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
33669,SRR30530658,SRX25954305,SRS22536191,SRP530279,PRJNA1156090,Single cell transcriptome sequencing analysis of endothelial cells in control and high glucose treated zebrafish embryos,GSE276251,Transcriptome Analysis,Artificially sweetened beverages containing noncaloric monosaccharides were suggested as healthier alternatives to sugar sweetened beverages. Nevertheless  the potential detrimental effects of these noncaloric monosaccharides on blood vessel function remain inadequately understood. Presently  we have established a zebrafish model that exhibits significant excessive angiogenesis induced by high glucose. Utilizing this model  we observed that glucose and noncaloric monosaccharides could induce excessive formation of blood vessels  especially intersegmental vessels ISVs. The excessively branched vessels were observed to be formed by ectopic activation of quiescent endothelial cells ECs into tip cells. Single cell transcriptomic sequencing analysis of the endothelial cells in the embryos exposed to high glucose revealed an augmented ratio of capillary ECs  proliferating ECs  and a series of upregulated proangiogenic genes. Overall design: Firstly  we isolated the EGFP positive cells from control and high glucose treated Tgfli1ep:EGFP CAAX transgenic embryos. Following the proteolytic dissociation of embryos  the EGFP positive cells were isolated by fluorescence activated cell sorting FACS. Around 300500 zebrafish embryos were used for the ECs collection for each stage. The isolated ECs were analyzed using a large scale scRNA seq 10X Genomics platform.,,pubmed:39365738;pubmed:39882604,,endothelial cells，high glucose,GSM8494124,,tissue:endothelial cells|cell type:endothelial cells|geo loc name:missing|collection date:missing,endothelial cells，high glucose,Cell Ranger 3.0.2 https://github.com/10XGenomics/cellranger was used to convert the raw sequencing data to single cell level gene counts matrix. The clustering of single cells and the marker genes in each cluster were analyzed by Seurat 3.0 https://satijalab.org/seurat/install.html Assembly: The reference genome fasta format and gene annotation gtf format files were downloaded from Ensembl database release version 94. Supplementary files format and content: Tab separated values files and matrix files.,endothelial cells,Embryos were treated with 6% glucose from 24 hpf to 72 hpf.,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell 3’Reagent Kits v3 from 10X Genomics Company.,Tgkdrl:EGFP embryos were raised in E3 solution at 28.5℃ to the indicated developmental stage.,cell type:endothelial cells,GSM8494124,GSM8494124: endothelial cells，high glucose; Danio rerio; RNA Seq,GSM8494124 r1,GSM8494124,1,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell three primeReagent Kits v3 from 10X Genomics Company.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP530279,,,lr57glu96hpf_R1.fq.gz lr57glu96hpf_R2.fq.gz,fastq fastq,196891371600.0,656304572.0,GSM8494124 r1,0:150 1:150,A:46034913013;C:37262343828;G:60636104680;T:52955473756;N:2536323,150,150,,,46034913013,37262343828,60636104680,52955473756,2536323,SRX25954305,SRS22536191,SRA1961613,Nantong University,Nantong University,,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2024-09-03,Multi-stage,Multi-stage,Endothelium,Cardiovascular System
33670,SRR30530659,SRX25954304,SRS22536190,SRP530279,PRJNA1156090,Single cell transcriptome sequencing analysis of endothelial cells in control and high glucose treated zebrafish embryos,GSE276251,Transcriptome Analysis,Artificially sweetened beverages containing noncaloric monosaccharides were suggested as healthier alternatives to sugar sweetened beverages. Nevertheless  the potential detrimental effects of these noncaloric monosaccharides on blood vessel function remain inadequately understood. Presently  we have established a zebrafish model that exhibits significant excessive angiogenesis induced by high glucose. Utilizing this model  we observed that glucose and noncaloric monosaccharides could induce excessive formation of blood vessels  especially intersegmental vessels ISVs. The excessively branched vessels were observed to be formed by ectopic activation of quiescent endothelial cells ECs into tip cells. Single cell transcriptomic sequencing analysis of the endothelial cells in the embryos exposed to high glucose revealed an augmented ratio of capillary ECs  proliferating ECs  and a series of upregulated proangiogenic genes. Overall design: Firstly  we isolated the EGFP positive cells from control and high glucose treated Tgfli1ep:EGFP CAAX transgenic embryos. Following the proteolytic dissociation of embryos  the EGFP positive cells were isolated by fluorescence activated cell sorting FACS. Around 300500 zebrafish embryos were used for the ECs collection for each stage. The isolated ECs were analyzed using a large scale scRNA seq 10X Genomics platform.,,pubmed:39365738;pubmed:39882604,,endothelial cells，control,GSM8494123,,tissue:endothelial cells|cell type:endothelial cells|geo loc name:missing|collection date:missing,endothelial cells，control,Cell Ranger 3.0.2 https://github.com/10XGenomics/cellranger was used to convert the raw sequencing data to single cell level gene counts matrix. The clustering of single cells and the marker genes in each cluster were analyzed by Seurat 3.0 https://satijalab.org/seurat/install.html Assembly: The reference genome fasta format and gene annotation gtf format files were downloaded from Ensembl database release version 94. Supplementary files format and content: Tab separated values files and matrix files.,endothelial cells,Embryos were treated with 6% glucose from 24 hpf to 72 hpf.,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell 3’Reagent Kits v3 from 10X Genomics Company.,Tgkdrl:EGFP embryos were raised in E3 solution at 28.5℃ to the indicated developmental stage.,cell type:endothelial cells,GSM8494123,GSM8494123: endothelial cells，control; Danio rerio; RNA Seq,GSM8494123 r1,GSM8494123,1,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell three primeReagent Kits v3 from 10X Genomics Company.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP530279,,,SH190424C_LR5796dpf_1_1_R1.fq.gz SH190424C_LR5796dpf_1_1_R2.fq.gz,fastq fastq,18351420300.0,61171401.0,GSM8494123 r1,0:150 1:150,A:3872504772;C:3434009784;G:6583451920;T:4461384217;N:69607,150,150,,,3872504772,3434009784,6583451920,4461384217,69607,SRX25954304,SRS22536190,SRA1961613,Nantong University,Nantong University,,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2024-09-03,Multi-stage,Multi-stage,Endothelium,Cardiovascular System
33671,SRR30530660,SRX25954304,SRS22536190,SRP530279,PRJNA1156090,Single cell transcriptome sequencing analysis of endothelial cells in control and high glucose treated zebrafish embryos,GSE276251,Transcriptome Analysis,Artificially sweetened beverages containing noncaloric monosaccharides were suggested as healthier alternatives to sugar sweetened beverages. Nevertheless  the potential detrimental effects of these noncaloric monosaccharides on blood vessel function remain inadequately understood. Presently  we have established a zebrafish model that exhibits significant excessive angiogenesis induced by high glucose. Utilizing this model  we observed that glucose and noncaloric monosaccharides could induce excessive formation of blood vessels  especially intersegmental vessels ISVs. The excessively branched vessels were observed to be formed by ectopic activation of quiescent endothelial cells ECs into tip cells. Single cell transcriptomic sequencing analysis of the endothelial cells in the embryos exposed to high glucose revealed an augmented ratio of capillary ECs  proliferating ECs  and a series of upregulated proangiogenic genes. Overall design: Firstly  we isolated the EGFP positive cells from control and high glucose treated Tgfli1ep:EGFP CAAX transgenic embryos. Following the proteolytic dissociation of embryos  the EGFP positive cells were isolated by fluorescence activated cell sorting FACS. Around 300500 zebrafish embryos were used for the ECs collection for each stage. The isolated ECs were analyzed using a large scale scRNA seq 10X Genomics platform.,,pubmed:39365738;pubmed:39882604,,endothelial cells，control,GSM8494123,,tissue:endothelial cells|cell type:endothelial cells|geo loc name:missing|collection date:missing,endothelial cells，control,Cell Ranger 3.0.2 https://github.com/10XGenomics/cellranger was used to convert the raw sequencing data to single cell level gene counts matrix. The clustering of single cells and the marker genes in each cluster were analyzed by Seurat 3.0 https://satijalab.org/seurat/install.html Assembly: The reference genome fasta format and gene annotation gtf format files were downloaded from Ensembl database release version 94. Supplementary files format and content: Tab separated values files and matrix files.,endothelial cells,Embryos were treated with 6% glucose from 24 hpf to 72 hpf.,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell 3’Reagent Kits v3 from 10X Genomics Company.,Tgkdrl:EGFP embryos were raised in E3 solution at 28.5℃ to the indicated developmental stage.,cell type:endothelial cells,GSM8494123,GSM8494123: endothelial cells，control; Danio rerio; RNA Seq,GSM8494123 r1,GSM8494123,1,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell three primeReagent Kits v3 from 10X Genomics Company.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP530279,,,SH190424C_LR5796dpf_1_2_R1.fq.gz SH190424C_LR5796dpf_1_2_R2.fq.gz,fastq fastq,36386960400.0,121289868.0,GSM8494123 r2,0:150 1:150,A:8890006445;C:6974694151;G:10814990376;T:9707137150;N:132278,150,150,,,8890006445,6974694151,10814990376,9707137150,132278,SRX25954304,SRS22536190,SRA1961613,Nantong University,Nantong University,,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2024-09-03,Multi-stage,Multi-stage,Endothelium,Cardiovascular System
33672,SRR30530661,SRX25954304,SRS22536190,SRP530279,PRJNA1156090,Single cell transcriptome sequencing analysis of endothelial cells in control and high glucose treated zebrafish embryos,GSE276251,Transcriptome Analysis,Artificially sweetened beverages containing noncaloric monosaccharides were suggested as healthier alternatives to sugar sweetened beverages. Nevertheless  the potential detrimental effects of these noncaloric monosaccharides on blood vessel function remain inadequately understood. Presently  we have established a zebrafish model that exhibits significant excessive angiogenesis induced by high glucose. Utilizing this model  we observed that glucose and noncaloric monosaccharides could induce excessive formation of blood vessels  especially intersegmental vessels ISVs. The excessively branched vessels were observed to be formed by ectopic activation of quiescent endothelial cells ECs into tip cells. Single cell transcriptomic sequencing analysis of the endothelial cells in the embryos exposed to high glucose revealed an augmented ratio of capillary ECs  proliferating ECs  and a series of upregulated proangiogenic genes. Overall design: Firstly  we isolated the EGFP positive cells from control and high glucose treated Tgfli1ep:EGFP CAAX transgenic embryos. Following the proteolytic dissociation of embryos  the EGFP positive cells were isolated by fluorescence activated cell sorting FACS. Around 300500 zebrafish embryos were used for the ECs collection for each stage. The isolated ECs were analyzed using a large scale scRNA seq 10X Genomics platform.,,pubmed:39365738;pubmed:39882604,,endothelial cells，control,GSM8494123,,tissue:endothelial cells|cell type:endothelial cells|geo loc name:missing|collection date:missing,endothelial cells，control,Cell Ranger 3.0.2 https://github.com/10XGenomics/cellranger was used to convert the raw sequencing data to single cell level gene counts matrix. The clustering of single cells and the marker genes in each cluster were analyzed by Seurat 3.0 https://satijalab.org/seurat/install.html Assembly: The reference genome fasta format and gene annotation gtf format files were downloaded from Ensembl database release version 94. Supplementary files format and content: Tab separated values files and matrix files.,endothelial cells,Embryos were treated with 6% glucose from 24 hpf to 72 hpf.,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell 3’Reagent Kits v3 from 10X Genomics Company.,Tgkdrl:EGFP embryos were raised in E3 solution at 28.5℃ to the indicated developmental stage.,cell type:endothelial cells,GSM8494123,GSM8494123: endothelial cells，control; Danio rerio; RNA Seq,GSM8494123 r1,GSM8494123,1,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell three primeReagent Kits v3 from 10X Genomics Company.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP530279,,,SH190424C_LR5796dpf_2_1_R1.fq.gz SH190424C_LR5796dpf_2_1_R2.fq.gz,fastq fastq,44811813000.0,149372710.0,GSM8494123 r3,0:150 1:150,A:10939691275;C:8613307673;G:13332283843;T:11926366839;N:163370,150,150,,,10939691275,8613307673,13332283843,11926366839,163370,SRX25954304,SRS22536190,SRA1961613,Nantong University,Nantong University,,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2024-09-03,Multi-stage,Multi-stage,Endothelium,Cardiovascular System
