metadata: run_metadata: 15 rows where devstage_curation_coarse = "Multi-stage" and tissue

15 rows where devstage_curation_coarse = "Multi-stage" and tissue_curation = "Endothelium"

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.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	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.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
30006	30006	SRR27663958	SRX23331822	SRS20194274	SRP484810	PRJNA1066877	p65 signaling dynamics drive the developmental progression of hematopoietic stem and progenitor cells through cell cycle regulation	GSE253758	Transcriptome Analysis	While hematopoietic stem and progenitor cells HSPCs and the signaling pathways that specify them have been well defined in vivo deriving functional HSPCs from human pluripotent stem cells hPSCs is still an outstanding challenge in the stem cell field. This has impaired efforts to use patient specific HSPCs and their derivatives to treat leukemia lymphoma anemia and solid cancers. Identifying the missing element to derive functional human HSPCs will be critical to advance these therapies. Here we found that in contrast to in vitro protocols where signaling pathways are typically manipulated statically the natural developmental progression of HSPC fate in the embryo requires a precise and temporally controlled oscillatory signaling dynamics. Particularly our work reveals that NF kB signaling works as an oscillatory clock that controls the developmental progression of HSPCs by driving phases of quiescence and proliferation precisely during embryonic development. This was revealed by live imaging of a custom NF kB zebrafish reporter line in conjunction with transcriptomic profiling and precise temporal manipulations of the NF kB family member p65 the driver of these signaling events. We also show that in vitro protocols of human hematopoietic differentiation from iPSCs depend on initial pro inflammatory signaling activation. In summary our results uncover the functional role of pro inflammatory signaling during HSPC specification revealed their oscillatory dynamics and define this signaling pathway as the main driver of HSPC fate progression. The integration of these dynamics in vitro will be fundamental to achieve the long standing goal of generating and expanding patient derived functional HSPCs. Overall design: To gain insights into how NF kB in endothelium was contributing to HSPC specification NFKB+ or NFKB endothelial cells kdrl+ were sorted and collected from 22hpf zebrafish embryos in triplicate and subject to RNA seq.	pubmed:39242546	NFKB biol rep 3	GSM8027552	tissue:endothelial cells\|cell type:endothelial cells\|genotype:NFKB:d2eGFP x kdrl:mCherry\|treatment:kdrl+/NFKB sorted\|geo loc name:missing\|collection date:missing	NFKB biol rep 3	Data was analyzed by ROSALIND® https://rosalind.bio/ with a HyperScale architecture developed by ROSALIND Inc. San Diego CA. Reads were trimmed using cutadapt. Reads were aligned to the Danio rerio genome build danRer10 using STAR. Individual sample reads were quantified using HTseq and normalized via Relative Log Expression RLE using DESeq2. Assembly: danRer10 Supplementary files format and content: comma delimited text files include fold change p values adjusted p values and normalized abundance values per sample for each gene	endothelial cells	22hpf NFKB:d2eGFP x kdrl:mCherry zebrafish embryos were screened with Leica M165FC stereomicroscope dechorionated with pronase Millipore Sigma; 11459643001 anesthetized in 1% tricaine Pentair; TRS5 and dissociated. Specifically the trunk region of each embryo was surgically isolated posterior to the yolk ball and anterior to the urogenital canal using a scalpel. The collected tissue was then gently vortexed at 28C for 5 20 mins with 50 µg/ml Liberase TM Millipore Sigma: 5401127001 in Dulbecco′s Phosphate Buffered Saline solution with Ca2+ and Mg2+ Millipore Sigma D8662. The resulting cell suspension was filtered through 30 µm nylon mesh Fisher Scientific; NC9084441 using a 21 gauge syringe Fisher Scientific; BD 309624 and stained with SYTOX™ Red Life Technologies; S34859 to exclude dead cells. Kdrl+/NFKB and kdrl+/NFKB+ cells were each sorted and collected with BD FACS Aria III. 7 000 cells per sample were collected by FACS in Eppendorf tubes containing 250 µl of RLT buffer.	RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer’s instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.	Zebrafish Danio rerio embryos and adults were mated staged raised and processed in a circulating aquarium system maintained at 26 °C on a 14 hr light/10 hr dark cycle.	cell type:endothelial cells\|genotype:NFKB:d2eGFP x kdrl:mCherry\|treatment:kdrl+/NFKB sorted	GSM8027552	GSM8027552: NFKB biol rep 3; Danio rerio; RNA Seq	GSM8027552 r1	GSM8027552	1	RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer's instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484810	loader:fastq load.py	6-RNA-1001_S6_L001_R1_001.fastq.gz	fastq	7566894200.0	75668942.0	GSM8027552 r1	0:100	A:2055514007;C:1776454819;G:1779667416;T:1955100553;N:157405	100		2055514007	1776454819	1779667416	1955100553	157405	SRX23331822	SRS20194274	SRA1788753	Iowa State University	Iowa State University	B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2024-01-19	Multi-stage	Multi-stage	Endothelium	Cardiovascular System
30007	30007	SRR27663959	SRX23331821	SRS20194275	SRP484810	PRJNA1066877	p65 signaling dynamics drive the developmental progression of hematopoietic stem and progenitor cells through cell cycle regulation	GSE253758	Transcriptome Analysis	While hematopoietic stem and progenitor cells HSPCs and the signaling pathways that specify them have been well defined in vivo deriving functional HSPCs from human pluripotent stem cells hPSCs is still an outstanding challenge in the stem cell field. This has impaired efforts to use patient specific HSPCs and their derivatives to treat leukemia lymphoma anemia and solid cancers. Identifying the missing element to derive functional human HSPCs will be critical to advance these therapies. Here we found that in contrast to in vitro protocols where signaling pathways are typically manipulated statically the natural developmental progression of HSPC fate in the embryo requires a precise and temporally controlled oscillatory signaling dynamics. Particularly our work reveals that NF kB signaling works as an oscillatory clock that controls the developmental progression of HSPCs by driving phases of quiescence and proliferation precisely during embryonic development. This was revealed by live imaging of a custom NF kB zebrafish reporter line in conjunction with transcriptomic profiling and precise temporal manipulations of the NF kB family member p65 the driver of these signaling events. We also show that in vitro protocols of human hematopoietic differentiation from iPSCs depend on initial pro inflammatory signaling activation. In summary our results uncover the functional role of pro inflammatory signaling during HSPC specification revealed their oscillatory dynamics and define this signaling pathway as the main driver of HSPC fate progression. The integration of these dynamics in vitro will be fundamental to achieve the long standing goal of generating and expanding patient derived functional HSPCs. Overall design: To gain insights into how NF kB in endothelium was contributing to HSPC specification NFKB+ or NFKB endothelial cells kdrl+ were sorted and collected from 22hpf zebrafish embryos in triplicate and subject to RNA seq.	pubmed:39242546	NFKB biol rep 2	GSM8027551	tissue:endothelial cells\|cell type:endothelial cells\|genotype:NFKB:d2eGFP x kdrl:mCherry\|treatment:kdrl+/NFKB sorted\|geo loc