metadata: run_metadata: 282 rows where technology = "unknown" and tissue

282 rows where technology = "unknown" 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.attributes	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.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
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
40968	40968	SRR3498282	SRX1756828	SRS1433359	SRP074847	PRJNA321312	mRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues	GSE81335	Transcriptome Analysis	Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages	parent bioproject:PRJNA321317	pubmed:28350988;pubmed:33273096	6dpf E1	GSM2150746	source name:Endothelial cell\|developmental stage:6 dpf\|tissue:Endothelial\|stain:GFP	6dpf E1	Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include FPKM values for each Sample .	Endothelial cell		Transgenic fish were treated with Liberase to dissociate the cells. post FACS sorting the GFP positive RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473.	developmental stage:6 dpf\|tissue:Endothelial\|stain:GFP	GSM2150746	GSM2150746: 6dpf E1; Danio rerio; RNA Seq	GSM2150746		1	Transgenic fish were treated with Liberase to dissociate the cells. post FACS sorting the GFP positive RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2150746	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina Genome Analyzer	SRP074847		EF_036_004_TGACCA_L002_R1.fastq.gz	fastq	446212036.0	5871211.0	GSM2150746 r1	0:76	A:121356950;C:99664887;G:97289960;T:122019647;N:5880592	76		121356950	99664887	97289960	122019647	5880592	SRX1756828	SRS1433359	SRA424807	GEO	Internal Medicine, Yale University	1	0.76652		0.13082		0.73985		0.47925		76		B		usable mapping rate	illumina	early_illumina	unknown	small_rna	trueseq	bulk	unknown	unknown	United States	2016-05-11	Larval	Larval	Endothelium	Cardiovascular System
40969	40969	SRR3498281	SRX1756827	SRS1433358	SRP074847	PRJNA321312	mRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues	GSE81335	Transcriptome Analysis	Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages	parent bioproject:PRJNA321317	pubmed:28350988;pubmed:33273096	72hpf E1	GSM2150745	source name:Endothelial cell\|developmental stage:72 hpf\|tissue:Endothelial\|stain:GFP	72hpf E1	Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include FPKM values for each Sample .	Endothelial cell		Transgenic fish were treated with Liberase to dissociate the cells. post FACS sorting the GFP positive RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473.	developmental stage:72 hpf\|tissue:Endothelial\|stain:GFP	GSM2150745	GSM2150745: 72hpf E1; Danio rerio; RNA Seq	GSM2150745		1	Transgenic fish were treated with Liberase to dissociate the cells. post FACS sorting the GFP positive RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2150745	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina Genome Analyzer	SRP074847		EF_035_003_TTAGGC_L002_R1.fastq.gz	fastq	533039908.0	7013683.0	GSM2150745 r1	0:76	A:141643030;C:119112106;G:118099940;T:147160011;N:7024821	76		141643030	119112106	118099940	147160011	7024821	SRX1756827	SRS1433358	SRA424807	GEO	Internal Medicine, Yale University	1	0.86605		0.1329		0.72253		0.49856		76		B		usable mapping rate	illumina	early_illumina	unknown	small_rna	trueseq	bulk	unknown	unknown	United States	2016-05-11	Larval	Larval	Endothelium	Cardiovascular System
40970	40970	SRR3498280	SRX1756826	SRS1433357	SRP074847	PRJNA321312	mRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues	GSE81335	Transcriptome Analysis	Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages	parent bioproject:PRJNA321317	pubmed:28350988;pubmed:33273096	48hpf E1	GSM2150744	source name:Endothelial cell\|developmental stage:48 hpf\|tissue:Endothelial\|stain:GFP	48hpf E1	Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include FPKM values for each Sample .	Endothelial cell		Transgenic fish were treated with Liberase to dissociate the cells. post FACS sorting the GFP positive RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473.	developmental stage:48 hpf\|tissue:Endothelial\|stain:GFP	GSM2150744	GSM2150744: 48hpf E1; Danio rerio; RNA Seq	GSM2150744		1	Transgenic fish were treated with Liberase to dissociate the cells. post FACS sorting the GFP positive RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2150744	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina Genome Analyzer	SRP074847		EF_034_002_CGATGT_L002_R1.fastq.gz	fastq	485202316.0	6384241.0	GSM2150744 r1	0:76	A:128473144;C:107489507;G:107138177;T:135707012;N:6394476	76		128473144	107489507	107138177	135707012	6394476	SRX1756826	SRS1433357	SRA424807	GEO	Internal Medicine, Yale University	1	0.89084		0.1385		0.71985		0.4908		76		B		usable mapping rate	illumina	early_illumina	unknown	small_rna	trueseq	bulk	unknown	unknown	United States	2016-05-11	Hatching	Embryo	Endothelium	Cardiovascular System
40971	40971	SRR3498279	SRX1756825	SRS1433356	SRP074847	PRJNA321312	mRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues	GSE81335	Transcriptome Analysis	Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages	parent bioproject:PRJNA321317	pubmed:28350988;pubmed:33273096	24hpf E1	GSM2150743	source name:Endothelial cell\|developmental stage:24 hpf\|tissue:Endothelial\|stain:GFP	24hpf E1	Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include FPKM values for each Sample .	Endothelial cell		Transgenic fish were treated with Liberase to dissociate the cells. post FACS sorting the GFP positive RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473.	developmental stage:24 hpf\|tissue:Endothelial\|stain:GFP	GSM2150743	GSM2150743: 24hpf E1; Danio rerio; RNA Seq	GSM2150743		1	Transgenic fish were treated with Liberase to dissociate the cells. post FACS sorting the GFP positive RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2150743	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina Genome Analyzer	SRP074847		EF_033_001_ATCACG_L002_R1.fastq.gz	fastq	426238476.0	5608401.0	GSM2150743 r1	0:76	A:113332066;C:95045840;G:93307502;T:118935708;N:5617360	76		113332066	95045840	93307502	118935708	5617360	SRX1756825	SRS1433356	SRA424807	GEO	Internal Medicine, Yale University	1	0.88651		0.15752		0.72805		0.48414		76		B		usable mapping rate	illumina	early_illumina	unknown	small_rna	trueseq	bulk	unknown	unknown	United States	2016-05-11	Pharyngula	Embryo	Endothelium	Cardiovascular System
40972	40972	SRR3498294	SRX1756840	SRS1433371	SRP074848	PRJNA321321	microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues	GSE81340	Transcriptome Analysis	Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate	parent bioproject:PRJNA321317	pubmed:28350988;pubmed:33273096	NoEndo 72hpf E2	GSM2150819	source name:Endothelial cell\|developmental stage:72hpf\|tissue:Endothelial\|stain:GFP	NoEndo 72hpf E2	Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...	Endothelial cell		Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473.	developmental stage:72hpf\|tissue:Endothelial\|stain:GFP	GSM2150819	GSM2150819: NoEndo 72hpf E2; Danio rerio; miRNA Seq	GSM2150819		1	Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2150819	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer	SRP074848		NoEndo_72hpf_E2.fastq.gz	fastq	797509876.0	10493551.0	GSM2150819 r1	0:76	A:182564842;C:199547592;G:199064466;T:216287390;N:45586	76		182564842	199547592	199064466	216287390	45586	SRX1756840	SRS1433371	SRA424808	GEO	Internal Medicine, Yale University	1	1e-05		0.0		1.0				76		T		under 1.2% mapping rate	illumina	early_illumina	unknown	size_fractionation	trueseq	bulk	unknown	unknown	United States	2016-05-11	Larval	Larval	Endothelium	Cardiovascular System
40973	40973	SRR3498293	SRX1756839	SRS1433370	SRP074848	PRJNA321321	microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues	GSE81340	Transcriptome Analysis	Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate	parent bioproject:PRJNA321317	pubmed:28350988;pubmed:33273096	NoEndo 72hpf E1	GSM2150818	source name:Endothelial cell\|developmental stage:72hpf\|tissue:Endothelial\|stain:GFP	NoEndo 72hpf E1	Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...	Endothelial cell		Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473.	developmental stage:72hpf\|tissue:Endothelial\|stain:GFP	GSM2150818	GSM2150818: NoEndo 72hpf E1; Danio rerio; miRNA Seq	GSM2150818		1	Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2150818	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer	SRP074848		NoEndo_72hpf_E1.fastq.gz	fastq	1864172232.0	24528582.0	GSM2150818 r1	0:76	A:426671762;C:469538477;G:458132395;T:509711525;N:118073	76		426671762	469538477	458132395	509711525	118073	SRX1756839	SRS1433370	SRA424808	GEO	Internal Medicine, Yale University	1	0.0		0.0		1.0				76		T		under 1.2% mapping rate	illumina	early_illumina	unknown	size_fractionation	trueseq	bulk	unknown	unknown	United States	2016-05-11	Larval	Larval	Endothelium	Cardiovascular System
40974	40974	SRR3498292	SRX1756838	SRS1433369	SRP074848	PRJNA321321	microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues	GSE81340	Transcriptome Analysis	Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate	parent bioproject:PRJNA321317	pubmed:28350988;pubmed:33273096	NoEndo 6dpf E1	GSM2150817	source name:Endothelial cell\|developmental stage:6dpf\|tissue:Endothelial\|stain:GFP	NoEndo 6dpf E1	Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...	Endothelial cell		Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473.	developmental stage:6dpf\|tissue:Endothelial\|stain:GFP	GSM2150817	GSM2150817: NoEndo 6dpf E1; Danio rerio; miRNA Seq	GSM2150817		1	Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2150817	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer	SRP074848		NoEndo_6dpf_E1.fastq.gz	fastq	1414849364.0	18616439.0	GSM2150817 r1	0:76	A:315250036;C:366906308;G:364673112;T:367938758;N:81150	76		315250036	366906308	364673112	367938758	81150	SRX1756838	SRS1433369	SRA424808	GEO	Internal Medicine, Yale University	1	1e-05		0.0		1.0				76		T		under 1.2% mapping rate	illumina	early_illumina	unknown	size_fractionation	trueseq	bulk	unknown	unknown	United States	2016-05-11	Larval	Larval	Endothelium	Cardiovascular System
40975	40975	SRR3498291	SRX1756837	SRS1433368	SRP074848	PRJNA321321	microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues	GSE81340	Transcriptome Analysis	Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate	parent bioproject:PRJNA321317	pubmed:28350988;pubmed:33273096	NoEndo 48hpf E2	GSM2150816	source name:Endothelial cell\|developmental stage:48hpf\|tissue:Endothelial\|stain:GFP	NoEndo 48hpf E2	Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...	Endothelial cell		Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473.	developmental stage:48hpf\|tissue:Endothelial\|stain:GFP	GSM2150816	GSM2150816: NoEndo 48hpf E2; Danio rerio; miRNA Seq	GSM2150816		1	Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2150816	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer	SRP074848		NoEndo_48hpf_E2.fastq.gz	fastq	553364740.0	7281115.0	GSM2150816 r1	0:76	A:129173344;C:134804122;G:141026546;T:148331467;N:29261	76		129173344	134804122	141026546	148331467	29261	SRX1756837	SRS1433368	SRA424808	GEO	Internal Medicine, Yale University	1	1e-05		0.0		0.99997		0.0		76		T		under 1.2% mapping rate	illumina	early_illumina	unknown	size_fractionation	trueseq	bulk	unknown	unknown	United States	2016-05-11	Hatching	Embryo	Endothelium	Cardiovascular System
40976	40976	SRR3498290	SRX1756836	SRS1433367	SRP074848	PRJNA321321	microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues	GSE81340	Transcriptome Analysis	Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate	parent bioproject:PRJNA321317	pubmed:28350988;pubmed:33273096	NoEndo 48hpf E1	GSM2150815	source name:Endothelial cell\|developmental stage:48hpf\|tissue:Endothelial\|stain:GFP	NoEndo 48hpf E1	Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...	Endothelial cell		Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473.	developmental stage:48hpf\|tissue:Endothelial\|stain:GFP	GSM2150815	GSM2150815: NoEndo 48hpf E1; Danio rerio; miRNA Seq	GSM2150815		1	Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2150815	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer	SRP074848		NoEndo_48hpf_E1.fastq.gz	fastq	1204752152.0	15852002.0	GSM2150815 r1	0:76	A:297517299;C:293969730;G:317491224;T:295696492;N:77407	76		297517299	293969730	317491224	295696492	77407	SRX1756836	SRS1433367	SRA424808	GEO	Internal Medicine, Yale University	1	0.0		0.0		1.0				76		T		under 1.2% mapping rate	illumina	early_illumina	unknown	size_fractionation	trueseq	bulk	unknown	unknown	United States	2016-05-11	Hatching	Embryo	Endothelium	Cardiovascular System
40977	40977	SRR3498289	SRX1756835	SRS1433366	SRP074848	PRJNA321321	microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues	GSE81340	Transcriptome Analysis	Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate	parent bioproject:PRJNA321317	pubmed:28350988;pubmed:33273096	NoEndo 24hpf E1	GSM2150814	source name:Endothelial cell\|developmental stage:24hpf\|tissue:Endothelial\|stain:GFP	NoEndo 24hpf E1	Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...	Endothelial cell		Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473.	developmental stage:24hpf\|tissue:Endothelial\|stain:GFP	GSM2150814	GSM2150814: NoEndo 24hpf E1; Danio rerio; miRNA Seq	GSM2150814		1	Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2150814	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer	SRP074848		NoEndo_24hpf_E1.fastq.gz	fastq	1422085704.0	18711654.0	GSM2150814 r1	0:76	A:347700492;C:356065333;G:376424133;T:341806001;N:89745	76		347700492	356065333	376424133	341806001	89745	SRX1756835	SRS1433366	SRA424808	GEO	Internal Medicine, Yale University	1	0.0		0.0		1.0				76		T		under 1.2% mapping rate	illumina	early_illumina	unknown	size_fractionation	trueseq	bulk	unknown	unknown	United States	2016-05-11	Pharyngula	Embryo	Endothelium	Cardiovascular System
40978	40978	SRR3498288	SRX1756834	SRS1433365	SRP074848	PRJNA321321	microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues	GSE81340	Transcriptome Analysis	Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate	parent bioproject:PRJNA321317	pubmed:28350988;pubmed:33273096	Endo 72hpf E2	GSM2150813	source name:Endothelial cell\|developmental stage:72hpf\|tissue:Endothelial\|stain:GFP	Endo 72hpf E2	Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...	Endothelial cell		Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473.	developmental stage:72hpf\|tissue:Endothelial\|stain:GFP	GSM2150813	GSM2150813: Endo 72hpf E2; Danio rerio; miRNA Seq	GSM2150813		1	Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2150813	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer	SRP074848		Endo_72hpf_E2.fastq.gz	fastq	438128980.0	5764855.0	GSM2150813 r1	0:76	A:101851745;C:114159902;G:115733669;T:106360221;N:23443	76		101851745	114159902	115733669	106360221	23443	SRX1756834	SRS1433365	SRA424808	GEO	Internal Medicine, Yale University	1	2e-05		1e-05		1.0				76		T		under 1.2% mapping rate	illumina	early_illumina	unknown	size_fractionation	trueseq	bulk	unknown	unknown	United States	2016-05-11	Larval	Larval	Endothelium	Cardiovascular System
40979	40979	SRR3498287	SRX1756833	SRS1433364	SRP074848	PRJNA321321	microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues	GSE81340	Transcriptome Analysis	Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate	parent bioproject:PRJNA321317	pubmed:28350988;pubmed:33273096	Endo 72hpf E1	GSM2150812	source name:Endothelial cell\|developmental stage:72hpf\|tissue:Endothelial\|stain:GFP	Endo 72hpf E1	Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...	Endothelial cell		Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473.	developmental stage:72hpf\|tissue:Endothelial\|stain:GFP	GSM2150812	GSM2150812: Endo 72hpf E1; Danio rerio; miRNA Seq	GSM2150812		1	Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2150812	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer	SRP074848		Endo_72hpf_E1.fastq.gz	fastq	1267915068.0	16683093.0	GSM2150812 r1	0:76	A:321606522;C:310505837;G:323829249;T:311892892;N:80568	76		321606522	310505837	323829249	311892892	80568	SRX1756833	SRS1433364	SRA424808	GEO	Internal Medicine, Yale University	1	0.0		0.0		1.0				76		T		under 1.2% mapping rate	illumina	early_illumina	unknown	size_fractionation	trueseq	bulk	unknown	unknown	United States	2016-05-11	Larval	Larval	Endothelium	Cardiovascular System
40980	40980	SRR3498286	SRX1756832	SRS1433363	SRP074848	PRJNA321321	microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues	GSE81340	Transcriptome Analysis	Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate	parent bioproject:PRJNA321317	pubmed:28350988;pubmed:33273096	Endo 6dpf E1	GSM2150811	source name:Endothelial cell\|developmental stage:6dpf\|tissue:Endothelial\|stain:GFP	Endo 6dpf E1	Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...	Endothelial cell		Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473.	developmental stage:6dpf\|tissue:Endothelial\|stain:GFP	GSM2150811	GSM2150811: Endo 6dpf E1; Danio rerio; miRNA Seq	GSM2150811		1	Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2150811	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer	SRP074848		Endo_6dpf_E1.fastq.gz	fastq	890474824.0	11716774.0	GSM2150811 r1	0:76	A:230419087;C:212029155;G:232306960;T:215672618;N:47004	76		230419087	212029155	232306960	215672618	47004	SRX1756832	SRS1433363	SRA424808	GEO	Internal Medicine, Yale University	1	2e-05		1e-05		1.0				76		T		under 1.2% mapping rate	illumina	early_illumina	unknown	size_fractionation	trueseq	bulk	unknown	unknown	United States	2016-05-11	Larval	Larval	Endothelium	Cardiovascular System
40981	40981	SRR3498285	SRX1756831	SRS1433362	SRP074848	PRJNA321321	microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues	GSE81340	Transcriptome Analysis	Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate	parent bioproject:PRJNA321317	pubmed:28350988;pubmed:33273096	Endo 48hpf E2	GSM2150810	source name:Endothelial cell\|developmental stage:48hpf\|tissue:Endothelial\|stain:GFP	Endo 48hpf E2	Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...	Endothelial cell		Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473.	developmental stage:48hpf\|tissue:Endothelial\|stain:GFP	GSM2150810	GSM2150810: Endo 48hpf E2; Danio rerio; miRNA Seq	GSM2150810		1	Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2150810	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer	SRP074848		Endo_48hpf_E2.fastq.gz	fastq	1254556624.0	16507324.0	GSM2150810 r1	0:76	A:316229540;C:323340793;G:307552357;T:307354555;N:79379	76		316229540	323340793	307552357	307354555	79379	SRX1756831	SRS1433362	SRA424808	GEO	Internal Medicine, Yale University	1	0.0		0.0		1.0				76		T		under 1.2% mapping rate	illumina	early_illumina	unknown	size_fractionation	trueseq	bulk	unknown	unknown	United States	2016-05-11	Hatching	Embryo	Endothelium	Cardiovascular System
40982	40982	SRR3498284	SRX1756830	SRS1433361	SRP074848	PRJNA321321	microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues	GSE81340	Transcriptome Analysis	Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate	parent bioproject:PRJNA321317	pubmed:28350988;pubmed:33273096	Endo 48hpf E1	GSM2150809	source name:Endothelial cell\|developmental stage:48hpf\|tissue:Endothelial\|stain:GFP	Endo 48hpf E1	Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...	Endothelial cell		Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473.	developmental stage:48hpf\|tissue:Endothelial\|stain:GFP	GSM2150809	GSM2150809: Endo 48hpf E1; Danio rerio; miRNA Seq	GSM2150809		1	Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2150809	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer	SRP074848		Endo_48hpf_E1.fastq.gz	fastq	1449497080.0	19072330.0	GSM2150809 r1	0:76	A:362564557;C:370330864;G:364749441;T:351760774;N:91444	76		362564557	370330864	364749441	351760774	91444	SRX1756830	SRS1433361	SRA424808	GEO	Internal Medicine, Yale University	1	0.0		0.0		1.0				76		T		under 1.2% mapping rate	illumina	early_illumina	unknown	size_fractionation	trueseq	bulk	unknown	unknown	United States	2016-05-11	Hatching	Embryo	Endothelium	Cardiovascular System