33673,SRR30530662,SRX25954304,SRS22536190,SRP530279,PRJNA1156090,Single cell transcriptome sequencing analysis of endothelial cells in control and high glucose treated zebrafish embryos,GSE276251,Transcriptome Analysis,Artificially sweetened beverages containing noncaloric monosaccharides were suggested as healthier alternatives to sugar sweetened beverages. Nevertheless  the potential detrimental effects of these noncaloric monosaccharides on blood vessel function remain inadequately understood. Presently  we have established a zebrafish model that exhibits significant excessive angiogenesis induced by high glucose. Utilizing this model  we observed that glucose and noncaloric monosaccharides could induce excessive formation of blood vessels  especially intersegmental vessels ISVs. The excessively branched vessels were observed to be formed by ectopic activation of quiescent endothelial cells ECs into tip cells. Single cell transcriptomic sequencing analysis of the endothelial cells in the embryos exposed to high glucose revealed an augmented ratio of capillary ECs  proliferating ECs  and a series of upregulated proangiogenic genes. Overall design: Firstly  we isolated the EGFP positive cells from control and high glucose treated Tgfli1ep:EGFP CAAX transgenic embryos. Following the proteolytic dissociation of embryos  the EGFP positive cells were isolated by fluorescence activated cell sorting FACS. Around 300500 zebrafish embryos were used for the ECs collection for each stage. The isolated ECs were analyzed using a large scale scRNA seq 10X Genomics platform.,,pubmed:39365738;pubmed:39882604,,endothelial cells，control,GSM8494123,,tissue:endothelial cells|cell type:endothelial cells|geo loc name:missing|collection date:missing,endothelial cells，control,Cell Ranger 3.0.2 https://github.com/10XGenomics/cellranger was used to convert the raw sequencing data to single cell level gene counts matrix. The clustering of single cells and the marker genes in each cluster were analyzed by Seurat 3.0 https://satijalab.org/seurat/install.html Assembly: The reference genome fasta format and gene annotation gtf format files were downloaded from Ensembl database release version 94. Supplementary files format and content: Tab separated values files and matrix files.,endothelial cells,Embryos were treated with 6% glucose from 24 hpf to 72 hpf.,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell 3’Reagent Kits v3 from 10X Genomics Company.,Tgkdrl:EGFP embryos were raised in E3 solution at 28.5℃ to the indicated developmental stage.,cell type:endothelial cells,GSM8494123,GSM8494123: endothelial cells，control; Danio rerio; RNA Seq,GSM8494123 r1,GSM8494123,1,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell three primeReagent Kits v3 from 10X Genomics Company.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP530279,,,SH190424C_LR5796dpf_2_2_R1.fq.gz SH190424C_LR5796dpf_2_2_R2.fq.gz,fastq fastq,22587582300.0,75291941.0,GSM8494123 r4,0:150 1:150,A:4762937825;C:4235264474;G:8108549401;T:5480746863;N:83737,150,150,,,4762937825,4235264474,8108549401,5480746863,83737,SRX25954304,SRS22536190,SRA1961613,Nantong University,Nantong University,,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2024-09-03,Multi-stage,Multi-stage,Endothelium,Cardiovascular System
33674,SRR30530663,SRX25954304,SRS22536190,SRP530279,PRJNA1156090,Single cell transcriptome sequencing analysis of endothelial cells in control and high glucose treated zebrafish embryos,GSE276251,Transcriptome Analysis,Artificially sweetened beverages containing noncaloric monosaccharides were suggested as healthier alternatives to sugar sweetened beverages. Nevertheless  the potential detrimental effects of these noncaloric monosaccharides on blood vessel function remain inadequately understood. Presently  we have established a zebrafish model that exhibits significant excessive angiogenesis induced by high glucose. Utilizing this model  we observed that glucose and noncaloric monosaccharides could induce excessive formation of blood vessels  especially intersegmental vessels ISVs. The excessively branched vessels were observed to be formed by ectopic activation of quiescent endothelial cells ECs into tip cells. Single cell transcriptomic sequencing analysis of the endothelial cells in the embryos exposed to high glucose revealed an augmented ratio of capillary ECs  proliferating ECs  and a series of upregulated proangiogenic genes. Overall design: Firstly  we isolated the EGFP positive cells from control and high glucose treated Tgfli1ep:EGFP CAAX transgenic embryos. Following the proteolytic dissociation of embryos  the EGFP positive cells were isolated by fluorescence activated cell sorting FACS. Around 300500 zebrafish embryos were used for the ECs collection for each stage. The isolated ECs were analyzed using a large scale scRNA seq 10X Genomics platform.,,pubmed:39365738;pubmed:39882604,,endothelial cells，control,GSM8494123,,tissue:endothelial cells|cell type:endothelial cells|geo loc name:missing|collection date:missing,endothelial cells，control,Cell Ranger 3.0.2 https://github.com/10XGenomics/cellranger was used to convert the raw sequencing data to single cell level gene counts matrix. The clustering of single cells and the marker genes in each cluster were analyzed by Seurat 3.0 https://satijalab.org/seurat/install.html Assembly: The reference genome fasta format and gene annotation gtf format files were downloaded from Ensembl database release version 94. Supplementary files format and content: Tab separated values files and matrix files.,endothelial cells,Embryos were treated with 6% glucose from 24 hpf to 72 hpf.,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell 3’Reagent Kits v3 from 10X Genomics Company.,Tgkdrl:EGFP embryos were raised in E3 solution at 28.5℃ to the indicated developmental stage.,cell type:endothelial cells,GSM8494123,GSM8494123: endothelial cells，control; Danio rerio; RNA Seq,GSM8494123 r1,GSM8494123,1,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell three primeReagent Kits v3 from 10X Genomics Company.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP530279,,,SH190424C_LR5796dpf_3_1_R1.fq.gz SH190424C_LR5796dpf_3_1_R2.fq.gz,fastq fastq,31458502200.0,104861674.0,GSM8494123 r5,0:150 1:150,A:7597642424;C:6175910515;G:9377029875;T:8307805635;N:113751,150,150,,,7597642424,6175910515,9377029875,8307805635,113751,SRX25954304,SRS22536190,SRA1961613,Nantong University,Nantong University,,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2024-09-03,Multi-stage,Multi-stage,Endothelium,Cardiovascular System
33675,SRR30530664,SRX25954304,SRS22536190,SRP530279,PRJNA1156090,Single cell transcriptome sequencing analysis of endothelial cells in control and high glucose treated zebrafish embryos,GSE276251,Transcriptome Analysis,Artificially sweetened beverages containing noncaloric monosaccharides were suggested as healthier alternatives to sugar sweetened beverages. Nevertheless  the potential detrimental effects of these noncaloric monosaccharides on blood vessel function remain inadequately understood. Presently  we have established a zebrafish model that exhibits significant excessive angiogenesis induced by high glucose. Utilizing this model  we observed that glucose and noncaloric monosaccharides could induce excessive formation of blood vessels  especially intersegmental vessels ISVs. The excessively branched vessels were observed to be formed by ectopic activation of quiescent endothelial cells ECs into tip cells. Single cell transcriptomic sequencing analysis of the endothelial cells in the embryos exposed to high glucose revealed an augmented ratio of capillary ECs  proliferating ECs  and a series of upregulated proangiogenic genes. Overall design: Firstly  we isolated the EGFP positive cells from control and high glucose treated Tgfli1ep:EGFP CAAX transgenic embryos. Following the proteolytic dissociation of embryos  the EGFP positive cells were isolated by fluorescence activated cell sorting FACS. Around 300500 zebrafish embryos were used for the ECs collection for each stage. The isolated ECs were analyzed using a large scale scRNA seq 10X Genomics platform.,,pubmed:39365738;pubmed:39882604,,endothelial cells，control,GSM8494123,,tissue:endothelial cells|cell type:endothelial cells|geo loc name:missing|collection date:missing,endothelial cells，control,Cell Ranger 3.0.2 https://github.com/10XGenomics/cellranger was used to convert the raw sequencing data to single cell level gene counts matrix. The clustering of single cells and the marker genes in each cluster were analyzed by Seurat 3.0 https://satijalab.org/seurat/install.html Assembly: The reference genome fasta format and gene annotation gtf format files were downloaded from Ensembl database release version 94. Supplementary files format and content: Tab separated values files and matrix files.,endothelial cells,Embryos were treated with 6% glucose from 24 hpf to 72 hpf.,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell 3’Reagent Kits v3 from 10X Genomics Company.,Tgkdrl:EGFP embryos were raised in E3 solution at 28.5℃ to the indicated developmental stage.,cell type:endothelial cells,GSM8494123,GSM8494123: endothelial cells，control; Danio rerio; RNA Seq,GSM8494123 r1,GSM8494123,1,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell three primeReagent Kits v3 from 10X Genomics Company.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP530279,,,SH190424C_LR5796dpf_3_2_R1.fq.gz SH190424C_LR5796dpf_3_2_R2.fq.gz,fastq fastq,15812987400.0,52709958.0,GSM8494123 r6,0:150 1:150,A:3317721700;C:3009997461;G:5662825685;T:3822382737;N:59817,150,150,,,3317721700,3009997461,5662825685,3822382737,59817,SRX25954304,SRS22536190,SRA1961613,Nantong University,Nantong University,,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2024-09-03,Multi-stage,Multi-stage,Endothelium,Cardiovascular System