name:missing\|collection date:missing	NFKB biol rep 2	Data was analyzed by ROSALIND® https://rosalind.bio/ with a HyperScale architecture developed by ROSALIND Inc. San Diego CA. Reads were trimmed using cutadapt. Reads were aligned to the Danio rerio genome build danRer10 using STAR. Individual sample reads were quantified using HTseq and normalized via Relative Log Expression RLE using DESeq2. Assembly: danRer10 Supplementary files format and content: comma delimited text files include fold change p values adjusted p values and normalized abundance values per sample for each gene	endothelial cells	22hpf NFKB:d2eGFP x kdrl:mCherry zebrafish embryos were screened with Leica M165FC stereomicroscope dechorionated with pronase Millipore Sigma; 11459643001 anesthetized in 1% tricaine Pentair; TRS5 and dissociated. Specifically the trunk region of each embryo was surgically isolated posterior to the yolk ball and anterior to the urogenital canal using a scalpel. The collected tissue was then gently vortexed at 28C for 5 20 mins with 50 µg/ml Liberase TM Millipore Sigma: 5401127001 in Dulbecco′s Phosphate Buffered Saline solution with Ca2+ and Mg2+ Millipore Sigma D8662. The resulting cell suspension was filtered through 30 µm nylon mesh Fisher Scientific; NC9084441 using a 21 gauge syringe Fisher Scientific; BD 309624 and stained with SYTOX™ Red Life Technologies; S34859 to exclude dead cells. Kdrl+/NFKB and kdrl+/NFKB+ cells were each sorted and collected with BD FACS Aria III. 7 000 cells per sample were collected by FACS in Eppendorf tubes containing 250 µl of RLT buffer.	RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer’s instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.	Zebrafish Danio rerio embryos and adults were mated staged raised and processed in a circulating aquarium system maintained at 26 °C on a 14 hr light/10 hr dark cycle.	cell type:endothelial cells\|genotype:NFKB:d2eGFP x kdrl:mCherry\|treatment:kdrl+/NFKB sorted	GSM8027551	GSM8027551: NFKB biol rep 2; Danio rerio; RNA Seq	GSM8027551 r1	GSM8027551	1	RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer's instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484810	loader:fastq load.py	5-RNA-0901_S5_L001_R1_001.fastq.gz	fastq	8077393600.0	80773936.0	GSM8027551 r1	0:100	A:2195547260;C:1863472493;G:1887149224;T:2131055526;N:169097	100		2195547260	1863472493	1887149224	2131055526	169097	SRX23331821	SRS20194275	SRA1788753	Iowa State University	Iowa State University	B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2024-01-19	Multi-stage	Multi-stage	Endothelium	Cardiovascular System
30008	30008	SRR27663960	SRX23331820	SRS20194273	SRP484810	PRJNA1066877	p65 signaling dynamics drive the developmental progression of hematopoietic stem and progenitor cells through cell cycle regulation	GSE253758	Transcriptome Analysis	While hematopoietic stem and progenitor cells HSPCs and the signaling pathways that specify them have been well defined in vivo deriving functional HSPCs from human pluripotent stem cells hPSCs is still an outstanding challenge in the stem cell field. This has impaired efforts to use patient specific HSPCs and their derivatives to treat leukemia lymphoma anemia and solid cancers. Identifying the missing element to derive functional human HSPCs will be critical to advance these therapies. Here we found that in contrast to in vitro protocols where signaling pathways are typically manipulated statically the natural developmental progression of HSPC fate in the embryo requires a precise and temporally controlled oscillatory signaling dynamics. Particularly our work reveals that NF kB signaling works as an oscillatory clock that controls the developmental progression of HSPCs by driving phases of quiescence and proliferation precisely during embryonic development. This was revealed by live imaging of a custom NF kB zebrafish reporter line in conjunction with transcriptomic profiling and precise temporal manipulations of the NF kB family member p65 the driver of these signaling events. We also show that in vitro protocols of human hematopoietic differentiation from iPSCs depend on initial pro inflammatory signaling activation. In summary our results uncover the functional role of pro inflammatory signaling during HSPC specification revealed their oscillatory dynamics and define this signaling pathway as the main driver of HSPC fate progression. The integration of these dynamics in vitro will be fundamental to achieve the long standing goal of generating and expanding patient derived functional HSPCs. Overall design: To gain insights into how NF kB in endothelium was contributing to HSPC specification NFKB+ or NFKB endothelial cells kdrl+ were sorted and collected from 22hpf zebrafish embryos in triplicate and subject to RNA seq.	pubmed:39242546	NFKB biol rep 1	GSM8027550	tissue:endothelial cells\|cell type:endothelial cells\|genotype:NFKB:d2eGFP x kdrl:mCherry\|treatment:kdrl+/NFKB sorted\|geo loc name:missing\|collection date:missing	NFKB biol rep 1	Data was analyzed by ROSALIND® https://rosalind.bio/ with a HyperScale architecture developed by ROSALIND Inc. San Diego CA. Reads were trimmed using cutadapt. Reads were aligned to the Danio rerio genome build danRer10 using STAR. Individual sample reads were quantified using HTseq and normalized via Relative Log Expression RLE using DESeq2. Assembly: danRer10 Supplementary files format and content: comma delimited text files include fold change p values adjusted p values and normalized abundance values per sample for each gene	endothelial cells	22hpf NFKB:d2eGFP x kdrl:mCherry zebrafish embryos were screened with Leica M165FC stereomicroscope dechorionated with pronase Millipore Sigma; 11459643001 anesthetized in 1% tricaine Pentair; TRS5 and dissociated. Specifically the trunk region of each embryo was surgically isolated posterior to the yolk ball and anterior to the urogenital canal using a scalpel. The collected tissue was then gently vortexed at 28C for 5 20 mins with 50 µg/ml Liberase TM Millipore Sigma: 5401127001 in Dulbecco′s Phosphate Buffered Saline solution with Ca2+ and Mg2+ Millipore Sigma D8662. The resulting cell suspension was filtered through 30 µm nylon mesh Fisher Scientific; NC9084441 using a 21 gauge syringe Fisher Scientific; BD 309624 and stained with SYTOX™ Red Life Technologies; S34859 to exclude dead cells. Kdrl+/NFKB and kdrl+/NFKB+ cells were each sorted and collected with BD FACS Aria III. 7 000 cells per sample were collected by FACS in Eppendorf tubes containing 250 µl of RLT buffer.	RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer’s instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.	Zebrafish Danio rerio embryos and adults were mated staged raised and processed in a circulating aquarium system maintained at 26 °C on a 14 hr light/10 hr dark cycle.	cell type:endothelial cells\|genotype:NFKB:d2eGFP x kdrl:mCherry\|treatment:kdrl+/NFKB sorted	GSM8027550	GSM8027550: NFKB biol rep 1; Danio rerio; RNA Seq	GSM8027550 r1	GSM8027550	1	RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer's instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484810	loader:fastq load.py	4-RNA-1001_S4_L001_R1_001.fastq.gz	fastq	6536957300.0	65369573.0	GSM8027550 r1	0:100	A:1764502914;C:1531091007;G:1533764634;T:1707464708;N:134037	100		1764502914	1531091007	1533764634	1707464708	134037	SRX23331820	SRS20194273	SRA1788753	Iowa State University	Iowa State University	B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2024-01-19	Multi-stage	Multi-stage	Endothelium	Cardiovascular System
