	strtseq	China	2021-11-18	Undetermined	Embryo	Endothelium	Cardiovascular System
67031	67031	SRR16973869	SRX13164733	SRS11095936	SRP346708	PRJNA781453	WGBS and RNA seq of Danio rerio in HSPC generation	GSE189072	Other	In this study we interrogated the role of DNA methylation in HSPC generation by taking advantage of dnmt1 knockout/knockdown embryos in zebrafish. First we generated a comprehensive DNA methylation landscape of EHT which revealed gradually hypermethylated regions associated with vasculogenesis. Taking advantage of dnmt1 deficient embryos we showed that the decreased DNA methylation blocked HSPC emergence. Mechanistically we demonstrated that the decreased DNA methylation increased the expression of arterial genes and Notch signaling thus contributing to defects in the EHT in dnmt1 deficient embryos. Herein we identified that DNA methylation as epigenetic regulator participates in the negative modulation of Notch signaling through inhibiting transcription during HSPC generation in zebrafish. Overall design: WGBS and RNA seq of Danio rerio in EC HE and HSPC.	pubmed:35502759	EC sib rep3 RNA	GSM5694243	tissue:endothelial cells\|developmental stage:EC\|genotype:sibling\|region:AGM	EC sib rep3 RNA	Basecalls perfomed using CASAVA2.19 WGBS and RNA seq raw sequencing reads were first trimmed for adapter and low quality sequences. Then mapped to GRCz11 using BS Seeker2v2.1.8 and hisat2v2.2.1 with parameters " t Y m 0.04 bt2 end to end" and " known splicesite infile p 30 k 10 dta t" separately. Student's T test was used to perform DMR analysis for WGBS data. Gene expression level was quantified by HTSeqv0.12.4 and differentially expressed genesDEGs were determined by DESeq2v1.30.1 Genome build: GRCz11 Supplementary files format and content: RNA seq raw count matrix Supplementary files format and content: raw count.txt raw counts Supplementary files format and content: EC sib.bed DMRs of EC sibling compared with HE sibling and HSC sibling Supplementary files format and content: HE sib.bed DMRs of HE sibling compared with EC sibling and HSC sibling Supplementary files format and content: HSC sib.bed DMRs of HSC sibling compared with EC sibling and HE sibling Supplementary files format and content: EC HE sib.bed DMRs of EC and HE sibling Supplementary files format and content: HE HSC sib.bed DMRs of HE and HSC sibling Supplementary files format and content: EC sib mut.bed DMRs of EC sibling and EC mutant Supplementary files format and content: HE sib mut.bed DMRs of HE sibling and HE mutant Supplementary files format and content: HSC sib mut.bed DMRs of HSC sibling and HSC mutant	endothelial cells	Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3′ biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification	developmental stage:EC\|genotype:sibling\|region:AGM	GSM5694243	GSM5694243: EC sib rep3 RNA; Danio rerio; RNA Seq	GSM5694243	1	Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3′ biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification	GEO Accession:GSM5694243	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP346708	loader:fastq load.py	EC_mut_3_1_RNA.fq.gz EC_mut_3_2_RNA.fq.gz	fastq fastq	5214231600.0	17380772.0	GSM5694243 r1	0:150 1:150	A:1518201912;C:1020669101;G:1094674332;T:1580669249;N:17006	150	150	1518201912	1020669101	1094674332	1580669249	17006	SRX13164733	SRS11095936	SRA1331007	GEO	Institute of Hematology and Blood Diseases Hospital	2	0.91916	0.91501	0.28949	0.28875	0.77536	0.77749	0.54408	0.54439	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	strtseq	China	2021-11-18	Undetermined	Embryo	Endothelium	Cardiovascular System
67032	67032	SRR16973868	SRX13164732	SRS11095935	SRP346708	PRJNA781453	WGBS and RNA seq of Danio rerio in HSPC generation	GSE189072	Other	In this study we interrogated the role of DNA methylation in HSPC generation by taking advantage of dnmt1 knockout/knockdown embryos in zebrafish. First we generated a comprehensive DNA methylation landscape of EHT which revealed gradually hypermethylated regions associated with vasculogenesis. Taking advantage of dnmt1 deficient embryos we showed that the decreased DNA methylation blocked HSPC emergence. Mechanistically we demonstrated that the decreased DNA methylation increased the expression of arterial genes and Notch signaling thus contributing to defects in the EHT in dnmt1 deficient embryos. Herein we identified that DNA methylation as epigenetic regulator participates in the negative modulation of Notch signaling through inhibiting transcription during HSPC generation in zebrafish. Overall design: WGBS and RNA seq of Danio rerio in EC HE and HSPC.	pubmed:35502759	EC sib rep2 RNA	GSM5694242	tissue:endothelial cells\|developmental stage:EC\|genotype:sibling\|region:AGM	EC sib rep2 RNA	Basecalls perfomed using CASAVA2.19 WGBS and RNA seq raw sequencing reads were first trimmed for adapter and low quality sequences. Then mapped to GRCz11 using BS Seeker2v2.1.8 and hisat2v2.2.1 with parameters " t Y m 0.04 bt2 end to end" and " known splicesite infile p 30 k 10 dta t" separately. Student's T test was used to perform DMR analysis for WGBS data. Gene expression level was quantified by HTSeqv0.12.4 and differentially expressed genesDEGs were determined by DESeq2v1.30.1 Genome build: GRCz11 Supplementary files format and content: RNA seq raw count matrix Supplementary