40983	40983	SRR3498283	SRX1756829	SRS1433360	SRP074848	PRJNA321321	microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues	GSE81340	Transcriptome Analysis	Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate	parent bioproject:PRJNA321317	pubmed:28350988;pubmed:33273096	Endo 24hpf E1	GSM2150808	source name:Endothelial cell\|developmental stage:24hpf\|tissue:Endothelial\|stain:GFP	Endo 24hpf E1	Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...	Endothelial cell		Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473.	developmental stage:24hpf\|tissue:Endothelial\|stain:GFP	GSM2150808	GSM2150808: Endo 24hpf E1; Danio rerio; miRNA Seq	GSM2150808		1	Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2150808	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer	SRP074848		Endo_24hpf_E1.fastq.gz	fastq	1527500440.0	20098690.0	GSM2150808 r1	0:76	A:356712587;C:354608109;G:432977038;T:383106520;N:96186	76		356712587	354608109	432977038	383106520	96186	SRX1756829	SRS1433360	SRA424808	GEO	Internal Medicine, Yale University	1	0.0		0.0		1.0				76		T		under 1.2% mapping rate	illumina	early_illumina	unknown	size_fractionation	trueseq	bulk	unknown	unknown	United States	2016-05-11	Pharyngula	Embryo	Endothelium	Cardiovascular System
41146	41146	SRR3742564	SRX1896783	SRS1539775	SRP077871	PRJNA327749	Gene expression profiles of endothelial cells from mutants and siblings of tsu3994	GSE83987	Transcriptome Analysis	Through RNA seq we report endothelial cells from mutants had 1063 up regulated and 132 down regulated genes >2.0 fold with false discovery rate <0.001 when compared to siblings. Overall design: Examination of gene exprssion profiles of endothelial cells from siblings and mutants of tsu3994		pubmed:28003365	Mt	GSM2224910	tissue:kdrl:GFP+ Endothelial cells\|genetic background:tsu3994;Tgkdrl;GFP cross\|genotype/variation:Morphologically mutant embryo\|Stage:44 hpf type:Endothelial cells	Mt	HCS3.3.20 RTA 2.5.2 and bcl2fastq2 v2.16 were used for basecalling. Sequenced reads were remove reads with adaptors and remove reads in which unknown bases are more than 10% remove reads in which unknown bases are more than 10%.We use Bowtie2 with parameters q phred64 sensitive dpad 0 gbar 99999999 mp 1 1 np 1 score min L 0 0.1 p 16 k 200 to map clean reads to reference gene and use BWA with parameters o 1 e 50 i 50 L k 2 l 31 t 4 q 10 to reference genome Danio rerio.GRCz10.dna.toplevel.fa . RSEM is a quantification tool that computed Maximum likelihood abundance estimates using the Expectation Maximization EM algorithm for its statistical model . FPKM fragment Per Kilobase of gene per Megabase of library size method is used in calculated expression level. Genome build: Zv10 Supplementary files format and content: tab delimited text files include FPKM values for each Sample	kdrl:GFP+ Endothelial cells		Morphologically normal siblings and mutant embryos from crosses of Tgkdrl:GFP; gbf1tsu3994/+ at 44 hpf were dechorionated and disintegrated completely to prepare single cell suspension. Then kdrl:GFP+ ECs were sorted by flow cytomer FACSAria BD and MoFlo XDP BeckMan and positive cells were confirmed by microscopy. Total mRNAs were extracted with RNeasy Mini Kit QIAGEN. The total RNA samples are first treated with DNase I to degrade any possible DNA contamination. Then the mRNA is enriched by using the oligo dT magnetic beads. Mixed with the fragmentation buffer the mRNA is fragmented into short fragments. Then the first strand of cDNA is synthesized by using random hexamer primer. Buffer dNTPs RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with magnetic beads. End reparation and 3’ end single nucleotide A adenine addition is then performed. Finally sequencing adaptors are ligated to the fragments. The fragments are enriched by PCR amplification.During the QC step Agilent 2100 Bioanaylzer and ABI StepOnePlus Real Time PCR System are used to qualify and quantify of the sample library. The library products are ready for sequencing via Illumina HiSeqTM 2000 or other sequencer when necessary.		genetic background:tsu3994;Tgkdrl;GFP cross\|genotype/variation:Morphologically mutant embryo\|Stage:44 hpf type:Endothelial cells	GSM2224910	GSM2224910: Mt; Danio rerio; RNA Seq	GSM2224910		1	Morphologically normal siblings and mutant embryos from crosses of Tgkdrl:GFP; gbf1tsu3994/+ at 44 hpf were dechorionated and disintegrated completely to prepare single cell suspension. Then kdrl:GFP+ ECs were sorted by flow cytomer FACSAria BD and MoFlo XDP BeckMan and positive cells were confirmed by microscopy. Total mRNAs were extracted with RNeasy Mini Kit QIAGEN. The total RNA samples are first treated with DNase I to degrade any possible DNA contamination. Then the mRNA is enriched by using the oligo dT magnetic beads. Mixed with the fragmentation buffer the mRNA is fragmented into short fragments. Then the first strand of cDNA is synthesized by using random hexamer primer. Buffer dNTPs RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with magnetic beads. End reparation and 3’ end single nucleotide A adenine addition is then performed. Finally sequencing adaptors are ligated to the fragments. The fragments are enriched by PCR amplification.During the QC step Agilent 2100 Bioanaylzer and ABI StepOnePlus Real Time PCR System are used to qualify and quantify of the sample library. The library products are ready for sequencing via Illumina HiSeqTM 2000 or other sequencer when necessary.	GEO Accession:GSM2224910	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP077871		160123_I114_FCH52M2BBXX_L2_WHFISoiqRAABRAAPEI-144_1.fq.gz	fastq	262444686.0	5356014.0	GSM2224910 r1	0:49	A:66548564;C:63544339;G:66582385;T:65755749;N:13649	49		66548564	63544339	66582385	65755749	13649	SRX1896783	SRS1539775	SRA437681	GEO	Anming Meng, School of Lifesciences, Tsinghua University	1	0.92714		0.05568		0.73423		0.48371		49		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2016-07-04	Pharyngula	Embryo	Endothelium	Cardiovascular System
41147	41147	SRR3742565	SRX1896783	SRS1539775	SRP077871	PRJNA327749	Gene expression profiles of endothelial cells from mutants and siblings of tsu3994	GSE83987	Transcriptome Analysis	Through RNA seq we report endothelial cells from mutants had 1063 up regulated and 132 down regulated genes >2.0 fold with false discovery rate <0.001 when compared to siblings. Overall design: Examination of gene exprssion profiles of endothelial cells from siblings and mutants of tsu3994		pubmed:28003365	Mt	GSM2224910	tissue:kdrl:GFP+ Endothelial cells\|genetic background:tsu3994;Tgkdrl;GFP cross\|genotype/variation:Morphologically mutant embryo\|Stage:44 hpf type:Endothelial cells	Mt	HCS3.3.20 RTA 2.5.2 and bcl2fastq2 v2.16 were used for basecalling. Sequenced reads were remove reads with adaptors and remove reads in which unknown bases are more than 10% remove reads in which unknown bases are more than 10%.We use Bowtie2 with parameters q phred64 sensitive dpad 0 gbar 99999999 mp 1 1 np 1 score min L 0 0.1 p 16 k 200 to map clean reads to reference gene and use BWA with parameters o 1 e 50 i 50 L k 2 l 31 t 4 q 10 to reference genome Danio rerio.GRCz10.dna.toplevel.fa . RSEM is a quantification tool that computed Maximum likelihood abundance estimates using the Expectation Maximization EM algorithm for its statistical model . FPKM fragment Per Kilobase of gene per Megabase of library size method is used in calculated expression level. Genome build: Zv10 Supplementary files format and content: tab delimited text files include FPKM values for each Sample	kdrl:GFP+ Endothelial cells		Morphologically normal siblings and mutant embryos from crosses of Tgkdrl:GFP; gbf1tsu3994/+ at 44 hpf were dechorionated and disintegrated completely to prepare single cell suspension. Then kdrl:GFP+ ECs were sorted by flow cytomer FACSAria BD and MoFlo XDP BeckMan and positive cells were confirmed by microscopy. Total mRNAs were extracted with RNeasy Mini Kit QIAGEN. The total RNA samples are first treated with DNase I to degrade any possible DNA contamination. Then the mRNA is enriched by using the oligo dT magnetic beads. Mixed with the fragmentation buffer the mRNA is fragmented into short fragments. Then the first strand of cDNA is synthesized by using random hexamer primer. Buffer dNTPs RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with magnetic beads. End reparation and 3’ end single nucleotide A adenine addition is then performed. Finally sequencing adaptors are ligated to the fragments. The fragments are enriched by PCR amplification.During the QC step Agilent 2100 Bioanaylzer and ABI StepOnePlus Real Time PCR System are used to qualify and quantify of the sample library. The library products are ready for sequencing via Illumina HiSeqTM 2000 or other sequencer when necessary.		genetic background:tsu3994;Tgkdrl;GFP cross\|genotype/variation:Morphologically mutant embryo\|Stage:44 hpf type:Endothelial cells	GSM2224910	GSM2224910: Mt; Danio rerio; RNA Seq	GSM2224910		1	Morphologically normal siblings and mutant embryos from crosses of Tgkdrl:GFP; gbf1tsu3994/+ at 44 hpf were dechorionated and disintegrated completely to prepare single cell suspension. Then kdrl:GFP+ ECs were sorted by flow cytomer FACSAria BD and MoFlo XDP BeckMan and positive cells were confirmed by microscopy. Total mRNAs were extracted with RNeasy Mini Kit QIAGEN. The total RNA samples are first treated with DNase I to degrade any possible DNA contamination. Then the mRNA is enriched by using the oligo dT magnetic beads. Mixed with the fragmentation buffer the mRNA is fragmented into short fragments. Then the first strand of cDNA is synthesized by using random hexamer primer. Buffer dNTPs RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with magnetic beads. End reparation and 3’ end single nucleotide A adenine addition is then performed. Finally sequencing adaptors are ligated to the fragments. The fragments are enriched by PCR amplification.During the QC step Agilent 2100 Bioanaylzer and ABI StepOnePlus Real Time PCR System are used to qualify and quantify of the sample library. The library products are ready for sequencing via Illumina HiSeqTM 2000 or other sequencer when necessary.	GEO Accession:GSM2224910	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP077871		160204_I136_FCH55MNBBXX_L6_WHFISoiqRAABRAAPEI-144_1.fq.gz	fastq	448147973.0	9145877.0	GSM2224910 r2	0:49	A:113623842;C:108767789;G:113689061;T:112055179;N:12102	49		113623842	108767789	113689061	112055179	12102	SRX1896783	SRS1539775	SRA437681	GEO	Anming Meng, School of Lifesciences, Tsinghua University	1	0.91636		0.05377		0.73545		0.48441		49		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2016-07-04	Pharyngula	Embryo	Endothelium	Cardiovascular System
41148	41148	SRR3742562	SRX1896782	SRS1539774	SRP077871	PRJNA327749	Gene expression profiles of endothelial cells from mutants and siblings of tsu3994	GSE83987	Transcriptome Analysis	Through RNA seq we report endothelial cells from mutants had 1063 up regulated and 132 down regulated genes >2.0 fold with false discovery rate <0.001 when compared to siblings. Overall design: Examination of gene exprssion profiles of endothelial cells from siblings and mutants of tsu3994		pubmed:28003365	Sib	GSM2224909	tissue:kdrl:GFP+ Endothelial cells\|genetic background:tsu3994;Tgkdrl;GFP cross\|genotype/variation:Morphologically normal siblings embryo\|Stage:44 hpf type:Endothelial cells	Sib	HCS3.3.20 RTA 2.5.2 and bcl2fastq2 v2.16 were used for basecalling. Sequenced reads were remove reads with adaptors and remove reads in which unknown bases are more than 10% remove reads in which unknown bases are more than 10%.We use Bowtie2 with parameters q phred64 sensitive dpad 0 gbar 99999999 mp 1 1 np 1 score min L 0 0.1 p 16 k 200 to map clean reads to reference gene and use BWA with parameters o 1 e 50 i 50 L k 2 l 31 t 4 q 10 to reference genome Danio rerio.GRCz10.dna.toplevel.fa . RSEM is a quantification tool that computed Maximum likelihood abundance estimates using the Expectation Maximization EM algorithm for its statistical model . FPKM fragment Per Kilobase of gene per Megabase of library size method is used in calculated expression level. Genome build: Zv10 Supplementary files format and content: tab delimited text files include FPKM values for each Sample	kdrl:GFP+ Endothelial cells		Morphologically normal siblings and mutant embryos from crosses of Tgkdrl:GFP; gbf1tsu3994/+ at 44 hpf were dechorionated and disintegrated completely to prepare single cell suspension. Then kdrl:GFP+ ECs were sorted by flow cytomer FACSAria BD and MoFlo XDP BeckMan and positive cells were confirmed by microscopy. Total mRNAs were extracted with RNeasy Mini Kit QIAGEN. The total RNA samples are first treated with DNase I to degrade any possible DNA contamination. Then the mRNA is enriched by using the oligo dT magnetic beads. Mixed with the fragmentation buffer the mRNA is fragmented into short fragments. Then the first strand of cDNA is synthesized by using random hexamer primer. Buffer dNTPs RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with magnetic beads. End reparation and 3’ end single nucleotide A adenine addition is then performed. Finally sequencing adaptors are ligated to the fragments. The fragments are enriched by PCR amplification.During the QC step Agilent 2100 Bioanaylzer and ABI StepOnePlus Real Time PCR System are used to qualify and quantify of the sample library. The library products are ready for sequencing via Illumina HiSeqTM 2000 or other sequencer when necessary.		genetic background:tsu3994;Tgkdrl;GFP cross\|genotype/variation:Morphologically normal siblings embryo\|Stage:44 hpf type:Endothelial cells	GSM2224909	GSM2224909: Sib; Danio rerio; RNA Seq	GSM2224909		1	Morphologically normal siblings and mutant embryos from crosses of Tgkdrl:GFP; gbf1tsu3994/+ at 44 hpf were dechorionated and disintegrated completely to prepare single cell suspension. Then kdrl:GFP+ ECs were sorted by flow cytomer FACSAria BD and MoFlo XDP BeckMan and positive cells were confirmed by microscopy. Total mRNAs were extracted with RNeasy Mini Kit QIAGEN. The total RNA samples are first treated with DNase I to degrade any possible DNA contamination. Then the mRNA is enriched by using the oligo dT magnetic beads. Mixed with the fragmentation buffer the mRNA is fragmented into short fragments. Then the first strand of cDNA is synthesized by using random hexamer primer. Buffer dNTPs RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with magnetic beads. End reparation and 3’ end single nucleotide A adenine addition is then performed. Finally sequencing adaptors are ligated to the fragments. The fragments are enriched by PCR amplification.During the QC step Agilent 2100 Bioanaylzer and ABI StepOnePlus Real Time PCR System are used to qualify and quantify of the sample library. The library products are ready for sequencing via Illumina HiSeqTM 2000 or other sequencer when necessary.	GEO Accession:GSM2224909	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP077871		160123_I114_FCH52M2BBXX_L2_WHFISoiqRAAARAAPEI-100_1.fq.gz	fastq	180708423.0	3687927.0	GSM2224909 r1	0:49	A:45675389;C:44261209;G:46002295;T:44768361;N:1169	49		45675389	44261209	46002295	44768361	1169	SRX1896782	SRS1539774	SRA437681	GEO	Anming Meng, School of Lifesciences, Tsinghua University	1	0.93956		0.0479		0.75276		0.47889		49		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2016-07-04	Pharyngula	Embryo	Endothelium	Cardiovascular System
41149	41149	SRR3742563	SRX1896782	SRS1539774	SRP077871	PRJNA327749	Gene expression profiles of endothelial cells from mutants and siblings of tsu3994	GSE83987	Transcriptome Analysis	Through RNA seq we report endothelial cells from mutants had 1063 up regulated and 132 down regulated genes >2.0 fold with false discovery rate <0.001 when compared to siblings. Overall design: Examination of gene exprssion profiles of endothelial cells from siblings and mutants of tsu3994		pubmed:28003365	Sib	GSM2224909	tissue:kdrl:GFP+ Endothelial cells\|genetic background:tsu3994;Tgkdrl;GFP cross\|genotype/variation:Morphologically normal siblings embryo\|Stage:44 hpf type:Endothelial cells	Sib	HCS3.3.20 RTA 2.5.2 and bcl2fastq2 v2.16 were used for basecalling. Sequenced reads were remove reads with adaptors and remove reads in which unknown bases are more than 10% remove reads in which unknown bases are more than 10%.We use Bowtie2 with parameters q phred64 sensitive dpad 0 gbar 99999999 mp 1 1 np 1 score min L 0 0.1 p 16 k 200 to map clean reads to reference gene and use BWA with parameters o 1 e 50 i 50 L k 2 l 31 t 4 q 10 to reference genome Danio rerio.GRCz10.dna.toplevel.fa . RSEM is a quantification tool that computed Maximum likelihood abundance estimates using the Expectation Maximization EM algorithm for its statistical model . FPKM fragment Per Kilobase of gene per Megabase of library size method is used in calculated expression level. Genome build: Zv10 Supplementary files format and content: tab delimited text files include FPKM values for each Sample	kdrl:GFP+ Endothelial cells		Morphologically normal siblings and mutant embryos from crosses of Tgkdrl:GFP; gbf1tsu3994/+ at 44 hpf were dechorionated and disintegrated completely to prepare single cell suspension. Then kdrl:GFP+ ECs were sorted by flow cytomer FACSAria BD and MoFlo XDP BeckMan and positive cells were confirmed by microscopy. Total mRNAs were extracted with RNeasy Mini Kit QIAGEN. The total RNA samples are first treated with DNase I to degrade any possible DNA contamination. Then the mRNA is enriched by using the oligo dT magnetic beads. Mixed with the fragmentation buffer the mRNA is fragmented into short fragments. Then the first strand of cDNA is synthesized by using random hexamer primer. Buffer dNTPs RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with magnetic beads. End reparation and 3’ end single nucleotide A adenine addition is then performed. Finally sequencing adaptors are ligated to the fragments. The fragments are enriched by PCR amplification.During the QC step Agilent 2100 Bioanaylzer and ABI StepOnePlus Real Time PCR System are used to qualify and quantify of the sample library. The library products are ready for sequencing via Illumina HiSeqTM 2000 or other sequencer when necessary.		genetic background:tsu3994;Tgkdrl;GFP cross\|genotype/variation:Morphologically normal siblings embryo\|Stage:44 hpf type:Endothelial cells	GSM2224909	GSM2224909: Sib; Danio rerio; RNA Seq	GSM2224909		1	Morphologically normal siblings and mutant embryos from crosses of Tgkdrl:GFP; gbf1tsu3994/+ at 44 hpf were dechorionated and disintegrated completely to prepare single cell suspension. Then kdrl:GFP+ ECs were sorted by flow cytomer FACSAria BD and MoFlo XDP BeckMan and positive cells were confirmed by microscopy. Total mRNAs were extracted with RNeasy Mini Kit QIAGEN. The total RNA samples are first treated with DNase I to degrade any possible DNA contamination. Then the mRNA is enriched by using the oligo dT magnetic beads. Mixed with the fragmentation buffer the mRNA is fragmented into short fragments. Then the first strand of cDNA is synthesized by using random hexamer primer. Buffer dNTPs RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with magnetic beads. End reparation and 3’ end single nucleotide A adenine addition is then performed. Finally sequencing adaptors are ligated to the fragments. The fragments are enriched by PCR amplification.During the QC step Agilent 2100 Bioanaylzer and ABI StepOnePlus Real Time PCR System are used to qualify and quantify of the sample library. The library products are ready for sequencing via Illumina HiSeqTM 2000 or other sequencer when necessary.	GEO Accession:GSM2224909	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP077871		160204_I136_FCH55MNBBXX_L6_WHFISoiqRAAARAAPEI-100_1.fq.gz	fastq	454459418.0	9274682.0	GSM2224909 r2	0:49	A:114982478;C:111450118;G:115561207;T:112452344;N:13271	49		114982478	111450118	115561207	112452344	13271	SRX1896782	SRS1539774	SRA437681	GEO	Anming Meng, School of Lifesciences, Tsinghua University	1	0.92536		0.04644		0.75103		0.47559		49		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2016-07-04	Pharyngula	Embryo	Endothelium	Cardiovascular System