30009	30009	SRR27663961	SRX23331819	SRS20194272	SRP484810	PRJNA1066877	p65 signaling dynamics drive the developmental progression of hematopoietic stem and progenitor cells through cell cycle regulation	GSE253758	Transcriptome Analysis	While hematopoietic stem and progenitor cells HSPCs and the signaling pathways that specify them have been well defined in vivo deriving functional HSPCs from human pluripotent stem cells hPSCs is still an outstanding challenge in the stem cell field. This has impaired efforts to use patient specific HSPCs and their derivatives to treat leukemia lymphoma anemia and solid cancers. Identifying the missing element to derive functional human HSPCs will be critical to advance these therapies. Here we found that in contrast to in vitro protocols where signaling pathways are typically manipulated statically the natural developmental progression of HSPC fate in the embryo requires a precise and temporally controlled oscillatory signaling dynamics. Particularly our work reveals that NF kB signaling works as an oscillatory clock that controls the developmental progression of HSPCs by driving phases of quiescence and proliferation precisely during embryonic development. This was revealed by live imaging of a custom NF kB zebrafish reporter line in conjunction with transcriptomic profiling and precise temporal manipulations of the NF kB family member p65 the driver of these signaling events. We also show that in vitro protocols of human hematopoietic differentiation from iPSCs depend on initial pro inflammatory signaling activation. In summary our results uncover the functional role of pro inflammatory signaling during HSPC specification revealed their oscillatory dynamics and define this signaling pathway as the main driver of HSPC fate progression. The integration of these dynamics in vitro will be fundamental to achieve the long standing goal of generating and expanding patient derived functional HSPCs. Overall design: To gain insights into how NF kB in endothelium was contributing to HSPC specification NFKB+ or NFKB endothelial cells kdrl+ were sorted and collected from 22hpf zebrafish embryos in triplicate and subject to RNA seq.	pubmed:39242546	NFKB+ biol rep 3	GSM8027549	tissue:endothelial cells\|cell type:endothelial cells\|genotype:NFKB:d2eGFP x kdrl:mCherry\|treatment:kdrl+/NFKB+ sorted\|geo loc name:missing\|collection date:missing	NFKB+ biol rep 3	Data was analyzed by ROSALIND® https://rosalind.bio/ with a HyperScale architecture developed by ROSALIND Inc. San Diego CA. Reads were trimmed using cutadapt. Reads were aligned to the Danio rerio genome build danRer10 using STAR. Individual sample reads were quantified using HTseq and normalized via Relative Log Expression RLE using DESeq2. Assembly: danRer10 Supplementary files format and content: comma delimited text files include fold change p values adjusted p values and normalized abundance values per sample for each gene	endothelial cells	22hpf NFKB:d2eGFP x kdrl:mCherry zebrafish embryos were screened with Leica M165FC stereomicroscope dechorionated with pronase Millipore Sigma; 11459643001 anesthetized in 1% tricaine Pentair; TRS5 and dissociated. Specifically the trunk region of each embryo was surgically isolated posterior to the yolk ball and anterior to the urogenital canal using a scalpel. The collected tissue was then gently vortexed at 28C for 5 20 mins with 50 µg/ml Liberase TM Millipore Sigma: 5401127001 in Dulbecco′s Phosphate Buffered Saline solution with Ca2+ and Mg2+ Millipore Sigma D8662. The resulting cell suspension was filtered through 30 µm nylon mesh Fisher Scientific; NC9084441 using a 21 gauge syringe Fisher Scientific; BD 309624 and stained with SYTOX™ Red Life Technologies; S34859 to exclude dead cells. Kdrl+/NFKB and kdrl+/NFKB+ cells were each sorted and collected with BD FACS Aria III. 7 000 cells per sample were collected by FACS in Eppendorf tubes containing 250 µl of RLT buffer.	RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer’s instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.	Zebrafish Danio rerio embryos and adults were mated staged raised and processed in a circulating aquarium system maintained at 26 °C on a 14 hr light/10 hr dark cycle.	cell type:endothelial cells\|genotype:NFKB:d2eGFP x kdrl:mCherry\|treatment:kdrl+/NFKB+ sorted	GSM8027549	GSM8027549: NFKB+ biol rep 3; Danio rerio; RNA Seq	GSM8027549 r1	GSM8027549	1	RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer's instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484810	loader:fastq load.py	3-RNA-1001_S3_L001_R1_001.fastq.gz	fastq	10375249700.0	103752497.0	GSM8027549 r1	0:100	A:2873369145;C:2335823279;G:2356855554;T:2808985435;N:216287	100		2873369145	2335823279	2356855554	2808985435	216287	SRX23331819	SRS20194272	SRA1788753	Iowa State University	Iowa State University	B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2024-01-19	Multi-stage	Multi-stage	Endothelium	Cardiovascular System
30010	30010	SRR27663962	SRX23331818	SRS20194271	SRP484810	PRJNA1066877	p65 signaling dynamics drive the developmental progression of hematopoietic stem and progenitor cells through cell cycle regulation	GSE253758	Transcriptome Analysis	While hematopoietic stem and progenitor cells HSPCs and the signaling pathways that specify them have been well defined in vivo deriving functional HSPCs from human pluripotent stem cells hPSCs is still an outstanding challenge in the stem cell field. This has impaired efforts to use patient specific HSPCs and their derivatives to treat leukemia lymphoma anemia and solid cancers. Identifying the missing element to derive functional human HSPCs will be critical to advance these therapies. Here we found that in contrast to in vitro protocols where signaling pathways are typically manipulated statically the natural developmental progression of HSPC fate in the embryo requires a precise and temporally controlled oscillatory signaling dynamics. Particularly our work reveals that NF kB signaling works as an oscillatory clock that controls the developmental progression of HSPCs by driving phases of quiescence and proliferation precisely during embryonic development. This was revealed by live imaging of a custom NF kB zebrafish reporter line in conjunction with transcriptomic profiling and precise temporal manipulations of the NF kB family member p65 the driver of these signaling events. We also show that in vitro protocols of human hematopoietic differentiation from iPSCs depend on initial pro inflammatory signaling activation. In summary our results uncover the functional role of pro inflammatory signaling during HSPC specification revealed their oscillatory dynamics and define this signaling pathway as the main driver of HSPC fate progression. The integration of these dynamics in vitro will be fundamental to achieve the long standing goal of generating and expanding patient derived functional HSPCs. Overall design: To gain insights into how NF kB in endothelium was contributing to HSPC specification NFKB+ or NFKB endothelial cells kdrl+ were sorted and collected from 22hpf zebrafish embryos in triplicate and subject to RNA seq.	pubmed:39242546	NFKB+ biol rep 2	GSM8027548	tissue:endothelial cells\|cell type:endothelial cells\|genotype:NFKB:d2eGFP x kdrl:mCherry\|treatment:kdrl+/NFKB+ sorted\|geo loc name:missing\|collection date:missing	NFKB+ biol rep 2	Data was analyzed by ROSALIND® https://rosalind.bio/ with a HyperScale architecture developed by ROSALIND Inc. San Diego CA. Reads were trimmed using cutadapt. Reads were aligned to the Danio rerio genome build danRer10 using STAR. Individual sample reads were quantified using HTseq and normalized via Relative Log Expression RLE using DESeq2. Assembly: danRer10 Supplementary files format and content: comma delimited text files include fold change p values adjusted p values and normalized abundance values per sample for each gene	endothelial cells	22hpf NFKB:d2eGFP x kdrl:mCherry zebrafish embryos were screened with Leica M165FC stereomicroscope dechorionated with pronase Millipore Sigma; 11459643001 anesthetized in 1% tricaine Pentair; TRS5 and dissociated. Specifically the trunk region of each embryo was surgically isolated posterior to the yolk ball and anterior to the urogenital canal using a scalpel. The collected tissue was then gently vortexed at 28C for 5 20 mins with 50 µg/ml Liberase TM Millipore Sigma: 5401127001 in Dulbecco′s Phosphate Buffered Saline solution with Ca2+ and Mg2+ Millipore Sigma D8662. The resulting cell suspension was filtered through 30 µm nylon mesh Fisher Scientific; NC9084441 using a 21 gauge syringe Fisher Scientific; BD 309624 and stained with SYTOX™ Red Life Technologies; S34859 to exclude dead cells. Kdrl+/NFKB and kdrl+/NFKB+ cells were each sorted and collected with BD FACS Aria III. 7 000 cells per sample were collected by FACS in Eppendorf tubes containing 250 µl of RLT buffer.	RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer’s instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.	Zebrafish Danio rerio embryos and adults were mated staged raised and processed in a circulating aquarium system maintained at 26 °C on a 14 hr light/10 hr dark cycle.	cell type:endothelial cells\|genotype:NFKB:d2eGFP x kdrl:mCherry\|treatment:kdrl+/NFKB+ sorted	GSM8027548	GSM8027548: NFKB+ biol rep 2; Danio rerio; RNA Seq	GSM8027548 r1	GSM8027548	1	RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer's instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484810	loader:fastq load.py	2-RNA-1001_S2_L001_R1_001.fastq.gz	fastq	5743794100.0	57437941.0	GSM8027548 r1	0:100	A:1588561398;C:1297479370;G:1310669617;T:1546965673;N:118042	100		1588561398	1297479370	1310669617	1546965673	118042	SRX23331818	SRS20194271	SRA1788753	Iowa State University	Iowa State University	B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2024-01-19	Multi-stage	Multi-stage	Endothelium	Cardiovascular System
30011	30011	SRR27663963	SRX23331817	SRS20194270	SRP484810	PRJNA1066877	p65 signaling dynamics drive the developmental progression of hematopoietic stem and progenitor cells through cell cycle regulation	GSE253758	Transcriptome Analysis	While hematopoietic stem and progenitor cells HSPCs and the signaling pathways that specify them have been well defined in vivo deriving functional HSPCs from human pluripotent stem cells hPSCs is still an outstanding challenge in the stem cell field. This has impaired efforts to use patient specific HSPCs and their derivatives to treat leukemia lymphoma anemia and solid cancers. Identifying the missing element to derive functional human HSPCs will be critical to advance these therapies. Here we found that in contrast to in vitro protocols where signaling pathways are typically manipulated statically the natural developmental progression of HSPC fate in the embryo requires a precise and temporally controlled oscillatory signaling dynamics. Particularly our work reveals that NF kB signaling works as an oscillatory clock that controls the developmental progression of HSPCs by driving phases of quiescence and proliferation precisely during embryonic development. This was revealed by live imaging of a custom NF kB zebrafish reporter line in conjunction with transcriptomic profiling and precise temporal manipulations of the NF kB family member p65 the driver of these signaling events. We also show that in vitro protocols of human hematopoietic differentiation from iPSCs depend on initial pro inflammatory signaling activation. In summary our results uncover the functional role of pro inflammatory signaling during HSPC specification revealed their oscillatory dynamics and define this signaling pathway as the main driver of HSPC fate progression. The integration of these dynamics in vitro will be fundamental to achieve the long standing goal of generating and expanding patient derived functional HSPCs. Overall design: To gain insights into how NF kB in endothelium was contributing to HSPC specification NFKB+ or NFKB endothelial cells kdrl+ were sorted and collected from 22hpf zebrafish embryos in triplicate and subject to RNA seq.	pubmed:39242546	NFKB+ biol rep 1	GSM8027547	tissue:endothelial cells\|cell type:endothelial cells\|genotype:NFKB:d2eGFP x kdrl:mCherry\|treatment:kdrl+/NFKB+ sorted\|geo loc name:missing\|collection date:missing	NFKB+ biol rep 1	Data was analyzed by ROSALIND® https://rosalind.bio/ with a HyperScale architecture developed by ROSALIND Inc. San Diego CA. Reads were trimmed using cutadapt. Reads were aligned to the Danio rerio genome build danRer10 using STAR. Individual sample reads were quantified using HTseq and normalized via Relative Log Expression RLE using DESeq2. Assembly: danRer10 Supplementary files format and content: comma delimited text files include fold change p values adjusted p values and normalized abundance values per sample for each gene	endothelial cells	22hpf NFKB:d2eGFP x kdrl:mCherry zebrafish embryos were screened with Leica M165FC stereomicroscope dechorionated with pronase Millipore Sigma; 11459643001 anesthetized in 1% tricaine Pentair; TRS5 and dissociated. Specifically the trunk region of each embryo was surgically isolated posterior to the yolk ball and anterior to the urogenital canal using a scalpel. The collected tissue was then gently vortexed at 28C for 5 20 mins with 50 µg/ml Liberase TM Millipore Sigma: 5401127001 in Dulbecco′s Phosphate Buffered Saline solution with Ca2+ and Mg2+ Millipore Sigma D8662. The resulting cell suspension was filtered through 30 µm nylon mesh Fisher Scientific; NC9084441 using a 21 gauge syringe Fisher Scientific; BD 309624 and stained with SYTOX™ Red Life Technologies; S34859 to exclude dead cells. Kdrl+/NFKB and kdrl+/NFKB+ cells were each sorted and collected with BD FACS Aria III. 7 000 cells per sample were collected by FACS in Eppendorf tubes containing 250 µl of RLT buffer.	RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer’s instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.	Zebrafish Danio rerio embryos and adults were mated staged raised and processed in a circulating aquarium system maintained at 26 °C on a 14 hr light/10 hr dark cycle.	cell type:endothelial cells\|genotype:NFKB:d2eGFP x kdrl:mCherry\|treatment:kdrl+/NFKB+ sorted	GSM8027547	GSM8027547: NFKB+ biol rep 1; Danio rerio; RNA Seq	GSM8027547 r1	GSM8027547	1	RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer's instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484810	loader:fastq load.py	1-RNA-0917_S1_L001_R1_001.fastq.gz	fastq	6201542500.0	62015425.0	GSM8027547 r1	0:100	A:1696049302;C:1431941155;G:1441395671;T:1632027072;N:129300	100		1696049302	1431941155	1441395671	1632027072	129300	SRX23331817	SRS20194270	SRA1788753	Iowa State University	Iowa State University	B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2024-01-19	Multi-stage	Multi-stage	Endothelium	Cardiovascular System