33676,SRR30530665,SRX25954304,SRS22536190,SRP530279,PRJNA1156090,Single cell transcriptome sequencing analysis of endothelial cells in control and high glucose treated zebrafish embryos,GSE276251,Transcriptome Analysis,Artificially sweetened beverages containing noncaloric monosaccharides were suggested as healthier alternatives to sugar sweetened beverages. Nevertheless  the potential detrimental effects of these noncaloric monosaccharides on blood vessel function remain inadequately understood. Presently  we have established a zebrafish model that exhibits significant excessive angiogenesis induced by high glucose. Utilizing this model  we observed that glucose and noncaloric monosaccharides could induce excessive formation of blood vessels  especially intersegmental vessels ISVs. The excessively branched vessels were observed to be formed by ectopic activation of quiescent endothelial cells ECs into tip cells. Single cell transcriptomic sequencing analysis of the endothelial cells in the embryos exposed to high glucose revealed an augmented ratio of capillary ECs  proliferating ECs  and a series of upregulated proangiogenic genes. Overall design: Firstly  we isolated the EGFP positive cells from control and high glucose treated Tgfli1ep:EGFP CAAX transgenic embryos. Following the proteolytic dissociation of embryos  the EGFP positive cells were isolated by fluorescence activated cell sorting FACS. Around 300500 zebrafish embryos were used for the ECs collection for each stage. The isolated ECs were analyzed using a large scale scRNA seq 10X Genomics platform.,,pubmed:39365738;pubmed:39882604,,endothelial cells，control,GSM8494123,,tissue:endothelial cells|cell type:endothelial cells|geo loc name:missing|collection date:missing,endothelial cells，control,Cell Ranger 3.0.2 https://github.com/10XGenomics/cellranger was used to convert the raw sequencing data to single cell level gene counts matrix. The clustering of single cells and the marker genes in each cluster were analyzed by Seurat 3.0 https://satijalab.org/seurat/install.html Assembly: The reference genome fasta format and gene annotation gtf format files were downloaded from Ensembl database release version 94. Supplementary files format and content: Tab separated values files and matrix files.,endothelial cells,Embryos were treated with 6% glucose from 24 hpf to 72 hpf.,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell 3’Reagent Kits v3 from 10X Genomics Company.,Tgkdrl:EGFP embryos were raised in E3 solution at 28.5℃ to the indicated developmental stage.,cell type:endothelial cells,GSM8494123,GSM8494123: endothelial cells，control; Danio rerio; RNA Seq,GSM8494123 r1,GSM8494123,1,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell three primeReagent Kits v3 from 10X Genomics Company.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP530279,,,SH190424C_LR5796dpf_4_1_R1.fq.gz SH190424C_LR5796dpf_4_1_R2.fq.gz,fastq fastq,19472976900.0,64909923.0,GSM8494123 r7,0:150 1:150,A:4109297307;C:3636046624;G:6996008921;T:4731548865;N:75183,150,150,,,4109297307,3636046624,6996008921,4731548865,75183,SRX25954304,SRS22536190,SRA1961613,Nantong University,Nantong University,,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2024-09-03,Multi-stage,Multi-stage,Endothelium,Cardiovascular System
33677,SRR30530666,SRX25954304,SRS22536190,SRP530279,PRJNA1156090,Single cell transcriptome sequencing analysis of endothelial cells in control and high glucose treated zebrafish embryos,GSE276251,Transcriptome Analysis,Artificially sweetened beverages containing noncaloric monosaccharides were suggested as healthier alternatives to sugar sweetened beverages. Nevertheless  the potential detrimental effects of these noncaloric monosaccharides on blood vessel function remain inadequately understood. Presently  we have established a zebrafish model that exhibits significant excessive angiogenesis induced by high glucose. Utilizing this model  we observed that glucose and noncaloric monosaccharides could induce excessive formation of blood vessels  especially intersegmental vessels ISVs. The excessively branched vessels were observed to be formed by ectopic activation of quiescent endothelial cells ECs into tip cells. Single cell transcriptomic sequencing analysis of the endothelial cells in the embryos exposed to high glucose revealed an augmented ratio of capillary ECs  proliferating ECs  and a series of upregulated proangiogenic genes. Overall design: Firstly  we isolated the EGFP positive cells from control and high glucose treated Tgfli1ep:EGFP CAAX transgenic embryos. Following the proteolytic dissociation of embryos  the EGFP positive cells were isolated by fluorescence activated cell sorting FACS. Around 300500 zebrafish embryos were used for the ECs collection for each stage. The isolated ECs were analyzed using a large scale scRNA seq 10X Genomics platform.,,pubmed:39365738;pubmed:39882604,,endothelial cells，control,GSM8494123,,tissue:endothelial cells|cell type:endothelial cells|geo loc name:missing|collection date:missing,endothelial cells，control,Cell Ranger 3.0.2 https://github.com/10XGenomics/cellranger was used to convert the raw sequencing data to single cell level gene counts matrix. The clustering of single cells and the marker genes in each cluster were analyzed by Seurat 3.0 https://satijalab.org/seurat/install.html Assembly: The reference genome fasta format and gene annotation gtf format files were downloaded from Ensembl database release version 94. Supplementary files format and content: Tab separated values files and matrix files.,endothelial cells,Embryos were treated with 6% glucose from 24 hpf to 72 hpf.,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell 3’Reagent Kits v3 from 10X Genomics Company.,Tgkdrl:EGFP embryos were raised in E3 solution at 28.5℃ to the indicated developmental stage.,cell type:endothelial cells,GSM8494123,GSM8494123: endothelial cells，control; Danio rerio; RNA Seq,GSM8494123 r1,GSM8494123,1,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell three primeReagent Kits v3 from 10X Genomics Company.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP530279,,,SH190424C_LR5796dpf_4_2_R1.fq.gz SH190424C_LR5796dpf_4_2_R2.fq.gz,fastq fastq,39005746200.0,130019154.0,GSM8494123 r8,0:150 1:150,A:9542890616;C:7456459618;G:11598648802;T:10407604379;N:142785,150,150,,,9542890616,7456459618,11598648802,10407604379,142785,SRX25954304,SRS22536190,SRA1961613,Nantong University,Nantong University,,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2024-09-03,Multi-stage,Multi-stage,Endothelium,Cardiovascular System
38364,SRR1793802,SRX869237,SRS840014,SRP053359,PRJNA274951,Lymphatic vessels arise from a niche of multipotent angioblasts within the floor of the cardinal vein,GSE65751,Transcriptome Analysis,How cells acquire their fate is a fundamental question in both developmental and regenerative biology. Multipotent progenitors undergo gradual cell fate restriction in response to temporal and positional cues from the microenvironment  the nature of which is far from being clear. In the case of the lymphatic system  venous endothelial cells are thought to give rise to lymphatic vessels  through a process of trans differentiation. Upon expression of a set of transcription factors  venous cells acquire a lymphatic fate  and bud out to generate the lymphatic vasculature. In this work we challenge this view and show that while lymphatic endothelial cells LECs do arise in the Cardinal Vein CV  they do so from a previously uncharacterized pool of multipotent angioblasts. Using lymphatic specific transgenic zebrafish  in combination with endothelial photoconvertible reporters  and long term live imaging  we demonstrate that these multipotent angioblasts can generate not only lymphatic  but also arterious  and venous fates. We further reveal that the underlying endoderm serves as a source of Wnt5b  which acts as a lymphatic inductive signal  promoting the angioblast to lymphatic transition. Moreover  Wnt5b induced lymphatic specification in human embryonic stem cells  derived vascular progenitors  suggesting that this process is evolutionary conserved. Our results uncover a novel mechanism of lymphatic vessel formation  whereby multipotent angioblasts and not venous endothelial cells give rise to the lymphatic endothelium  and provide the first characterization of their inductive niche. More broadly  our findings highlight the CV as a plastic and heterogeneous structure containing different cell populations  analogous to the hematopoietic niche in the aortic floor. Overall design: Following Kaede photoconversion of dorsal or ventral halves of the PCV in Tgfli1:gal4;uasKaede embryos at 24 hpf  6 embryos per group were used for FACS isolation of Kaede photconverted red ECs.,,pubmed:25992545,,d red ZF sample 0012,GSM1604058,,tissue:Dorsal endothelial cells|strain:Tgfli1:gal4; uasKaede|developmental stage:24hpf,d red ZF sample 0012,Libraries were sequenced on the Illumina HiSeq2500 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 20. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et al. 2012 demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations. Reads with the same unique molecular identifiers UMIs were colapsed for transcript counting. Genome build: Zv9 Supplementary files format and content: Tabular expression matrix includes number of transcript molecules.,Dorsal endothelial cells,,RNA was isolated using TRIzol with addition of ERCC spike ins and GenElute LPA Sigma The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL Seq multiplexing barocdes with slite modification were used. Each CEL Seq primer cointained a barcode and a unique moleculare identifier Teemu  et al. 2011,The vPCV vs dPCV endothelial cells were analyzed at 24hpf,strain:Tgfli1:gal4;uasKaede|developmental stage:24hpf,GSM1604058,GSM1604058: d red ZF sample 0012; Danio rerio; RNA Seq,GSM1604058,,1,RNA was isolated using TRIzol with addition of ERCC spike ins and GenElute LPA Sigma The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL Seq multiplexing barocdes with slite modification were used. Each CEL Seq primer cointained a barcode and a unique moleculare identifier Teemu  et al. 2011,GEO Accession:GSM1604058,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP053359,,,d_red_ZF_sample_0012.fastq.gz,fastq,136949295.0,3912837.0,GSM1604058 r1,0:35,A:38967686;C:29235653;G:29781723;T:38764742;N:199491,35,,,,38967686,29235653,29781723,38764742,199491,SRX869237,SRS840014,SRA236924,GEO,"Itai Yanai, Biology, Technion - Israel Institute of Technology",1,0.50546,,0.22201,,0.91524,,0.49457,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2015-02-09,Pharyngula,Embryo,Endothelium,Cardiovascular System
38365,SRR1793801,SRX869236,SRS840015,SRP053359,PRJNA274951,Lymphatic vessels arise from a niche of multipotent angioblasts within the floor of the cardinal vein,GSE65751,Transcriptome Analysis,How cells acquire their fate is a fundamental question in both developmental and regenerative biology. Multipotent progenitors undergo gradual cell fate restriction in response to temporal and positional cues from the microenvironment  the nature of which is far from being clear. In the case of the lymphatic system  venous endothelial cells are thought to give rise to lymphatic vessels  through a process of trans differentiation. Upon expression of a set of transcription factors  venous cells acquire a lymphatic fate  and bud out to generate the lymphatic vasculature. In this work we challenge this view and show that while lymphatic endothelial cells LECs do arise in the Cardinal Vein CV  they do so from a previously uncharacterized pool of multipotent angioblasts. Using lymphatic specific transgenic zebrafish  in combination with endothelial photoconvertible reporters  and long term live imaging  we demonstrate that these multipotent angioblasts can generate not only lymphatic  but also arterious  and venous fates. We further reveal that the underlying endoderm serves as a source of Wnt5b  which acts as a lymphatic inductive signal  promoting the angioblast to lymphatic transition. Moreover  Wnt5b induced lymphatic specification in human embryonic stem cells  derived vascular progenitors  suggesting that this process is evolutionary conserved. Our results uncover a novel mechanism of lymphatic vessel formation  whereby multipotent angioblasts and not venous endothelial cells give rise to the lymphatic endothelium  and provide the first characterization of their inductive niche. More broadly  our findings highlight the CV as a plastic and heterogeneous structure containing different cell populations  analogous to the hematopoietic niche in the aortic floor. Overall design: Following Kaede photoconversion of dorsal or ventral halves of the PCV in Tgfli1:gal4;uasKaede embryos at 24 hpf  6 embryos per group were used for FACS isolation of Kaede photconverted red ECs.,,pubmed:25992545,,d red ZF sample 0008,GSM1604057,,tissue:Dorsal endothelial cells|strain:Tgfli1:gal4; uasKaede|developmental stage:24hpf,d red ZF sample 0008,Libraries were sequenced on the Illumina HiSeq2500 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 20. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et al. 2012 demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations. Reads with the same unique molecular identifiers UMIs were colapsed for transcript counting. Genome build: Zv9 Supplementary files format and content: Tabular expression matrix includes number of transcript molecules.,Dorsal endothelial cells,,RNA was isolated using TRIzol with addition of ERCC spike ins and GenElute LPA Sigma The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL Seq multiplexing barocdes with slite modification were used. Each CEL Seq primer cointained a barcode and a unique moleculare identifier Teemu  et al. 2011,The vPCV vs dPCV endothelial cells were analyzed at 24hpf,strain:Tgfli1:gal4;uasKaede|developmental stage:24hpf,GSM1604057,GSM1604057: d red ZF sample 0008; Danio rerio; RNA Seq,GSM1604057,,1,RNA was isolated using TRIzol with addition of ERCC spike ins and GenElute LPA Sigma The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL Seq multiplexing barocdes with slite modification were used. Each CEL Seq primer cointained a barcode and a unique moleculare identifier Teemu  et al. 2011,GEO Accession:GSM1604057,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP053359,,,d_red_ZF_sample_0008.fastq.gz,fastq,230204380.0,6577268.0,GSM1604057 r1,0:35,A:63286154;C:49924891;G:50948035;T:65703538;N:341762,35,,,,63286154,49924891,50948035,65703538,341762,SRX869236,SRS840015,SRA236924,GEO,"Itai Yanai, Biology, Technion - Israel Institute of Technology",1,0.59898,,0.14092,,0.89073,,0.49292,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2015-02-09,Pharyngula,Embryo,Endothelium,Cardiovascular System
