rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,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.spot_descriptor,experiment.study_ref,run.title,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.r3_length,run.r4_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,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse
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,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,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,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,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,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,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,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,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,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
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,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,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,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,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,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,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,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
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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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
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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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
52781,SRR9207184,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_236897_242_1_pair.fq.gz WTCHG_236897_242_2_pair.fq.gz,fastq fastq,2063492969.0,14026048.0,GSM3855049 r2,0:74.82 1:72.30,A:533045811;C:480334040;G:492421855;T:557653783;N:37480,74,72,,,533045811,480334040,492421855,557653783,37480,SRX5978257,SRS4884512,SRA894667,GEO,Oxford University,2,0.95243,0.79788,0.04971,0.04343,0.7878,0.81016,0.48035,0.46512,74,74,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
52782,SRR9207181,SRX5978256,SRS4884511,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 R1med rep3,GSM3855048,,source name:aortic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected,RNA seq Wt DP R1med 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.,aortic 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:aortic endothelium|genotype/variation:non injected,GSM3855048,GSM3855048: Wt DP R1med rep3; Danio rerio; RNA Seq,GSM3855048,,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:GSM3855048,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP200560,,,WTCHG_236896_265_1_pair.fq.gz WTCHG_236896_265_2_pair.fq.gz,fastq fastq,1745443128.0,11892304.0,GSM3855048 r1,0:74.86 1:71.91,A:453150216;C:403838492;G:414952890;T:473474634;N:26896,74,71,,,453150216,403838492,414952890,473474634,26896,SRX5978256,SRS4884511,SRA894667,GEO,Oxford University,2,0.95301,0.78351,0.0658,0.06097,0.78368,0.80941,0.47251,0.4445,75,74,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
52783,SRR9207182,SRX5978256,SRS4884511,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 R1med rep3,GSM3855048,,source name:aortic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected,RNA seq Wt DP R1med 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.,aortic 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:aortic endothelium|genotype/variation:non injected,GSM3855048,GSM3855048: Wt DP R1med rep3; Danio rerio; RNA Seq,GSM3855048,,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:GSM3855048,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP200560,,,WTCHG_236897_265_1_pair.fq.gz WTCHG_236897_265_2_pair.fq.gz,fastq fastq,1728817726.0,11782024.0,GSM3855048 r2,0:74.82 1:71.91,A:448845759;C:398200726;G:409703125;T:472037424;N:30692,74,71,,,448845759,398200726,409703125,472037424,30692,SRX5978256,SRS4884511,SRA894667,GEO,Oxford University,2,0.9518,0.77329,0.06602,0.05955,0.78423,0.81051,0.47776,0.46478,74,74,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