33669	33669	SRR30530658	SRX25954305	SRS22536191	SRP530279	PRJNA1156090	Single cell transcriptome sequencing analysis of endothelial cells in control and high glucose treated zebrafish embryos	GSE276251	Transcriptome Analysis	Artificially sweetened beverages containing noncaloric monosaccharides were suggested as healthier alternatives to sugar sweetened beverages. Nevertheless the potential detrimental effects of these noncaloric monosaccharides on blood vessel function remain inadequately understood. Presently we have established a zebrafish model that exhibits significant excessive angiogenesis induced by high glucose. Utilizing this model we observed that glucose and noncaloric monosaccharides could induce excessive formation of blood vessels especially intersegmental vessels ISVs. The excessively branched vessels were observed to be formed by ectopic activation of quiescent endothelial cells ECs into tip cells. Single cell transcriptomic sequencing analysis of the endothelial cells in the embryos exposed to high glucose revealed an augmented ratio of capillary ECs proliferating ECs and a series of upregulated proangiogenic genes. Overall design: Firstly we isolated the EGFP positive cells from control and high glucose treated Tgfli1ep:EGFP CAAX transgenic embryos. Following the proteolytic dissociation of embryos the EGFP positive cells were isolated by fluorescence activated cell sorting FACS. Around 300500 zebrafish embryos were used for the ECs collection for each stage. The isolated ECs were analyzed using a large scale scRNA seq 10X Genomics platform.	pubmed:39365738;pubmed:39882604	endothelial cells，high glucose	GSM8494124	tissue:endothelial cells\|cell type:endothelial cells\|geo loc name:missing\|collection date:missing	endothelial cells，high glucose	Cell Ranger 3.0.2 https://github.com/10XGenomics/cellranger was used to convert the raw sequencing data to single cell level gene counts matrix. The clustering of single cells and the marker genes in each cluster were analyzed by Seurat 3.0 https://satijalab.org/seurat/install.html Assembly: The reference genome fasta format and gene annotation gtf format files were downloaded from Ensembl database release version 94. Supplementary files format and content: Tab separated values files and matrix files.	endothelial cells	Embryos were treated with 6% glucose from 24 hpf to 72 hpf.	Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS and then went through library preparation following the standard protocol named Chromium Single Cell 3’Reagent Kits v3 from 10X Genomics Company.	Tgkdrl:EGFP embryos were raised in E3 solution at 28.5℃ to the indicated developmental stage.	cell type:endothelial cells	GSM8494124	GSM8494124: endothelial cells，high glucose; Danio rerio; RNA Seq	GSM8494124 r1	GSM8494124	1	Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS and then went through library preparation following the standard protocol named Chromium Single Cell three primeReagent Kits v3 from 10X Genomics Company.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP530279		lr57glu96hpf_R1.fq.gz lr57glu96hpf_R2.fq.gz	fastq fastq	196891371600.0	656304572.0	GSM8494124 r1	0:150 1:150	A:46034913013;C:37262343828;G:60636104680;T:52955473756;N:2536323	150	150	46034913013	37262343828	60636104680	52955473756	2536323	SRX25954305	SRS22536191	SRA1961613	Nantong University	Nantong University	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2024-09-03	Multi-stage	Multi-stage	Endothelium	Cardiovascular System
33670	33670	SRR30530659	SRX25954304	SRS22536190	SRP530279	PRJNA1156090	Single cell transcriptome sequencing analysis of endothelial cells in control and high glucose treated zebrafish embryos	GSE276251	Transcriptome Analysis	Artificially sweetened beverages containing noncaloric monosaccharides were suggested as healthier alternatives to sugar sweetened beverages. Nevertheless the potential detrimental effects of these noncaloric monosaccharides on blood vessel function remain inadequately understood. Presently we have established a zebrafish model that exhibits significant excessive angiogenesis induced by high glucose. Utilizing this model we observed that glucose and noncaloric monosaccharides could induce excessive formation of blood vessels especially intersegmental vessels ISVs. The excessively branched vessels were observed to be formed by ectopic activation of quiescent endothelial cells ECs into tip cells. Single cell transcriptomic sequencing analysis of the endothelial cells in the embryos exposed to high glucose revealed an augmented ratio of capillary ECs proliferating ECs and a series of upregulated proangiogenic genes. Overall design: Firstly we isolated the EGFP positive cells from control and high glucose treated Tgfli1ep:EGFP CAAX transgenic embryos. Following the proteolytic dissociation of embryos the EGFP positive cells were isolated by fluorescence activated cell sorting FACS. Around 300500 zebrafish embryos were used for the ECs collection for each stage. The isolated ECs were analyzed using a large scale scRNA seq 10X Genomics platform.	pubmed:39365738;pubmed:39882604	endothelial cells，control	GSM8494123	tissue:endothelial cells\|cell type:endothelial cells\|geo loc name:missing\|collection date:missing	endothelial cells，control	Cell Ranger 3.0.2 https://github.com/10XGenomics/cellranger was used to convert the raw sequencing data to single cell level gene counts matrix. The clustering of single cells and the marker genes in each cluster were analyzed by Seurat 3.0 https://satijalab.org/seurat/install.html Assembly: The reference genome fasta format and gene annotation gtf format files were downloaded from Ensembl database release version 94. Supplementary files format and content: Tab separated values files and matrix files.	endothelial cells	Embryos were treated with 6% glucose from 24 hpf to 72 hpf.	Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS and then went through library preparation following the standard protocol named Chromium Single Cell 3’Reagent Kits v3 from 10X Genomics Company.	Tgkdrl:EGFP embryos were raised in E3 solution at 28.5℃ to the indicated developmental stage.	cell type:endothelial cells	GSM8494123	GSM8494123: endothelial cells，control; Danio rerio; RNA Seq	GSM8494123 r1	GSM8494123	1	Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS and then went through library preparation following the standard protocol named Chromium Single Cell three primeReagent Kits v3 from 10X Genomics Company.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP530279		SH190424C_LR5796dpf_1_1_R1.fq.gz SH190424C_LR5796dpf_1_1_R2.fq.gz	fastq fastq	18351420300.0	61171401.0	GSM8494123 r1	0:150 1:150	A:3872504772;C:3434009784;G:6583451920;T:4461384217;N:69607	150	150	3872504772	3434009784	6583451920	4461384217	69607	SRX25954304	SRS22536190	SRA1961613	Nantong University	Nantong University	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2024-09-03	Multi-stage	Multi-stage	Endothelium	Cardiovascular System
33671	33671	SRR30530660	SRX25954304	SRS22536190	SRP530279	PRJNA1156090	Single cell transcriptome sequencing analysis of endothelial cells in control and high glucose treated zebrafish embryos	GSE276251	Transcriptome Analysis	Artificially sweetened beverages containing noncaloric monosaccharides were suggested as healthier alternatives to sugar sweetened beverages. Nevertheless the potential detrimental effects of these noncaloric monosaccharides on blood vessel function remain inadequately understood. Presently we have established a zebrafish model that exhibits significant excessive angiogenesis induced by high glucose. Utilizing this model we observed that glucose and noncaloric monosaccharides could induce excessive formation of blood vessels especially intersegmental vessels ISVs. The excessively branched vessels were observed to be formed by ectopic activation of quiescent endothelial cells ECs into tip cells. Single cell transcriptomic sequencing analysis of the endothelial cells in the embryos exposed to high glucose revealed an augmented ratio of capillary ECs proliferating ECs and a series of upregulated proangiogenic genes. Overall design: Firstly we isolated the EGFP positive cells from control and high glucose treated Tgfli1ep:EGFP CAAX transgenic embryos. Following the proteolytic dissociation of embryos the EGFP positive cells were isolated by fluorescence activated cell sorting FACS. Around 300500 zebrafish embryos were used for the ECs collection for each stage. The isolated ECs were analyzed using a large scale scRNA seq 10X Genomics platform.	