38366,SRR1793800,SRX869235,SRS840013,SRP053359,PRJNA274951,Lymphatic vessels arise from a niche of multipotent angioblasts within the floor of the cardinal vein,GSE65751,Transcriptome Analysis,How cells acquire their fate is a fundamental question in both developmental and regenerative biology. Multipotent progenitors undergo gradual cell fate restriction in response to temporal and positional cues from the microenvironment  the nature of which is far from being clear. In the case of the lymphatic system  venous endothelial cells are thought to give rise to lymphatic vessels  through a process of trans differentiation. Upon expression of a set of transcription factors  venous cells acquire a lymphatic fate  and bud out to generate the lymphatic vasculature. In this work we challenge this view and show that while lymphatic endothelial cells LECs do arise in the Cardinal Vein CV  they do so from a previously uncharacterized pool of multipotent angioblasts. Using lymphatic specific transgenic zebrafish  in combination with endothelial photoconvertible reporters  and long term live imaging  we demonstrate that these multipotent angioblasts can generate not only lymphatic  but also arterious  and venous fates. We further reveal that the underlying endoderm serves as a source of Wnt5b  which acts as a lymphatic inductive signal  promoting the angioblast to lymphatic transition. Moreover  Wnt5b induced lymphatic specification in human embryonic stem cells  derived vascular progenitors  suggesting that this process is evolutionary conserved. Our results uncover a novel mechanism of lymphatic vessel formation  whereby multipotent angioblasts and not venous endothelial cells give rise to the lymphatic endothelium  and provide the first characterization of their inductive niche. More broadly  our findings highlight the CV as a plastic and heterogeneous structure containing different cell populations  analogous to the hematopoietic niche in the aortic floor. Overall design: Following Kaede photoconversion of dorsal or ventral halves of the PCV in Tgfli1:gal4;uasKaede embryos at 24 hpf  6 embryos per group were used for FACS isolation of Kaede photconverted red ECs.,,pubmed:25992545,,V red ZF sample 0011,GSM1604056,,tissue:Ventral endothelial cells|strain:Tgfli1:gal4; uasKaede|developmental stage:24hpf,V red ZF sample 0011,Libraries were sequenced on the Illumina HiSeq2500 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 20. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et al. 2012 demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations. Reads with the same unique molecular identifiers UMIs were colapsed for transcript counting. Genome build: Zv9 Supplementary files format and content: Tabular expression matrix includes number of transcript molecules.,Ventral endothelial cells,,RNA was isolated using TRIzol with addition of ERCC spike ins and GenElute LPA Sigma The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL Seq multiplexing barocdes with slite modification were used. Each CEL Seq primer cointained a barcode and a unique moleculare identifier Teemu  et al. 2011,The vPCV vs dPCV endothelial cells were analyzed at 24hpf,strain:Tgfli1:gal4;uasKaede|developmental stage:24hpf,GSM1604056,GSM1604056: V red ZF sample 0011; Danio rerio; RNA Seq,GSM1604056,,1,RNA was isolated using TRIzol with addition of ERCC spike ins and GenElute LPA Sigma The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL Seq multiplexing barocdes with slite modification were used. Each CEL Seq primer cointained a barcode and a unique moleculare identifier Teemu  et al. 2011,GEO Accession:GSM1604056,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP053359,,,V_red_ZF_sample_0011.fastq.gz,fastq,146319705.0,4180563.0,GSM1604056 r1,0:35,A:40991954;C:30892087;G:32112709;T:42103782;N:219173,35,,,,40991954,30892087,32112709,42103782,219173,SRX869235,SRS840013,SRA236924,GEO,"Itai Yanai, Biology, Technion - Israel Institute of Technology",1,0.57038,,0.16086,,0.89014,,0.53016,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2015-02-09,Pharyngula,Embryo,Endothelium,Cardiovascular System
38367,SRR1793799,SRX869234,SRS840016,SRP053359,PRJNA274951,Lymphatic vessels arise from a niche of multipotent angioblasts within the floor of the cardinal vein,GSE65751,Transcriptome Analysis,How cells acquire their fate is a fundamental question in both developmental and regenerative biology. Multipotent progenitors undergo gradual cell fate restriction in response to temporal and positional cues from the microenvironment  the nature of which is far from being clear. In the case of the lymphatic system  venous endothelial cells are thought to give rise to lymphatic vessels  through a process of trans differentiation. Upon expression of a set of transcription factors  venous cells acquire a lymphatic fate  and bud out to generate the lymphatic vasculature. In this work we challenge this view and show that while lymphatic endothelial cells LECs do arise in the Cardinal Vein CV  they do so from a previously uncharacterized pool of multipotent angioblasts. Using lymphatic specific transgenic zebrafish  in combination with endothelial photoconvertible reporters  and long term live imaging  we demonstrate that these multipotent angioblasts can generate not only lymphatic  but also arterious  and venous fates. We further reveal that the underlying endoderm serves as a source of Wnt5b  which acts as a lymphatic inductive signal  promoting the angioblast to lymphatic transition. Moreover  Wnt5b induced lymphatic specification in human embryonic stem cells  derived vascular progenitors  suggesting that this process is evolutionary conserved. Our results uncover a novel mechanism of lymphatic vessel formation  whereby multipotent angioblasts and not venous endothelial cells give rise to the lymphatic endothelium  and provide the first characterization of their inductive niche. More broadly  our findings highlight the CV as a plastic and heterogeneous structure containing different cell populations  analogous to the hematopoietic niche in the aortic floor. Overall design: Following Kaede photoconversion of dorsal or ventral halves of the PCV in Tgfli1:gal4;uasKaede embryos at 24 hpf  6 embryos per group were used for FACS isolation of Kaede photconverted red ECs.,,pubmed:25992545,,V red ZF sample 0007,GSM1604055,,tissue:Ventral endothelial cells|strain:Tgfli1:gal4; uasKaede|developmental stage:24hpf,V red ZF sample 0007,Libraries were sequenced on the Illumina HiSeq2500 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 20. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et al. 2012 demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations. Reads with the same unique molecular identifiers UMIs were colapsed for transcript counting. Genome build: Zv9 Supplementary files format and content: Tabular expression matrix includes number of transcript molecules.,Ventral endothelial cells,,RNA was isolated using TRIzol with addition of ERCC spike ins and GenElute LPA Sigma The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL Seq multiplexing barocdes with slite modification were used. Each CEL Seq primer cointained a barcode and a unique moleculare identifier Teemu  et al. 2011,The vPCV vs dPCV endothelial cells were analyzed at 24hpf,strain:Tgfli1:gal4;uasKaede|developmental stage:24hpf,GSM1604055,GSM1604055: V red ZF sample 0007; Danio rerio; RNA Seq,GSM1604055,,1,RNA was isolated using TRIzol with addition of ERCC spike ins and GenElute LPA Sigma The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL Seq multiplexing barocdes with slite modification were used. Each CEL Seq primer cointained a barcode and a unique moleculare identifier Teemu  et al. 2011,GEO Accession:GSM1604055,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP053359,,,V_red_ZF_sample_0007.fastq.gz,fastq,219537045.0,6272487.0,GSM1604055 r1,0:35,A:61562432;C:46586451;G:48274564;T:62792331;N:321267,35,,,,61562432,46586451,48274564,62792331,321267,SRX869234,SRS840016,SRA236924,GEO,"Itai Yanai, Biology, Technion - Israel Institute of Technology",1,0.57949,,0.1659,,0.88187,,0.51446,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2015-02-09,Pharyngula,Embryo,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
40972,SRR3498294,SRX1756840,SRS1433371,SRP074848,PRJNA321321,microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues,GSE81340,Transcriptome Analysis,Proper functioning of tissues requires cells to behave in uniform  well organized ways. Conversely  many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here  we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably  lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate,parent bioproject:PRJNA321317,pubmed:28350988;pubmed:33273096,,NoEndo 72hpf E2,GSM2150819,,source name:Endothelial cell|developmental stage:72hpf|tissue:Endothelial|stain:GFP,NoEndo 72hpf E2,Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software  Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...,Endothelial cell,,Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols,Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473.,developmental stage:72hpf|tissue:Endothelial|stain:GFP,GSM2150819,GSM2150819: NoEndo 72hpf E2; Danio rerio; miRNA Seq,GSM2150819,,1,Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM2150819,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer,,SRP074848,,,NoEndo_72hpf_E2.fastq.gz,fastq,797509876.0,10493551.0,GSM2150819 r1,0:76,A:182564842;C:199547592;G:199064466;T:216287390;N:45586,76,,,,182564842,199547592,199064466,216287390,45586,SRX1756840,SRS1433371,SRA424808,GEO,"Internal Medicine, Yale University",1,1e-05,,0.0,,1.0,,,,76,,T,,under 1.2% mapping rate,illumina,early_illumina,unknown,size_fractionation,trueseq,bulk,unknown,unknown,,United States,2016-05-11,Larval,Larval,Endothelium,Cardiovascular System
40973,SRR3498293,SRX1756839,SRS1433370,SRP074848,PRJNA321321,microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues,GSE81340,Transcriptome Analysis,Proper functioning of tissues requires cells to behave in uniform  well organized ways. Conversely  many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here  we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably  lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate,parent bioproject:PRJNA321317,pubmed:28350988;pubmed:33273096,,NoEndo 72hpf E1,GSM2150818,,source name:Endothelial cell|developmental stage:72hpf|tissue:Endothelial|stain:GFP,NoEndo 72hpf E1,Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software  Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...,Endothelial cell,,Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols,Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473.,developmental stage:72hpf|tissue:Endothelial|stain:GFP,GSM2150818,GSM2150818: NoEndo 72hpf E1; Danio rerio; miRNA Seq,GSM2150818,,1,Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM2150818,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer,,SRP074848,,,NoEndo_72hpf_E1.fastq.gz,fastq,1864172232.0,24528582.0,GSM2150818 r1,0:76,A:426671762;C:469538477;G:458132395;T:509711525;N:118073,76,,,,426671762,469538477,458132395,509711525,118073,SRX1756839,SRS1433370,SRA424808,GEO,"Internal Medicine, Yale University",1,0.0,,0.0,,1.0,,,,76,,T,,under 1.2% mapping rate,illumina,early_illumina,unknown,size_fractionation,trueseq,bulk,unknown,unknown,,United States,2016-05-11,Larval,Larval,Endothelium,Cardiovascular System
