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33 rows where devstage_curation = "Undetermined" and tissue_curation = "Endothelium"

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technology 2

experiment.library_strategy 2

experiment.library_selection 2

experiment.library_layout 2

tissue_curation_coarse 1

tissue_curation 1

  • Endothelium · 33 ✖

experiment.platform 1

experiment.library_source 1

devstage_curation_coarse 1

devstage_curation 1

  • Undetermined · 33 ✖
Link 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
41681 41681 SRR5119926 SRX2435201 SRS1870197 SRP095331 PRJNA358009 CXCL8 and CXCR1 Remodel the Vascular Niche to Promote Hematopoietic Stem and Progenitor Cell Colonization and Engraftment [wt vs kdrl:cxcr1] GSE92542 Transcriptome Analysis The microenvironment is an important regulator of hematopoietic stem and progenitor cell HSPC biology. Interactions between the niche and stem cells have been difficult to track but recent advances marking fluorescent HSPCs have allowed exquisite visualization in the caudal hematopoietic tissue CHT of the developing zebrafish. Sinusoidal endothelial cells interact closely with HSPCs as they colonize this niche. Here we show that the chemokine cxcl8 and its receptor cxcr1 are abundantly expressed by zebrafish endothelial cells and we identify cxcl8/cxcr1 signaling as a positive regulator of HSPC colonization using genetic gain and loss of function techniques. Single cell tracking experiments demonstrated that this effect is due to an increase in HSPC “cuddling” by endothelial cells thereby increasing CHT residency time and allowing more HSPC cell divisions to occur. Enhanced cxcl8/cxcr1 signaling was associated with an increase in the volume of the CHT and induction of cxcl12a expression favoring HSPC colonization. Finally using parabiotic zebrafish we show that cxcr1 acts stem cell non autonomously to improve the efficiency of donor HSPC engraftment. This work identifies a mechanism by which the hematopoietic niche remodels to promote HSPC engraftment and suggests that cxcl8/cxcr1 signaling is a potential therapeutic target in patients undergoing hematopoietic stem cell transplantation. Overall design: Kdrl:mcherry and kdrl:mcherry;kdrl:cxcr1 zebrafish were dissociated and endothelial cells purified by FACS. RNA seq libraries were prepared from endothelial cells purified from two independent clutches of fish four libraries total. parent bioproject:PRJNA358001 pubmed:28351983   wt clutch2 GSM2432105   tissue:endothelial cells|cell type:endothelial cells wt clutch2 Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using cutadapt then mapped to Ensembl GRCz10 whole genome using Tophat 2.0.11 without xxx splicing form calls Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts Genome build: GRCz10 Supplementary files format and content: excel files include RPKM values for each Sample endothelial cells   Freshly sorted cells were lysed in Trizol LS and total RNA was extracted by isopropanol precipitation. Libraries were prepared using the SMARTer Universal Low Input RNA kit followed by the Low Input Library Prep Kit for Illumina Clontech Laboratories. Zebrafish embryos were grown under standard conditions in a 28 degree incubator. cell type:endothelial cells GSM2432105 GSM2432105: wt clutch2; Danio rerio; RNA Seq GSM2432105   1 Freshly sorted cells were lysed in Trizol LS and total RNA was extracted by isopropanol precipitation. Libraries were prepared using the SMARTer Universal Low Input RNA kit followed by the Low Input Library Prep Kit for Illumina Clontech Laboratories. GEO Accession:GSM2432105 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP095331     BB-IL8-7_GATCAG_R2.fastq.gz BB-IL8-7_GATCAG_R1.fastq.gz fastq fastq 6054362200.0 30271811.0 GSM2432105 r1 0:100 1:100 A:1586036726;C:1442511502;G:1449390272;T:1575855416;N:568284 100 100     1586036726 1442511502 1449390272 1575855416 568284 SRX2435201 SRS1870197 SRA505250 GEO Oncology/Hematology, Boston Children's Hospital 2 0.68659 0.68507 0.22283 0.22137 0.76067 0.76343 0.57225 0.58743 100 100 B B biological fallback assumption illumina hiseq_era full_length random_priming smarter bulk unknown unknown   United States 2016-12-19 Undetermined Embryo Endothelium Cardiovascular System