52784,SRR9207179,SRX5978255,SRS4884510,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 R1med rep2,GSM3855047,,source name:aortic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected,RNA seq Wt DP R1med 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.,aortic 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:aortic endothelium|genotype/variation:non injected,GSM3855047,GSM3855047: Wt DP R1med rep2; Danio rerio; RNA Seq,GSM3855047,,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:GSM3855047,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP200560,,,WTCHG_236896_250_1_pair.fq.gz WTCHG_236896_250_2_pair.fq.gz,fastq fastq,2096576707.0,14262609.0,GSM3855047 r1,0:74.87 1:72.13,A:536583711;C:491572815;G:509433296;T:558953949;N:32936,74,72,,,536583711,491572815,509433296,558953949,32936,SRX5978255,SRS4884510,SRA894667,GEO,Oxford University,2,0.95719,0.76406,0.04256,0.03937,0.7989,0.82856,0.40968,0.4591,75,74,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
52785,SRR9207180,SRX5978255,SRS4884510,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 R1med rep2,GSM3855047,,source name:aortic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected,RNA seq Wt DP R1med 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.,aortic 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:aortic endothelium|genotype/variation:non injected,GSM3855047,GSM3855047: Wt DP R1med rep2; Danio rerio; RNA Seq,GSM3855047,,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:GSM3855047,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP200560,,,WTCHG_236897_250_1_pair.fq.gz WTCHG_236897_250_2_pair.fq.gz,fastq fastq,2081468598.0,14169082.0,GSM3855047 r2,0:74.83 1:72.07,A:532025059;C:484883611;G:503099767;T:561423564;N:36597,74,72,,,532025059,484883611,503099767,561423564,36597,SRX5978255,SRS4884510,SRA894667,GEO,Oxford University,2,0.95742,0.74712,0.04275,0.03741,0.79922,0.82866,0.40398,0.46313,74,74,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
52786,SRR9207177,SRX5978254,SRS4884509,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 R1med rep1,GSM3855046,,source name:aortic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected,RNA seq Wt DP R1med 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.,aortic 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:aortic endothelium|genotype/variation:non injected,GSM3855046,GSM3855046: Wt DP R1med rep1; Danio rerio; RNA Seq,GSM3855046,,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:GSM3855046,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP200560,,,WTCHG_236896_243_1_pair.fq.gz WTCHG_236896_243_2_pair.fq.gz,fastq fastq,2011950216.0,13680917.0,GSM3855046 r1,0:74.86 1:72.20,A:511635564;C:476475475;G:489688294;T:534119393;N:31490,74,72,,,511635564,476475475,489688294,534119393,31490,SRX5978254,SRS4884509,SRA894667,GEO,Oxford University,2,0.9571,0.78471,0.03658,0.03396,0.80247,0.8268,0.48025,0.46265,74,74,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
52787,SRR9207178,SRX5978254,SRS4884509,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 R1med rep1,GSM3855046,,source name:aortic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected,RNA seq Wt DP R1med 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.,aortic 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:aortic endothelium|genotype/variation:non injected,GSM3855046,GSM3855046: Wt DP R1med rep1; Danio rerio; RNA Seq,GSM3855046,,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:GSM3855046,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP200560,,,WTCHG_236897_243_1_pair.fq.gz WTCHG_236897_243_2_pair.fq.gz,fastq fastq,1979368927.0,13461179.0,GSM3855046 r2,0:74.83 1:72.21,A:503539205;C:467446638;G:480794441;T:527553577;N:35066,74,72,,,503539205,467446638,480794441,527553577,35066,SRX5978254,SRS4884509,SRA894667,GEO,Oxford University,2,0.95558,0.78357,0.03711,0.03412,0.80318,0.82664,0.42185,0.46216,74,64,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
52788,SRR9207175,SRX5978253,SRS4884508,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 R1lo rep3,GSM3855045,,source name:aortic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected,RNA seq Wt DP R1lo 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.,aortic 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:aortic endothelium|genotype/variation:non injected,GSM3855045,GSM3855045: Wt DP R1lo rep3; Danio rerio; RNA Seq,GSM3855045,,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:GSM3855045,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP200560,,,WTCHG_236896_266_1_pair.fq.gz WTCHG_236896_266_2_pair.fq.gz,fastq fastq,2022090059.0,13752247.0,GSM3855045 r1,0:74.84 1:72.20,A:529671943;C:466470156;G:476864148;T:549051395;N:32417,74,72,,,529671943,466470156,476864148,549051395,32417,SRX5978253,SRS4884508,SRA894667,GEO,Oxford University,2,0.94638,0.80375,0.07924,0.06889,0.76098,0.78636,0.4888,0.46168,74,74,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