files format and content: raw count.txt raw counts Supplementary files format and content: EC sib.bed DMRs of EC sibling compared with HE sibling and HSC sibling Supplementary files format and content: HE sib.bed DMRs of HE sibling compared with EC sibling and HSC sibling Supplementary files format and content: HSC sib.bed DMRs of HSC sibling compared with EC sibling and HE sibling Supplementary files format and content: EC HE sib.bed DMRs of EC and HE sibling Supplementary files format and content: HE HSC sib.bed DMRs of HE and HSC sibling Supplementary files format and content: EC sib mut.bed DMRs of EC sibling and EC mutant Supplementary files format and content: HE sib mut.bed DMRs of HE sibling and HE mutant Supplementary files format and content: HSC sib mut.bed DMRs of HSC sibling and HSC mutant	endothelial cells	Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3′ biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification	developmental stage:EC\|genotype:sibling\|region:AGM	GSM5694242	GSM5694242: EC sib rep2 RNA; Danio rerio; RNA Seq	GSM5694242	1	Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3′ biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification	GEO Accession:GSM5694242	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP346708		EC_mut_2_1_RNA.fq.gz EC_mut_2_2_RNA.fq.gz	fastq fastq	3551728200.0	11839094.0	GSM5694242 r1	0:150 1:150	A:1033665824;C:697141333;G:748608593;T:1072309959;N:2491	150	150	1033665824	697141333	748608593	1072309959	2491	SRX13164732	SRS11095935	SRA1331007	GEO	Institute of Hematology and Blood Diseases Hospital	2	0.91086	0.91055	0.22761	0.22617	0.76611	0.77388	0.54742	0.54539	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	strtseq	China	2021-11-18	Undetermined	Embryo	Endothelium	Cardiovascular System
67033	67033	SRR16973867	SRX13164731	SRS11095934	SRP346708	PRJNA781453	WGBS and RNA seq of Danio rerio in HSPC generation	GSE189072	Other	In this study we interrogated the role of DNA methylation in HSPC generation by taking advantage of dnmt1 knockout/knockdown embryos in zebrafish. First we generated a comprehensive DNA methylation landscape of EHT which revealed gradually hypermethylated regions associated with vasculogenesis. Taking advantage of dnmt1 deficient embryos we showed that the decreased DNA methylation blocked HSPC emergence. Mechanistically we demonstrated that the decreased DNA methylation increased the expression of arterial genes and Notch signaling thus contributing to defects in the EHT in dnmt1 deficient embryos. Herein we identified that DNA methylation as epigenetic regulator participates in the negative modulation of Notch signaling through inhibiting transcription during HSPC generation in zebrafish. Overall design: WGBS and RNA seq of Danio rerio in EC HE and HSPC.	pubmed:35502759	EC sib rep1 RNA	GSM5694241	tissue:endothelial cells\|developmental stage:EC\|genotype:sibling\|region:AGM	EC sib rep1 RNA	Basecalls perfomed using CASAVA2.19 WGBS and RNA seq raw sequencing reads were first trimmed for adapter and low quality sequences. Then mapped to GRCz11 using BS Seeker2v2.1.8 and hisat2v2.2.1 with parameters " t Y m 0.04 bt2 end to end" and " known splicesite infile p 30 k 10 dta t" separately. Student's T test was used to perform DMR analysis for WGBS data. Gene expression level was quantified by HTSeqv0.12.4 and differentially expressed genesDEGs were determined by DESeq2v1.30.1 Genome build: GRCz11 Supplementary files format and content: RNA seq raw count matrix Supplementary files format and content: raw count.txt raw counts Supplementary files format and content: EC sib.bed DMRs of EC sibling compared with HE sibling and HSC sibling Supplementary files format and content: HE sib.bed DMRs of HE sibling compared with EC sibling and HSC sibling Supplementary files format and content: HSC sib.bed DMRs of HSC sibling compared with EC sibling and HE sibling Supplementary files format and content: EC HE sib.bed DMRs of EC and HE sibling Supplementary files format and content: HE HSC sib.bed DMRs of HE and HSC sibling Supplementary files format and content: EC sib mut.bed DMRs of EC sibling and EC mutant Supplementary files format and content: HE sib mut.bed DMRs of HE sibling and HE mutant Supplementary files format and content: HSC sib mut.bed DMRs of HSC sibling and HSC mutant	endothelial cells	Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3′ biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification	developmental stage:EC\|genotype:sibling\|region:AGM	GSM5694241	GSM5694241: EC sib rep1 RNA; Danio rerio; RNA Seq	GSM5694241	1	Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3′ biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification	GEO Accession:GSM5694241	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP346708		EC_mut_1_1_RNA.fq.gz EC_mut_1_2_RNA.fq.gz	fastq fastq	4174024500.0	13913415.0	GSM5694241 r1	0:150 1:150	A:1198561312;C:807832743;G:886085495;T:1281504164;N:40786	150	150	1198561312	807832743	886085495	1281504164	40786	SRX13164731	SRS11095934	SRA1331007	GEO	Institute of Hematology and Blood Diseases Hospital	2	0.9162	0.91249	0.25639	0.25487	0.7767	0.78186	0.45792	0.43528	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	strtseq	China	2021-11-18	Undetermined	Embryo	Endothelium	Cardiovascular 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");;