41682 41682 SRR5119925 SRX2435200 SRS1870195 SRP095331 PRJNA358009 CXCL8 and CXCR1 Remodel the Vascular Niche to Promote Hematopoietic Stem and Progenitor Cell Colonization and Engraftment [wt vs kdrl:cxcr1] GSE92542 Transcriptome Analysis The microenvironment is an important regulator of hematopoietic stem and progenitor cell HSPC biology. Interactions between the niche and stem cells have been difficult to track but recent advances marking fluorescent HSPCs have allowed exquisite visualization in the caudal hematopoietic tissue CHT of the developing zebrafish. Sinusoidal endothelial cells interact closely with HSPCs as they colonize this niche. Here we show that the chemokine cxcl8 and its receptor cxcr1 are abundantly expressed by zebrafish endothelial cells and we identify cxcl8/cxcr1 signaling as a positive regulator of HSPC colonization using genetic gain and loss of function techniques. Single cell tracking experiments demonstrated that this effect is due to an increase in HSPC “cuddling” by endothelial cells thereby increasing CHT residency time and allowing more HSPC cell divisions to occur. Enhanced cxcl8/cxcr1 signaling was associated with an increase in the volume of the CHT and induction of cxcl12a expression favoring HSPC colonization. Finally using parabiotic zebrafish we show that cxcr1 acts stem cell non autonomously to improve the efficiency of donor HSPC engraftment. This work identifies a mechanism by which the hematopoietic niche remodels to promote HSPC engraftment and suggests that cxcl8/cxcr1 signaling is a potential therapeutic target in patients undergoing hematopoietic stem cell transplantation. Overall design: Kdrl:mcherry and kdrl:mcherry;kdrl:cxcr1 zebrafish were dissociated and endothelial cells purified by FACS. RNA seq libraries were prepared from endothelial cells purified from two independent clutches of fish four libraries total. parent bioproject:PRJNA358001 pubmed:28351983   wt clutch1 GSM2432104   tissue:endothelial cells|cell type:endothelial cells wt clutch1 Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using cutadapt then mapped to Ensembl GRCz10 whole genome using Tophat 2.0.11 without xxx splicing form calls Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts Genome build: GRCz10 Supplementary files format and content: excel files include RPKM values for each Sample endothelial cells   Freshly sorted cells were lysed in Trizol LS and total RNA was extracted by isopropanol precipitation. Libraries were prepared using the SMARTer Universal Low Input RNA kit followed by the Low Input Library Prep Kit for Illumina Clontech Laboratories. Zebrafish embryos were grown under standard conditions in a 28 degree incubator. cell type:endothelial cells GSM2432104 GSM2432104: wt clutch1; Danio rerio; RNA Seq GSM2432104   1 Freshly sorted cells were lysed in Trizol LS and total RNA was extracted by isopropanol precipitation. Libraries were prepared using the SMARTer Universal Low Input RNA kit followed by the Low Input Library Prep Kit for Illumina Clontech Laboratories. GEO Accession:GSM2432104 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP095331     BB-IL8-3_TGACCA_R1.fastq.gz BB-IL8-3_TGACCA_R2.fastq.gz fastq fastq 4718160000.0 23590800.0 GSM2432104 r1 0:100 1:100 A:1285175152;C:1075055485;G:1078285328;T:1279202852;N:441183 100 100     1285175152 1075055485 1078285328 1279202852 441183 SRX2435200 SRS1870195 SRA505250 GEO Oncology/Hematology, Boston Children's Hospital 2 0.79676 0.7947 0.26445 0.26272 0.71652 0.71924 0.55157 0.55957 100 100 B B biological fallback assumption illumina hiseq_era full_length random_priming smarter bulk unknown unknown   United States 2016-12-19 Undetermined Embryo Endothelium Cardiovascular System