52789,SRR9207176,SRX5978253,SRS4884508,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 R1lo rep3,GSM3855045,,source name:aortic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected,RNA seq Wt DP R1lo 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.,aortic 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:aortic endothelium|genotype/variation:non injected,GSM3855045,GSM3855045: Wt DP R1lo rep3; Danio rerio; RNA Seq,GSM3855045,,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:GSM3855045,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP200560,,,WTCHG_236897_266_1_pair.fq.gz WTCHG_236897_266_2_pair.fq.gz,fastq fastq,1996491732.0,13581226.0,GSM3855045 r2,0:74.81 1:72.20,A:522970179;C:458424995;G:469211257;T:545848558;N:36743,74,72,,,522970179,458424995,469211257,545848558,36743,SRX5978253,SRS4884508,SRA894667,GEO,Oxford University,2,0.94571,0.7947,0.08062,0.06773,0.76116,0.78591,0.49549,0.46742,74,74,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
52790,SRR9207173,SRX5978252,SRS4884507,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 R1lo rep2,GSM3855044,,source name:aortic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected,RNA seq Wt DP R1lo 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.,aortic 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:aortic endothelium|genotype/variation:non injected,GSM3855044,GSM3855044: Wt DP R1lo rep2; Danio rerio; RNA Seq,GSM3855044,,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:GSM3855044,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP200560,,,WTCHG_236896_251_1_pair.fq.gz WTCHG_236896_251_2_pair.fq.gz,fastq fastq,2166575163.0,14709523.0,GSM3855044 r1,0:74.86 1:72.43,A:559933570;C:510454967;G:520888591;T:575264053;N:33982,74,72,,,559933570,510454967,520888591,575264053,33982,SRX5978252,SRS4884507,SRA894667,GEO,Oxford University,2,0.95094,0.8211,0.0594,0.05292,0.76664,0.79253,0.4795,0.4638,74,74,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
52791,SRR9207174,SRX5978252,SRS4884507,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 R1lo rep2,GSM3855044,,source name:aortic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected,RNA seq Wt DP R1lo 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.,aortic 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:aortic endothelium|genotype/variation:non injected,GSM3855044,GSM3855044: Wt DP R1lo rep2; Danio rerio; RNA Seq,GSM3855044,,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:GSM3855044,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP200560,,,WTCHG_236897_251_1_pair.fq.gz WTCHG_236897_251_2_pair.fq.gz,fastq fastq,2148630324.0,14593830.0,GSM3855044 r2,0:74.83 1:72.40,A:555362600;C:503529612;G:514542689;T:575156489;N:38934,74,72,,,555362600,503529612,514542689,575156489,38934,SRX5978252,SRS4884507,SRA894667,GEO,Oxford University,2,0.95053,0.81036,0.06102,0.05199,0.76897,0.79354,0.47523,0.46186,74,74,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
52792,SRR9207171,SRX5978251,SRS4884506,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 R1lo rep1,GSM3855043,,source name:aortic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected,RNA seq Wt DP R1lo 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.,aortic 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:aortic endothelium|genotype/variation:non injected,GSM3855043,GSM3855043: Wt DP R1lo rep1; Danio rerio; RNA Seq,GSM3855043,,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:GSM3855043,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP200560,,,WTCHG_236896_244_1_pair.fq.gz WTCHG_236896_244_2_pair.fq.gz,fastq fastq,1899807957.0,12921335.0,GSM3855043 r1,0:74.85 1:72.17,A:494455972;C:440267035;G:451386907;T:513668319;N:29724,74,72,,,494455972,440267035,451386907,513668319,29724,SRX5978251,SRS4884506,SRA894667,GEO,Oxford University,2,0.94888,0.79567,0.06354,0.05518,0.77041,0.79837,0.48973,0.47834,75,73,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
52793,SRR9207172,SRX5978251,SRS4884506,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 R1lo rep1,GSM3855043,,source name:aortic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected,RNA seq Wt DP R1lo 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.,aortic 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:aortic endothelium|genotype/variation:non injected,GSM3855043,GSM3855043: Wt DP R1lo rep1; Danio rerio; RNA Seq,GSM3855043,,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:GSM3855043,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP200560,,,WTCHG_236897_244_1_pair.fq.gz WTCHG_236897_244_2_pair.fq.gz,fastq fastq,1882109620.0,12807285.0,GSM3855043 r2,0:74.82 1:72.14,A:489932533;C:433346981;G:444869178;T:513927823;N:33105,74,72,,,489932533,433346981,444869178,513927823,33105,SRX5978251,SRS4884506,SRA894667,GEO,Oxford University,2,0.94837,0.78199,0.06553,0.05587,0.77068,0.79967,0.48984,0.47719,74,74,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