41681	41681	SRR5119926	SRX2435201	SRS1870197	SRP095331	PRJNA358009	CXCL8 and CXCR1 Remodel the Vascular Niche to Promote Hematopoietic Stem and Progenitor Cell Colonization and Engraftment [wt vs kdrl:cxcr1]	GSE92542	Transcriptome Analysis	The microenvironment is an important regulator of hematopoietic stem and progenitor cell HSPC biology. Interactions between the niche and stem cells have been difficult to track but recent advances marking fluorescent HSPCs have allowed exquisite visualization in the caudal hematopoietic tissue CHT of the developing zebrafish. Sinusoidal endothelial cells interact closely with HSPCs as they colonize this niche. Here we show that the chemokine cxcl8 and its receptor cxcr1 are abundantly expressed by zebrafish endothelial cells and we identify cxcl8/cxcr1 signaling as a positive regulator of HSPC colonization using genetic gain and loss of function techniques. Single cell tracking experiments demonstrated that this effect is due to an increase in HSPC “cuddling” by endothelial cells thereby increasing CHT residency time and allowing more HSPC cell divisions to occur. Enhanced cxcl8/cxcr1 signaling was associated with an increase in the volume of the CHT and induction of cxcl12a expression favoring HSPC colonization. Finally using parabiotic zebrafish we show that cxcr1 acts stem cell non autonomously to improve the efficiency of donor HSPC engraftment. This work identifies a mechanism by which the hematopoietic niche remodels to promote HSPC engraftment and suggests that cxcl8/cxcr1 signaling is a potential therapeutic target in patients undergoing hematopoietic stem cell transplantation. Overall design: Kdrl:mcherry and kdrl:mcherry;kdrl:cxcr1 zebrafish were dissociated and endothelial cells purified by FACS. RNA seq libraries were prepared from endothelial cells purified from two independent clutches of fish four libraries total.	parent bioproject:PRJNA358001	pubmed:28351983	wt clutch2	GSM2432105	tissue:endothelial cells\|cell type:endothelial cells	wt clutch2	Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using cutadapt then mapped to Ensembl GRCz10 whole genome using Tophat 2.0.11 without xxx splicing form calls Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts Genome build: GRCz10 Supplementary files format and content: excel files include RPKM values for each Sample	endothelial cells		Freshly sorted cells were lysed in Trizol LS and total RNA was extracted by isopropanol precipitation. Libraries were prepared using the SMARTer Universal Low Input RNA kit followed by the Low Input Library Prep Kit for Illumina Clontech Laboratories.	Zebrafish embryos were grown under standard conditions in a 28 degree incubator.	cell type:endothelial cells	GSM2432105	GSM2432105: wt clutch2; Danio rerio; RNA Seq	GSM2432105		1	Freshly sorted cells were lysed in Trizol LS and total RNA was extracted by isopropanol precipitation. Libraries were prepared using the SMARTer Universal Low Input RNA kit followed by the Low Input Library Prep Kit for Illumina Clontech Laboratories.	GEO Accession:GSM2432105	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP095331		BB-IL8-7_GATCAG_R2.fastq.gz BB-IL8-7_GATCAG_R1.fastq.gz	fastq fastq	6054362200.0	30271811.0	GSM2432105 r1	0:100 1:100	A:1586036726;C:1442511502;G:1449390272;T:1575855416;N:568284	100	100	1586036726	1442511502	1449390272	1575855416	568284	SRX2435201	SRS1870197	SRA505250	GEO	Oncology/Hematology, Boston Children's Hospital	2	0.68659	0.68507	0.22283	0.22137	0.76067	0.76343	0.57225	0.58743	100	100	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	smarter	bulk	unknown	unknown	United States	2016-12-19	Undetermined	Embryo	Endothelium	Cardiovascular System
41682	41682	SRR5119925	SRX2435200	SRS1870195	SRP095331	PRJNA358009	CXCL8 and CXCR1 Remodel the Vascular Niche to Promote Hematopoietic Stem and Progenitor Cell Colonization and Engraftment [wt vs kdrl:cxcr1]	GSE92542	Transcriptome Analysis	The microenvironment is an important regulator of hematopoietic stem and progenitor cell HSPC biology. Interactions between the niche and stem cells have been difficult to track but recent advances marking fluorescent HSPCs have allowed exquisite visualization in the caudal hematopoietic tissue CHT of the developing zebrafish. Sinusoidal endothelial cells interact closely with HSPCs as they colonize this niche. Here we show that the chemokine cxcl8 and its receptor cxcr1 are abundantly expressed by zebrafish endothelial cells and we identify cxcl8/cxcr1 signaling as a positive regulator of HSPC colonization using genetic gain and loss of function techniques. Single cell tracking experiments demonstrated that this effect is due to an increase in HSPC “cuddling” by endothelial cells thereby increasing CHT residency time and allowing more HSPC cell divisions to occur. Enhanced cxcl8/cxcr1 signaling was associated with an increase in the volume of the CHT and induction of cxcl12a expression favoring HSPC colonization. Finally using parabiotic zebrafish we show that cxcr1 acts stem cell non autonomously to improve the efficiency of donor HSPC engraftment. This work identifies a mechanism by which the hematopoietic niche remodels to promote HSPC engraftment and suggests that cxcl8/cxcr1 signaling is a potential therapeutic target in patients undergoing hematopoietic stem cell transplantation. Overall design: Kdrl:mcherry and kdrl:mcherry;kdrl:cxcr1 zebrafish were dissociated and endothelial cells purified by FACS. RNA seq libraries were prepared from endothelial cells purified from two independent clutches of fish four libraries total.	parent bioproject:PRJNA358001	pubmed:28351983	wt clutch1	GSM2432104	tissue:endothelial cells\|cell type:endothelial cells	wt clutch1	Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using cutadapt then mapped to Ensembl GRCz10 whole genome using Tophat 2.0.11 without xxx splicing form calls Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts Genome build: GRCz10 Supplementary files format and content: excel files include RPKM values for each Sample	endothelial cells		Freshly sorted cells were lysed in Trizol LS and total RNA was extracted by isopropanol precipitation. Libraries were prepared using the SMARTer Universal Low Input RNA kit followed by the Low Input Library Prep Kit for Illumina Clontech Laboratories.	Zebrafish embryos were grown under standard conditions in a 28 degree incubator.	cell type:endothelial cells	GSM2432104	GSM2432104: wt clutch1; Danio rerio; RNA Seq	GSM2432104		1	Freshly sorted cells were lysed in Trizol LS and total RNA was extracted by isopropanol precipitation. Libraries were prepared using the SMARTer Universal Low Input RNA kit followed by the Low Input Library Prep Kit for Illumina Clontech Laboratories.	GEO Accession:GSM2432104	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP095331		BB-IL8-3_TGACCA_R1.fastq.gz BB-IL8-3_TGACCA_R2.fastq.gz	fastq fastq	4718160000.0	23590800.0	GSM2432104 r1	0:100 1:100	A:1285175152;C:1075055485;G:1078285328;T:1279202852;N:441183	100	100	1285175152	1075055485	1078285328	1279202852	441183	SRX2435200	SRS1870195	SRA505250	GEO	Oncology/Hematology, Boston Children's Hospital	2	0.79676	0.7947	0.26445	0.26272	0.71652	0.71924	0.55157	0.55957	100	100	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	smarter	bulk	unknown	unknown	United States	2016-12-19	Undetermined	Embryo	Endothelium	Cardiovascular System
41683	41683	SRR5119924	SRX2435199	SRS1870196	SRP095331	PRJNA358009	CXCL8 and CXCR1 Remodel the Vascular Niche to Promote Hematopoietic Stem and Progenitor Cell Colonization and Engraftment [wt vs kdrl:cxcr1]	GSE92542	Transcriptome Analysis	The microenvironment is an important regulator of hematopoietic stem and progenitor cell HSPC biology. Interactions between the niche and stem cells have been difficult to track but recent advances marking fluorescent HSPCs have allowed exquisite visualization in the caudal hematopoietic tissue CHT of the developing zebrafish. Sinusoidal endothelial cells interact closely with HSPCs as they colonize this niche. Here we show that the chemokine cxcl8 and its receptor cxcr1 are abundantly expressed by zebrafish endothelial cells and we identify cxcl8/cxcr1 signaling as a positive regulator of HSPC colonization using genetic gain and loss of function techniques. Single cell tracking experiments demonstrated that this effect is due to an increase in HSPC “cuddling” by endothelial cells thereby increasing CHT residency time and allowing more HSPC cell divisions to occur. Enhanced cxcl8/cxcr1 signaling was associated with an increase in the volume of the CHT and induction of cxcl12a expression favoring HSPC colonization. Finally using parabiotic zebrafish we show that cxcr1 acts stem cell non autonomously to improve the efficiency of donor HSPC engraftment. This work identifies a mechanism by which the hematopoietic niche remodels to promote HSPC engraftment and suggests that cxcl8/cxcr1 signaling is a potential therapeutic target in patients undergoing hematopoietic stem cell transplantation. Overall design: Kdrl:mcherry and kdrl:mcherry;kdrl:cxcr1 zebrafish were dissociated and endothelial cells purified by FACS. RNA seq libraries were prepared from endothelial cells purified from two independent clutches of fish four libraries total.	parent bioproject:PRJNA358001	pubmed:28351983	kdrl:cxcr1 clutch2	GSM2432103	tissue:endothelial cells\|cell type:endothelial cells	kdrl:cxcr1 clutch2	Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using cutadapt then mapped to Ensembl GRCz10 whole genome using Tophat 2.0.11 without xxx splicing form calls Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts Genome build: GRCz10 Supplementary files format and content: excel files include RPKM values for each Sample	endothelial cells		Freshly sorted cells were lysed in Trizol LS and total RNA was extracted by isopropanol precipitation. Libraries were prepared using the SMARTer Universal Low Input RNA kit followed by the Low Input Library Prep Kit for Illumina Clontech Laboratories.	Zebrafish embryos were grown under standard conditions in a 28 degree incubator.	cell type:endothelial cells	GSM2432103	GSM2432103: kdrl:cxcr1 clutch2; Danio rerio; RNA Seq	GSM2432103		1	Freshly sorted cells were lysed in Trizol LS and total RNA was extracted by isopropanol precipitation. Libraries were prepared using the SMARTer Universal Low Input RNA kit followed by the Low Input Library Prep Kit for Illumina Clontech Laboratories.	GEO Accession:GSM2432103	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP095331		BB-IL8-5_GCCAAT_R1.fastq.gz BB-IL8-5_GCCAAT_R2.fastq.gz	fastq fastq	4575871400.0	22879357.0	GSM2432103 r1	0:100 1:100	A:1212272291;C:1077863805;G:1079802103;T:1205507838;N:425363	100	100	1212272291	1077863805	1079802103	1205507838	425363	SRX2435199	SRS1870196	SRA505250	GEO	Oncology/Hematology, Boston Children's Hospital	2	0.79788	0.79581	0.25639	0.25339	0.74888	0.75195	0.55512	0.56401	100	100	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	smarter	bulk	unknown	unknown	United States	2016-12-19	Undetermined	Embryo	Endothelium	Cardiovascular System
41684	41684	SRR5119923	SRX2435198	SRS1870193	SRP095331	PRJNA358009	CXCL8 and CXCR1 Remodel the Vascular Niche to Promote Hematopoietic Stem and Progenitor Cell Colonization and Engraftment [wt vs kdrl:cxcr1]	GSE92542	Transcriptome Analysis	The microenvironment is an important regulator of hematopoietic stem and progenitor cell HSPC biology. Interactions between the niche and stem cells have been difficult to track but recent advances marking fluorescent HSPCs have allowed exquisite visualization in the caudal hematopoietic tissue CHT of the developing zebrafish. Sinusoidal endothelial cells interact closely with HSPCs as they colonize this niche. Here we show that the chemokine cxcl8 and its receptor cxcr1 are abundantly expressed by zebrafish endothelial cells and we identify cxcl8/cxcr1 signaling as a positive regulator of HSPC colonization using genetic gain and loss of function techniques. Single cell tracking experiments demonstrated that this effect is due to an increase in HSPC “cuddling” by endothelial cells thereby increasing CHT residency time and allowing more HSPC cell divisions to occur. Enhanced cxcl8/cxcr1 signaling was associated with an increase in the volume of the CHT and induction of cxcl12a expression favoring HSPC colonization. Finally using parabiotic zebrafish we show that cxcr1 acts stem cell non autonomously to improve the efficiency of donor HSPC engraftment. This work identifies a mechanism by which the hematopoietic niche remodels to promote HSPC engraftment and suggests that cxcl8/cxcr1 signaling is a potential therapeutic target in patients undergoing hematopoietic stem cell transplantation. Overall design: Kdrl:mcherry and kdrl:mcherry;kdrl:cxcr1 zebrafish were dissociated and endothelial cells purified by FACS. RNA seq libraries were prepared from endothelial cells purified from two independent clutches of fish four libraries total.	parent bioproject:PRJNA358001	pubmed:28351983	kdrl:cxcr1 clutch1	GSM2432102	tissue:endothelial cells\|cell type:endothelial cells	kdrl:cxcr1 clutch1	Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using cutadapt then mapped to Ensembl GRCz10 whole genome using Tophat 2.0.11 without xxx splicing form calls Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts Genome build: GRCz10 Supplementary files format and content: excel files include RPKM values for each Sample	endothelial cells		Freshly sorted cells were lysed in Trizol LS and total RNA was extracted by isopropanol precipitation. Libraries were prepared using the SMARTer Universal Low Input RNA kit followed by the Low Input Library Prep Kit for Illumina Clontech Laboratories.	Zebrafish embryos were grown under standard conditions in a 28 degree incubator.	cell type:endothelial cells	GSM2432102	GSM2432102: kdrl:cxcr1 clutch1; Danio rerio; RNA Seq	GSM2432102		1	Freshly sorted cells were lysed in Trizol LS and total RNA was extracted by isopropanol precipitation. Libraries were prepared using the SMARTer Universal Low Input RNA kit followed by the Low Input Library Prep Kit for Illumina Clontech Laboratories.	GEO Accession:GSM2432102	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP095331		BB-IL8-1_ATCACG_R1.fastq.gz BB-IL8-1_ATCACG_R2.fastq.gz	fastq fastq	5384509000.0	26922545.0	GSM2432102 r1	0:100 1:100	A:1457197772;C:1237507818;G:1239484699;T:1449819489;N:499222	100	100	1457197772	1237507818	1239484699	1449819489	499222	SRX2435198	SRS1870193	SRA505250	GEO	Oncology/Hematology, Boston Children's Hospital	2	0.80446	0.79238	0.24797	0.24691	0.72423	0.72681	0.57301	0.46021	100	100	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	smarter	bulk	unknown	unknown	United States	2016-12-19	Undetermined	Embryo	Endothelium	Cardiovascular System
41827	41827	SRR5251446	SRX2557171	SRS1974564	SRP099466	PRJNA374579	microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos	PRJNA374579	Other	Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.			QuantSeq mutant miRNAs WT miR139 B1	nicoli mutmir AG01645	strain:TU/AB\|age:27.0\|sex:pooled male and female\|tissue:endothelial cells\|molecule:mRNA\|condition:miR 139\|replicate:1\|BioSampleModel:Model organism or animal									QuantSeq mutant miRNAs WT miR139 B1	AG01645.1	AG01645.1	1			OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP099466		AG01645.1_R1.fastq.gz	fastq	1574284140.0	20714265.0	AG01645.1 R1.fastq.gz	0:76	A:485471345;C:270854124;G:374164721;T:443766613;N:27337	76		485471345	270854124	374164721	443766613	27337	SRX2557171	SRS1974564	SRA537606	Yale University\|Genetics	Yale University	1	0.82142		0.14068		0.8002		0.5444		76		B		usable mapping rate	illumina	hiseq_era	unknown	small_rna	lexogen	bulk	unknown	unknown	United States	2017-03-27	Undetermined	Embryo	Endothelium	Cardiovascular System
41828	41828	SRR5251445	SRX2557170	SRS1974563	SRP099466	PRJNA374579	microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos	PRJNA374579	Other	Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.			QuantSeq mutant miRNAs WT miR139 B2	nicoli mutmir AG01646	strain:TU/AB\|age:27.0\|sex:pooled male and female\|tissue:endothelial cells\|molecule:mRNA\|condition:miR 139\|replicate:2\|BioSampleModel:Model organism or animal									QuantSeq mutant miRNAs WT miR139 B2	AG01646.1	AG01646.1	1			OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP099466		AG01646.1_R1.fastq.gz	fastq	1484740104.0	19536054.0	AG01646.1 R1.fastq.gz	0:76	A:453388316;C:246477203;G:365031959;T:419816346;N:26280	76		453388316	246477203	365031959	419816346	26280	SRX2557170	SRS1974563	SRA537606	Yale University\|Genetics	Yale University	1	0.82649		0.1897		0.79862		0.52759		76		B		usable mapping rate	illumina	hiseq_era	unknown	small_rna	lexogen	bulk	unknown	unknown	United States	2017-03-28	Undetermined	Embryo	Endothelium	Cardiovascular System
41829	41829	SRR5251444	SRX2557169	SRS1974562	SRP099466	PRJNA374579	microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos	PRJNA374579	Other	Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.			QuantSeq mutant miRNAs WT miR139 B3	nicoli mutmir AG01647	strain:TU/AB\|age:27.0\|sex:pooled male and female\|tissue:endothelial cells\|molecule:mRNA\|condition:miR 139\|replicate:3\|BioSampleModel:Model organism or animal									QuantSeq mutant miRNAs WT miR139 B3	AG01647.1	AG01647.1	1			OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP099466		AG01647.1_R1.fastq.gz	fastq	881298660.0	11596035.0	AG01647.1 R1.fastq.gz	0:76	A:270675838;C:160127586;G:228157662;T:222301246;N:36328	76		270675838	160127586	228157662	222301246	36328	SRX2557169	SRS1974562	SRA537606	Yale University\|Genetics	Yale University	1	0.76133		0.15034		0.83341		0.56596		76		B		usable mapping rate	illumina	hiseq_era	unknown	small_rna	lexogen	bulk	unknown	unknown	United States	2017-03-28	Undetermined	Embryo	Endothelium	Cardiovascular System
41830	41830	SRR5251443	SRX2557168	SRS1974561	SRP099466	PRJNA374579	microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos	PRJNA374579	Other	Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.			QuantSeq mutant miRNAs Mut miR139 B1	nicoli mutmir AG01648	strain:TU/AB\|age:27.0\|sex:pooled male and female\|tissue:endothelial cells\|genotype:miR 139 ya302/ya302\|molecule:mRNA\|condition:miR 139\|replicate:1\|BioSampleModel:Model organism or animal									QuantSeq mutant miRNAs Mut miR139 B1	AG01648.1	AG01648.1	1			OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP099466		AG01648.1_R1.fastq.gz	fastq	637896880.0	8393380.0	AG01648.1 R1.fastq.gz	0:76	A:192829278;C:112701153;G:153321271;T:179019095;N:26083	76		192829278	112701153	153321271	179019095	26083	SRX2557168	SRS1974561	SRA537606	Yale University\|Genetics	Yale University	1	0.75971		0.1181		0.82171		0.56797		76		B		usable mapping rate	illumina	hiseq_era	unknown	small_rna	lexogen	bulk	unknown	unknown	United States	2017-03-28	Undetermined	Embryo	Endothelium	Cardiovascular System
41831	41831	SRR5251442	SRX2557167	SRS1974560	SRP099466	PRJNA374579	microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos	PRJNA374579	Other	Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.			QuantSeq mutant miRNAs Mut miR139 B2	nicoli mutmir AG01649	strain:TU/AB\|age:27.0\|sex:pooled male and female\|tissue:endothelial cells\|genotype:miR 139 ya302/ya302\|molecule:mRNA\|condition:miR 139\|replicate:2\|BioSampleModel:Model organism or animal									QuantSeq mutant miRNAs Mut miR139 B2	AG01649.1	AG01649.1	1			OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP099466		AG01649.1_R1.fastq.gz	fastq	849868328.0	11182478.0	AG01649.1 R1.fastq.gz	0:76	A:258225905;C:148467172;G:205165181;T:237974100;N:35970	76		258225905	148467172	205165181	237974100	35970	SRX2557167	SRS1974560	SRA537606	Yale University\|Genetics	Yale University	1	0.75096		0.14506		0.81507		0.5545		76		B		usable mapping rate	illumina	hiseq_era	unknown	small_rna	lexogen	bulk	unknown	unknown	United States	2017-03-28	Undetermined	Embryo	Endothelium	Cardiovascular System
41832	41832	SRR5251441	SRX2557166	SRS1974559	SRP099466	PRJNA374579	microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos	PRJNA374579	Other	Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.			QuantSeq mutant miRNAs Mut miR139 B3	nicoli mutmir AG01650	strain:TU/AB\|age:27.0\|sex:pooled male and female\|tissue:endothelial cells\|genotype:miR 139 ya302/ya302\|molecule:mRNA\|condition:miR 139\|replicate:3\|BioSampleModel:Model organism or animal									QuantSeq mutant miRNAs Mut miR139 B3	AG01650.1	AG01650.1	1			OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP099466		AG01650.1_R1.fastq.gz	fastq	998464668.0	13137693.0	AG01650.1 R1.fastq.gz	0:76	A:311526420;C:176545041;G:251852786;T:258497630;N:42791	76		311526420	176545041	251852786	258497630	42791	SRX2557166	SRS1974559	SRA537606	Yale University\|Genetics	Yale University	1	0.76479		0.11192		0.82674		0.54621		76		B		usable mapping rate	illumina	hiseq_era	unknown	small_rna	lexogen	bulk	unknown	unknown	United States	2017-03-28	Undetermined	Embryo	Endothelium	Cardiovascular System