pubmed:39365738;pubmed:39882604	endothelial cells，control	GSM8494123	tissue:endothelial cells\|cell type:endothelial cells\|geo loc name:missing\|collection date:missing	endothelial cells，control	Cell Ranger 3.0.2 https://github.com/10XGenomics/cellranger was used to convert the raw sequencing data to single cell level gene counts matrix. The clustering of single cells and the marker genes in each cluster were analyzed by Seurat 3.0 https://satijalab.org/seurat/install.html Assembly: The reference genome fasta format and gene annotation gtf format files were downloaded from Ensembl database release version 94. Supplementary files format and content: Tab separated values files and matrix files.	endothelial cells	Embryos were treated with 6% glucose from 24 hpf to 72 hpf.	Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS and then went through library preparation following the standard protocol named Chromium Single Cell 3’Reagent Kits v3 from 10X Genomics Company.	Tgkdrl:EGFP embryos were raised in E3 solution at 28.5℃ to the indicated developmental stage.	cell type:endothelial cells	GSM8494123	GSM8494123: endothelial cells，control; Danio rerio; RNA Seq	GSM8494123 r1	GSM8494123	1	Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS and then went through library preparation following the standard protocol named Chromium Single Cell three primeReagent Kits v3 from 10X Genomics Company.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP530279		SH190424C_LR5796dpf_1_2_R1.fq.gz SH190424C_LR5796dpf_1_2_R2.fq.gz	fastq fastq	36386960400.0	121289868.0	GSM8494123 r2	0:150 1:150	A:8890006445;C:6974694151;G:10814990376;T:9707137150;N:132278	150	150	8890006445	6974694151	10814990376	9707137150	132278	SRX25954304	SRS22536190	SRA1961613	Nantong University	Nantong University	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2024-09-03	Multi-stage	Multi-stage	Endothelium	Cardiovascular System
33672	33672	SRR30530661	SRX25954304	SRS22536190	SRP530279	PRJNA1156090	Single cell transcriptome sequencing analysis of endothelial cells in control and high glucose treated zebrafish embryos	GSE276251	Transcriptome Analysis	Artificially sweetened beverages containing noncaloric monosaccharides were suggested as healthier alternatives to sugar sweetened beverages. Nevertheless the potential detrimental effects of these noncaloric monosaccharides on blood vessel function remain inadequately understood. Presently we have established a zebrafish model that exhibits significant excessive angiogenesis induced by high glucose. Utilizing this model we observed that glucose and noncaloric monosaccharides could induce excessive formation of blood vessels especially intersegmental vessels ISVs. The excessively branched vessels were observed to be formed by ectopic activation of quiescent endothelial cells ECs into tip cells. Single cell transcriptomic sequencing analysis of the endothelial cells in the embryos exposed to high glucose revealed an augmented ratio of capillary ECs proliferating ECs and a series of upregulated proangiogenic genes. Overall design: Firstly we isolated the EGFP positive cells from control and high glucose treated Tgfli1ep:EGFP CAAX transgenic embryos. Following the proteolytic dissociation of embryos the EGFP positive cells were isolated by fluorescence activated cell sorting FACS. Around 300500 zebrafish embryos were used for the ECs collection for each stage. The isolated ECs were analyzed using a large scale scRNA seq 10X Genomics platform.	pubmed:39365738;pubmed:39882604	endothelial cells，control	GSM8494123	tissue:endothelial cells\|cell type:endothelial cells\|geo loc name:missing\|collection date:missing	endothelial cells，control	Cell Ranger 3.0.2 https://github.com/10XGenomics/cellranger was used to convert the raw sequencing data to single cell level gene counts matrix. The clustering of single cells and the marker genes in each cluster were analyzed by Seurat 3.0 https://satijalab.org/seurat/install.html Assembly: The reference genome fasta format and gene annotation gtf format files were downloaded from Ensembl database release version 94. Supplementary files format and content: Tab separated values files and matrix files.	endothelial cells	Embryos were treated with 6% glucose from 24 hpf to 72 hpf.	Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS and then went through library preparation following the standard protocol named Chromium Single Cell 3’Reagent Kits v3 from 10X Genomics Company.	Tgkdrl:EGFP embryos were raised in E3 solution at 28.5℃ to the indicated developmental stage.	cell type:endothelial cells	GSM8494123	GSM8494123: endothelial cells，control; Danio rerio; RNA Seq	GSM8494123 r1	GSM8494123	1	Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS and then went through library preparation following the standard protocol named Chromium Single Cell three primeReagent Kits v3 from 10X Genomics Company.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP530279		SH190424C_LR5796dpf_2_1_R1.fq.gz SH190424C_LR5796dpf_2_1_R2.fq.gz	fastq fastq	44811813000.0	149372710.0	GSM8494123 r3	0:150 1:150	A:10939691275;C:8613307673;G:13332283843;T:11926366839;N:163370	150	150	10939691275	8613307673	13332283843	11926366839	163370	SRX25954304	SRS22536190	SRA1961613	Nantong University	Nantong University	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2024-09-03	Multi-stage	Multi-stage	Endothelium	Cardiovascular System
33673	33673	SRR30530662	SRX25954304	SRS22536190	SRP530279	PRJNA1156090	Single cell transcriptome sequencing analysis of endothelial cells in control and high glucose treated zebrafish embryos	GSE276251	Transcriptome Analysis	Artificially sweetened beverages containing noncaloric monosaccharides were suggested as healthier alternatives to sugar sweetened beverages. Nevertheless the potential detrimental effects of these noncaloric monosaccharides on blood vessel function remain inadequately understood. Presently we have established a zebrafish model that exhibits significant excessive angiogenesis induced by high glucose. Utilizing this model we observed that glucose and noncaloric monosaccharides could induce excessive formation of blood vessels especially intersegmental vessels ISVs. The excessively branched vessels were observed to be formed by ectopic activation of quiescent endothelial cells ECs into tip cells. Single cell transcriptomic sequencing analysis of the endothelial cells in the embryos exposed to high glucose revealed an augmented ratio of capillary ECs proliferating ECs and a series of upregulated proangiogenic genes. Overall design: Firstly we isolated the EGFP positive cells from control and high glucose treated Tgfli1ep:EGFP CAAX transgenic embryos. Following the proteolytic dissociation of embryos the EGFP positive cells were isolated by fluorescence activated cell sorting FACS. Around 300500 zebrafish embryos were used for the ECs collection for each stage. The isolated ECs were analyzed using a large scale scRNA seq 10X Genomics platform.	pubmed:39365738;pubmed:39882604	endothelial cells，control	GSM8494123	tissue:endothelial cells\|cell type:endothelial cells\|geo loc name:missing\|collection date:missing	endothelial cells，control	Cell Ranger 3.0.2 https://github.com/10XGenomics/cellranger was used to convert the raw sequencing data to single cell level gene counts matrix. The clustering of single cells and the marker genes in each cluster were analyzed by Seurat 3.0 https://satijalab.org/seurat/install.html Assembly: The reference genome fasta format and gene annotation gtf format files were downloaded from Ensembl database release version 94. Supplementary files format and content: Tab separated values files and matrix files.	