52800,SRR9207163,SRX5978247,SRS4884502,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 DN rep3,GSM3855039,,source name:non endothelial tissue|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:non injected,RNA seq Wt 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:non injected,GSM3855039,GSM3855039: Wt DN rep3; Danio rerio; RNA Seq,GSM3855039,,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:GSM3855039,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP200560,,,WTCHG_236896_267_1_pair.fq.gz WTCHG_236896_267_2_pair.fq.gz,fastq fastq,1812059909.0,12410104.0,GSM3855039 r1,0:74.81 1:71.21,A:491620609;C:383394578;G:398030819;T:538985491;N:28412,74,71,,,491620609,383394578,398030819,538985491,28412,SRX5978247,SRS4884502,SRA894667,GEO,Oxford University,2,0.93321,0.68178,0.15093,0.11867,0.75282,0.79468,0.51285,0.51101,75,74,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
52801,SRR9207164,SRX5978247,SRS4884502,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 DN rep3,GSM3855039,,source name:non endothelial tissue|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:non injected,RNA seq Wt 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:non injected,GSM3855039,GSM3855039: Wt DN rep3; Danio rerio; RNA Seq,GSM3855039,,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:GSM3855039,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP200560,,,WTCHG_236897_267_1_pair.fq.gz WTCHG_236897_267_2_pair.fq.gz,fastq fastq,1798726377.0,12321488.0,GSM3855039 r2,0:74.77 1:71.21,A:487870380;C:378213454;G:393167780;T:539442882;N:31881,74,71,,,487870380,378213454,393167780,539442882,31881,SRX5978247,SRS4884502,SRA894667,GEO,Oxford University,2,0.93183,0.67372,0.15009,0.11547,0.7555,0.79705,0.52465,0.50781,74,54,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
52802,SRR9207161,SRX5978246,SRS4884501,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 DN rep2,GSM3855038,,source name:non endothelial tissue|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:non injected,RNA seq Wt 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:non injected,GSM3855038,GSM3855038: Wt DN rep2; Danio rerio; RNA Seq,GSM3855038,,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:GSM3855038,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP200560,,,WTCHG_236896_252_1_pair.fq.gz WTCHG_236896_252_2_pair.fq.gz,fastq fastq,2146316233.0,14628161.0,GSM3855038 r1,0:74.84 1:71.88,A:566578244;C:489485503;G:504442873;T:585776104;N:33509,74,71,,,566578244,489485503,504442873,585776104,33509,SRX5978246,SRS4884501,SRA894667,GEO,Oxford University,2,0.94696,0.79752,0.10017,0.0872,0.74572,0.78165,0.50212,0.49488,74,74,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
52803,SRR9207162,SRX5978246,SRS4884501,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 DN rep2,GSM3855038,,source name:non endothelial tissue|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:non injected,RNA seq Wt 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:non injected,GSM3855038,GSM3855038: Wt DN rep2; Danio rerio; RNA Seq,GSM3855038,,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:GSM3855038,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP200560,,,WTCHG_236897_252_1_pair.fq.gz WTCHG_236897_252_2_pair.fq.gz,fastq fastq,2135407349.0,14569323.0,GSM3855038 r2,0:74.81 1:71.76,A:563322304;C:482982247;G:498831126;T:590234332;N:37340,74,71,,,563322304,482982247,498831126,590234332,37340,SRX5978246,SRS4884501,SRA894667,GEO,Oxford University,2,0.94623,0.77703,0.10192,0.08638,0.74582,0.78289,0.50539,0.48024,74,74,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
52804,SRR9207159,SRX5978245,SRS4884500,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 DN rep1,GSM3855037,,source name:non endothelial tissue|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:non injected,RNA seq Wt 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:non injected,GSM3855037,GSM3855037: Wt DN rep1; Danio rerio; RNA Seq,GSM3855037,,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:GSM3855037,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP200560,,,WTCHG_236896_245_2_pair.fq.gz WTCHG_236896_245_1_pair.fq.gz,fastq fastq,1719181139.0,11738270.0,GSM3855037 r1,0:74.81 1:71.65,A:459579950;C:379670678;G:392006300;T:487897820;N:26391,74,71,,,459579950,379670678,392006300,487897820,26391,SRX5978245,SRS4884500,SRA894667,GEO,Oxford University,2,0.93052,0.73058,0.11005,0.09187,0.7587,0.79375,0.50611,0.48538,75,73,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