41833	41833	SRR5251440	SRX2557165	SRS1974558	SRP099466	PRJNA374579	microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos	PRJNA374579	Other	Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.			QuantSeq mutant miRNAs WT miR24 B1	nicoli mutmir AG01651	strain:TU/AB\|age:51.0\|sex:pooled male and female\|tissue:endothelial cells\|molecule:mRNA\|condition:miR 24\|replicate:1\|BioSampleModel:Model organism or animal									QuantSeq mutant miRNAs WT miR24 B1	AG01651.1	AG01651.1	1			OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP099466		AG01651.1_R1.fastq.gz	fastq	570492252.0	7506477.0	AG01651.1 R1.fastq.gz	0:76	A:162512811;C:104071716;G:135730697;T:168149427;N:27601	76		162512811	104071716	135730697	168149427	27601	SRX2557165	SRS1974558	SRA537606	Yale University\|Genetics	Yale University	1	0.73988		0.10157		0.86647		0.54252		76		B		usable mapping rate	illumina	hiseq_era	unknown	small_rna	lexogen	bulk	unknown	unknown	United States	2017-03-28	Undetermined	Embryo	Endothelium	Cardiovascular System
41834	41834	SRR5251439	SRX2557164	SRS1974557	SRP099466	PRJNA374579	microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos	PRJNA374579	Other	Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.			QuantSeq mutant miRNAs WT miR24 B2	nicoli mutmir AG01652	strain:TU/AB\|age:51.0\|sex:pooled male and female\|tissue:endothelial cells\|molecule:mRNA\|condition:miR 24\|replicate:2\|BioSampleModel:Model organism or animal									QuantSeq mutant miRNAs WT miR24 B2	AG01652.1	AG01652.1	1			OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP099466		AG01652.1_R1.fastq.gz	fastq	1072886148.0	14116923.0	AG01652.1 R1.fastq.gz	0:76	A:338399596;C:192703439;G:242960887;T:298769761;N:52465	76		338399596	192703439	242960887	298769761	52465	SRX2557164	SRS1974557	SRA537606	Yale University\|Genetics	Yale University	1	0.76456		0.11024		0.89197		0.59214		76		B		usable mapping rate	illumina	hiseq_era	unknown	small_rna	lexogen	bulk	unknown	unknown	United States	2017-03-28	Undetermined	Embryo	Endothelium	Cardiovascular System
41835	41835	SRR5251438	SRX2557163	SRS1974556	SRP099466	PRJNA374579	microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos	PRJNA374579	Other	Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.			QuantSeq mutant miRNAs WT miR24 B3	nicoli mutmir AG01653	strain:TU/AB\|age:51.0\|sex:pooled male and female\|tissue:endothelial cells\|molecule:mRNA\|condition:miR 24\|replicate:3\|BioSampleModel:Model organism or animal									QuantSeq mutant miRNAs WT miR24 B3	AG01653.1	AG01653.1	1			OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP099466		AG01653.1_R1.fastq.gz	fastq	1016374144.0	13373344.0	AG01653.1 R1.fastq.gz	0:76	A:310958343;C:168702106;G:223420046;T:313241363;N:52286	76		310958343	168702106	223420046	313241363	52286	SRX2557163	SRS1974556	SRA537606	Yale University\|Genetics	Yale University	1	0.75735		0.12224		0.79756		0.55136		76		B		usable mapping rate	illumina	hiseq_era	unknown	small_rna	lexogen	bulk	unknown	unknown	United States	2017-02-13	Undetermined	Embryo	Endothelium	Cardiovascular System
41836	41836	SRR5251437	SRX2557162	SRS1974555	SRP099466	PRJNA374579	microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos	PRJNA374579	Other	Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.			QuantSeq mutant miRNAs Mut miR24 B1	nicoli mutmir AG01654	strain:TU/AB\|age:51.0\|sex:pooled male and female\|tissue:endothelial cells\|genotype:miR 24 ya324/? ya325/? ya326/? ya327/?\|molecule:mRNA\|condition:miR 24\|replicate:1\|BioSampleModel:Model organism or animal									QuantSeq mutant miRNAs Mut miR24 B1	AG01654.1	AG01654.1	1			OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP099466		AG01654.1_R1.fastq.gz	fastq	782170112.0	10291712.0	AG01654.1 R1.fastq.gz	0:76	A:238316720;C:132163709;G:179301544;T:232350598;N:37541	76		238316720	132163709	179301544	232350598	37541	SRX2557162	SRS1974555	SRA537606	Yale University\|Genetics	Yale University	1	0.7683		0.10712		0.80034		0.55804		76		B		usable mapping rate	illumina	hiseq_era	unknown	small_rna	lexogen	bulk	unknown	unknown	United States	2017-03-28	Undetermined	Embryo	Endothelium	Cardiovascular System
41837	41837	SRR5251436	SRX2557161	SRS1974554	SRP099466	PRJNA374579	microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos	PRJNA374579	Other	Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.			QuantSeq mutant miRNAs Mut miR24 B2	nicoli mutmir AG01655	strain:TU/AB\|age:51.0\|sex:pooled male and female\|tissue:endothelial cells\|genotype:miR 24 ya324/? ya325/? ya326/? ya327/?\|molecule:mRNA\|condition:miR 24\|replicate:2\|BioSampleModel:Model organism or animal									QuantSeq mutant miRNAs Mut miR24 B2	AG01655.1	AG01655.1	1			OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP099466		AG01655.1_R1.fastq.gz	fastq	1053946340.0	13867715.0	AG01655.1 R1.fastq.gz	0:76	A:318351311;C:191163031;G:240348413;T:304030367;N:53218	76		318351311	191163031	240348413	304030367	53218	SRX2557161	SRS1974554	SRA537606	Yale University\|Genetics	Yale University	1	0.77588		0.07983		0.83934		0.56228		76		B		usable mapping rate	illumina	hiseq_era	unknown	small_rna	lexogen	bulk	unknown	unknown	United States	2017-03-28	Undetermined	Embryo	Endothelium	Cardiovascular System
41838	41838	SRR5251435	SRX2557160	SRS1974553	SRP099466	PRJNA374579	microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos	PRJNA374579	Other	Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.			QuantSeq mutant miRNAs Mut miR24 B3	nicoli mutmir AG01656	strain:TU/AB\|age:51.0\|sex:pooled male and female\|tissue:endothelial cells\|genotype:miR 24 ya324/? ya325/? ya326/? ya327/?\|molecule:mRNA\|condition:miR 24\|replicate:3\|BioSampleModel:Model organism or animal									QuantSeq mutant miRNAs Mut miR24 B3	AG01656.1	AG01656.1	1			OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP099466		AG01656.1_R1.fastq.gz	fastq	1182467736.0	15558786.0	AG01656.1 R1.fastq.gz	0:76	A:344465226;C:204677242;G:269228338;T:364036735;N:60195	76		344465226	204677242	269228338	364036735	60195	SRX2557160	SRS1974553	SRA537606	Yale University\|Genetics	Yale University	1	0.78956		0.13495		0.81517		0.56342		76		B		usable mapping rate	illumina	hiseq_era	unknown	small_rna	lexogen	bulk	unknown	unknown	United States	2017-02-13	Undetermined	Embryo	Endothelium	Cardiovascular System
41839	41839	SRR5251434	SRX2557159	SRS1974552	SRP099466	PRJNA374579	microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos	PRJNA374579	Other	Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.			QuantSeq mutant miRNAs WT miR223 B1	nicoli mutmir AG01657	strain:TU/AB\|age:27.0\|sex:pooled male and female\|tissue:endothelial cells\|molecule:mRNA\|condition:miR 223\|replicate:1\|BioSampleModel:Model organism or animal									QuantSeq mutant miRNAs WT miR223 B1	AG01657.1	AG01657.1	1			OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP099466		AG01657.1_R1.fastq.gz	fastq	536336712.0	7057062.0	AG01657.1 R1.fastq.gz	0:76	A:158301607;C:93070120;G:121382262;T:163555487;N:27236	76		158301607	93070120	121382262	163555487	27236	SRX2557159	SRS1974552	SRA537606	Yale University\|Genetics	Yale University	1	0.76425		0.1278		0.84222		0.55305		76		B		usable mapping rate	illumina	hiseq_era	unknown	small_rna	lexogen	bulk	unknown	unknown	United States	2017-02-13	Undetermined	Embryo	Endothelium	Cardiovascular System
41840	41840	SRR5251433	SRX2557158	SRS1974551	SRP099466	PRJNA374579	microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos	PRJNA374579	Other	Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.			QuantSeq mutant miRNAs WT miR223 B2	nicoli mutmir AG01658	strain:TU/AB\|age:27.0\|sex:pooled male and female\|tissue:endothelial cells\|molecule:mRNA\|condition:miR 223\|replicate:2\|BioSampleModel:Model organism or animal									QuantSeq mutant miRNAs WT miR223 B2	AG01658.1	AG01658.1	1			OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP099466		AG01658.1_R1.fastq.gz	fastq	798581856.0	10507656.0	AG01658.1 R1.fastq.gz	0:76	A:241352089;C:134327379;G:183394123;T:239469845;N:38420	76		241352089	134327379	183394123	239469845	38420	SRX2557158	SRS1974551	SRA537606	Yale University\|Genetics	Yale University	1	0.76221		0.13398		0.82459		0.55228		76		B		usable mapping rate	illumina	hiseq_era	unknown	small_rna	lexogen	bulk	unknown	unknown	United States	2017-03-28	Undetermined	Embryo	Endothelium	Cardiovascular System
41841	41841	SRR5251432	SRX2557157	SRS1974550	SRP099466	PRJNA374579	microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos	PRJNA374579	Other	Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.			QuantSeq mutant miRNAs WT miR223 B3	nicoli mutmir AG01659	strain:TU/AB\|age:27.0\|sex:pooled male and female\|tissue:endothelial cells\|molecule:mRNA\|condition:miR 223\|replicate:3\|BioSampleModel:Model organism or animal									QuantSeq mutant miRNAs WT miR223 B3	AG01659.1	AG01659.1	1			OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP099466		AG01659.1_R1.fastq.gz	fastq	1093998948.0	14394723.0	AG01659.1 R1.fastq.gz	0:76	A:330741822;C:186325335;G:249557623;T:327320449;N:53719	76		330741822	186325335	249557623	327320449	53719	SRX2557157	SRS1974550	SRA537606	Yale University\|Genetics	Yale University	1	0.77108		0.14674		0.80955		0.55819		76		B		usable mapping rate	illumina	hiseq_era	unknown	small_rna	lexogen	bulk	unknown	unknown	United States	2017-03-28	Undetermined	Embryo	Endothelium	Cardiovascular System
41842	41842	SRR5251431	SRX2557156	SRS1974549	SRP099466	PRJNA374579	microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos	PRJNA374579	Other	Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.			QuantSeq mutant miRNAs Mut miR223 B1	nicoli mutmir AG01660	strain:TU/AB\|age:27.0\|sex:pooled male and female\|tissue:endothelial cells\|genotype:miR 223 ya304/ya304\|molecule:mRNA\|condition:miR 223\|replicate:1\|BioSampleModel:Model organism or animal									QuantSeq mutant miRNAs Mut miR223 B1	AG01660.1	AG01660.1	1			OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP099466		AG01660.1_R1.fastq.gz	fastq	849905492.0	11182967.0	AG01660.1 R1.fastq.gz	0:76	A:250953875;C:146191904;G:190040699;T:262674911;N:44103	76		250953875	146191904	190040699	262674911	44103	SRX2557156	SRS1974549	SRA537606	Yale University\|Genetics	Yale University	1	0.7687		0.14192		0.82842		0.5344		76		B		usable mapping rate	illumina	hiseq_era	unknown	small_rna	lexogen	bulk	unknown	unknown	United States	2017-02-13	Undetermined	Embryo	Endothelium	Cardiovascular System
41843	41843	SRR5251430	SRX2557155	SRS1974548	SRP099466	PRJNA374579	microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos	PRJNA374579	Other	Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.			QuantSeq mutant miRNAs Mut miR223 B2	nicoli mutmir AG01661	strain:TU/AB\|age:27.0\|sex:pooled male and female\|tissue:endothelial cells\|genotype:miR 223 ya304/ya304\|molecule:mRNA\|condition:miR 223\|replicate:2\|BioSampleModel:Model organism or animal									QuantSeq mutant miRNAs Mut miR223 B2	AG01661.1	AG01661.1	1			OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP099466		AG01661.1_R1.fastq.gz	fastq	840115400.0	11054150.0	AG01661.1 R1.fastq.gz	0:76	A:257057495;C:141775085;G:188281166;T:252960590;N:41064	76		257057495	141775085	188281166	252960590	41064	SRX2557155	SRS1974548	SRA537606	Yale University\|Genetics	Yale University	1	0.74292		0.10759		0.83615		0.55136		76		B		usable mapping rate	illumina	hiseq_era	unknown	small_rna	lexogen	bulk	unknown	unknown	United States	2017-03-28	Undetermined	Embryo	Endothelium	Cardiovascular System
42141	42141	SRR5443688	SRX2733020	SRS2120917	SRP103805	PRJNA382558	mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish.	GSE97649	Transcriptome Analysis	48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate with 6 brains used per samples. Overall design: wild type vs mutant		pubmed:26253536	48hpf zebrafish FAC sorted endothelial cell mutant 3	GSM2574373	tissue:purified endothelial cell\|transgene:kdrl eGFP\|genotype:mafba uq4bh mutant	48hpf zebrafish FAC sorted endothelial cell mutant 3	adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample	purified endothelial cell		48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols		transgene:kdrl eGFP\|genotype:mafba uq4bh mutant	GSM2574373	GSM2574373: 48hpf zebrafish FAC sorted endothelial cell mutant 3; Danio rerio; RNA Seq	GSM2574373		1	48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2574373	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP103805		M3_S6_L001_R1_001.fastq.gz	fastq	1290470348.0	17096427.0	GSM2574373 r1	0:75.48 1:0	A:320847705;C:319435806;G:300073193;T:350044923;N:68721	75	0	320847705	319435806	300073193	350044923	68721	SRX2733020	SRS2120917	SRA553927	GEO	Australian Institute for Bioengineering and Nanotechnology	1	0.94339		0.05762		0.72232		0.50799		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Australia	2017-04-11	Hatching	Embryo	Endothelium	Cardiovascular System
42142	42142	SRR5443689	SRX2733020	SRS2120917	SRP103805	PRJNA382558	mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish.	GSE97649	Transcriptome Analysis	48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate with 6 brains used per samples. Overall design: wild type vs mutant		pubmed:26253536	48hpf zebrafish FAC sorted endothelial cell mutant 3	GSM2574373	tissue:purified endothelial cell\|transgene:kdrl eGFP\|genotype:mafba uq4bh mutant	48hpf zebrafish FAC sorted endothelial cell mutant 3	adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample	purified endothelial cell		48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols		transgene:kdrl eGFP\|genotype:mafba uq4bh mutant	GSM2574373	GSM2574373: 48hpf zebrafish FAC sorted endothelial cell mutant 3; Danio rerio; RNA Seq	GSM2574373		1	48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2574373	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP103805		M3_S6_L002_R1_001.fastq.gz	fastq	1274417413.0	16883601.0	GSM2574373 r2	0:75.48 1:0	A:316659737;C:315517172;G:296527344;T:345645123;N:68037	75	0	316659737	315517172	296527344	345645123	68037	SRX2733020	SRS2120917	SRA553927	GEO	Australian Institute for Bioengineering and Nanotechnology	1	0.94193		0.05753		0.7236		0.50991		75		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Australia	2017-04-11	Hatching	Embryo	Endothelium	Cardiovascular System
42143	42143	SRR5443690	SRX2733020	SRS2120917	SRP103805	PRJNA382558	mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish.	GSE97649	Transcriptome Analysis	48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate with 6 brains used per samples. Overall design: wild type vs mutant		pubmed:26253536	48hpf zebrafish FAC sorted endothelial cell mutant 3	GSM2574373	tissue:purified endothelial cell\|transgene:kdrl eGFP\|genotype:mafba uq4bh mutant	48hpf zebrafish FAC sorted endothelial cell mutant 3	adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample	purified endothelial cell		48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols		transgene:kdrl eGFP\|genotype:mafba uq4bh mutant	GSM2574373	GSM2574373: 48hpf zebrafish FAC sorted endothelial cell mutant 3; Danio rerio; RNA Seq	GSM2574373		1	48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2574373	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP103805		M3_S6_L003_R1_001.fastq.gz	fastq	1267650302.0	16794051.0	GSM2574373 r3	0:75.48 1:0	A:316851687;C:313922763;G:294562163;T:342271337;N:42352	75	0	316851687	313922763	294562163	342271337	42352	SRX2733020	SRS2120917	SRA553927	GEO	Australian Institute for Bioengineering and Nanotechnology	1	0.93935		0.05711		0.72421		0.51344		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Australia	2017-04-11	Hatching	Embryo	Endothelium	Cardiovascular System
42144	42144	SRR5443691	SRX2733020	SRS2120917	SRP103805	PRJNA382558	mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish.	GSE97649	Transcriptome Analysis	48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate with 6 brains used per samples. Overall design: wild type vs mutant		pubmed:26253536	48hpf zebrafish FAC sorted endothelial cell mutant 3	GSM2574373	tissue:purified endothelial cell\|transgene:kdrl eGFP\|genotype:mafba uq4bh mutant	48hpf zebrafish FAC sorted endothelial cell mutant 3	adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample	purified endothelial cell		48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols		transgene:kdrl eGFP\|genotype:mafba uq4bh mutant	GSM2574373	GSM2574373: 48hpf zebrafish FAC sorted endothelial cell mutant 3; Danio rerio; RNA Seq	GSM2574373		1	48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2574373	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP103805		M3_S6_L004_R1_001.fastq.gz	fastq	1272371755.0	16856553.0	GSM2574373 r4	0:75.48 1:0	A:317627046;C:315030569;G:295859300;T:343808592;N:46248	75	0	317627046	315030569	295859300	343808592	46248	SRX2733020	SRS2120917	SRA553927	GEO	Australian Institute for Bioengineering and Nanotechnology	1	0.94038		0.05657		0.72391		0.5115		75		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Australia	2017-04-11	Hatching	Embryo	Endothelium	Cardiovascular System
42145	42145	SRR5443684	SRX2733019	SRS2120916	SRP103805	PRJNA382558	mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish.	GSE97649	Transcriptome Analysis	48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate with 6 brains used per samples. Overall design: wild type vs mutant		pubmed:26253536	48hpf zebrafish FAC sorted endothelial cell mutant 2	GSM2574372	tissue:purified endothelial cell\|transgene:kdrl eGFP\|genotype:mafba uq4bh mutant	48hpf zebrafish FAC sorted endothelial cell mutant 2	adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample	purified endothelial cell		48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols		transgene:kdrl eGFP\|genotype:mafba uq4bh mutant	GSM2574372	GSM2574372: 48hpf zebrafish FAC sorted endothelial cell mutant 2; Danio rerio; RNA Seq	GSM2574372		1	48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2574372	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP103805		M2_S4_L001_R1_001.fastq.gz	fastq	1110761224.0	14715439.0	GSM2574372 r1	0:75.48 1:0	A:275638341;C:274879264;G:260426963;T:299738013;N:78643	75	0	275638341	274879264	260426963	299738013	78643	SRX2733019	SRS2120916	SRA553927	GEO	Australian Institute for Bioengineering and Nanotechnology	1	0.93377		0.0583		0.73697		0.503		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Australia	2017-04-11	Hatching	Embryo	Endothelium	Cardiovascular System
42146	42146	SRR5443685	SRX2733019	SRS2120916	SRP103805	PRJNA382558	mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish.	GSE97649	Transcriptome Analysis	48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate with 6 brains used per samples. Overall design: wild type vs mutant		pubmed:26253536	48hpf zebrafish FAC sorted endothelial cell mutant 2	GSM2574372	tissue:purified endothelial cell\|transgene:kdrl eGFP\|genotype:mafba uq4bh mutant	48hpf zebrafish FAC sorted endothelial cell mutant 2	adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample	purified endothelial cell		48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols		transgene:kdrl eGFP\|genotype:mafba uq4bh mutant	GSM2574372	GSM2574372: 48hpf zebrafish FAC sorted endothelial cell mutant 2; Danio rerio; RNA Seq	GSM2574372		1	48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2574372	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP103805		M2_S4_L002_R1_001.fastq.gz	fastq	1096460187.0	14525794.0	GSM2574372 r2	0:75.48 1:0	A:271912949;C:271463678;G:257186071;T:295823949;N:73540	75	0	271912949	271463678	257186071	295823949	73540	SRX2733019	SRS2120916	SRA553927	GEO	Australian Institute for Bioengineering and Nanotechnology	1	0.9322		0.05825		0.74054		0.50344		75		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Australia	2017-04-11	Hatching	Embryo	Endothelium	Cardiovascular System