40974,SRR3498292,SRX1756838,SRS1433369,SRP074848,PRJNA321321,microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues,GSE81340,Transcriptome Analysis,Proper functioning of tissues requires cells to behave in uniform  well organized ways. Conversely  many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here  we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably  lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate,parent bioproject:PRJNA321317,pubmed:28350988;pubmed:33273096,,NoEndo 6dpf E1,GSM2150817,,source name:Endothelial cell|developmental stage:6dpf|tissue:Endothelial|stain:GFP,NoEndo 6dpf E1,Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software  Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...,Endothelial cell,,Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols,Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473.,developmental stage:6dpf|tissue:Endothelial|stain:GFP,GSM2150817,GSM2150817: NoEndo 6dpf E1; Danio rerio; miRNA Seq,GSM2150817,,1,Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM2150817,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer,,SRP074848,,,NoEndo_6dpf_E1.fastq.gz,fastq,1414849364.0,18616439.0,GSM2150817 r1,0:76,A:315250036;C:366906308;G:364673112;T:367938758;N:81150,76,,,,315250036,366906308,364673112,367938758,81150,SRX1756838,SRS1433369,SRA424808,GEO,"Internal Medicine, Yale University",1,1e-05,,0.0,,1.0,,,,76,,T,,under 1.2% mapping rate,illumina,early_illumina,unknown,size_fractionation,trueseq,bulk,unknown,unknown,,United States,2016-05-11,Larval,Larval,Endothelium,Cardiovascular System
40975,SRR3498291,SRX1756837,SRS1433368,SRP074848,PRJNA321321,microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues,GSE81340,Transcriptome Analysis,Proper functioning of tissues requires cells to behave in uniform  well organized ways. Conversely  many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here  we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably  lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate,parent bioproject:PRJNA321317,pubmed:28350988;pubmed:33273096,,NoEndo 48hpf E2,GSM2150816,,source name:Endothelial cell|developmental stage:48hpf|tissue:Endothelial|stain:GFP,NoEndo 48hpf E2,Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software  Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...,Endothelial cell,,Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols,Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473.,developmental stage:48hpf|tissue:Endothelial|stain:GFP,GSM2150816,GSM2150816: NoEndo 48hpf E2; Danio rerio; miRNA Seq,GSM2150816,,1,Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM2150816,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer,,SRP074848,,,NoEndo_48hpf_E2.fastq.gz,fastq,553364740.0,7281115.0,GSM2150816 r1,0:76,A:129173344;C:134804122;G:141026546;T:148331467;N:29261,76,,,,129173344,134804122,141026546,148331467,29261,SRX1756837,SRS1433368,SRA424808,GEO,"Internal Medicine, Yale University",1,1e-05,,0.0,,0.99997,,0.0,,76,,T,,under 1.2% mapping rate,illumina,early_illumina,unknown,size_fractionation,trueseq,bulk,unknown,unknown,,United States,2016-05-11,Hatching,Embryo,Endothelium,Cardiovascular System
40976,SRR3498290,SRX1756836,SRS1433367,SRP074848,PRJNA321321,microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues,GSE81340,Transcriptome Analysis,Proper functioning of tissues requires cells to behave in uniform  well organized ways. Conversely  many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here  we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably  lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate,parent bioproject:PRJNA321317,pubmed:28350988;pubmed:33273096,,NoEndo 48hpf E1,GSM2150815,,source name:Endothelial cell|developmental stage:48hpf|tissue:Endothelial|stain:GFP,NoEndo 48hpf E1,Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software  Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...,Endothelial cell,,Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols,Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473.,developmental stage:48hpf|tissue:Endothelial|stain:GFP,GSM2150815,GSM2150815: NoEndo 48hpf E1; Danio rerio; miRNA Seq,GSM2150815,,1,Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM2150815,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer,,SRP074848,,,NoEndo_48hpf_E1.fastq.gz,fastq,1204752152.0,15852002.0,GSM2150815 r1,0:76,A:297517299;C:293969730;G:317491224;T:295696492;N:77407,76,,,,297517299,293969730,317491224,295696492,77407,SRX1756836,SRS1433367,SRA424808,GEO,"Internal Medicine, Yale University",1,0.0,,0.0,,1.0,,,,76,,T,,under 1.2% mapping rate,illumina,early_illumina,unknown,size_fractionation,trueseq,bulk,unknown,unknown,,United States,2016-05-11,Hatching,Embryo,Endothelium,Cardiovascular System
40977,SRR3498289,SRX1756835,SRS1433366,SRP074848,PRJNA321321,microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues,GSE81340,Transcriptome Analysis,Proper functioning of tissues requires cells to behave in uniform  well organized ways. Conversely  many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here  we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably  lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate,parent bioproject:PRJNA321317,pubmed:28350988;pubmed:33273096,,NoEndo 24hpf E1,GSM2150814,,source name:Endothelial cell|developmental stage:24hpf|tissue:Endothelial|stain:GFP,NoEndo 24hpf E1,Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software  Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...,Endothelial cell,,Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols,Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473.,developmental stage:24hpf|tissue:Endothelial|stain:GFP,GSM2150814,GSM2150814: NoEndo 24hpf E1; Danio rerio; miRNA Seq,GSM2150814,,1,Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM2150814,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer,,SRP074848,,,NoEndo_24hpf_E1.fastq.gz,fastq,1422085704.0,18711654.0,GSM2150814 r1,0:76,A:347700492;C:356065333;G:376424133;T:341806001;N:89745,76,,,,347700492,356065333,376424133,341806001,89745,SRX1756835,SRS1433366,SRA424808,GEO,"Internal Medicine, Yale University",1,0.0,,0.0,,1.0,,,,76,,T,,under 1.2% mapping rate,illumina,early_illumina,unknown,size_fractionation,trueseq,bulk,unknown,unknown,,United States,2016-05-11,Pharyngula,Embryo,Endothelium,Cardiovascular System
40978,SRR3498288,SRX1756834,SRS1433365,SRP074848,PRJNA321321,microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues,GSE81340,Transcriptome Analysis,Proper functioning of tissues requires cells to behave in uniform  well organized ways. Conversely  many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here  we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably  lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate,parent bioproject:PRJNA321317,pubmed:28350988;pubmed:33273096,,Endo 72hpf E2,GSM2150813,,source name:Endothelial cell|developmental stage:72hpf|tissue:Endothelial|stain:GFP,Endo 72hpf E2,Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software  Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...,Endothelial cell,,Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols,Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473.,developmental stage:72hpf|tissue:Endothelial|stain:GFP,GSM2150813,GSM2150813: Endo 72hpf E2; Danio rerio; miRNA Seq,GSM2150813,,1,Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM2150813,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer,,SRP074848,,,Endo_72hpf_E2.fastq.gz,fastq,438128980.0,5764855.0,GSM2150813 r1,0:76,A:101851745;C:114159902;G:115733669;T:106360221;N:23443,76,,,,101851745,114159902,115733669,106360221,23443,SRX1756834,SRS1433365,SRA424808,GEO,"Internal Medicine, Yale University",1,2e-05,,1e-05,,1.0,,,,76,,T,,under 1.2% mapping rate,illumina,early_illumina,unknown,size_fractionation,trueseq,bulk,unknown,unknown,,United States,2016-05-11,Larval,Larval,Endothelium,Cardiovascular System
40979,SRR3498287,SRX1756833,SRS1433364,SRP074848,PRJNA321321,microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues,GSE81340,Transcriptome Analysis,Proper functioning of tissues requires cells to behave in uniform  well organized ways. Conversely  many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here  we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably  lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate,parent bioproject:PRJNA321317,pubmed:28350988;pubmed:33273096,,Endo 72hpf E1,GSM2150812,,source name:Endothelial cell|developmental stage:72hpf|tissue:Endothelial|stain:GFP,Endo 72hpf E1,Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software  Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...,Endothelial cell,,Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols,Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473.,developmental stage:72hpf|tissue:Endothelial|stain:GFP,GSM2150812,GSM2150812: Endo 72hpf E1; Danio rerio; miRNA Seq,GSM2150812,,1,Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM2150812,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer,,SRP074848,,,Endo_72hpf_E1.fastq.gz,fastq,1267915068.0,16683093.0,GSM2150812 r1,0:76,A:321606522;C:310505837;G:323829249;T:311892892;N:80568,76,,,,321606522,310505837,323829249,311892892,80568,SRX1756833,SRS1433364,SRA424808,GEO,"Internal Medicine, Yale University",1,0.0,,0.0,,1.0,,,,76,,T,,under 1.2% mapping rate,illumina,early_illumina,unknown,size_fractionation,trueseq,bulk,unknown,unknown,,United States,2016-05-11,Larval,Larval,Endothelium,Cardiovascular System
40980,SRR3498286,SRX1756832,SRS1433363,SRP074848,PRJNA321321,microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues,GSE81340,Transcriptome Analysis,Proper functioning of tissues requires cells to behave in uniform  well organized ways. Conversely  many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here  we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably  lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate,parent bioproject:PRJNA321317,pubmed:28350988;pubmed:33273096,,Endo 6dpf E1,GSM2150811,,source name:Endothelial cell|developmental stage:6dpf|tissue:Endothelial|stain:GFP,Endo 6dpf E1,Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software  Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...,Endothelial cell,,Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols,Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473.,developmental stage:6dpf|tissue:Endothelial|stain:GFP,GSM2150811,GSM2150811: Endo 6dpf E1; Danio rerio; miRNA Seq,GSM2150811,,1,Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM2150811,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer,,SRP074848,,,Endo_6dpf_E1.fastq.gz,fastq,890474824.0,11716774.0,GSM2150811 r1,0:76,A:230419087;C:212029155;G:232306960;T:215672618;N:47004,76,,,,230419087,212029155,232306960,215672618,47004,SRX1756832,SRS1433363,SRA424808,GEO,"Internal Medicine, Yale University",1,2e-05,,1e-05,,1.0,,,,76,,T,,under 1.2% mapping rate,illumina,early_illumina,unknown,size_fractionation,trueseq,bulk,unknown,unknown,,United States,2016-05-11,Larval,Larval,Endothelium,Cardiovascular System