endothelial cells	Embryos were treated with 6% glucose from 24 hpf to 72 hpf.	Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS and then went through library preparation following the standard protocol named Chromium Single Cell 3’Reagent Kits v3 from 10X Genomics Company.	Tgkdrl:EGFP embryos were raised in E3 solution at 28.5℃ to the indicated developmental stage.	cell type:endothelial cells	GSM8494123	GSM8494123: endothelial cells，control; Danio rerio; RNA Seq	GSM8494123 r1	GSM8494123	1	Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS and then went through library preparation following the standard protocol named Chromium Single Cell three primeReagent Kits v3 from 10X Genomics Company.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP530279		SH190424C_LR5796dpf_2_2_R1.fq.gz SH190424C_LR5796dpf_2_2_R2.fq.gz	fastq fastq	22587582300.0	75291941.0	GSM8494123 r4	0:150 1:150	A:4762937825;C:4235264474;G:8108549401;T:5480746863;N:83737	150	150	4762937825	4235264474	8108549401	5480746863	83737	SRX25954304	SRS22536190	SRA1961613	Nantong University	Nantong University	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2024-09-03	Multi-stage	Multi-stage	Endothelium	Cardiovascular System
33674	33674	SRR30530663	SRX25954304	SRS22536190	SRP530279	PRJNA1156090	Single cell transcriptome sequencing analysis of endothelial cells in control and high glucose treated zebrafish embryos	GSE276251	Transcriptome Analysis	Artificially sweetened beverages containing noncaloric monosaccharides were suggested as healthier alternatives to sugar sweetened beverages. Nevertheless the potential detrimental effects of these noncaloric monosaccharides on blood vessel function remain inadequately understood. Presently we have established a zebrafish model that exhibits significant excessive angiogenesis induced by high glucose. Utilizing this model we observed that glucose and noncaloric monosaccharides could induce excessive formation of blood vessels especially intersegmental vessels ISVs. The excessively branched vessels were observed to be formed by ectopic activation of quiescent endothelial cells ECs into tip cells. Single cell transcriptomic sequencing analysis of the endothelial cells in the embryos exposed to high glucose revealed an augmented ratio of capillary ECs proliferating ECs and a series of upregulated proangiogenic genes. Overall design: Firstly we isolated the EGFP positive cells from control and high glucose treated Tgfli1ep:EGFP CAAX transgenic embryos. Following the proteolytic dissociation of embryos the EGFP positive cells were isolated by fluorescence activated cell sorting FACS. Around 300500 zebrafish embryos were used for the ECs collection for each stage. The isolated ECs were analyzed using a large scale scRNA seq 10X Genomics platform.	pubmed:39365738;pubmed:39882604	endothelial cells，control	GSM8494123	tissue:endothelial cells\|cell type:endothelial cells\|geo loc name:missing\|collection date:missing	endothelial cells，control	Cell Ranger 3.0.2 https://github.com/10XGenomics/cellranger was used to convert the raw sequencing data to single cell level gene counts matrix. The clustering of single cells and the marker genes in each cluster were analyzed by Seurat 3.0 https://satijalab.org/seurat/install.html Assembly: The reference genome fasta format and gene annotation gtf format files were downloaded from Ensembl database release version 94. Supplementary files format and content: Tab separated values files and matrix files.	endothelial cells	Embryos were treated with 6% glucose from 24 hpf to 72 hpf.	Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS and then went through library preparation following the standard protocol named Chromium Single Cell 3’Reagent Kits v3 from 10X Genomics Company.	Tgkdrl:EGFP embryos were raised in E3 solution at 28.5℃ to the indicated developmental stage.	cell type:endothelial cells	GSM8494123	GSM8494123: endothelial cells，control; Danio rerio; RNA Seq	GSM8494123 r1	GSM8494123	1	Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS and then went through library preparation following the standard protocol named Chromium Single Cell three primeReagent Kits v3 from 10X Genomics Company.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP530279		SH190424C_LR5796dpf_3_1_R1.fq.gz SH190424C_LR5796dpf_3_1_R2.fq.gz	fastq fastq	31458502200.0	104861674.0	GSM8494123 r5	0:150 1:150	A:7597642424;C:6175910515;G:9377029875;T:8307805635;N:113751	150	150	7597642424	6175910515	9377029875	8307805635	113751	SRX25954304	SRS22536190	SRA1961613	Nantong University	Nantong University	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2024-09-03	Multi-stage	Multi-stage	Endothelium	Cardiovascular System
33675	33675	SRR30530664	SRX25954304	SRS22536190	SRP530279	PRJNA1156090	Single cell transcriptome sequencing analysis of endothelial cells in control and high glucose treated zebrafish embryos	GSE276251	Transcriptome Analysis	Artificially sweetened beverages containing noncaloric monosaccharides were suggested as healthier alternatives to sugar sweetened beverages. Nevertheless the potential detrimental effects of these noncaloric monosaccharides on blood vessel function remain inadequately understood. Presently we have established a zebrafish model that exhibits significant excessive angiogenesis induced by high glucose. Utilizing this model we observed that glucose and noncaloric monosaccharides could induce excessive formation of blood vessels especially intersegmental vessels ISVs. The excessively branched vessels were observed to be formed by ectopic activation of quiescent endothelial cells ECs into tip cells. Single cell transcriptomic sequencing analysis of the endothelial cells in the embryos exposed to high glucose revealed an augmented ratio of capillary ECs proliferating ECs and a series of upregulated proangiogenic genes. Overall design: Firstly we isolated the EGFP positive cells from control and high glucose treated Tgfli1ep:EGFP CAAX transgenic embryos. Following the proteolytic dissociation of embryos the EGFP positive cells were isolated by fluorescence activated cell sorting FACS. Around 300500 zebrafish embryos were used for the ECs collection for each stage. The isolated ECs were analyzed using a large scale scRNA seq 10X Genomics platform.	pubmed:39365738;pubmed:39882604	endothelial cells，control	GSM8494123	tissue:endothelial cells\|cell type:endothelial cells\|geo loc name:missing\|collection date:missing	endothelial cells，control	Cell Ranger 3.0.2 https://github.com/10XGenomics/cellranger was used to convert the raw sequencing data to single cell level gene counts matrix. The clustering of single cells and the marker genes in each cluster were analyzed by Seurat 3.0 https://satijalab.org/seurat/install.html Assembly: The reference genome fasta format and gene annotation gtf format files were downloaded from Ensembl database release version 94. Supplementary files format and content: Tab separated values files and matrix files.	endothelial cells	Embryos were treated with 6% glucose from 24 hpf to 72 hpf.	Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS and then went through library preparation following the standard protocol named Chromium Single Cell 3’Reagent Kits v3 from 10X Genomics Company.	Tgkdrl:EGFP embryos were raised in E3 solution at 28.5℃ to the indicated developmental stage.	cell type:endothelial cells	GSM8494123	GSM8494123: endothelial cells，control; Danio rerio; RNA Seq	GSM8494123 r1	GSM8494123	1	Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS and then went through library preparation following the standard protocol named Chromium Single Cell three primeReagent Kits v3 from 10X Genomics Company.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP530279		SH190424C_LR5796dpf_3_2_R1.fq.gz SH190424C_LR5796dpf_3_2_R2.fq.gz	fastq fastq	15812987400.0	52709958.0	GSM8494123 r6	0:150 1:150	A:3317721700;C:3009997461;G:5662825685;T:3822382737;N:59817	150	150	3317721700	3009997461	5662825685	3822382737	59817	SRX25954304	SRS22536190	SRA1961613	Nantong University	Nantong University	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2024-09-03	Multi-stage	Multi-stage	Endothelium	Cardiovascular System