42147	42147	SRR5443686	SRX2733019	SRS2120916	SRP103805	PRJNA382558	mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish.	GSE97649	Transcriptome Analysis	48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate with 6 brains used per samples. Overall design: wild type vs mutant		pubmed:26253536	48hpf zebrafish FAC sorted endothelial cell mutant 2	GSM2574372	tissue:purified endothelial cell\|transgene:kdrl eGFP\|genotype:mafba uq4bh mutant	48hpf zebrafish FAC sorted endothelial cell mutant 2	adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample	purified endothelial cell		48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols		transgene:kdrl eGFP\|genotype:mafba uq4bh mutant	GSM2574372	GSM2574372: 48hpf zebrafish FAC sorted endothelial cell mutant 2; Danio rerio; RNA Seq	GSM2574372		1	48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2574372	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP103805		M2_S4_L003_R1_001.fastq.gz	fastq	1091010366.0	14453885.0	GSM2574372 r3	0:75.48 1:0	A:272182496;C:270174883;G:255585422;T:293013773;N:53792	75	0	272182496	270174883	255585422	293013773	53792	SRX2733019	SRS2120916	SRA553927	GEO	Australian Institute for Bioengineering and Nanotechnology	1	0.93152		0.05837		0.74168		0.50083		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Australia	2017-04-11	Hatching	Embryo	Endothelium	Cardiovascular System
42148	42148	SRR5443687	SRX2733019	SRS2120916	SRP103805	PRJNA382558	mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish.	GSE97649	Transcriptome Analysis	48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate with 6 brains used per samples. Overall design: wild type vs mutant		pubmed:26253536	48hpf zebrafish FAC sorted endothelial cell mutant 2	GSM2574372	tissue:purified endothelial cell\|transgene:kdrl eGFP\|genotype:mafba uq4bh mutant	48hpf zebrafish FAC sorted endothelial cell mutant 2	adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample	purified endothelial cell		48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols		transgene:kdrl eGFP\|genotype:mafba uq4bh mutant	GSM2574372	GSM2574372: 48hpf zebrafish FAC sorted endothelial cell mutant 2; Danio rerio; RNA Seq	GSM2574372		1	48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2574372	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP103805		M2_S4_L004_R1_001.fastq.gz	fastq	1094982987.0	14506489.0	GSM2574372 r4	0:75.48 1:0	A:272880331;C:271041484;G:256630523;T:294374054;N:56595	75	0	272880331	271041484	256630523	294374054	56595	SRX2733019	SRS2120916	SRA553927	GEO	Australian Institute for Bioengineering and Nanotechnology	1	0.93087		0.05679		0.73791		0.51669		74		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Australia	2017-04-11	Hatching	Embryo	Endothelium	Cardiovascular System
42149	42149	SRR5443680	SRX2733018	SRS2120918	SRP103805	PRJNA382558	mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish.	GSE97649	Transcriptome Analysis	48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate with 6 brains used per samples. Overall design: wild type vs mutant		pubmed:26253536	48hpf zebrafish FAC sorted endothelial cell mutant 1	GSM2574371	tissue:purified endothelial cell\|transgene:kdrl eGFP\|genotype:mafba uq4bh mutant	48hpf zebrafish FAC sorted endothelial cell mutant 1	adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample	purified endothelial cell		48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols		transgene:kdrl eGFP\|genotype:mafba uq4bh mutant	GSM2574371	GSM2574371: 48hpf zebrafish FAC sorted endothelial cell mutant 1; Danio rerio; RNA Seq	GSM2574371		1	48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2574371	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP103805		M1_S2_L001_R1_001.fastq.gz	fastq	1191104867.0	15788220.0	GSM2574371 r1	0:75.44 1:0	A:291253611;C:297887900;G:280714676;T:321180057;N:68623	75	0	291253611	297887900	280714676	321180057	68623	SRX2733018	SRS2120918	SRA553927	GEO	Australian Institute for Bioengineering and Nanotechnology	1	0.93937		0.05486		0.73841		0.50505		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Australia	2017-04-11	Hatching	Embryo	Endothelium	Cardiovascular System
42150	42150	SRR5443681	SRX2733018	SRS2120918	SRP103805	PRJNA382558	mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish.	GSE97649	Transcriptome Analysis	48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate with 6 brains used per samples. Overall design: wild type vs mutant		pubmed:26253536	48hpf zebrafish FAC sorted endothelial cell mutant 1	GSM2574371	tissue:purified endothelial cell\|transgene:kdrl eGFP\|genotype:mafba uq4bh mutant	48hpf zebrafish FAC sorted endothelial cell mutant 1	adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample	purified endothelial cell		48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols		transgene:kdrl eGFP\|genotype:mafba uq4bh mutant	GSM2574371	GSM2574371: 48hpf zebrafish FAC sorted endothelial cell mutant 1; Danio rerio; RNA Seq	GSM2574371		1	48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2574371	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP103805		M1_S2_L002_R1_001.fastq.gz	fastq	1175231750.0	15577911.0	GSM2574371 r2	0:75.44 1:0	A:287141469;C:293942288;G:277159611;T:316919071;N:69311	75	0	287141469	293942288	277159611	316919071	69311	SRX2733018	SRS2120918	SRA553927	GEO	Australian Institute for Bioengineering and Nanotechnology	1	0.93883		0.05461		0.73841		0.50615		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Australia	2017-04-11	Hatching	Embryo	Endothelium	Cardiovascular System
42151	42151	SRR5443682	SRX2733018	SRS2120918	SRP103805	PRJNA382558	mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish.	GSE97649	Transcriptome Analysis	48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate with 6 brains used per samples. Overall design: wild type vs mutant		pubmed:26253536	48hpf zebrafish FAC sorted endothelial cell mutant 1	GSM2574371	tissue:purified endothelial cell\|transgene:kdrl eGFP\|genotype:mafba uq4bh mutant	48hpf zebrafish FAC sorted endothelial cell mutant 1	adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample	purified endothelial cell		48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols		transgene:kdrl eGFP\|genotype:mafba uq4bh mutant	GSM2574371	GSM2574371: 48hpf zebrafish FAC sorted endothelial cell mutant 1; Danio rerio; RNA Seq	GSM2574371		1	48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2574371	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP103805		M1_S2_L003_R1_001.fastq.gz	fastq	1170671016.0	15517791.0	GSM2574371 r3	0:75.44 1:0	A:287726896;C:292922993;G:275775803;T:314197498;N:47826	75	0	287726896	292922993	275775803	314197498	47826	SRX2733018	SRS2120918	SRA553927	GEO	Australian Institute for Bioengineering and Nanotechnology	1	0.93571		0.05459		0.74168		0.50894		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Australia	2017-04-11	Hatching	Embryo	Endothelium	Cardiovascular System
42152	42152	SRR5443683	SRX2733018	SRS2120918	SRP103805	PRJNA382558	mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish.	GSE97649	Transcriptome Analysis	48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate with 6 brains used per samples. Overall design: wild type vs mutant		pubmed:26253536	48hpf zebrafish FAC sorted endothelial cell mutant 1	GSM2574371	tissue:purified endothelial cell\|transgene:kdrl eGFP\|genotype:mafba uq4bh mutant	48hpf zebrafish FAC sorted endothelial cell mutant 1	adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample	purified endothelial cell		48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols		transgene:kdrl eGFP\|genotype:mafba uq4bh mutant	GSM2574371	GSM2574371: 48hpf zebrafish FAC sorted endothelial cell mutant 1; Danio rerio; RNA Seq	GSM2574371		1	48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2574371	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP103805		M1_S2_L004_R1_001.fastq.gz	fastq	1174626578.0	15569716.0	GSM2574371 r4	0:75.44 1:0	A:288367287;C:293885435;G:276774483;T:315550752;N:48621	75	0	288367287	293885435	276774483	315550752	48621	SRX2733018	SRS2120918	SRA553927	GEO	Australian Institute for Bioengineering and Nanotechnology	1	0.93712		0.05466		0.73969		0.50987		74		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Australia	2017-04-11	Hatching	Embryo	Endothelium	Cardiovascular System
42153	42153	SRR5443676	SRX2733017	SRS2120915	SRP103805	PRJNA382558	mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish.	GSE97649	Transcriptome Analysis	48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate with 6 brains used per samples. Overall design: wild type vs mutant		pubmed:26253536	48hpf zebrafish FAC sorted endothelial cell wt 3	GSM2574370	tissue:purified endothelial cell\|transgene:kdrl eGFP\|genotype:wildtype	48hpf zebrafish FAC sorted endothelial cell wt 3	adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample	purified endothelial cell		48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols		transgene:kdrl eGFP\|genotype:wildtype	GSM2574370	GSM2574370: 48hpf zebrafish FAC sorted endothelial cell wt 3; Danio rerio; RNA Seq	GSM2574370		1	48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2574370	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP103805		S3_S5_L001_R1_001.fastq.gz	fastq	1200317760.0	15909907.0	GSM2574370 r1	0:75.44 1:0	A:296365402;C:297373974;G:283266985;T:323244649;N:66750	75	0	296365402	297373974	283266985	323244649	66750	SRX2733017	SRS2120915	SRA553927	GEO	Australian Institute for Bioengineering and Nanotechnology	1	0.92986		0.05547		0.72805		0.50801		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Australia	2017-04-11	Hatching	Embryo	Endothelium	Cardiovascular System
42154	42154	SRR5443677	SRX2733017	SRS2120915	SRP103805	PRJNA382558	mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish.	GSE97649	Transcriptome Analysis	48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate with 6 brains used per samples. Overall design: wild type vs mutant		pubmed:26253536	48hpf zebrafish FAC sorted endothelial cell wt 3	GSM2574370	tissue:purified endothelial cell\|transgene:kdrl eGFP\|genotype:wildtype	48hpf zebrafish FAC sorted endothelial cell wt 3	adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample	purified endothelial cell		48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols		transgene:kdrl eGFP\|genotype:wildtype	GSM2574370	GSM2574370: 48hpf zebrafish FAC sorted endothelial cell wt 3; Danio rerio; RNA Seq	GSM2574370		1	48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2574370	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP103805		S3_S5_L002_R1_001.fastq.gz	fastq	1186590046.0	15727830.0	GSM2574370 r2	0:75.45 1:0	A:292748835;C:294033369;G:280237781;T:319506249;N:63812	75	0	292748835	294033369	280237781	319506249	63812	SRX2733017	SRS2120915	SRA553927	GEO	Australian Institute for Bioengineering and Nanotechnology	1	0.92874		0.05356		0.72839		0.51335		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Australia	2017-04-11	Hatching	Embryo	Endothelium	Cardiovascular System
42155	42155	SRR5443678	SRX2733017	SRS2120915	SRP103805	PRJNA382558	mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish.	GSE97649	Transcriptome Analysis	48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate with 6 brains used per samples. Overall design: wild type vs mutant		pubmed:26253536	48hpf zebrafish FAC sorted endothelial cell wt 3	GSM2574370	tissue:purified endothelial cell\|transgene:kdrl eGFP\|genotype:wildtype	48hpf zebrafish FAC sorted endothelial cell wt 3	adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample	purified endothelial cell		48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols		transgene:kdrl eGFP\|genotype:wildtype	GSM2574370	GSM2574370: 48hpf zebrafish FAC sorted endothelial cell wt 3; Danio rerio; RNA Seq	GSM2574370		1	48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2574370	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP103805		S3_S5_L003_R1_001.fastq.gz	fastq	1179030774.0	15627890.0	GSM2574370 r3	0:75.44 1:0	A:292569213;C:292307681;G:278072717;T:316039886;N:41277	75	0	292569213	292307681	278072717	316039886	41277	SRX2733017	SRS2120915	SRA553927	GEO	Australian Institute for Bioengineering and Nanotechnology	1	0.92502		0.0542		0.73129		0.50553		75		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Australia	2017-04-11	Hatching	Embryo	Endothelium	Cardiovascular System
42156	42156	SRR5443679	SRX2733017	SRS2120915	SRP103805	PRJNA382558	mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish.	GSE97649	Transcriptome Analysis	48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate with 6 brains used per samples. Overall design: wild type vs mutant		pubmed:26253536	48hpf zebrafish FAC sorted endothelial cell wt 3	GSM2574370	tissue:purified endothelial cell\|transgene:kdrl eGFP\|genotype:wildtype	48hpf zebrafish FAC sorted endothelial cell wt 3	adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample	purified endothelial cell		48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols		transgene:kdrl eGFP\|genotype:wildtype	GSM2574370	GSM2574370: 48hpf zebrafish FAC sorted endothelial cell wt 3; Danio rerio; RNA Seq	GSM2574370		1	48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2574370	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP103805		S3_S5_L004_R1_001.fastq.gz	fastq	1186517148.0	15727062.0	GSM2574370 r4	0:75.44 1:0	A:294065343;C:294086528;G:279977232;T:318344594;N:43451	75	0	294065343	294086528	279977232	318344594	43451	SRX2733017	SRS2120915	SRA553927	GEO	Australian Institute for Bioengineering and Nanotechnology	1	0.92801		0.05486		0.7263		0.51617		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Australia	2017-04-11	Hatching	Embryo	Endothelium	Cardiovascular System
42157	42157	SRR5443672	SRX2733016	SRS2120914	SRP103805	PRJNA382558	mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish.	GSE97649	Transcriptome Analysis	48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate with 6 brains used per samples. Overall design: wild type vs mutant		pubmed:26253536	48hpf zebrafish FAC sorted endothelial cell wt 2	GSM2574369	tissue:purified endothelial cell\|transgene:kdrl eGFP\|genotype:wildtype	48hpf zebrafish FAC sorted endothelial cell wt 2	adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample	purified endothelial cell		48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols		transgene:kdrl eGFP\|genotype:wildtype	GSM2574369	GSM2574369: 48hpf zebrafish FAC sorted endothelial cell wt 2; Danio rerio; RNA Seq	GSM2574369		1	48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2574369	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP103805		S2_S3_L001_R1_001.fastq.gz	fastq	1118226721.0	14818796.0	GSM2574369 r1	0:75.46 1:0	A:277321886;C:276240373;G:264607012;T:299984813;N:72637	75	0	277321886	276240373	264607012	299984813	72637	SRX2733016	SRS2120914	SRA553927	GEO	Australian Institute for Bioengineering and Nanotechnology	1	0.92813		0.0608		0.73511		0.49445		75		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Australia	2017-04-11	Hatching	Embryo	Endothelium	Cardiovascular System
42158	42158	SRR5443673	SRX2733016	SRS2120914	SRP103805	PRJNA382558	mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish.	GSE97649	Transcriptome Analysis	48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate with 6 brains used per samples. Overall design: wild type vs mutant		pubmed:26253536	48hpf zebrafish FAC sorted endothelial cell wt 2	GSM2574369	tissue:purified endothelial cell\|transgene:kdrl eGFP\|genotype:wildtype	48hpf zebrafish FAC sorted endothelial cell wt 2	adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample	purified endothelial cell		48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols		transgene:kdrl eGFP\|genotype:wildtype	GSM2574369	GSM2574369: 48hpf zebrafish FAC sorted endothelial cell wt 2; Danio rerio; RNA Seq	GSM2574369		1	48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2574369	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP103805		S2_S3_L002_R1_001.fastq.gz	fastq	1097382503.0	14542648.0	GSM2574369 r2	0:75.46 1:0	A:271913618;C:271165534;G:259952446;T:294280610;N:70295	75	0	271913618	271165534	259952446	294280610	70295	SRX2733016	SRS2120914	SRA553927	GEO	Australian Institute for Bioengineering and Nanotechnology	1	0.92628		0.05901		0.73434		0.50436		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Australia	2017-04-11	Hatching	Embryo	Endothelium	Cardiovascular System
42159	42159	SRR5443674	SRX2733016	SRS2120914	SRP103805	PRJNA382558	mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish.	GSE97649	Transcriptome Analysis	48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate with 6 brains used per samples. Overall design: wild type vs mutant		pubmed:26253536	48hpf zebrafish FAC sorted endothelial cell wt 2	GSM2574369	tissue:purified endothelial cell\|transgene:kdrl eGFP\|genotype:wildtype	48hpf zebrafish FAC sorted endothelial cell wt 2	adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample	purified endothelial cell		48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols		transgene:kdrl eGFP\|genotype:wildtype	GSM2574369	GSM2574369: 48hpf zebrafish FAC sorted endothelial cell wt 2; Danio rerio; RNA Seq	GSM2574369		1	48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2574369	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP103805		S2_S3_L003_R1_001.fastq.gz	fastq	1100385244.0	14582533.0	GSM2574369 r3	0:75.46 1:0	A:274241238;C:272082346;G:260277831;T:293731839;N:51990	75	0	274241238	272082346	260277831	293731839	51990	SRX2733016	SRS2120914	SRA553927	GEO	Australian Institute for Bioengineering and Nanotechnology	1	0.92524		0.06015		0.73805		0.50957		71		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Australia	2017-04-11	Hatching	Embryo	Endothelium	Cardiovascular System
42160	42160	SRR5443675	SRX2733016	SRS2120914	SRP103805	PRJNA382558	mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish.	GSE97649	Transcriptome Analysis	48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate with 6 brains used per samples. Overall design: wild type vs mutant		pubmed:26253536	48hpf zebrafish FAC sorted endothelial cell wt 2	GSM2574369	tissue:purified endothelial cell\|transgene:kdrl eGFP\|genotype:wildtype	48hpf zebrafish FAC sorted endothelial cell wt 2	adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample	purified endothelial cell		48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols		transgene:kdrl eGFP\|genotype:wildtype	GSM2574369	GSM2574369: 48hpf zebrafish FAC sorted endothelial cell wt 2; Danio rerio; RNA Seq	GSM2574369		1	48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2574369	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP103805		S2_S3_L004_R1_001.fastq.gz	fastq	1100058192.0	14577978.0	GSM2574369 r4	0:75.46 1:0	A:273957130;C:271919703;G:260365193;T:293764097;N:52069	75	0	273957130	271919703	260365193	293764097	52069	SRX2733016	SRS2120914	SRA553927	GEO	Australian Institute for Bioengineering and Nanotechnology	1	0.92546		0.06173		0.73985		0.52271		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Australia	2017-04-11	Hatching	Embryo	Endothelium	Cardiovascular System
42161	42161	SRR5443668	SRX2733015	SRS2120913	SRP103805	PRJNA382558	mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish.	GSE97649	Transcriptome Analysis	48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate with 6 brains used per samples. Overall design: wild type vs mutant		pubmed:26253536	48hpf zebrafish FAC sorted endothelial cell wt 1	GSM2574368	tissue:purified endothelial cell\|transgene:kdrl eGFP\|genotype:wildtype	48hpf zebrafish FAC sorted endothelial cell wt 1	adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample	purified endothelial cell		48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols		transgene:kdrl eGFP\|genotype:wildtype	GSM2574368	GSM2574368: 48hpf zebrafish FAC sorted endothelial cell wt 1; Danio rerio; RNA Seq	GSM2574368		1	48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2574368	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP103805		S1_S1_L001_R1_001.fastq.gz	fastq	1086391308.0	14398072.0	GSM2574368 r1	0:75.45 1:0	A:265407098;C:273473167;G:256935933;T:290517430;N:57680	75	0	265407098	273473167	256935933	290517430	57680	SRX2733015	SRS2120913	SRA553927	GEO	Australian Institute for Bioengineering and Nanotechnology	1	0.93916		0.05822		0.73785		0.51199		75		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Australia	2017-04-11	Hatching	Embryo	Endothelium	Cardiovascular System
42162	42162	SRR5443669	SRX2733015	SRS2120913	SRP103805	PRJNA382558	mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish.	GSE97649	Transcriptome Analysis	48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate with 6 brains used per samples. Overall design: wild type vs mutant		pubmed:26253536	48hpf zebrafish FAC sorted endothelial cell wt 1	GSM2574368	tissue:purified endothelial cell\|transgene:kdrl eGFP\|genotype:wildtype	48hpf zebrafish FAC sorted endothelial cell wt 1	adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample	purified endothelial cell		48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols		transgene:kdrl eGFP\|genotype:wildtype	GSM2574368	GSM2574368: 48hpf zebrafish FAC sorted endothelial cell wt 1; Danio rerio; RNA Seq	GSM2574368		1	48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2574368	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP103805		S1_S1_L002_R1_001.fastq.gz	fastq	1073108602.0	14221959.0	GSM2574368 r2	0:75.45 1:0	A:261964537;C:270187564;G:253958473;T:286941827;N:56201	75	0	261964537	270187564	253958473	286941827	56201	SRX2733015	SRS2120913	SRA553927	GEO	Australian Institute for Bioengineering and Nanotechnology	1	0.93746		0.05835		0.73734		0.50609		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Australia	2017-04-11	Hatching	Embryo	Endothelium	Cardiovascular System