40981,SRR3498285,SRX1756831,SRS1433362,SRP074848,PRJNA321321,microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues,GSE81340,Transcriptome Analysis,Proper functioning of tissues requires cells to behave in uniform  well organized ways. Conversely  many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here  we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably  lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate,parent bioproject:PRJNA321317,pubmed:28350988;pubmed:33273096,,Endo 48hpf E2,GSM2150810,,source name:Endothelial cell|developmental stage:48hpf|tissue:Endothelial|stain:GFP,Endo 48hpf E2,Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software  Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...,Endothelial cell,,Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols,Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473.,developmental stage:48hpf|tissue:Endothelial|stain:GFP,GSM2150810,GSM2150810: Endo 48hpf E2; Danio rerio; miRNA Seq,GSM2150810,,1,Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM2150810,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer,,SRP074848,,,Endo_48hpf_E2.fastq.gz,fastq,1254556624.0,16507324.0,GSM2150810 r1,0:76,A:316229540;C:323340793;G:307552357;T:307354555;N:79379,76,,,,316229540,323340793,307552357,307354555,79379,SRX1756831,SRS1433362,SRA424808,GEO,"Internal Medicine, Yale University",1,0.0,,0.0,,1.0,,,,76,,T,,under 1.2% mapping rate,illumina,early_illumina,unknown,size_fractionation,trueseq,bulk,unknown,unknown,,United States,2016-05-11,Hatching,Embryo,Endothelium,Cardiovascular System
40982,SRR3498284,SRX1756830,SRS1433361,SRP074848,PRJNA321321,microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues,GSE81340,Transcriptome Analysis,Proper functioning of tissues requires cells to behave in uniform  well organized ways. Conversely  many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here  we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably  lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate,parent bioproject:PRJNA321317,pubmed:28350988;pubmed:33273096,,Endo 48hpf E1,GSM2150809,,source name:Endothelial cell|developmental stage:48hpf|tissue:Endothelial|stain:GFP,Endo 48hpf E1,Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software  Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...,Endothelial cell,,Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols,Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473.,developmental stage:48hpf|tissue:Endothelial|stain:GFP,GSM2150809,GSM2150809: Endo 48hpf E1; Danio rerio; miRNA Seq,GSM2150809,,1,Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM2150809,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer,,SRP074848,,,Endo_48hpf_E1.fastq.gz,fastq,1449497080.0,19072330.0,GSM2150809 r1,0:76,A:362564557;C:370330864;G:364749441;T:351760774;N:91444,76,,,,362564557,370330864,364749441,351760774,91444,SRX1756830,SRS1433361,SRA424808,GEO,"Internal Medicine, Yale University",1,0.0,,0.0,,1.0,,,,76,,T,,under 1.2% mapping rate,illumina,early_illumina,unknown,size_fractionation,trueseq,bulk,unknown,unknown,,United States,2016-05-11,Hatching,Embryo,Endothelium,Cardiovascular System
40983,SRR3498283,SRX1756829,SRS1433360,SRP074848,PRJNA321321,microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues,GSE81340,Transcriptome Analysis,Proper functioning of tissues requires cells to behave in uniform  well organized ways. Conversely  many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here  we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably  lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate,parent bioproject:PRJNA321317,pubmed:28350988;pubmed:33273096,,Endo 24hpf E1,GSM2150808,,source name:Endothelial cell|developmental stage:24hpf|tissue:Endothelial|stain:GFP,Endo 24hpf E1,Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software  Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...,Endothelial cell,,Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols,Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473.,developmental stage:24hpf|tissue:Endothelial|stain:GFP,GSM2150808,GSM2150808: Endo 24hpf E1; Danio rerio; miRNA Seq,GSM2150808,,1,Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM2150808,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer,,SRP074848,,,Endo_24hpf_E1.fastq.gz,fastq,1527500440.0,20098690.0,GSM2150808 r1,0:76,A:356712587;C:354608109;G:432977038;T:383106520;N:96186,76,,,,356712587,354608109,432977038,383106520,96186,SRX1756829,SRS1433360,SRA424808,GEO,"Internal Medicine, Yale University",1,0.0,,0.0,,1.0,,,,76,,T,,under 1.2% mapping rate,illumina,early_illumina,unknown,size_fractionation,trueseq,bulk,unknown,unknown,,United States,2016-05-11,Pharyngula,Embryo,Endothelium,Cardiovascular System
41146,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
41827,SRR5251446,SRX2557171,SRS1974564,SRP099466,PRJNA374579,microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos,PRJNA374579,Other,Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.,,,,QuantSeq mutant miRNAs   WT miR139 B1,nicoli mutmir AG01645,,strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|molecule:mRNA|condition:miR 139|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,QuantSeq mutant miRNAs   WT miR139 B1,AG01645.1,AG01645.1,1,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP099466,,,AG01645.1_R1.fastq.gz,fastq,1574284140.0,20714265.0,AG01645.1 R1.fastq.gz,0:76,A:485471345;C:270854124;G:374164721;T:443766613;N:27337,76,,,,485471345,270854124,374164721,443766613,27337,SRX2557171,SRS1974564,SRA537606,Yale University|Genetics,Yale University,1,0.82142,,0.14068,,0.8002,,0.5444,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,lexogen,bulk,unknown,unknown,,United States,2017-03-27,Undetermined,Embryo,Endothelium,Cardiovascular System
41828,SRR5251445,SRX2557170,SRS1974563,SRP099466,PRJNA374579,microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos,PRJNA374579,Other,Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.,,,,QuantSeq mutant miRNAs   WT miR139 B2,nicoli mutmir AG01646,,strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|molecule:mRNA|condition:miR 139|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,QuantSeq mutant miRNAs   WT miR139 B2,AG01646.1,AG01646.1,1,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP099466,,,AG01646.1_R1.fastq.gz,fastq,1484740104.0,19536054.0,AG01646.1 R1.fastq.gz,0:76,A:453388316;C:246477203;G:365031959;T:419816346;N:26280,76,,,,453388316,246477203,365031959,419816346,26280,SRX2557170,SRS1974563,SRA537606,Yale University|Genetics,Yale University,1,0.82649,,0.1897,,0.79862,,0.52759,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,lexogen,bulk,unknown,unknown,,United States,2017-03-28,Undetermined,Embryo,Endothelium,Cardiovascular System
41829,SRR5251444,SRX2557169,SRS1974562,SRP099466,PRJNA374579,microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos,PRJNA374579,Other,Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.,,,,QuantSeq mutant miRNAs   WT miR139 B3,nicoli mutmir AG01647,,strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|molecule:mRNA|condition:miR 139|replicate:3|BioSampleModel:Model organism or animal,,,,,,,,,QuantSeq mutant miRNAs   WT miR139 B3,AG01647.1,AG01647.1,1,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP099466,,,AG01647.1_R1.fastq.gz,fastq,881298660.0,11596035.0,AG01647.1 R1.fastq.gz,0:76,A:270675838;C:160127586;G:228157662;T:222301246;N:36328,76,,,,270675838,160127586,228157662,222301246,36328,SRX2557169,SRS1974562,SRA537606,Yale University|Genetics,Yale University,1,0.76133,,0.15034,,0.83341,,0.56596,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,lexogen,bulk,unknown,unknown,,United States,2017-03-28,Undetermined,Embryo,Endothelium,Cardiovascular System
41830,SRR5251443,SRX2557168,SRS1974561,SRP099466,PRJNA374579,microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos,PRJNA374579,Other,Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.,,,,QuantSeq mutant miRNAs   Mut miR139 B1,nicoli mutmir AG01648,,strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|genotype:miR 139 ya302/ya302|molecule:mRNA|condition:miR 139|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,QuantSeq mutant miRNAs   Mut miR139 B1,AG01648.1,AG01648.1,1,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP099466,,,AG01648.1_R1.fastq.gz,fastq,637896880.0,8393380.0,AG01648.1 R1.fastq.gz,0:76,A:192829278;C:112701153;G:153321271;T:179019095;N:26083,76,,,,192829278,112701153,153321271,179019095,26083,SRX2557168,SRS1974561,SRA537606,Yale University|Genetics,Yale University,1,0.75971,,0.1181,,0.82171,,0.56797,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,lexogen,bulk,unknown,unknown,,United States,2017-03-28,Undetermined,Embryo,Endothelium,Cardiovascular System
41831,SRR5251442,SRX2557167,SRS1974560,SRP099466,PRJNA374579,microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos,PRJNA374579,Other,Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.,,,,QuantSeq mutant miRNAs   Mut miR139 B2,nicoli mutmir AG01649,,strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|genotype:miR 139 ya302/ya302|molecule:mRNA|condition:miR 139|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,QuantSeq mutant miRNAs   Mut miR139 B2,AG01649.1,AG01649.1,1,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP099466,,,AG01649.1_R1.fastq.gz,fastq,849868328.0,11182478.0,AG01649.1 R1.fastq.gz,0:76,A:258225905;C:148467172;G:205165181;T:237974100;N:35970,76,,,,258225905,148467172,205165181,237974100,35970,SRX2557167,SRS1974560,SRA537606,Yale University|Genetics,Yale University,1,0.75096,,0.14506,,0.81507,,0.5545,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,lexogen,bulk,unknown,unknown,,United States,2017-03-28,Undetermined,Embryo,Endothelium,Cardiovascular System
41832,SRR5251441,SRX2557166,SRS1974559,SRP099466,PRJNA374579,microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos,PRJNA374579,Other,Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.,,,,QuantSeq mutant miRNAs   Mut miR139 B3,nicoli mutmir AG01650,,strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|genotype:miR 139 ya302/ya302|molecule:mRNA|condition:miR 139|replicate:3|BioSampleModel:Model organism or animal,,,,,,,,,QuantSeq mutant miRNAs   Mut miR139 B3,AG01650.1,AG01650.1,1,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP099466,,,AG01650.1_R1.fastq.gz,fastq,998464668.0,13137693.0,AG01650.1 R1.fastq.gz,0:76,A:311526420;C:176545041;G:251852786;T:258497630;N:42791,76,,,,311526420,176545041,251852786,258497630,42791,SRX2557166,SRS1974559,SRA537606,Yale University|Genetics,Yale University,1,0.76479,,0.11192,,0.82674,,0.54621,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,lexogen,bulk,unknown,unknown,,United States,2017-03-28,Undetermined,Embryo,Endothelium,Cardiovascular System
41833,SRR5251440,SRX2557165,SRS1974558,SRP099466,PRJNA374579,microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos,PRJNA374579,Other,Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.,,,,QuantSeq mutant miRNAs   WT miR24 B1,nicoli mutmir AG01651,,strain:TU/AB|age:51.0|sex:pooled male and female|tissue:endothelial cells|molecule:mRNA|condition:miR 24|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,QuantSeq mutant miRNAs   WT miR24 B1,AG01651.1,AG01651.1,1,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP099466,,,AG01651.1_R1.fastq.gz,fastq,570492252.0,7506477.0,AG01651.1 R1.fastq.gz,0:76,A:162512811;C:104071716;G:135730697;T:168149427;N:27601,76,,,,162512811,104071716,135730697,168149427,27601,SRX2557165,SRS1974558,SRA537606,Yale University|Genetics,Yale University,1,0.73988,,0.10157,,0.86647,,0.54252,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,lexogen,bulk,unknown,unknown,,United States,2017-03-28,Undetermined,Embryo,Endothelium,Cardiovascular System
41834,SRR5251439,SRX2557164,SRS1974557,SRP099466,PRJNA374579,microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos,PRJNA374579,Other,Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.,,,,QuantSeq mutant miRNAs   WT miR24 B2,nicoli mutmir AG01652,,strain:TU/AB|age:51.0|sex:pooled male and female|tissue:endothelial cells|molecule:mRNA|condition:miR 24|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,QuantSeq mutant miRNAs   WT miR24 B2,AG01652.1,AG01652.1,1,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP099466,,,AG01652.1_R1.fastq.gz,fastq,1072886148.0,14116923.0,AG01652.1 R1.fastq.gz,0:76,A:338399596;C:192703439;G:242960887;T:298769761;N:52465,76,,,,338399596,192703439,242960887,298769761,52465,SRX2557164,SRS1974557,SRA537606,Yale University|Genetics,Yale University,1,0.76456,,0.11024,,0.89197,,0.59214,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,lexogen,bulk,unknown,unknown,,United States,2017-03-28,Undetermined,Embryo,Endothelium,Cardiovascular System