33676	33676	SRR30530665	SRX25954304	SRS22536190	SRP530279	PRJNA1156090	Single cell transcriptome sequencing analysis of endothelial cells in control and high glucose treated zebrafish embryos	GSE276251	Transcriptome Analysis	Artificially sweetened beverages containing noncaloric monosaccharides were suggested as healthier alternatives to sugar sweetened beverages. Nevertheless the potential detrimental effects of these noncaloric monosaccharides on blood vessel function remain inadequately understood. Presently we have established a zebrafish model that exhibits significant excessive angiogenesis induced by high glucose. Utilizing this model we observed that glucose and noncaloric monosaccharides could induce excessive formation of blood vessels especially intersegmental vessels ISVs. The excessively branched vessels were observed to be formed by ectopic activation of quiescent endothelial cells ECs into tip cells. Single cell transcriptomic sequencing analysis of the endothelial cells in the embryos exposed to high glucose revealed an augmented ratio of capillary ECs proliferating ECs and a series of upregulated proangiogenic genes. Overall design: Firstly we isolated the EGFP positive cells from control and high glucose treated Tgfli1ep:EGFP CAAX transgenic embryos. Following the proteolytic dissociation of embryos the EGFP positive cells were isolated by fluorescence activated cell sorting FACS. Around 300500 zebrafish embryos were used for the ECs collection for each stage. The isolated ECs were analyzed using a large scale scRNA seq 10X Genomics platform.	pubmed:39365738;pubmed:39882604	endothelial cells，control	GSM8494123	tissue:endothelial cells\|cell type:endothelial cells\|geo loc name:missing\|collection date:missing	endothelial cells，control	Cell Ranger 3.0.2 https://github.com/10XGenomics/cellranger was used to convert the raw sequencing data to single cell level gene counts matrix. The clustering of single cells and the marker genes in each cluster were analyzed by Seurat 3.0 https://satijalab.org/seurat/install.html Assembly: The reference genome fasta format and gene annotation gtf format files were downloaded from Ensembl database release version 94. Supplementary files format and content: Tab separated values files and matrix files.	endothelial cells	Embryos were treated with 6% glucose from 24 hpf to 72 hpf.	Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS and then went through library preparation following the standard protocol named Chromium Single Cell 3’Reagent Kits v3 from 10X Genomics Company.	Tgkdrl:EGFP embryos were raised in E3 solution at 28.5℃ to the indicated developmental stage.	cell type:endothelial cells	GSM8494123	GSM8494123: endothelial cells，control; Danio rerio; RNA Seq	GSM8494123 r1	GSM8494123	1	Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS and then went through library preparation following the standard protocol named Chromium Single Cell three primeReagent Kits v3 from 10X Genomics Company.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP530279		SH190424C_LR5796dpf_4_1_R1.fq.gz SH190424C_LR5796dpf_4_1_R2.fq.gz	fastq fastq	19472976900.0	64909923.0	GSM8494123 r7	0:150 1:150	A:4109297307;C:3636046624;G:6996008921;T:4731548865;N:75183	150	150	4109297307	3636046624	6996008921	4731548865	75183	SRX25954304	SRS22536190	SRA1961613	Nantong University	Nantong University	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2024-09-03	Multi-stage	Multi-stage	Endothelium	Cardiovascular System
33677	33677	SRR30530666	SRX25954304	SRS22536190	SRP530279	PRJNA1156090	Single cell transcriptome sequencing analysis of endothelial cells in control and high glucose treated zebrafish embryos	GSE276251	Transcriptome Analysis	Artificially sweetened beverages containing noncaloric monosaccharides were suggested as healthier alternatives to sugar sweetened beverages. Nevertheless the potential detrimental effects of these noncaloric monosaccharides on blood vessel function remain inadequately understood. Presently we have established a zebrafish model that exhibits significant excessive angiogenesis induced by high glucose. Utilizing this model we observed that glucose and noncaloric monosaccharides could induce excessive formation of blood vessels especially intersegmental vessels ISVs. The excessively branched vessels were observed to be formed by ectopic activation of quiescent endothelial cells ECs into tip cells. Single cell transcriptomic sequencing analysis of the endothelial cells in the embryos exposed to high glucose revealed an augmented ratio of capillary ECs proliferating ECs and a series of upregulated proangiogenic genes. Overall design: Firstly we isolated the EGFP positive cells from control and high glucose treated Tgfli1ep:EGFP CAAX transgenic embryos. Following the proteolytic dissociation of embryos the EGFP positive cells were isolated by fluorescence activated cell sorting FACS. Around 300500 zebrafish embryos were used for the ECs collection for each stage. The isolated ECs were analyzed using a large scale scRNA seq 10X Genomics platform.	pubmed:39365738;pubmed:39882604	endothelial cells，control	GSM8494123	tissue:endothelial cells\|cell type:endothelial cells\|geo loc name:missing\|collection date:missing	endothelial cells，control	Cell Ranger 3.0.2 https://github.com/10XGenomics/cellranger was used to convert the raw sequencing data to single cell level gene counts matrix. The clustering of single cells and the marker genes in each cluster were analyzed by Seurat 3.0 https://satijalab.org/seurat/install.html Assembly: The reference genome fasta format and gene annotation gtf format files were downloaded from Ensembl database release version 94. Supplementary files format and content: Tab separated values files and matrix files.	endothelial cells	Embryos were treated with 6% glucose from 24 hpf to 72 hpf.	Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS and then went through library preparation following the standard protocol named Chromium Single Cell 3’Reagent Kits v3 from 10X Genomics Company.	Tgkdrl:EGFP embryos were raised in E3 solution at 28.5℃ to the indicated developmental stage.	cell type:endothelial cells	GSM8494123	GSM8494123: endothelial cells，control; Danio rerio; RNA Seq	GSM8494123 r1	GSM8494123	1	Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS and then went through library preparation following the standard protocol named Chromium Single Cell three primeReagent Kits v3 from 10X Genomics Company.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP530279		SH190424C_LR5796dpf_4_2_R1.fq.gz SH190424C_LR5796dpf_4_2_R2.fq.gz	fastq fastq	39005746200.0	130019154.0	GSM8494123 r8	0:150 1:150	A:9542890616;C:7456459618;G:11598648802;T:10407604379;N:142785	150	150	9542890616	7456459618	11598648802	10407604379	142785	SRX25954304	SRS22536190	SRA1961613	Nantong University	Nantong University	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2024-09-03	Multi-stage	Multi-stage	Endothelium	Cardiovascular System

Advanced export

JSON shape: default, array, newline-delimited

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");;