42163	42163	SRR5443670	SRX2733015	SRS2120913	SRP103805	PRJNA382558	mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish.	GSE97649	Transcriptome Analysis	48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate with 6 brains used per samples. Overall design: wild type vs mutant		pubmed:26253536	48hpf zebrafish FAC sorted endothelial cell wt 1	GSM2574368	tissue:purified endothelial cell\|transgene:kdrl eGFP\|genotype:wildtype	48hpf zebrafish FAC sorted endothelial cell wt 1	adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample	purified endothelial cell		48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols		transgene:kdrl eGFP\|genotype:wildtype	GSM2574368	GSM2574368: 48hpf zebrafish FAC sorted endothelial cell wt 1; Danio rerio; RNA Seq	GSM2574368		1	48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2574368	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP103805		S1_S1_L003_R1_001.fastq.gz	fastq	1064653834.0	14110138.0	GSM2574368 r3	0:75.45 1:0	A:261657368;C:268193214;G:251551872;T:283215565;N:35815	75	0	261657368	268193214	251551872	283215565	35815	SRX2733015	SRS2120913	SRA553927	GEO	Australian Institute for Bioengineering and Nanotechnology	1	0.93651		0.05738		0.74042		0.51489		74		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Australia	2017-04-11	Hatching	Embryo	Endothelium	Cardiovascular System
42164	42164	SRR5443671	SRX2733015	SRS2120913	SRP103805	PRJNA382558	mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish.	GSE97649	Transcriptome Analysis	48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate with 6 brains used per samples. Overall design: wild type vs mutant		pubmed:26253536	48hpf zebrafish FAC sorted endothelial cell wt 1	GSM2574368	tissue:purified endothelial cell\|transgene:kdrl eGFP\|genotype:wildtype	48hpf zebrafish FAC sorted endothelial cell wt 1	adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample	purified endothelial cell		48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols		transgene:kdrl eGFP\|genotype:wildtype	GSM2574368	GSM2574368: 48hpf zebrafish FAC sorted endothelial cell wt 1; Danio rerio; RNA Seq	GSM2574368		1	48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2574368	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP103805		S1_S1_L004_R1_001.fastq.gz	fastq	1072543375.0	14214599.0	GSM2574368 r4	0:75.45 1:0	A:263268340;C:270054371;G:253632532;T:285551360;N:36772	75	0	263268340	270054371	253632532	285551360	36772	SRX2733015	SRS2120913	SRA553927	GEO	Australian Institute for Bioengineering and Nanotechnology	1	0.93658		0.05706		0.73935		0.5115		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Australia	2017-04-11	Hatching	Embryo	Endothelium	Cardiovascular System
47740	47740	SRR6848349	SRX3803619	SRS3055252	SRP135898	PRJNA438687	Transcriptome profiling of endothelial cells from wild type hhex mutants and hhex overexpression zebrafish embryos	GSE111963	Transcriptome Analysis	We used high throughput sequencing to identify differential expression in siblings hhex mutants and hhex overexpression endothelial cells at 48 hpf. Overall design: FACS sorted endothelial cells from siblings hhex mutants and hhex overexpression at 48 hpf		pubmed:30006544	hhex overexpression rep2	GSM3045716	tissue:FACS sorted endothelial cells\|genotype/variation:hhex overexpression\|age:48 hpf\|strain:AB\|cell type:endothelial cells	hhex overexpression rep2	The resulting raw reads were assessed for quality adapter content and duplication rates with FastQC Andrews S. 2010 FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reaper version 13 100 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides Davis et al. Kraken: A set of tools for quality control and analysis of high throughput sequence data. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter “ outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10% Dobin et al. STAR: ultrafast universal RNA seq aligner. The number of reads aligning to genes was counted with featureCounts 1.4.5 p1 tool from the Subread package Liao et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.62 Love et al. Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Only genes with a minimum fold change of + 1.5 log2 + 0.59 a maximum Benjamini Hochberg corrected p value of 0.05 and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers Activities at the Universal Protein Resource UniProt. Genome build: DanCer10 GRCz10.87 Supplementary files format and content: tab delimited text files include library size normlized counts per peak	FACS sorted endothelial cells		For isolating endothelial cells from Tgkdrl:EGFPs843 siblings and Tgkdrl:EGFPs843 hhex mutant at 48 hpf embryos were divided based on the absence of PLs. Then embryos were rinsed in HBSS Gibco followed by dissociation in TrypLE express Gibco at 28°C with repeated pipetting. Endothelial cells were isolated using BD Aria sorter and sorted for EGFP+ or tdTomato+/EGFP+ signals for Tgkdrl:EGFPs843 Tgfli1a:tdTomato 2A hhexbns136. RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. 6ng total RNA was used as input for SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian Kit Clontech. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry resulting in minimum of 30M reads per library with 1x75bp single end setup.		genotype/variation:hhex overexpression\|age:48 hpf\|strain:AB\|cell type:endothelial cells	GSM3045716	GSM3045716: hhex overexpression rep2; Danio rerio; RNA Seq	GSM3045716		1	For isolating endothelial cells from Tgkdrl:EGFPs843 siblings and Tgkdrl:EGFPs843 hhex mutant at 48 hpf embryos were divided based on the absence of PLs. Then embryos were rinsed in HBSS Gibco followed by dissociation in TrypLE express Gibco at 28°C with repeated pipetting. Endothelial cells were isolated using BD Aria sorter and sorted for EGFP+ or tdTomato+/EGFP+ signals for Tgkdrl:EGFPs843 Tgfli1a:tdTomato 2A hhexbns136. RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. 6ng total RNA was used as input for SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian Kit Clontech. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry resulting in minimum of 30M reads per library with 1x75bp single end setup.	GEO Accession:GSM3045716	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP135898		Sebastien_OE_2_R1.fastq.gz	fastq	2514724985.0	34768823.0	GSM3045716 r1	0:72.33 1:0	A:565805246;C:704077993;G:741187599;T:503446013;N:208134	72	0	565805246	704077993	741187599	503446013	208134	SRX3803619	SRS3055252	SRA667127	GEO	MPI for heart and lung research	1	0.94763		0.26354		0.80702		0.62768		74		B		usable mapping rate	illumina	nextseq	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	Germany	2018-03-16	Hatching	Embryo	Endothelium	Cardiovascular System
47741	47741	SRR6848348	SRX3803618	SRS3055251	SRP135898	PRJNA438687	Transcriptome profiling of endothelial cells from wild type hhex mutants and hhex overexpression zebrafish embryos	GSE111963	Transcriptome Analysis	We used high throughput sequencing to identify differential expression in siblings hhex mutants and hhex overexpression endothelial cells at 48 hpf. Overall design: FACS sorted endothelial cells from siblings hhex mutants and hhex overexpression at 48 hpf		pubmed:30006544	hhex overexpression rep1	GSM3045715	tissue:FACS sorted endothelial cells\|genotype/variation:hhex overexpression\|age:48 hpf\|strain:AB\|cell type:endothelial cells	hhex overexpression rep1	The resulting raw reads were assessed for quality adapter content and duplication rates with FastQC Andrews S. 2010 FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reaper version 13 100 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides Davis et al. Kraken: A set of tools for quality control and analysis of high throughput sequence data. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter “ outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10% Dobin et al. STAR: ultrafast universal RNA seq aligner. The number of reads aligning to genes was counted with featureCounts 1.4.5 p1 tool from the Subread package Liao et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.62 Love et al. Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Only genes with a minimum fold change of + 1.5 log2 + 0.59 a maximum Benjamini Hochberg corrected p value of 0.05 and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers Activities at the Universal Protein Resource UniProt. Genome build: DanCer10 GRCz10.87 Supplementary files format and content: tab delimited text files include library size normlized counts per peak	FACS sorted endothelial cells		For isolating endothelial cells from Tgkdrl:EGFPs843 siblings and Tgkdrl:EGFPs843 hhex mutant at 48 hpf embryos were divided based on the absence of PLs. Then embryos were rinsed in HBSS Gibco followed by dissociation in TrypLE express Gibco at 28°C with repeated pipetting. Endothelial cells were isolated using BD Aria sorter and sorted for EGFP+ or tdTomato+/EGFP+ signals for Tgkdrl:EGFPs843 Tgfli1a:tdTomato 2A hhexbns136. RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. 6ng total RNA was used as input for SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian Kit Clontech. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry resulting in minimum of 30M reads per library with 1x75bp single end setup.		genotype/variation:hhex overexpression\|age:48 hpf\|strain:AB\|cell type:endothelial cells	GSM3045715	GSM3045715: hhex overexpression rep1; Danio rerio; RNA Seq	GSM3045715		1	For isolating endothelial cells from Tgkdrl:EGFPs843 siblings and Tgkdrl:EGFPs843 hhex mutant at 48 hpf embryos were divided based on the absence of PLs. Then embryos were rinsed in HBSS Gibco followed by dissociation in TrypLE express Gibco at 28°C with repeated pipetting. Endothelial cells were isolated using BD Aria sorter and sorted for EGFP+ or tdTomato+/EGFP+ signals for Tgkdrl:EGFPs843 Tgfli1a:tdTomato 2A hhexbns136. RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. 6ng total RNA was used as input for SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian Kit Clontech. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry resulting in minimum of 30M reads per library with 1x75bp single end setup.	GEO Accession:GSM3045715	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP135898		Sebastien_OE_1_R1.fastq.gz	fastq	2201523348.0	30479961.0	GSM3045715 r1	0:72.23 1:0	A:510844407;C:602803512;G:634953285;T:452682176;N:239968	72	0	510844407	602803512	634953285	452682176	239968	SRX3803618	SRS3055251	SRA667127	GEO	MPI for heart and lung research	1	0.94219		0.27653		0.80466		0.66516		75		B		usable mapping rate	illumina	nextseq	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	Germany	2018-03-16	Hatching	Embryo	Endothelium	Cardiovascular System
47742	47742	SRR6848347	SRX3803617	SRS3055250	SRP135898	PRJNA438687	Transcriptome profiling of endothelial cells from wild type hhex mutants and hhex overexpression zebrafish embryos	GSE111963	Transcriptome Analysis	We used high throughput sequencing to identify differential expression in siblings hhex mutants and hhex overexpression endothelial cells at 48 hpf. Overall design: FACS sorted endothelial cells from siblings hhex mutants and hhex overexpression at 48 hpf		pubmed:30006544	hhex mutant rep2	GSM3045714	tissue:FACS sorted endothelial cells\|genotype/variation:hhex mutant\|age:48 hpf\|strain:AB\|cell type:endothelial cells	hhex mutant rep2	The resulting raw reads were assessed for quality adapter content and duplication rates with FastQC Andrews S. 2010 FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reaper version 13 100 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides Davis et al. Kraken: A set of tools for quality control and analysis of high throughput sequence data. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter “ outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10% Dobin et al. STAR: ultrafast universal RNA seq aligner. The number of reads aligning to genes was counted with featureCounts 1.4.5 p1 tool from the Subread package Liao et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.62 Love et al. Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Only genes with a minimum fold change of + 1.5 log2 + 0.59 a maximum Benjamini Hochberg corrected p value of 0.05 and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers Activities at the Universal Protein Resource UniProt. Genome build: DanCer10 GRCz10.87 Supplementary files format and content: tab delimited text files include library size normlized counts per peak	FACS sorted endothelial cells		For isolating endothelial cells from Tgkdrl:EGFPs843 siblings and Tgkdrl:EGFPs843 hhex mutant at 48 hpf embryos were divided based on the absence of PLs. Then embryos were rinsed in HBSS Gibco followed by dissociation in TrypLE express Gibco at 28°C with repeated pipetting. Endothelial cells were isolated using BD Aria sorter and sorted for EGFP+ or tdTomato+/EGFP+ signals for Tgkdrl:EGFPs843 Tgfli1a:tdTomato 2A hhexbns136. RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. 6ng total RNA was used as input for SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian Kit Clontech. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry resulting in minimum of 30M reads per library with 1x75bp single end setup.		genotype/variation:hhex mutant\|age:48 hpf\|strain:AB\|cell type:endothelial cells	GSM3045714	GSM3045714: hhex mutant rep2; Danio rerio; RNA Seq	GSM3045714		1	For isolating endothelial cells from Tgkdrl:EGFPs843 siblings and Tgkdrl:EGFPs843 hhex mutant at 48 hpf embryos were divided based on the absence of PLs. Then embryos were rinsed in HBSS Gibco followed by dissociation in TrypLE express Gibco at 28°C with repeated pipetting. Endothelial cells were isolated using BD Aria sorter and sorted for EGFP+ or tdTomato+/EGFP+ signals for Tgkdrl:EGFPs843 Tgfli1a:tdTomato 2A hhexbns136. RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. 6ng total RNA was used as input for SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian Kit Clontech. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry resulting in minimum of 30M reads per library with 1x75bp single end setup.	GEO Accession:GSM3045714	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP135898		Sebastien_Mut_2_R1.fastq.gz	fastq	2377033794.0	32865413.0	GSM3045714 r1	0:72.33 1:0	A:531221225;C:668093793;G:704926379;T:472544720;N:247677	72	0	531221225	668093793	704926379	472544720	247677	SRX3803617	SRS3055250	SRA667127	GEO	MPI for heart and lung research	1	0.93202		0.25789		0.81617		0.66408		74		B		usable mapping rate	illumina	nextseq	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	Germany	2018-03-16	Hatching	Embryo	Endothelium	Cardiovascular System
47743	47743	SRR6848346	SRX3803616	SRS3055249	SRP135898	PRJNA438687	Transcriptome profiling of endothelial cells from wild type hhex mutants and hhex overexpression zebrafish embryos	GSE111963	Transcriptome Analysis	We used high throughput sequencing to identify differential expression in siblings hhex mutants and hhex overexpression endothelial cells at 48 hpf. Overall design: FACS sorted endothelial cells from siblings hhex mutants and hhex overexpression at 48 hpf		pubmed:30006544	hhex mutant rep1	GSM3045713	tissue:FACS sorted endothelial cells\|genotype/variation:hhex mutant\|age:48 hpf\|strain:AB\|cell type:endothelial cells	hhex mutant rep1	The resulting raw reads were assessed for quality adapter content and duplication rates with FastQC Andrews S. 2010 FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reaper version 13 100 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides Davis et al. Kraken: A set of tools for quality control and analysis of high throughput sequence data. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter “ outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10% Dobin et al. STAR: ultrafast universal RNA seq aligner. The number of reads aligning to genes was counted with featureCounts 1.4.5 p1 tool from the Subread package Liao et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.62 Love et al. Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Only genes with a minimum fold change of + 1.5 log2 + 0.59 a maximum Benjamini Hochberg corrected p value of 0.05 and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers Activities at the Universal Protein Resource UniProt. Genome build: DanCer10 GRCz10.87 Supplementary files format and content: tab delimited text files include library size normlized counts per peak	FACS sorted endothelial cells		For isolating endothelial cells from Tgkdrl:EGFPs843 siblings and Tgkdrl:EGFPs843 hhex mutant at 48 hpf embryos were divided based on the absence of PLs. Then embryos were rinsed in HBSS Gibco followed by dissociation in TrypLE express Gibco at 28°C with repeated pipetting. Endothelial cells were isolated using BD Aria sorter and sorted for EGFP+ or tdTomato+/EGFP+ signals for Tgkdrl:EGFPs843 Tgfli1a:tdTomato 2A hhexbns136. RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. 6ng total RNA was used as input for SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian Kit Clontech. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry resulting in minimum of 30M reads per library with 1x75bp single end setup.		genotype/variation:hhex mutant\|age:48 hpf\|strain:AB\|cell type:endothelial cells	GSM3045713	GSM3045713: hhex mutant rep1; Danio rerio; RNA Seq	GSM3045713		1	For isolating endothelial cells from Tgkdrl:EGFPs843 siblings and Tgkdrl:EGFPs843 hhex mutant at 48 hpf embryos were divided based on the absence of PLs. Then embryos were rinsed in HBSS Gibco followed by dissociation in TrypLE express Gibco at 28°C with repeated pipetting. Endothelial cells were isolated using BD Aria sorter and sorted for EGFP+ or tdTomato+/EGFP+ signals for Tgkdrl:EGFPs843 Tgfli1a:tdTomato 2A hhexbns136. RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. 6ng total RNA was used as input for SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian Kit Clontech. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry resulting in minimum of 30M reads per library with 1x75bp single end setup.	GEO Accession:GSM3045713	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP135898		Sebastien_Mut_1_R1.fastq.gz	fastq	2492708175.0	34527636.0	GSM3045713 r1	0:72.19 1:0	A:555859455;C:702003394;G:740775583;T:493818885;N:250858	72	0	555859455	702003394	740775583	493818885	250858	SRX3803616	SRS3055249	SRA667127	GEO	MPI for heart and lung research	1	0.93924		0.25343		0.81889		0.6311		75		B		usable mapping rate	illumina	nextseq	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	Germany	2018-03-16	Hatching	Embryo	Endothelium	Cardiovascular System