41835,SRR5251438,SRX2557163,SRS1974556,SRP099466,PRJNA374579,microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos,PRJNA374579,Other,Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.,,,,QuantSeq mutant miRNAs   WT miR24 B3,nicoli mutmir AG01653,,strain:TU/AB|age:51.0|sex:pooled male and female|tissue:endothelial cells|molecule:mRNA|condition:miR 24|replicate:3|BioSampleModel:Model organism or animal,,,,,,,,,QuantSeq mutant miRNAs   WT miR24 B3,AG01653.1,AG01653.1,1,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP099466,,,AG01653.1_R1.fastq.gz,fastq,1016374144.0,13373344.0,AG01653.1 R1.fastq.gz,0:76,A:310958343;C:168702106;G:223420046;T:313241363;N:52286,76,,,,310958343,168702106,223420046,313241363,52286,SRX2557163,SRS1974556,SRA537606,Yale University|Genetics,Yale University,1,0.75735,,0.12224,,0.79756,,0.55136,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,lexogen,bulk,unknown,unknown,,United States,2017-02-13,Undetermined,Embryo,Endothelium,Cardiovascular System
41836,SRR5251437,SRX2557162,SRS1974555,SRP099466,PRJNA374579,microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos,PRJNA374579,Other,Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.,,,,QuantSeq mutant miRNAs   Mut miR24 B1,nicoli mutmir AG01654,,strain:TU/AB|age:51.0|sex:pooled male and female|tissue:endothelial cells|genotype:miR 24 ya324/? ya325/? ya326/? ya327/?|molecule:mRNA|condition:miR 24|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,QuantSeq mutant miRNAs   Mut miR24 B1,AG01654.1,AG01654.1,1,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP099466,,,AG01654.1_R1.fastq.gz,fastq,782170112.0,10291712.0,AG01654.1 R1.fastq.gz,0:76,A:238316720;C:132163709;G:179301544;T:232350598;N:37541,76,,,,238316720,132163709,179301544,232350598,37541,SRX2557162,SRS1974555,SRA537606,Yale University|Genetics,Yale University,1,0.7683,,0.10712,,0.80034,,0.55804,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,lexogen,bulk,unknown,unknown,,United States,2017-03-28,Undetermined,Embryo,Endothelium,Cardiovascular System
41837,SRR5251436,SRX2557161,SRS1974554,SRP099466,PRJNA374579,microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos,PRJNA374579,Other,Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.,,,,QuantSeq mutant miRNAs   Mut miR24 B2,nicoli mutmir AG01655,,strain:TU/AB|age:51.0|sex:pooled male and female|tissue:endothelial cells|genotype:miR 24 ya324/? ya325/? ya326/? ya327/?|molecule:mRNA|condition:miR 24|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,QuantSeq mutant miRNAs   Mut miR24 B2,AG01655.1,AG01655.1,1,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP099466,,,AG01655.1_R1.fastq.gz,fastq,1053946340.0,13867715.0,AG01655.1 R1.fastq.gz,0:76,A:318351311;C:191163031;G:240348413;T:304030367;N:53218,76,,,,318351311,191163031,240348413,304030367,53218,SRX2557161,SRS1974554,SRA537606,Yale University|Genetics,Yale University,1,0.77588,,0.07983,,0.83934,,0.56228,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,lexogen,bulk,unknown,unknown,,United States,2017-03-28,Undetermined,Embryo,Endothelium,Cardiovascular System
41838,SRR5251435,SRX2557160,SRS1974553,SRP099466,PRJNA374579,microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos,PRJNA374579,Other,Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.,,,,QuantSeq mutant miRNAs   Mut miR24 B3,nicoli mutmir AG01656,,strain:TU/AB|age:51.0|sex:pooled male and female|tissue:endothelial cells|genotype:miR 24 ya324/? ya325/? ya326/? ya327/?|molecule:mRNA|condition:miR 24|replicate:3|BioSampleModel:Model organism or animal,,,,,,,,,QuantSeq mutant miRNAs   Mut miR24 B3,AG01656.1,AG01656.1,1,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP099466,,,AG01656.1_R1.fastq.gz,fastq,1182467736.0,15558786.0,AG01656.1 R1.fastq.gz,0:76,A:344465226;C:204677242;G:269228338;T:364036735;N:60195,76,,,,344465226,204677242,269228338,364036735,60195,SRX2557160,SRS1974553,SRA537606,Yale University|Genetics,Yale University,1,0.78956,,0.13495,,0.81517,,0.56342,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,lexogen,bulk,unknown,unknown,,United States,2017-02-13,Undetermined,Embryo,Endothelium,Cardiovascular System
41839,SRR5251434,SRX2557159,SRS1974552,SRP099466,PRJNA374579,microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos,PRJNA374579,Other,Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.,,,,QuantSeq mutant miRNAs   WT miR223 B1,nicoli mutmir AG01657,,strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|molecule:mRNA|condition:miR 223|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,QuantSeq mutant miRNAs   WT miR223 B1,AG01657.1,AG01657.1,1,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP099466,,,AG01657.1_R1.fastq.gz,fastq,536336712.0,7057062.0,AG01657.1 R1.fastq.gz,0:76,A:158301607;C:93070120;G:121382262;T:163555487;N:27236,76,,,,158301607,93070120,121382262,163555487,27236,SRX2557159,SRS1974552,SRA537606,Yale University|Genetics,Yale University,1,0.76425,,0.1278,,0.84222,,0.55305,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,lexogen,bulk,unknown,unknown,,United States,2017-02-13,Undetermined,Embryo,Endothelium,Cardiovascular System
41840,SRR5251433,SRX2557158,SRS1974551,SRP099466,PRJNA374579,microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos,PRJNA374579,Other,Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.,,,,QuantSeq mutant miRNAs   WT miR223 B2,nicoli mutmir AG01658,,strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|molecule:mRNA|condition:miR 223|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,QuantSeq mutant miRNAs   WT miR223 B2,AG01658.1,AG01658.1,1,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP099466,,,AG01658.1_R1.fastq.gz,fastq,798581856.0,10507656.0,AG01658.1 R1.fastq.gz,0:76,A:241352089;C:134327379;G:183394123;T:239469845;N:38420,76,,,,241352089,134327379,183394123,239469845,38420,SRX2557158,SRS1974551,SRA537606,Yale University|Genetics,Yale University,1,0.76221,,0.13398,,0.82459,,0.55228,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,lexogen,bulk,unknown,unknown,,United States,2017-03-28,Undetermined,Embryo,Endothelium,Cardiovascular System
41841,SRR5251432,SRX2557157,SRS1974550,SRP099466,PRJNA374579,microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos,PRJNA374579,Other,Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.,,,,QuantSeq mutant miRNAs   WT miR223 B3,nicoli mutmir AG01659,,strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|molecule:mRNA|condition:miR 223|replicate:3|BioSampleModel:Model organism or animal,,,,,,,,,QuantSeq mutant miRNAs   WT miR223 B3,AG01659.1,AG01659.1,1,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP099466,,,AG01659.1_R1.fastq.gz,fastq,1093998948.0,14394723.0,AG01659.1 R1.fastq.gz,0:76,A:330741822;C:186325335;G:249557623;T:327320449;N:53719,76,,,,330741822,186325335,249557623,327320449,53719,SRX2557157,SRS1974550,SRA537606,Yale University|Genetics,Yale University,1,0.77108,,0.14674,,0.80955,,0.55819,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,lexogen,bulk,unknown,unknown,,United States,2017-03-28,Undetermined,Embryo,Endothelium,Cardiovascular System
41842,SRR5251431,SRX2557156,SRS1974549,SRP099466,PRJNA374579,microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos,PRJNA374579,Other,Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.,,,,QuantSeq mutant miRNAs   Mut miR223 B1,nicoli mutmir AG01660,,strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|genotype:miR 223 ya304/ya304|molecule:mRNA|condition:miR 223|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,QuantSeq mutant miRNAs   Mut miR223 B1,AG01660.1,AG01660.1,1,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP099466,,,AG01660.1_R1.fastq.gz,fastq,849905492.0,11182967.0,AG01660.1 R1.fastq.gz,0:76,A:250953875;C:146191904;G:190040699;T:262674911;N:44103,76,,,,250953875,146191904,190040699,262674911,44103,SRX2557156,SRS1974549,SRA537606,Yale University|Genetics,Yale University,1,0.7687,,0.14192,,0.82842,,0.5344,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,lexogen,bulk,unknown,unknown,,United States,2017-02-13,Undetermined,Embryo,Endothelium,Cardiovascular System
41843,SRR5251430,SRX2557155,SRS1974548,SRP099466,PRJNA374579,microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos,PRJNA374579,Other,Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.,,,,QuantSeq mutant miRNAs   Mut miR223 B2,nicoli mutmir AG01661,,strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|genotype:miR 223 ya304/ya304|molecule:mRNA|condition:miR 223|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,QuantSeq mutant miRNAs   Mut miR223 B2,AG01661.1,AG01661.1,1,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP099466,,,AG01661.1_R1.fastq.gz,fastq,840115400.0,11054150.0,AG01661.1 R1.fastq.gz,0:76,A:257057495;C:141775085;G:188281166;T:252960590;N:41064,76,,,,257057495,141775085,188281166,252960590,41064,SRX2557155,SRS1974548,SRA537606,Yale University|Genetics,Yale University,1,0.74292,,0.10759,,0.83615,,0.55136,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,lexogen,bulk,unknown,unknown,,United States,2017-03-28,Undetermined,Embryo,Endothelium,Cardiovascular System
42141,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
49040,SRR7633494,SRX4497225,SRS3618225,SRP155992,PRJNA483985,Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA,GSE118000,Transcriptome Analysis,We injected zebrafish embryos with human APOL1 mRNA  dissociated embryos at xxx days of age  and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting  mRNA was extracted from purified cells and used to generate cDNA libraries  which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham  APOL1 G0  APOL1 G2,,pubmed:31158233,,G2 endo 03,GSM3317066,,tissue:zebrafish endothelium|line:fli:EGFP|treatment:human APOL1 G2 mRNA,G2 endo 03,Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered  sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2,zebrafish endothelium,Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL  or phenol red,RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech,Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf,line:fli:EGFP|treatment:human APOL1 G2 mRNA,GSM3317066,GSM3317066: G2 endo 03; Danio rerio; RNA Seq,GSM3317066,,1,RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech,GEO Accession:GSM3317066,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP155992,,,BA_S18_trimmed.fastq.gz,fastq,950344310.0,18847513.0,GSM3317066 r1,0:50.42 1:0,A:270135652;C:209210468;G:202674675;T:268256430;N:67085,50,0,,,270135652,209210468,202674675,268256430,67085,SRX4497225,SRS3618225,SRA749599,GEO,"Duke Molecular Physiology Institute, Duke University Medical Center",1,0.89759,,0.1428,,0.69132,,0.4729,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2018-08-01,Larval,Larval,Endothelium,Cardiovascular System
49041,SRR7633493,SRX4497224,SRS3618224,SRP155992,PRJNA483985,Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA,GSE118000,Transcriptome Analysis,We injected zebrafish embryos with human APOL1 mRNA  dissociated embryos at xxx days of age  and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting  mRNA was extracted from purified cells and used to generate cDNA libraries  which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham  APOL1 G0  APOL1 G2,,pubmed:31158233,,G2 endo 02,GSM3317065,,tissue:zebrafish endothelium|line:fli:EGFP|treatment:human APOL1 G2 mRNA,G2 endo 02,Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered  sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2,zebrafish endothelium,Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL  or phenol red,RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech,Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf,line:fli:EGFP|treatment:human APOL1 G2 mRNA,GSM3317065,GSM3317065: G2 endo 02; Danio rerio; RNA Seq,GSM3317065,,1,RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech,GEO Accession:GSM3317065,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP155992,,,BA_S17_trimmed.fastq.gz,fastq,1635110054.0,32380584.0,GSM3317065 r1,0:50.50 1:0,A:462134552;C:361057634;G:349465446;T:462337205;N:115217,50,0,,,462134552,361057634,349465446,462337205,115217,SRX4497224,SRS3618224,SRA749599,GEO,"Duke Molecular Physiology Institute, Duke University Medical Center",1,0.80201,,0.12711,,0.70471,,0.44427,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2018-08-01,Larval,Larval,Endothelium,Cardiovascular System