52805,SRR9207160,SRX5978245,SRS4884500,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 DN rep1,GSM3855037,,source name:non endothelial tissue|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:non injected,RNA seq Wt 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:non injected,GSM3855037,GSM3855037: Wt DN rep1; Danio rerio; RNA Seq,GSM3855037,,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:GSM3855037,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP200560,,,WTCHG_236897_245_1_pair.fq.gz WTCHG_236897_245_2_pair.fq.gz,fastq fastq,1710103502.0,11683422.0,GSM3855037 r2,0:74.77 1:71.60,A:456758769;C:375069094;G:387904698;T:490340725;N:30216,74,71,,,456758769,375069094,387904698,490340725,30216,SRX5978245,SRS4884500,SRA894667,GEO,Oxford University,2,0.93089,0.71617,0.1094,0.08897,0.75879,0.79667,0.51735,0.49687,74,74,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
55747,SRR10753218,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read2_indexN707-S517=Aug1_Cell_49.fastq.gz run1696_lane2_read1_indexN707-S517=Aug1_Cell_49.fastq.gz,fastq fastq,283120950.0,1887473.0,GSM4230287 r1,0:75 1:75,A:78921390;C:62364350;G:62670695;T:79125765;N:38750,75,75,,,78921390,62364350,62670695,79125765,38750,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.90632,0.92036,0.16158,0.16744,0.93332,0.93389,0.4857,0.48751,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55748,SRR10753219,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read2_indexN709-S502=Aug1_Cell_58.fastq.gz run1696_lane2_read1_indexN709-S502=Aug1_Cell_58.fastq.gz,fastq fastq,245846550.0,1638977.0,GSM4230287 r10,0:75 1:75,A:67896939;C:54764431;G:55135813;T:68016031;N:33336,75,75,,,67896939,54764431,55135813,68016031,33336,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.90267,0.90773,0.18676,0.18997,0.92983,0.92971,0.49203,0.49454,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55749,SRR10753220,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read2_indexN710-S503=Aug1_Cell_59.fastq.gz run1696_lane2_read1_indexN710-S503=Aug1_Cell_59.fastq.gz,fastq fastq,254226450.0,1694843.0,GSM4230287 r11,0:75 1:75,A:72181308;C:54619189;G:54984718;T:72405980;N:35255,75,75,,,72181308,54619189,54984718,72405980,35255,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.89184,0.89943,0.33071,0.3348,0.90538,0.90514,0.54519,0.54232,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55750,SRR10753221,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN711-S504=Aug1_Cell_60.fastq.gz run1696_lane2_read2_indexN711-S504=Aug1_Cell_60.fastq.gz,fastq fastq,272723400.0,1818156.0,GSM4230287 r12,0:75 1:75,A:75891977;C:60178887;G:60639000;T:75975500;N:38036,75,75,,,75891977,60178887,60639000,75975500,38036,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.91617,0.92262,0.19662,0.20134,0.93072,0.9307,0.43264,0.43459,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55751,SRR10753222,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read2_indexN712-S505=Aug1_Cell_61.fastq.gz run1696_lane2_read1_indexN712-S505=Aug1_Cell_61.fastq.gz,fastq fastq,328643250.0,2190955.0,GSM4230287 r13,0:75 1:75,A:91428860;C:72391345;G:72874053;T:91904041;N:44951,75,75,,,91428860,72391345,72874053,91904041,44951,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.90728,0.91292,0.20245,0.20556,0.91701,0.91664,0.47925,0.47785,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55752,SRR10753223,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN701-S506=Aug1_Cell_62.fastq.gz run1696_lane2_read2_indexN701-S506=Aug1_Cell_62.fastq.gz,fastq fastq,393051600.0,2620344.0,GSM4230287 r14,0:75 1:75,A:107520133;C:88489033;G:89202131;T:107788164;N:52139,75,75,,,107520133,88489033,89202131,107788164,52139,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.91538,0.92003,0.14754,0.14967,0.89438,0.89572,0.48906,0.46829,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55753,SRR10753224,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN702-S507=Aug1_Cell_63.fastq.gz run1696_lane2_read2_indexN702-S507=Aug1_Cell_63.fastq.gz,fastq fastq,266633850.0,1777559.0,GSM4230287 r15,0:75 