47744	47744	SRR6848345	SRX3803615	SRS3055248	SRP135898	PRJNA438687	Transcriptome profiling of endothelial cells from wild type hhex mutants and hhex overexpression zebrafish embryos	GSE111963	Transcriptome Analysis	We used high throughput sequencing to identify differential expression in siblings hhex mutants and hhex overexpression endothelial cells at 48 hpf. Overall design: FACS sorted endothelial cells from siblings hhex mutants and hhex overexpression at 48 hpf		pubmed:30006544	Sibling rep2	GSM3045712	tissue:FACS sorted endothelial cells\|genotype/variation:wild type\|age:48 hpf\|strain:AB\|cell type:endothelial cells	Sibling rep2	The resulting raw reads were assessed for quality adapter content and duplication rates with FastQC Andrews S. 2010 FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reaper version 13 100 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides Davis et al. Kraken: A set of tools for quality control and analysis of high throughput sequence data. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter “ outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10% Dobin et al. STAR: ultrafast universal RNA seq aligner. The number of reads aligning to genes was counted with featureCounts 1.4.5 p1 tool from the Subread package Liao et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.62 Love et al. Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Only genes with a minimum fold change of + 1.5 log2 + 0.59 a maximum Benjamini Hochberg corrected p value of 0.05 and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers Activities at the Universal Protein Resource UniProt. Genome build: DanCer10 GRCz10.87 Supplementary files format and content: tab delimited text files include library size normlized counts per peak	FACS sorted endothelial cells		For isolating endothelial cells from Tgkdrl:EGFPs843 siblings and Tgkdrl:EGFPs843 hhex mutant at 48 hpf embryos were divided based on the absence of PLs. Then embryos were rinsed in HBSS Gibco followed by dissociation in TrypLE express Gibco at 28°C with repeated pipetting. Endothelial cells were isolated using BD Aria sorter and sorted for EGFP+ or tdTomato+/EGFP+ signals for Tgkdrl:EGFPs843 Tgfli1a:tdTomato 2A hhexbns136. RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. 6ng total RNA was used as input for SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian Kit Clontech. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry resulting in minimum of 30M reads per library with 1x75bp single end setup.		genotype/variation:wild type\|age:48 hpf\|strain:AB\|cell type:endothelial cells	GSM3045712	GSM3045712: Sibling rep2; Danio rerio; RNA Seq	GSM3045712		1	For isolating endothelial cells from Tgkdrl:EGFPs843 siblings and Tgkdrl:EGFPs843 hhex mutant at 48 hpf embryos were divided based on the absence of PLs. Then embryos were rinsed in HBSS Gibco followed by dissociation in TrypLE express Gibco at 28°C with repeated pipetting. Endothelial cells were isolated using BD Aria sorter and sorted for EGFP+ or tdTomato+/EGFP+ signals for Tgkdrl:EGFPs843 Tgfli1a:tdTomato 2A hhexbns136. RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. 6ng total RNA was used as input for SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian Kit Clontech. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry resulting in minimum of 30M reads per library with 1x75bp single end setup.	GEO Accession:GSM3045712	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP135898		Sebastien_WT_2_R1.fastq.gz	fastq	2451974351.0	33830383.0	GSM3045712 r1	0:72.48 1:0	A:557370317;C:679644672;G:720300776;T:494468929;N:189657	72	0	557370317	679644672	720300776	494468929	189657	SRX3803615	SRS3055248	SRA667127	GEO	MPI for heart and lung research	1	0.91674		0.25327		0.80868		0.70337		75		B		usable mapping rate	illumina	nextseq	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	Germany	2018-03-16	Hatching	Embryo	Endothelium	Cardiovascular System
47745	47745	SRR6848344	SRX3803614	SRS3055247	SRP135898	PRJNA438687	Transcriptome profiling of endothelial cells from wild type hhex mutants and hhex overexpression zebrafish embryos	GSE111963	Transcriptome Analysis	We used high throughput sequencing to identify differential expression in siblings hhex mutants and hhex overexpression endothelial cells at 48 hpf. Overall design: FACS sorted endothelial cells from siblings hhex mutants and hhex overexpression at 48 hpf		pubmed:30006544	Sibling rep1	GSM3045711	tissue:FACS sorted endothelial cells\|genotype/variation:wild type\|age:48 hpf\|strain:AB\|cell type:endothelial cells	Sibling rep1	The resulting raw reads were assessed for quality adapter content and duplication rates with FastQC Andrews S. 2010 FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reaper version 13 100 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides Davis et al. Kraken: A set of tools for quality control and analysis of high throughput sequence data. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter “ outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10% Dobin et al. STAR: ultrafast universal RNA seq aligner. The number of reads aligning to genes was counted with featureCounts 1.4.5 p1 tool from the Subread package Liao et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.62 Love et al. Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Only genes with a minimum fold change of + 1.5 log2 + 0.59 a maximum Benjamini Hochberg corrected p value of 0.05 and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers Activities at the Universal Protein Resource UniProt. Genome build: DanCer10 GRCz10.87 Supplementary files format and content: tab delimited text files include library size normlized counts per peak	FACS sorted endothelial cells		For isolating endothelial cells from Tgkdrl:EGFPs843 siblings and Tgkdrl:EGFPs843 hhex mutant at 48 hpf embryos were divided based on the absence of PLs. Then embryos were rinsed in HBSS Gibco followed by dissociation in TrypLE express Gibco at 28°C with repeated pipetting. Endothelial cells were isolated using BD Aria sorter and sorted for EGFP+ or tdTomato+/EGFP+ signals for Tgkdrl:EGFPs843 Tgfli1a:tdTomato 2A hhexbns136. RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. 6ng total RNA was used as input for SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian Kit Clontech. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry resulting in minimum of 30M reads per library with 1x75bp single end setup.		genotype/variation:wild type\|age:48 hpf\|strain:AB\|cell type:endothelial cells	GSM3045711	GSM3045711: Sibling rep1; Danio rerio; RNA Seq	GSM3045711		1	For isolating endothelial cells from Tgkdrl:EGFPs843 siblings and Tgkdrl:EGFPs843 hhex mutant at 48 hpf embryos were divided based on the absence of PLs. Then embryos were rinsed in HBSS Gibco followed by dissociation in TrypLE express Gibco at 28°C with repeated pipetting. Endothelial cells were isolated using BD Aria sorter and sorted for EGFP+ or tdTomato+/EGFP+ signals for Tgkdrl:EGFPs843 Tgfli1a:tdTomato 2A hhexbns136. RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. 6ng total RNA was used as input for SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian Kit Clontech. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry resulting in minimum of 30M reads per library with 1x75bp single end setup.	GEO Accession:GSM3045711	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP135898		Sebastien_WT_1_R1.fastq.gz	fastq	2685019288.0	37185023.0	GSM3045711 r1	0:72.21 1:0	A:629322492;C:731250924;G:769793846;T:554311522;N:340504	72	0	629322492	731250924	769793846	554311522	340504	SRX3803614	SRS3055247	SRA667127	GEO	MPI for heart and lung research	1	0.90551		0.24697		0.80695		0.65765		75		B		usable mapping rate	illumina	nextseq	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	Germany	2018-03-16	Hatching	Embryo	Endothelium	Cardiovascular System
50604	50604	SRR8169175	SRX4989831	SRS4025849	SRP168005	PRJNA504385	Endothelial transcriptome of 1dpf Zebrafish empryo	PRJNA504385	Other	The study aimed to identify endothelial specific transcript isoforms in 24hpf zebrafish embryo. The polyA RNA sequencing was performed on Illumina GA II platform.			Endothelial cells	EC	strain:Tgfli1:EGFP gata1a: dsRed\|age:1 dpf stage:1 dpf applicable\|tissue:Endothelium\|cell type:Endothelial\|BioSampleModel:Model organism or animal									Endothelial cells	EC	EC	PolyA RNA Seq			RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina Genome Analyzer IIx	SRP168005		EC_R1.fastq EC_R2.fastq	fastq fastq	3373890496.0	22196648.0	EC R1.fastq	0:76 1:76	A:984631808;C:769706826;G:812424195;T:790813473;N:16314194	76	76	984631808	769706826	812424195	790813473	16314194	SRX4989831	SRS4025849	SRA805845	CSIR-Institute of Genomics and Integrative Biology\|GN Ramachandran Knowledge Center	CSIR-Institute of Genomics and Integrative Biology	2	0.92323	0.92543	0.07989	0.0849	0.76842	0.77964	0.46181	0.47429	76	76	B	B	biological fallback assumption	illumina	early_illumina	unknown	poly_a	unknown	bulk	unknown	unknown	India	2019-12-06	Pharyngula	Embryo	Endothelium	Cardiovascular System
50605	50605	SRR8169176	SRX4989830	SRS4025850	SRP168005	PRJNA504385	Endothelial transcriptome of 1dpf Zebrafish empryo	PRJNA504385	Other	The study aimed to identify endothelial specific transcript isoforms in 24hpf zebrafish embryo. The polyA RNA sequencing was performed on Illumina GA II platform.			Non endothelial cells	NEC	strain:Tgfli1:EGFP gata1a: dsRed\|age:1 dpf stage:1 dpf applicable\|tissue:Whole organism devoid of endothelium\|BioSampleModel:Model organism or animal									Non endothelial cells	NEC	NEC	PolyA RNA Seq			RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina Genome Analyzer IIx	SRP168005		NEC_R2.fastq NEC_R1.fastq	fastq fastq	3903685432.0	25682141.0	NEC R1.fastq	0:76 1:76	A:1078599801;C:913868400;G:942281029;T:950473482;N:18462720	76	76	1078599801	913868400	942281029	950473482	18462720	SRX4989830	SRS4025850	SRA805845	CSIR-Institute of Genomics and Integrative Biology\|GN Ramachandran Knowledge Center	CSIR-Institute of Genomics and Integrative Biology	2	0.93037	0.92641	0.10373	0.11231	0.72644	0.74081	0.48329	0.48409	76	76	B	B	biological fallback assumption	illumina	early_illumina	unknown	poly_a	unknown	bulk	unknown	unknown	India	2019-12-06	Pharyngula	Embryo	Endothelium	Cardiovascular System
52238	52238	SRR9044114	SRX5820656	SRS4749302	SRP197695	PRJNA542436	Regulation of hematopoiesis and endothelium function by endocytic trafficking	PRJNA542436	Other	Endocytic trafficking in endothelium				CT1	strain:AB\|isolate:ctrl MO fluorescence activated cell sorting 1\|cultivar:not applicable\|ecotype:not applicable\|age:1 year\|sex:male and female\|tissue:fli1a+ endothelium\|BioSampleModel:Model organism or animal									RNA seq of endothelial cells1	ct1 20191	ct1 20191	ctrl MO 1			RNA-Seq	TRANSCRIPTOMIC	RT-PCR	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP197695		CT1.gz	fastq	3222866250.0	21485775.0	CT1.gz	0:150 1:0	A:845914701;C:771891741;G:774348916;T:830705072;N:5820	150	0	845914701	771891741	774348916	830705072	5820	SRX5820656	SRS4749302	SRA885405	Chinese academy of sciences\|institute of zoology	Chinese academy of sciences	1	0.95232		0.09195		0.7837		0.45885		150		B		usable mapping rate	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2020-01-17	Adult	Adult	Endothelium	Cardiovascular System
52239	52239	SRR9044115	SRX5820655	SRS4749299	SRP197695	PRJNA542436	Regulation of hematopoiesis and endothelium function by endocytic trafficking	PRJNA542436	Other	Endocytic trafficking in endothelium				CT2	strain:AB\|isolate:ctrl MO fluorescence activated cell sorting 2\|cultivar:not applicable\|ecotype:not applicable\|age:1 year\|sex:male and female\|tissue:fli1a+ endothelium\|BioSampleModel:Model organism or animal									RNA seq of endothelial cells2	ct1 20192	ct1 20192	ctrl MO 2			RNA-Seq	TRANSCRIPTOMIC	RT-PCR	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP197695		CT2.gz	fastq	3992117700.0	26614118.0	CT2.gz	0:150 1:0	A:1040923084;C:961956867;G:964333886;T:1024896832;N:7031	150	0	1040923084	961956867	964333886	1024896832	7031	SRX5820655	SRS4749299	SRA885405	Chinese academy of sciences\|institute of zoology	Chinese academy of sciences	1	0.95545		0.087		0.78488		0.46466		150		B		usable mapping rate	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2019-05-11	Adult	Adult	Endothelium	Cardiovascular System
52240	52240	SRR9044116	SRX5820654	SRS4749301	SRP197695	PRJNA542436	Regulation of hematopoiesis and endothelium function by endocytic trafficking	PRJNA542436	Other	Endocytic trafficking in endothelium				SCMO1	strain:AB\|isolate:5c MO fluorescence activated cell sorting 3\|cultivar:not applicable\|ecotype:not applicable\|age:1 year\|sex:male and female\|tissue:fli1a+ endothelium\|BioSampleModel:Model organism or animal									RNA seq of endothelial cells3	5c 20191	5c 20191	5c MO 1			RNA-Seq	TRANSCRIPTOMIC	RT-PCR	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP197695		SCMO1.gz	fastq	2137379550.0	14249197.0	SCMO1.gz	0:150 1:0	A:558129907;C:517045618;G:515434728;T:546767387;N:1910	150	0	558129907	517045618	515434728	546767387	1910	SRX5820654	SRS4749301	SRA885405	Chinese academy of sciences\|institute of zoology	Chinese academy of sciences	1	0.94546		0.08686		0.78709		0.56163		150		B		usable mapping rate	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2020-01-17	Adult	Adult	Endothelium	Cardiovascular System
52241	52241	SRR9044117	SRX5820653	SRS4749300	SRP197695	PRJNA542436	Regulation of hematopoiesis and endothelium function by endocytic trafficking	PRJNA542436	Other	Endocytic trafficking in endothelium				SCMO2	strain:AB\|isolate:5c MO fluorescence activated cell sorting 4\|cultivar:not applicable\|ecotype:not applicable\|age:1 year\|sex:male and female\|tissue:fli1a+ endothelium\|BioSampleModel:Model organism or animal									RNA seq of endothelial cells4	5c 20192	5c 20192	5c MO 2			RNA-Seq	TRANSCRIPTOMIC	RT-PCR	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP197695		SCMO2.gz	fastq	3909804300.0	26065362.0	SCMO2.gz	0:150 1:0	A:1033271905;C:928576644;G:928527559;T:1019420939;N:7253	150	0	1033271905	928576644	928527559	1019420939	7253	SRX5820653	SRS4749300	SRA885405	Chinese academy of sciences\|institute of zoology	Chinese academy of sciences	1	0.94475		0.096		0.7867		0.55845		150		B		usable mapping rate	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2020-01-17	Adult	Adult	Endothelium	Cardiovascular System
52764	52764	SRR9207199	SRX5978265	SRS4884520	SRP200560	PRJNA547066	RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf	GSE132259	Transcriptome Analysis	The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.	parent bioproject:PRJNA546805	pubmed:31395869	RNA seq MO DP R1hi rep3	GSM3855057	source name:haemogenic endothelium\|age:28 hpf 30 hpf\|cell isolation:FACS isolated cells\|tissue:haemogenic endothelium\|genotype/variation:runx1 morpholino injected	RNA seq MO DP R1hi rep3	Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value.	haemogenic endothelium	double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino	whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.	TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf.	age:28 hpf 30 hpf\|cell isolation:FACS isolated cells\|tissue:haemogenic endothelium\|genotype/variation:runx1 morpholino injected	GSM3855057	GSM3855057: MO DP R1hi rep3; Danio rerio; RNA Seq	GSM3855057		1	whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.	GEO Accession:GSM3855057	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP200560		WTCHG_236896_268_1_pair.fq.gz WTCHG_236896_268_2_pair.fq.gz	fastq fastq	1927186907.0	13135764.0	GSM3855057 r1	0:74.85 1:71.86	A:495349382;C:442938837;G:459765161;T:529104158;N:29369	74	71	495349382	442938837	459765161	529104158	29369	SRX5978265	SRS4884520	SRA894667	GEO	Oxford University	2	0.9511	0.71957	0.05876	0.04975	0.80322	0.83463	0.41847	0.47909	75	64	B	B	biological fallback assumption	illumina	hiseq_era	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United Kingdom	2019-06-05	Pharyngula	Embryo	Endothelium	Cardiovascular System
52765	52765	SRR9207200	SRX5978265	SRS4884520	SRP200560	PRJNA547066	RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf	GSE132259	Transcriptome Analysis	The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.	parent bioproject:PRJNA546805	pubmed:31395869	RNA seq MO DP R1hi rep3	GSM3855057	source name:haemogenic endothelium\|age:28 hpf 30 hpf\|cell isolation:FACS isolated cells\|tissue:haemogenic endothelium\|genotype/variation:runx1 morpholino injected	RNA seq MO DP R1hi rep3	Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value.	haemogenic endothelium	double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino	whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.	TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf.	age:28 hpf 30 hpf\|cell isolation:FACS isolated cells\|tissue:haemogenic endothelium\|genotype/variation:runx1 morpholino injected	GSM3855057	GSM3855057: MO DP R1hi rep3; Danio rerio; RNA Seq	GSM3855057		1	whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.	GEO Accession:GSM3855057	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP200560		WTCHG_236897_268_1_pair.fq.gz WTCHG_236897_268_2_pair.fq.gz	fastq fastq	1909528693.0	13017658.0	GSM3855057 r2	0:74.82 1:71.87	A:490710971;C:436487071;G:453444216;T:528853285;N:33150	74	71	490710971	436487071	453444216	528853285	33150	SRX5978265	SRS4884520	SRA894667	GEO	Oxford University	2	0.94988	0.70903	0.05941	0.04918	0.80346	0.83597	0.42243	0.48127	74	69	B	B	mate2-mate1 similar by mapping diff	illumina	hiseq_era	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United Kingdom	2019-06-05	Pharyngula	Embryo	Endothelium	Cardiovascular System
52766	52766	SRR9207197	SRX5978264	SRS4884519	SRP200560	PRJNA547066	RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf	GSE132259	Transcriptome Analysis	The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.	parent bioproject:PRJNA546805	pubmed:31395869	RNA seq MO DP R1hi rep2	GSM3855056	source name:haemogenic endothelium\|age:28 hpf 30 hpf\|cell isolation:FACS isolated cells\|tissue:haemogenic endothelium\|genotype/variation:runx1 morpholino injected	RNA seq MO DP R1hi rep2	Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value.	haemogenic endothelium	double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino	whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.	TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf.	age:28 hpf 30 hpf\|cell isolation:FACS isolated cells\|tissue:haemogenic endothelium\|genotype/variation:runx1 morpholino injected	GSM3855056	GSM3855056: MO DP R1hi rep2; Danio rerio; RNA Seq	GSM3855056		1	whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.	GEO Accession:GSM3855056	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP200560		WTCHG_236896_253_2_pair.fq.gz WTCHG_236896_253_1_pair.fq.gz	fastq fastq	2328318316.0	15846855.0	GSM3855056 r1	0:74.86 1:72.07	A:595900608;C:546479100;G:562297908;T:623605072;N:35628	74	72	595900608	546479100	562297908	623605072	35628	SRX5978264	SRS4884519	SRA894667	GEO	Oxford University	2	0.95426	0.78099	0.04531	0.04107	0.79285	0.81738	0.47636	0.47393	74	74	B	B	biological fallback assumption	illumina	hiseq_era	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United Kingdom	2019-06-05	Pharyngula	Embryo	Endothelium	Cardiovascular System
52767	52767	SRR9207198	SRX5978264	SRS4884519	SRP200560	PRJNA547066	RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf	GSE132259	Transcriptome Analysis	The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.	parent bioproject:PRJNA546805	pubmed:31395869	RNA seq MO DP R1hi rep2	GSM3855056	source name:haemogenic endothelium\|age:28 hpf 30 hpf\|cell isolation:FACS isolated cells\|tissue:haemogenic endothelium\|genotype/variation:runx1 morpholino injected	RNA seq MO DP R1hi rep2	Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value.	haemogenic endothelium	double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino	whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.	TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf.	age:28 hpf 30 hpf\|cell isolation:FACS isolated cells\|tissue:haemogenic endothelium\|genotype/variation:runx1 morpholino injected	GSM3855056	GSM3855056: MO DP R1hi rep2; Danio rerio; RNA Seq	GSM3855056		1	whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.	GEO Accession:GSM3855056	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP200560		WTCHG_236897_253_1_pair.fq.gz WTCHG_236897_253_2_pair.fq.gz	fastq fastq	2302889916.0	15678935.0	GSM3855056 r2	0:74.83 1:72.05	A:589414837;C:537423117;G:553631542;T:622379721;N:40699	74	72	589414837	537423117	553631542	622379721	40699	SRX5978264	SRS4884519	SRA894667	GEO	Oxford University	2	0.95316	0.76729	0.04543	0.04	0.79368	0.81994	0.4793	0.45619	74	73	B	B	biological fallback assumption	illumina	hiseq_era	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United Kingdom	2019-06-05	Pharyngula	Embryo	Endothelium	Cardiovascular System