41683 41683 SRR5119924 SRX2435199 SRS1870196 SRP095331 PRJNA358009 CXCL8 and CXCR1 Remodel the Vascular Niche to Promote Hematopoietic Stem and Progenitor Cell Colonization and Engraftment [wt vs kdrl:cxcr1] GSE92542 Transcriptome Analysis The microenvironment is an important regulator of hematopoietic stem and progenitor cell HSPC biology. Interactions between the niche and stem cells have been difficult to track but recent advances marking fluorescent HSPCs have allowed exquisite visualization in the caudal hematopoietic tissue CHT of the developing zebrafish. Sinusoidal endothelial cells interact closely with HSPCs as they colonize this niche. Here we show that the chemokine cxcl8 and its receptor cxcr1 are abundantly expressed by zebrafish endothelial cells and we identify cxcl8/cxcr1 signaling as a positive regulator of HSPC colonization using genetic gain and loss of function techniques. Single cell tracking experiments demonstrated that this effect is due to an increase in HSPC “cuddling” by endothelial cells thereby increasing CHT residency time and allowing more HSPC cell divisions to occur. Enhanced cxcl8/cxcr1 signaling was associated with an increase in the volume of the CHT and induction of cxcl12a expression favoring HSPC colonization. Finally using parabiotic zebrafish we show that cxcr1 acts stem cell non autonomously to improve the efficiency of donor HSPC engraftment. This work identifies a mechanism by which the hematopoietic niche remodels to promote HSPC engraftment and suggests that cxcl8/cxcr1 signaling is a potential therapeutic target in patients undergoing hematopoietic stem cell transplantation. Overall design: Kdrl:mcherry and kdrl:mcherry;kdrl:cxcr1 zebrafish were dissociated and endothelial cells purified by FACS. RNA seq libraries were prepared from endothelial cells purified from two independent clutches of fish four libraries total. parent bioproject:PRJNA358001 pubmed:28351983   kdrl:cxcr1 clutch2 GSM2432103   tissue:endothelial cells|cell type:endothelial cells kdrl:cxcr1 clutch2 Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using cutadapt then mapped to Ensembl GRCz10 whole genome using Tophat 2.0.11 without xxx splicing form calls Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts Genome build: GRCz10 Supplementary files format and content: excel files include RPKM values for each Sample endothelial cells   Freshly sorted cells were lysed in Trizol LS and total RNA was extracted by isopropanol precipitation. Libraries were prepared using the SMARTer Universal Low Input RNA kit followed by the Low Input Library Prep Kit for Illumina Clontech Laboratories. Zebrafish embryos were grown under standard conditions in a 28 degree incubator. cell type:endothelial cells GSM2432103 GSM2432103: kdrl:cxcr1 clutch2; Danio rerio; RNA Seq GSM2432103   1 Freshly sorted cells were lysed in Trizol LS and total RNA was extracted by isopropanol precipitation. Libraries were prepared using the SMARTer Universal Low Input RNA kit followed by the Low Input Library Prep Kit for Illumina Clontech Laboratories. GEO Accession:GSM2432103 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP095331     BB-IL8-5_GCCAAT_R1.fastq.gz BB-IL8-5_GCCAAT_R2.fastq.gz fastq fastq 4575871400.0 22879357.0 GSM2432103 r1 0:100 1:100 A:1212272291;C:1077863805;G:1079802103;T:1205507838;N:425363 100 100     1212272291 1077863805 1079802103 1205507838 425363 SRX2435199 SRS1870196 SRA505250 GEO Oncology/Hematology, Boston Children's Hospital 2 0.79788 0.79581 0.25639 0.25339 0.74888 0.75195 0.55512 0.56401 100 100 B B biological fallback assumption illumina hiseq_era full_length random_priming smarter bulk unknown unknown   United States 2016-12-19 Undetermined Embryo Endothelium Cardiovascular System
41684 41684 SRR5119923 SRX2435198 SRS1870193 SRP095331 PRJNA358009 CXCL8 and CXCR1 Remodel the Vascular Niche to Promote Hematopoietic Stem and Progenitor Cell Colonization and Engraftment [wt vs kdrl:cxcr1] GSE92542 Transcriptome Analysis The microenvironment is an important regulator of hematopoietic stem and progenitor cell HSPC biology. Interactions between the niche and stem cells have been difficult to track but recent advances marking fluorescent HSPCs have allowed exquisite visualization in the caudal hematopoietic tissue CHT of the developing zebrafish. Sinusoidal endothelial cells interact closely with HSPCs as they colonize this niche. Here we show that the chemokine cxcl8 and its receptor cxcr1 are abundantly expressed by zebrafish endothelial cells and we identify cxcl8/cxcr1 signaling as a positive regulator of HSPC colonization using genetic gain and loss of function techniques. Single cell tracking experiments demonstrated that this effect is due to an increase in HSPC “cuddling” by endothelial cells thereby