1:75,A:75310904;C:57522159;G:58016352;T:75748192;N:36243,75,75,,,75310904,57522159,58016352,75748192,36243,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.8963,0.91004,0.26603,0.27276,0.92064,0.91993,0.49301,0.49362,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55754,SRR10753225,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN703-S508=Aug1_Cell_64.fastq.gz run1696_lane2_read2_indexN703-S508=Aug1_Cell_64.fastq.gz,fastq fastq,320260050.0,2135067.0,GSM4230287 r16,0:75 1:75,A:88326766;C:70952312;G:71719762;T:89217755;N:43455,75,75,,,88326766,70952312,71719762,89217755,43455,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.90631,0.91303,0.17305,0.1758,0.91226,0.91194,0.4751,0.47508,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55755,SRR10753226,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read2_indexN709-S517=Aug1_Cell_65.fastq.gz run1696_lane2_read1_indexN709-S517=Aug1_Cell_65.fastq.gz,fastq fastq,237092850.0,1580619.0,GSM4230287 r17,0:75 1:75,A:65593919;C:52797142;G:53078356;T:65591887;N:31546,75,75,,,65593919,52797142,53078356,65591887,31546,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.9084,0.91253,0.16047,0.16296,0.91291,0.91232,0.47821,0.48265,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55756,SRR10753227,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN710-S502=Aug1_Cell_66.fastq.gz run1696_lane2_read2_indexN710-S502=Aug1_Cell_66.fastq.gz,fastq fastq,203466600.0,1356444.0,GSM4230287 r18,0:75 1:75,A:57338640;C:43614133;G:44244871;T:58241187;N:27769,75,75,,,57338640,43614133,44244871,58241187,27769,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.88694,0.89395,0.35775,0.36017,0.93371,0.93428,0.64977,0.64812,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55757,SRR10753228,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN711-S503=Aug1_Cell_67.fastq.gz run1696_lane2_read2_indexN711-S503=Aug1_Cell_67.fastq.gz,fastq fastq,382760100.0,2551734.0,GSM4230287 r19,0:75 1:75,A:104074844;C:86846190;G:87465046;T:104321801;N:52219,75,75,,,104074844,86846190,87465046,104321801,52219,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.92294,0.92788,0.14352,0.14599,0.91845,0.91782,0.48227,0.48103,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55758,SRR10753229,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN708-S502=Aug1_Cell_50.fastq.gz run1696_lane2_read2_indexN708-S502=Aug1_Cell_50.fastq.gz,fastq fastq,267098700.0,1780658.0,GSM4230287 r2,0:75 1:75,A:74382570;C:58775515;G:59120917;T:74783242;N:36456,75,75,,,74382570,58775515,59120917,74783242,36456,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.90724,0.91983,0.2402,0.24535,0.92547,0.92533,0.45641,0.4586,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55759,SRR10753230,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN712-S504=Aug1_Cell_68.fastq.gz run1696_lane2_read2_indexN712-S504=Aug1_Cell_68.fastq.gz,fastq fastq,318756750.0,2125045.0,GSM4230287 r20,0:75 1:75,A:87025537;C:72058246;G:72667582;T:86962614;N:42771,75,75,,,87025537,72058246,72667582,86962614,42771,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.91149,0.91879,0.14134,0.14484,0.9181,0.91839,0.48713,0.48686,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55760,SRR10753231,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN701-S505=Aug1_Cell_69.fastq.gz run1696_lane2_read2_indexN701-S505=Aug1_Cell_69.fastq.gz,fastq fastq,284858550.0,1899057.0,GSM4230287 r21,0:75 1:75,A:78978323;C:63093139;G:63404944;T:79343904;N:38240,75,75,,,78978323,63093139,63404944,79343904,38240,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.91426,0.92025,0.1863,0.18952,0.92855,0.92849,0.50311,0.50162,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55761,SRR10753232,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN702-S506=Aug1_Cell_70.fastq.gz run1696_lane2_read2_indexN702-S506=Aug1_Cell_70.fastq.gz,fastq fastq,284898300.0,1899322.0,GSM4230287 r22,0:75 1:75,A:78397302;C:63504322;G:64181815;T:78775032;N:39829,75,75,,,78397302,63504322,64181815,78775032,39829,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.90463,0.9098,0.13564,0.137,0.90382,0.90461,0.48397,0.4914,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55762,SRR10753233,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN703-S507=Aug1_Cell_71.fastq.gz run1696_lane2_read2_indexN703-S507=Aug1_Cell_71.fastq.gz,fastq fastq,320753850.0,2138359.0,GSM4230287 r23,0:75 1:75,A:88975252;C:70589715;G:71455216;T:89691991;N:41676,75,75,,,88975252,70589715,71455216,89691991,41676,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.87801,0.88372,0.22781,0.23132,0.9036,0.90408,0.47968,0.48892,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System