52768	52768	SRR9207195	SRX5978263	SRS4884518	SRP200560	PRJNA547066	RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf	GSE132259	Transcriptome Analysis	The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.	parent bioproject:PRJNA546805	pubmed:31395869	RNA seq MO DP R1hi rep1	GSM3855055	source name:haemogenic endothelium\|age:28 hpf 30 hpf\|cell isolation:FACS isolated cells\|tissue:haemogenic endothelium\|genotype/variation:runx1 morpholino injected	RNA seq MO DP R1hi rep1	Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value.	haemogenic endothelium	double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino	whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.	TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf.	age:28 hpf 30 hpf\|cell isolation:FACS isolated cells\|tissue:haemogenic endothelium\|genotype/variation:runx1 morpholino injected	GSM3855055	GSM3855055: MO DP R1hi rep1; Danio rerio; RNA Seq	GSM3855055		1	whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.	GEO Accession:GSM3855055	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP200560		WTCHG_236896_246_1_pair.fq.gz WTCHG_236896_246_2_pair.fq.gz	fastq fastq	2117580563.0	14386411.0	GSM3855055 r1	0:74.87 1:72.33	A:541407670;C:500318189;G:514959635;T:560861522;N:33547	74	72	541407670	500318189	514959635	560861522	33547	SRX5978263	SRS4884518	SRA894667	GEO	Oxford University	2	0.95698	0.79806	0.0412	0.03838	0.79683	0.82073	0.4361	0.47246	75	74	B	B	biological fallback assumption	illumina	hiseq_era	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United Kingdom	2019-06-05	Pharyngula	Embryo	Endothelium	Cardiovascular System
52769	52769	SRR9207196	SRX5978263	SRS4884518	SRP200560	PRJNA547066	RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf	GSE132259	Transcriptome Analysis	The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.	parent bioproject:PRJNA546805	pubmed:31395869	RNA seq MO DP R1hi rep1	GSM3855055	source name:haemogenic endothelium\|age:28 hpf 30 hpf\|cell isolation:FACS isolated cells\|tissue:haemogenic endothelium\|genotype/variation:runx1 morpholino injected	RNA seq MO DP R1hi rep1	Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value.	haemogenic endothelium	double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino	whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.	TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf.	age:28 hpf 30 hpf\|cell isolation:FACS isolated cells\|tissue:haemogenic endothelium\|genotype/variation:runx1 morpholino injected	GSM3855055	GSM3855055: MO DP R1hi rep1; Danio rerio; RNA Seq	GSM3855055		1	whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.	GEO Accession:GSM3855055	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP200560		WTCHG_236897_246_1_pair.fq.gz WTCHG_236897_246_2_pair.fq.gz	fastq fastq	2093566860.0	14226227.0	GSM3855055 r2	0:74.83 1:72.33	A:535219614;C:492666345;G:507484718;T:558158640;N:37543	74	72	535219614	492666345	507484718	558158640	37543	SRX5978263	SRS4884518	SRA894667	GEO	Oxford University	2	0.95586	0.7889	0.04114	0.03868	0.79689	0.82104	0.43998	0.46953	74	47	B	B	biological fallback assumption	illumina	hiseq_era	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United Kingdom	2019-06-05	Pharyngula	Embryo	Endothelium	Cardiovascular System
52770	52770	SRR9207193	SRX5978262	SRS4884517	SRP200560	PRJNA547066	RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf	GSE132259	Transcriptome Analysis	The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.	parent bioproject:PRJNA546805	pubmed:31395869	RNA seq MO DN rep3	GSM3855054	source name:non endothelial tissue\|age:28 hpf 30 hpf\|cell isolation:FACS isolated cells\|tissue:non endothelial tissue\|genotype/variation:runx1 morpholino injected	RNA seq MO DN rep3	Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value.	non endothelial tissue	double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino	whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.	TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf.	age:28 hpf 30 hpf\|cell isolation:FACS isolated cells\|tissue:non endothelial tissue\|genotype/variation:runx1 morpholino injected	GSM3855054	GSM3855054: MO DN rep3; Danio rerio; RNA Seq	GSM3855054		1	whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.	GEO Accession:GSM3855054	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP200560		WTCHG_236896_269_1_pair.fq.gz WTCHG_236896_269_2_pair.fq.gz	fastq fastq	2046617161.0	13945847.0	GSM3855054 r1	0:74.83 1:71.93	A:534129043;C:466415284;G:478200001;T:567840465;N:32368	74	71	534129043	466415284	478200001	567840465	32368	SRX5978262	SRS4884517	SRA894667	GEO	Oxford University	2	0.94896	0.77373	0.08658	0.07153	0.73519	0.76715	0.49305	0.48341	75	74	B	B	biological fallback assumption	illumina	hiseq_era	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United Kingdom	2019-06-05	Pharyngula	Embryo	Endothelium	Cardiovascular System
52771	52771	SRR9207194	SRX5978262	SRS4884517	SRP200560	PRJNA547066	RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf	GSE132259	Transcriptome Analysis	The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.	parent bioproject:PRJNA546805	pubmed:31395869	RNA seq MO DN rep3	GSM3855054	source name:non endothelial tissue\|age:28 hpf 30 hpf\|cell isolation:FACS isolated cells\|tissue:non endothelial tissue\|genotype/variation:runx1 morpholino injected	RNA seq MO DN rep3	Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value.	non endothelial tissue	double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino	whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.	TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf.	age:28 hpf 30 hpf\|cell isolation:FACS isolated cells\|tissue:non endothelial tissue\|genotype/variation:runx1 morpholino injected	GSM3855054	GSM3855054: MO DN rep3; Danio rerio; RNA Seq	GSM3855054		1	whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.	GEO Accession:GSM3855054	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP200560		WTCHG_236897_269_1_pair.fq.gz WTCHG_236897_269_2_pair.fq.gz	fastq fastq	2013937570.0	13725739.0	GSM3855054 r2	0:74.79 1:71.93	A:525460437;C:456678849;G:468917277;T:562845673;N:35334	74	71	525460437	456678849	468917277	562845673	35334	SRX5978262	SRS4884517	SRA894667	GEO	Oxford University	2	0.94917	0.76456	0.08857	0.07125	0.73541	0.76777	0.49906	0.49093	74	44	B	B	biological fallback assumption	illumina	hiseq_era	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United Kingdom	2019-06-05	Pharyngula	Embryo	Endothelium	Cardiovascular System
52772	52772	SRR9207191	SRX5978261	SRS4884516	SRP200560	PRJNA547066	RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf	GSE132259	Transcriptome Analysis	The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.	parent bioproject:PRJNA546805	pubmed:31395869	RNA seq MO DN rep2	GSM3855053	source name:non endothelial tissue\|age:28 hpf 30 hpf\|cell isolation:FACS isolated cells\|tissue:non endothelial tissue\|genotype/variation:runx1 morpholino injected	RNA seq MO DN rep2	Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value.	non endothelial tissue	double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino	whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.	TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf.	age:28 hpf 30 hpf\|cell isolation:FACS isolated cells\|tissue:non endothelial tissue\|genotype/variation:runx1 morpholino injected	GSM3855053	GSM3855053: MO DN rep2; Danio rerio; RNA Seq	GSM3855053		1	whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.	GEO Accession:GSM3855053	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP200560		WTCHG_236896_254_1_pair.fq.gz WTCHG_236896_254_2_pair.fq.gz	fastq fastq	2491569443.0	17007413.0	GSM3855053 r1	0:74.84 1:71.66	A:650887336;C:562551977;G:579971830;T:698120812;N:37488	74	71	650887336	562551977	579971830	698120812	37488	SRX5978261	SRS4884516	SRA894667	GEO	Oxford University	2	0.95058	0.74758	0.08565	0.06922	0.74817	0.78344	0.49706	0.48533	74	74	B	B	biological fallback assumption	illumina	hiseq_era	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United Kingdom	2019-06-05	Pharyngula	Embryo	Endothelium	Cardiovascular System
52773	52773	SRR9207192	SRX5978261	SRS4884516	SRP200560	PRJNA547066	RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf	GSE132259	Transcriptome Analysis	The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.	parent bioproject:PRJNA546805	pubmed:31395869	RNA seq MO DN rep2	GSM3855053	source name:non endothelial tissue\|age:28 hpf 30 hpf\|cell isolation:FACS isolated cells\|tissue:non endothelial tissue\|genotype/variation:runx1 morpholino injected	RNA seq MO DN rep2	Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value.	non endothelial tissue	double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino	whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.	TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf.	age:28 hpf 30 hpf\|cell isolation:FACS isolated cells\|tissue:non endothelial tissue\|genotype/variation:runx1 morpholino injected	GSM3855053	GSM3855053: MO DN rep2; Danio rerio; RNA Seq	GSM3855053		1	whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.	GEO Accession:GSM3855053	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP200560		WTCHG_236897_254_1_pair.fq.gz WTCHG_236897_254_2_pair.fq.gz	fastq fastq	2467826388.0	16847563.0	GSM3855053 r2	0:74.80 1:71.67	A:644767348;C:554488060;G:572473532;T:696053759;N:43689	74	71	644767348	554488060	572473532	696053759	43689	SRX5978261	SRS4884516	SRA894667	GEO	Oxford University	2	0.95097	0.73759	0.0857	0.0679	0.74805	0.78307	0.50597	0.48761	74	59	B	B	biological fallback assumption	illumina	hiseq_era	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United Kingdom	2019-06-05	Pharyngula	Embryo	Endothelium	Cardiovascular System
52774	52774	SRR9207189	SRX5978260	SRS4884515	SRP200560	PRJNA547066	RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf	GSE132259	Transcriptome Analysis	The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.	parent bioproject:PRJNA546805	pubmed:31395869	RNA seq MO DN rep1	GSM3855052	source name:non endothelial tissue\|age:28 hpf 30 hpf\|cell isolation:FACS isolated cells\|tissue:non endothelial tissue\|genotype/variation:runx1 morpholino injected	RNA seq MO DN rep1	Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value.	non endothelial tissue	double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino	whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.	TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf.	age:28 hpf 30 hpf\|cell isolation:FACS isolated cells\|tissue:non endothelial tissue\|genotype/variation:runx1 morpholino injected	GSM3855052	GSM3855052: MO DN rep1; Danio rerio; RNA Seq	GSM3855052		1	whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.	GEO Accession:GSM3855052	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP200560		WTCHG_236896_247_1_pair.fq.gz WTCHG_236896_247_2_pair.fq.gz	fastq fastq	1764365530.0	12029530.0	GSM3855052 r1	0:74.84 1:71.83	A:466613214;C:395400217;G:407881798;T:494443051;N:27250	74	71	466613214	395400217	407881798	494443051	27250	SRX5978260	SRS4884515	SRA894667	GEO	Oxford University	2	0.95055	0.76043	0.0868	0.07313	0.75436	0.79295	0.51961	0.5131	75	74	B	B	biological fallback assumption	illumina	hiseq_era	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United Kingdom	2019-06-05	Pharyngula	Embryo	Endothelium	Cardiovascular System
52775	52775	SRR9207190	SRX5978260	SRS4884515	SRP200560	PRJNA547066	RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf	GSE132259	Transcriptome Analysis	The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.	parent bioproject:PRJNA546805	pubmed:31395869	RNA seq MO DN rep1	GSM3855052	source name:non endothelial tissue\|age:28 hpf 30 hpf\|cell isolation:FACS isolated cells\|tissue:non endothelial tissue\|genotype/variation:runx1 morpholino injected	RNA seq MO DN rep1	Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value.	non endothelial tissue	double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino	whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.	TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf.	age:28 hpf 30 hpf\|cell isolation:FACS isolated cells\|tissue:non endothelial tissue\|genotype/variation:runx1 morpholino injected	GSM3855052	GSM3855052: MO DN rep1; Danio rerio; RNA Seq	GSM3855052		1	whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.	GEO Accession:GSM3855052	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP200560		WTCHG_236897_247_1_pair.fq.gz WTCHG_236897_247_2_pair.fq.gz	fastq fastq	1746830974.0	11912737.0	GSM3855052 r2	0:74.80 1:71.83	A:461791276;C:389648653;G:402516938;T:492843307;N:30800	74	71	461791276	389648653	402516938	492843307	30800	SRX5978260	SRS4884515	SRA894667	GEO	Oxford University	2	0.94945	0.75002	0.08645	0.07146	0.75564	0.79247	0.52424	0.51007	74	74	B	B	biological fallback assumption	illumina	hiseq_era	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United Kingdom	2019-06-05	Pharyngula	Embryo	Endothelium	Cardiovascular System
52776	52776	SRR9207187	SRX5978259	SRS4884514	SRP200560	PRJNA547066	RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf	GSE132259	Transcriptome Analysis	The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.	parent bioproject:PRJNA546805	pubmed:31395869	RNA seq Wt DP R1hi rep3	GSM3855051	source name:haemogenic endothelium\|age:28 hpf 30 hpf\|cell isolation:FACS isolated cells\|tissue:haemogenic endothelium\|genotype/variation:non injected	RNA seq Wt DP R1hi rep3	Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value.	haemogenic endothelium	double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino	whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.	TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf.	age:28 hpf 30 hpf\|cell isolation:FACS isolated cells\|tissue:haemogenic endothelium\|genotype/variation:non injected	GSM3855051	GSM3855051: Wt DP R1hi rep3; Danio rerio; RNA Seq	GSM3855051		1	whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.	GEO Accession:GSM3855051	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP200560		WTCHG_236896_256_1_pair.fq.gz WTCHG_236896_256_2_pair.fq.gz	fastq fastq	2404346186.0	16361688.0	GSM3855051 r1	0:74.85 1:72.10	A:623840845;C:555338266;G:572145582;T:652983438;N:38055	74	72	623840845	555338266	572145582	652983438	38055	SRX5978259	SRS4884514	SRA894667	GEO	Oxford University	2	0.95156	0.77737	0.06227	0.05592	0.78013	0.80811	0.47747	0.46476	75	74	B	B	biological fallback assumption	illumina	hiseq_era	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United Kingdom	2019-06-05	Pharyngula	Embryo	Endothelium	Cardiovascular System
52777	52777	SRR9207188	SRX5978259	SRS4884514	SRP200560	PRJNA547066	RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf	GSE132259	Transcriptome Analysis	The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.	parent bioproject:PRJNA546805	pubmed:31395869	RNA seq Wt DP R1hi rep3	GSM3855051	source name:haemogenic endothelium\|age:28 hpf 30 hpf\|cell isolation:FACS isolated cells\|tissue:haemogenic endothelium\|genotype/variation:non injected	RNA seq Wt DP R1hi rep3	Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value.	haemogenic endothelium	double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino	whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.	TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf.	age:28 hpf 30 hpf\|cell isolation:FACS isolated cells\|tissue:haemogenic endothelium\|genotype/variation:non injected	GSM3855051	GSM3855051: Wt DP R1hi rep3; Danio rerio; RNA Seq	GSM3855051		1	whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.	GEO Accession:GSM3855051	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP200560		WTCHG_236897_256_1_pair.fq.gz WTCHG_236897_256_2_pair.fq.gz	fastq fastq	2376933896.0	16184470.0	GSM3855051 r2	0:74.81 1:72.05	A:616256503;C:545472678;G:562708331;T:652453993;N:42391	74	72	616256503	545472678	562708331	652453993	42391	SRX5978259	SRS4884514	SRA894667	GEO	Oxford University	2	0.95009	0.76216	0.06391	0.05506	0.78131	0.81051	0.48169	0.4736	74	74	B	B	biological fallback assumption	illumina	hiseq_era	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United Kingdom	2019-06-05	Pharyngula	Embryo	Endothelium	Cardiovascular System
52778	52778	SRR9207185	SRX5978258	SRS4884513	SRP200560	PRJNA547066	RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf	GSE132259	Transcriptome Analysis	The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.	parent bioproject:PRJNA546805	pubmed:31395869	RNA seq Wt DP R1hi rep2	GSM3855050	source name:haemogenic endothelium\|age:28 hpf 30 hpf\|cell isolation:FACS isolated cells\|tissue:haemogenic endothelium\|genotype/variation:non injected	RNA seq Wt DP R1hi rep2	Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value.	haemogenic endothelium	double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino	whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.	TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf.	age:28 hpf 30 hpf\|cell isolation:FACS isolated cells\|tissue:haemogenic endothelium\|genotype/variation:non injected	GSM3855050	GSM3855050: Wt DP R1hi rep2; Danio rerio; RNA Seq	GSM3855050		1	whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.	GEO Accession:GSM3855050	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP200560		WTCHG_236896_249_1_pair.fq.gz WTCHG_236896_249_2_pair.fq.gz	fastq fastq	2143701223.0	14577609.0	GSM3855050 r1	0:74.85 1:72.21	A:556710384;C:496467692;G:509166690;T:581322427;N:34030	74	72	556710384	496467692	509166690	581322427	34030	SRX5978258	SRS4884513	SRA894667	GEO	Oxford University	2	0.94754	0.79028	0.06346	0.05688	0.7811	0.80754	0.47106	0.45364	75	74	B	B	biological fallback assumption	illumina	hiseq_era	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United Kingdom	2019-06-05	Pharyngula	Embryo	Endothelium	Cardiovascular System
52779	52779	SRR9207186	SRX5978258	SRS4884513	SRP200560	PRJNA547066	RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf	GSE132259	Transcriptome Analysis	The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.	parent bioproject:PRJNA546805	pubmed:31395869	RNA seq Wt DP R1hi rep2	GSM3855050	source name:haemogenic endothelium\|age:28 hpf 30 hpf\|cell isolation:FACS isolated cells\|tissue:haemogenic endothelium\|genotype/variation:non injected	RNA seq Wt DP R1hi rep2	Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value.	haemogenic endothelium	double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino	whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.	TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf.	age:28 hpf 30 hpf\|cell isolation:FACS isolated cells\|tissue:haemogenic endothelium\|genotype/variation:non injected	GSM3855050	GSM3855050: Wt DP R1hi rep2; Danio rerio; RNA Seq	GSM3855050		1	whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.	GEO Accession:GSM3855050	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP200560		WTCHG_236897_249_1_pair.fq.gz WTCHG_236897_249_2_pair.fq.gz	fastq fastq	2117035142.0	14401911.0	GSM3855050 r2	0:74.82 1:72.18	A:549829321;C:487941130;G:501062541;T:578164319;N:37831	74	72	549829321	487941130	501062541	578164319	37831	SRX5978258	SRS4884513	SRA894667	GEO	Oxford University	2	0.9478	0.78326	0.06392	0.05622	0.78271	0.80764	0.46978	0.44622	74	74	B	B	biological fallback assumption	illumina	hiseq_era	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United Kingdom	2019-06-05	Pharyngula	Embryo	Endothelium	Cardiovascular System
52780	52780	SRR9207183	SRX5978257	SRS4884512	SRP200560	PRJNA547066	RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf	GSE132259	Transcriptome Analysis	The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.	parent bioproject:PRJNA546805	pubmed:31395869	RNA seq Wt DP R1hi rep1	GSM3855049	source name:haemogenic endothelium\|age:28 hpf 30 hpf\|cell isolation:FACS isolated cells\|tissue:haemogenic endothelium\|genotype/variation:non injected	RNA seq Wt DP R1hi rep1	Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value.	haemogenic endothelium	double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino	whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.	TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf.	age:28 hpf 30 hpf\|cell isolation:FACS isolated cells\|tissue:haemogenic endothelium\|genotype/variation:non injected	GSM3855049	GSM3855049: Wt DP R1hi rep1; Danio rerio; RNA Seq	GSM3855049		1	whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.	GEO Accession:GSM3855049	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP200560		WTCHG_236896_242_1_pair.fq.gz WTCHG_236896_242_2_pair.fq.gz	fastq fastq	2095674074.0	14243567.0	GSM3855049 r1	0:74.85 1:72.28	A:541444792;C:489580880;G:501484244;T:563130979;N:33179	74	72	541444792	489580880	501484244	563130979	33179	SRX5978257	SRS4884512	SRA894667	GEO	Oxford University	2	0.95275	0.80515	0.0503	0.0447	0.78827	0.81028	0.47691	0.47164	74	74	B	B	biological fallback assumption	illumina	hiseq_era	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United Kingdom	2019-06-05	Pharyngula	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");;