increasing CHT residency time and allowing more HSPC cell divisions to occur. Enhanced cxcl8/cxcr1 signaling was associated with an increase in the volume of the CHT and induction of cxcl12a expression favoring HSPC colonization. Finally using parabiotic zebrafish we show that cxcr1 acts stem cell non autonomously to improve the efficiency of donor HSPC engraftment. This work identifies a mechanism by which the hematopoietic niche remodels to promote HSPC engraftment and suggests that cxcl8/cxcr1 signaling is a potential therapeutic target in patients undergoing hematopoietic stem cell transplantation. Overall design: Kdrl:mcherry and kdrl:mcherry;kdrl:cxcr1 zebrafish were dissociated and endothelial cells purified by FACS. RNA seq libraries were prepared from endothelial cells purified from two independent clutches of fish four libraries total. parent bioproject:PRJNA358001 pubmed:28351983   kdrl:cxcr1 clutch1 GSM2432102   tissue:endothelial cells|cell type:endothelial cells kdrl:cxcr1 clutch1 Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using cutadapt then mapped to Ensembl GRCz10 whole genome using Tophat 2.0.11 without xxx splicing form calls Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts Genome build: GRCz10 Supplementary files format and content: excel files include RPKM values for each Sample endothelial cells   Freshly sorted cells were lysed in Trizol LS and total RNA was extracted by isopropanol precipitation. Libraries were prepared using the SMARTer Universal Low Input RNA kit followed by the Low Input Library Prep Kit for Illumina Clontech Laboratories. Zebrafish embryos were grown under standard conditions in a 28 degree incubator. cell type:endothelial cells GSM2432102 GSM2432102: kdrl:cxcr1 clutch1; Danio rerio; RNA Seq GSM2432102   1 Freshly sorted cells were lysed in Trizol LS and total RNA was extracted by isopropanol precipitation. Libraries were prepared using the SMARTer Universal Low Input RNA kit followed by the Low Input Library Prep Kit for Illumina Clontech Laboratories. GEO Accession:GSM2432102 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP095331     BB-IL8-1_ATCACG_R1.fastq.gz BB-IL8-1_ATCACG_R2.fastq.gz fastq fastq 5384509000.0 26922545.0 GSM2432102 r1 0:100 1:100 A:1457197772;C:1237507818;G:1239484699;T:1449819489;N:499222 100 100     1457197772 1237507818 1239484699 1449819489 499222 SRX2435198 SRS1870193 SRA505250 GEO Oncology/Hematology, Boston Children's Hospital 2 0.80446 0.79238 0.24797 0.24691 0.72423 0.72681 0.57301 0.46021 100 100 B B biological fallback assumption illumina hiseq_era full_length random_priming smarter bulk unknown unknown   United States 2016-12-19 Undetermined Embryo Endothelium Cardiovascular System
41827 41827 SRR5251446 SRX2557171 SRS1974564 SRP099466 PRJNA374579 microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos PRJNA374579 Other Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.       QuantSeq mutant miRNAs WT miR139 B1 nicoli mutmir AG01645   strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|molecule:mRNA|condition:miR 139|replicate:1|BioSampleModel:Model organism or animal                 QuantSeq mutant miRNAs WT miR139 B1 AG01645.1 AG01645.1 1     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP099466     AG01645.1_R1.fastq.gz fastq 1574284140.0 20714265.0 AG01645.1 R1.fastq.gz 0:76 A:485471345;C:270854124;G:374164721;T:443766613;N:27337 76       485471345 270854124 374164721 443766613 27337 SRX2557171 SRS1974564 SRA537606 Yale University|Genetics Yale University 1 0.82142   0.14068   0.8002   0.5444   76   B   usable mapping rate illumina hiseq_era unknown small_rna lexogen bulk unknown unknown   United States 2017-03-27 Undetermined Embryo Endothelium Cardiovascular System
41828 41828 SRR5251445 SRX2557170 SRS1974563 SRP099466 PRJNA374579 microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos PRJNA374579 Other Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.       QuantSeq mutant miRNAs WT miR139 B2 nicoli mutmir AG01646   strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|molecule:mRNA|condition:miR 139|replicate:2|BioSampleModel:Model organism or animal                 QuantSeq mutant miRNAs WT miR139 B2 AG01646.1 AG01646.1 1     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP099466     AG01646.1_R1.fastq.gz fastq 1484740104.0 19536054.0 AG01646.1 R1.fastq.gz 0:76 A:453388316;C:246477203;G:365031959;T:419816346;N:26280 76       453388316 246477203 365031959 419816346 26280 SRX2557170 SRS1974563 SRA537606 Yale University|Genetics Yale University 1 0.82649   0.1897   0.79862   0.52759   76   B   usable mapping rate illumina hiseq_era unknown small_rna lexogen bulk unknown unknown   United States 2017-03-28 Undetermined Embryo Endothelium Cardiovascular System