49042,SRR7633492,SRX4497223,SRS3618223,SRP155992,PRJNA483985,Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA,GSE118000,Transcriptome Analysis,We injected zebrafish embryos with human APOL1 mRNA  dissociated embryos at xxx days of age  and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting  mRNA was extracted from purified cells and used to generate cDNA libraries  which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham  APOL1 G0  APOL1 G2,,pubmed:31158233,,G2 endo 01,GSM3317064,,tissue:zebrafish endothelium|line:fli:EGFP|treatment:human APOL1 G2 mRNA,G2 endo 01,Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered  sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2,zebrafish endothelium,Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL  or phenol red,RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech,Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf,line:fli:EGFP|treatment:human APOL1 G2 mRNA,GSM3317064,GSM3317064: G2 endo 01; Danio rerio; RNA Seq,GSM3317064,,1,RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech,GEO Accession:GSM3317064,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP155992,,,BA_S16_trimmed.fastq.gz,fastq,1302352614.0,25794210.0,GSM3317064 r1,0:50.49 1:0,A:370194702;C:286011167;G:276758200;T:369297736;N:90809,50,0,,,370194702,286011167,276758200,369297736,90809,SRX4497223,SRS3618223,SRA749599,GEO,"Duke Molecular Physiology Institute, Duke University Medical Center",1,0.89468,,0.15745,,0.69447,,0.47938,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2018-08-01,Larval,Larval,Endothelium,Cardiovascular System
49043,SRR7633491,SRX4497222,SRS3618222,SRP155992,PRJNA483985,Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA,GSE118000,Transcriptome Analysis,We injected zebrafish embryos with human APOL1 mRNA  dissociated embryos at xxx days of age  and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting  mRNA was extracted from purified cells and used to generate cDNA libraries  which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham  APOL1 G0  APOL1 G2,,pubmed:31158233,,G0 endo 03,GSM3317063,,tissue:zebrafish endothelium|line:fli:EGFP|treatment:human APOL1 G0 mRNA,G0 endo 03,Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered  sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2,zebrafish endothelium,Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL  or phenol red,RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech,Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf,line:fli:EGFP|treatment:human APOL1 G0 mRNA,GSM3317063,GSM3317063: G0 endo 03; Danio rerio; RNA Seq,GSM3317063,,1,RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech,GEO Accession:GSM3317063,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP155992,,,BA_S15_trimmed.fastq.gz,fastq,1248556473.0,24725241.0,GSM3317063 r1,0:50.50 1:0,A:350256976;C:280431139;G:270771772;T:347009294;N:87292,50,0,,,350256976,280431139,270771772,347009294,87292,SRX4497222,SRS3618222,SRA749599,GEO,"Duke Molecular Physiology Institute, Duke University Medical Center",1,0.90514,,0.13266,,0.69236,,0.47977,,49,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2018-08-01,Larval,Larval,Endothelium,Cardiovascular System
49044,SRR7633490,SRX4497221,SRS3618221,SRP155992,PRJNA483985,Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA,GSE118000,Transcriptome Analysis,We injected zebrafish embryos with human APOL1 mRNA  dissociated embryos at xxx days of age  and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting  mRNA was extracted from purified cells and used to generate cDNA libraries  which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham  APOL1 G0  APOL1 G2,,pubmed:31158233,,G0 endo 02,GSM3317062,,tissue:zebrafish endothelium|line:fli:EGFP|treatment:human APOL1 G0 mRNA,G0 endo 02,Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered  sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2,zebrafish endothelium,Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL  or phenol red,RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech,Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf,line:fli:EGFP|treatment:human APOL1 G0 mRNA,GSM3317062,GSM3317062: G0 endo 02; Danio rerio; RNA Seq,GSM3317062,,1,RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech,GEO Accession:GSM3317062,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP155992,,,BA_S14_trimmed.fastq.gz,fastq,372093672.0,7456111.0,GSM3317062 r1,0:49.90 1:0,A:113486766;C:74400549;G:71245468;T:112935661;N:25228,49,0,,,113486766,74400549,71245468,112935661,25228,SRX4497221,SRS3618221,SRA749599,GEO,"Duke Molecular Physiology Institute, Duke University Medical Center",1,0.89644,,0.12968,,0.70658,,0.47231,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2018-08-01,Larval,Larval,Endothelium,Cardiovascular System
49045,SRR7633489,SRX4497220,SRS3618220,SRP155992,PRJNA483985,Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA,GSE118000,Transcriptome Analysis,We injected zebrafish embryos with human APOL1 mRNA  dissociated embryos at xxx days of age  and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting  mRNA was extracted from purified cells and used to generate cDNA libraries  which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham  APOL1 G0  APOL1 G2,,pubmed:31158233,,G0 endo 01,GSM3317061,,tissue:zebrafish endothelium|line:fli:EGFP|treatment:human APOL1 G0 mRNA,G0 endo 01,Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered  sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2,zebrafish endothelium,Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL  or phenol red,RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech,Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf,line:fli:EGFP|treatment:human APOL1 G0 mRNA,GSM3317061,GSM3317061: G0 endo 01; Danio rerio; RNA Seq,GSM3317061,,1,RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech,GEO Accession:GSM3317061,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP155992,,,BA_S13_trimmed.fastq.gz,fastq,1450133780.0,28705598.0,GSM3317061 r1,0:50.52 1:0,A:407543677;C:323333189;G:313321100;T:405835253;N:100561,50,0,,,407543677,323333189,313321100,405835253,100561,SRX4497220,SRS3618220,SRA749599,GEO,"Duke Molecular Physiology Institute, Duke University Medical Center",1,0.8994,,0.13347,,0.6942,,0.47759,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2018-08-01,Larval,Larval,Endothelium,Cardiovascular System
49046,SRR7633488,SRX4497219,SRS3618219,SRP155992,PRJNA483985,Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA,GSE118000,Transcriptome Analysis,We injected zebrafish embryos with human APOL1 mRNA  dissociated embryos at xxx days of age  and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting  mRNA was extracted from purified cells and used to generate cDNA libraries  which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham  APOL1 G0  APOL1 G2,,pubmed:31158233,,control endo 03,GSM3317060,,tissue:zebrafish endothelium|line:fli:EGFP|treatment:control,control endo 03,Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered  sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2,zebrafish endothelium,Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL  or phenol red,RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech,Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf,line:fli:EGFP|treatment:control,GSM3317060,GSM3317060: control endo 03; Danio rerio; RNA Seq,GSM3317060,,1,RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech,GEO Accession:GSM3317060,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP155992,,,BA_S12_trimmed.fastq.gz,fastq,1720199608.0,34019943.0,GSM3317060 r1,0:50.56 1:0,A:474252335;C:393152371;G:382256277;T:470417173;N:121452,50,0,,,474252335,393152371,382256277,470417173,121452,SRX4497219,SRS3618219,SRA749599,GEO,"Duke Molecular Physiology Institute, Duke University Medical Center",1,0.90252,,0.11709,,0.69668,,0.47424,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2018-08-01,Larval,Larval,Endothelium,Cardiovascular System
49047,SRR7633487,SRX4497218,SRS3618218,SRP155992,PRJNA483985,Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA,GSE118000,Transcriptome Analysis,We injected zebrafish embryos with human APOL1 mRNA  dissociated embryos at xxx days of age  and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting  mRNA was extracted from purified cells and used to generate cDNA libraries  which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham  APOL1 G0  APOL1 G2,,pubmed:31158233,,control endo 02,GSM3317059,,tissue:zebrafish endothelium|line:fli:EGFP|treatment:control,control endo 02,Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered  sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2,zebrafish endothelium,Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL  or phenol red,RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech,Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf,line:fli:EGFP|treatment:control,GSM3317059,GSM3317059: control endo 02; Danio rerio; RNA Seq,GSM3317059,,1,RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech,GEO Accession:GSM3317059,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP155992,,,BA_S11_trimmed.fastq.gz,fastq,322327295.0,6605687.0,GSM3317059 r1,0:48.80 1:0,A:109722776;C:53179948;G:51091267;T:108312123;N:21181,48,0,,,109722776,53179948,51091267,108312123,21181,SRX4497218,SRS3618218,SRA749599,GEO,"Duke Molecular Physiology Institute, Duke University Medical Center",1,0.8922,,0.1261,,0.72811,,0.46128,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2018-08-01,Larval,Larval,Endothelium,Cardiovascular System
49048,SRR7633486,SRX4497217,SRS3618217,SRP155992,PRJNA483985,Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA,GSE118000,Transcriptome Analysis,We injected zebrafish embryos with human APOL1 mRNA  dissociated embryos at xxx days of age  and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting  mRNA was extracted from purified cells and used to generate cDNA libraries  which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham  APOL1 G0  APOL1 G2,,pubmed:31158233,,control endo 01,GSM3317058,,tissue:zebrafish endothelium|line:fli:EGFP|treatment:control,control endo 01,Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered  sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2,zebrafish endothelium,Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL  or phenol red,RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech,Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf,line:fli:EGFP|treatment:control,GSM3317058,GSM3317058: control endo 01; Danio rerio; RNA Seq,GSM3317058,,1,RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech,GEO Accession:GSM3317058,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP155992,,,BA_S10_trimmed.fastq.gz,fastq,1484074935.0,29385409.0,GSM3317058 r1,0:50.50 1:0,A:411414710;C:336260838;G:326730208;T:409563857;N:105322,50,0,,,411414710,336260838,326730208,409563857,105322,SRX4497217,SRS3618217,SRA749599,GEO,"Duke Molecular Physiology Institute, Duke University Medical Center",1,0.88777,,0.11462,,0.70102,,0.47353,,49,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2018-08-01,Larval,Larval,Endothelium,Cardiovascular System
50604,SRR8169175,SRX4989831,SRS4025849,SRP168005,PRJNA504385,Endothelial transcriptome of 1dpf Zebrafish empryo,PRJNA504385,Other,The study aimed to identify endothelial specific transcript isoforms in 24hpf zebrafish embryo. The polyA RNA sequencing was performed on Illumina GA II platform.,,,,Endothelial cells,EC,,strain:Tgfli1:EGFP  gata1a: dsRed|age:1 dpf stage:1 dpf applicable|tissue:Endothelium|cell type:Endothelial|BioSampleModel:Model organism or animal,,,,,,,,,Endothelial cells,EC,EC,PolyA RNA Seq,,,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina Genome Analyzer IIx,,SRP168005,,,EC_R1.fastq EC_R2.fastq,fastq fastq,3373890496.0,22196648.0,EC R1.fastq,0:76 1:76,A:984631808;C:769706826;G:812424195;T:790813473;N:16314194,76,76,,,984631808,769706826,812424195,790813473,16314194,SRX4989831,SRS4025849,SRA805845,CSIR-Institute of Genomics and Integrative Biology|GN Ramachandran Knowledge Center,CSIR-Institute of Genomics and Integrative Biology,2,0.92323,0.92543,0.07989,0.0849,0.76842,0.77964,0.46181,0.47429,76,76,B,B,biological fallback assumption,illumina,early_illumina,unknown,poly_a,unknown,bulk,unknown,unknown,,India,2019-12-06,Pharyngula,Embryo,Endothelium,Cardiovascular System