41829 41829 SRR5251444 SRX2557169 SRS1974562 SRP099466 PRJNA374579 microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos PRJNA374579 Other Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.       QuantSeq mutant miRNAs WT miR139 B3 nicoli mutmir AG01647   strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|molecule:mRNA|condition:miR 139|replicate:3|BioSampleModel:Model organism or animal                 QuantSeq mutant miRNAs WT miR139 B3 AG01647.1 AG01647.1 1     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP099466     AG01647.1_R1.fastq.gz fastq 881298660.0 11596035.0 AG01647.1 R1.fastq.gz 0:76 A:270675838;C:160127586;G:228157662;T:222301246;N:36328 76       270675838 160127586 228157662 222301246 36328 SRX2557169 SRS1974562 SRA537606 Yale University|Genetics Yale University 1 0.76133   0.15034   0.83341   0.56596   76   B   usable mapping rate illumina hiseq_era unknown small_rna lexogen bulk unknown unknown   United States 2017-03-28 Undetermined Embryo Endothelium Cardiovascular System
41830 41830 SRR5251443 SRX2557168 SRS1974561 SRP099466 PRJNA374579 microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos PRJNA374579 Other Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.       QuantSeq mutant miRNAs Mut miR139 B1 nicoli mutmir AG01648   strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|genotype:miR 139 ya302/ya302|molecule:mRNA|condition:miR 139|replicate:1|BioSampleModel:Model organism or animal                 QuantSeq mutant miRNAs Mut miR139 B1 AG01648.1 AG01648.1 1     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP099466     AG01648.1_R1.fastq.gz fastq 637896880.0 8393380.0 AG01648.1 R1.fastq.gz 0:76 A:192829278;C:112701153;G:153321271;T:179019095;N:26083 76       192829278 112701153 153321271 179019095 26083 SRX2557168 SRS1974561 SRA537606 Yale University|Genetics Yale University 1 0.75971   0.1181   0.82171   0.56797   76   B   usable mapping rate illumina hiseq_era unknown small_rna lexogen bulk unknown unknown   United States 2017-03-28 Undetermined Embryo Endothelium Cardiovascular System
41831 41831 SRR5251442 SRX2557167 SRS1974560 SRP099466 PRJNA374579 microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos PRJNA374579 Other Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.       QuantSeq mutant miRNAs Mut miR139 B2 nicoli mutmir AG01649   strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|genotype:miR 139 ya302/ya302|molecule:mRNA|condition:miR 139|replicate:2|BioSampleModel:Model organism or animal                 QuantSeq mutant miRNAs Mut miR139 B2 AG01649.1 AG01649.1 1     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP099466     AG01649.1_R1.fastq.gz fastq 849868328.0 11182478.0 AG01649.1 R1.fastq.gz 0:76 A:258225905;C:148467172;G:205165181;T:237974100;N:35970 76       258225905 148467172 205165181 237974100 35970 SRX2557167 SRS1974560 SRA537606 Yale University|Genetics Yale University 1 0.75096   0.14506   0.81507   0.5545   76   B   usable mapping rate illumina hiseq_era unknown small_rna lexogen bulk unknown unknown   United States 2017-03-28 Undetermined Embryo Endothelium Cardiovascular System
41832 41832 SRR5251441 SRX2557166 SRS1974559 SRP099466 PRJNA374579 microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos PRJNA374579 Other Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.       QuantSeq mutant miRNAs Mut miR139 B3 nicoli mutmir AG01650   strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|genotype:miR 139 ya302/ya302|molecule:mRNA|condition:miR 139|replicate:3|BioSampleModel:Model organism or animal                 QuantSeq mutant miRNAs Mut miR139 B3 AG01650.1 AG01650.1 1     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP099466     AG01650.1_R1.fastq.gz fastq 998464668.0 13137693.0 AG01650.1 R1.fastq.gz 0:76 A:311526420;C:176545041;G:251852786;T:258497630;N:42791 76       311526420 176545041 251852786 258497630 42791 SRX2557166 SRS1974559 SRA537606 Yale University|Genetics Yale University 1 0.76479   0.11192   0.82674   0.54621   76   B   usable mapping rate illumina hiseq_era unknown small_rna lexogen bulk unknown unknown   United States 2017-03-28 Undetermined Embryo Endothelium Cardiovascular System
41833 41833 SRR5251440 SRX2557165 SRS1974558 SRP099466 PRJNA374579 microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos PRJNA374579 Other Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.       QuantSeq mutant miRNAs WT miR24 B1 nicoli mutmir AG01651   strain:TU/AB|age:51.0|sex:pooled male and female|tissue:endothelial cells|molecule:mRNA|condition:miR 24|replicate:1|BioSampleModel:Model organism or animal                 QuantSeq mutant miRNAs WT miR24 B1 AG01651.1 AG01651.1 1     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP099466     AG01651.1_R1.fastq.gz fastq 570492252.0 7506477.0 AG01651.1 R1.fastq.gz 0:76 A:162512811;C:104071716;G:135730697;T:168149427;N:27601 76       162512811 104071716 135730697 168149427 27601 SRX2557165 SRS1974558 SRA537606 Yale University|Genetics Yale University 1 0.73988   0.10157   0.86647   0.54252   76   B   usable mapping rate illumina hiseq_era unknown small_rna lexogen bulk unknown unknown   United States 2017-03-28 Undetermined Embryo Endothelium Cardiovascular System
41834 41834 SRR5251439 SRX2557164 SRS1974557 SRP099466 PRJNA374579 microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos PRJNA374579 Other Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.       QuantSeq mutant miRNAs WT miR24 B2 nicoli mutmir AG01652   strain:TU/AB|age:51.0|sex:pooled male and female|tissue:endothelial cells|molecule:mRNA|condition:miR 24|replicate:2|BioSampleModel:Model organism or animal                 QuantSeq mutant miRNAs WT miR24 B2 AG01652.1 AG01652.1 1     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP099466     AG01652.1_R1.fastq.gz fastq 1072886148.0 14116923.0 AG01652.1 R1.fastq.gz 0:76 A:338399596;C:192703439;G:242960887;T:298769761;N:52465 76       338399596 192703439 242960887 298769761 52465 SRX2557164 SRS1974557 SRA537606 Yale University|Genetics Yale University 1 0.76456   0.11024   0.89197   0.59214   76   B   usable mapping rate illumina hiseq_era unknown small_rna lexogen bulk unknown unknown   United States 2017-03-28 Undetermined Embryo Endothelium Cardiovascular System
41835 41835 SRR5251438 SRX2557163 SRS1974556 SRP099466 PRJNA374579 microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos PRJNA374579 Other Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.       QuantSeq mutant miRNAs WT miR24 B3 nicoli mutmir AG01653   strain:TU/AB|age:51.0|sex:pooled male and female|tissue:endothelial cells|molecule:mRNA|condition:miR 24|replicate:3|BioSampleModel:Model organism or animal                 QuantSeq mutant miRNAs WT miR24 B3 AG01653.1 AG01653.1 1     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP099466     AG01653.1_R1.fastq.gz fastq 1016374144.0 13373344.0 AG01653.1 R1.fastq.gz 0:76 A:310958343;C:168702106;G:223420046;T:313241363;N:52286 76       310958343 168702106 223420046 313241363 52286 SRX2557163 SRS1974556 SRA537606 Yale University|Genetics Yale University 1 0.75735   0.12224   0.79756   0.55136   76   B   usable mapping rate illumina hiseq_era unknown small_rna lexogen bulk unknown unknown   United States 2017-02-13 Undetermined Embryo Endothelium Cardiovascular System
41836 41836 SRR5251437 SRX2557162 SRS1974555 SRP099466 PRJNA374579 microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos PRJNA374579 Other Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.       QuantSeq mutant miRNAs Mut miR24 B1 nicoli mutmir AG01654   strain:TU/AB|age:51.0|sex:pooled male and female|tissue:endothelial cells|genotype:miR 24 ya324/? ya325/? ya326/? ya327/?|molecule:mRNA|condition:miR 24|replicate:1|BioSampleModel:Model organism or animal                 QuantSeq mutant miRNAs Mut miR24 B1 AG01654.1 AG01654.1 1     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP099466     AG01654.1_R1.fastq.gz fastq 782170112.0 10291712.0 AG01654.1 R1.fastq.gz 0:76 A:238316720;C:132163709;G:179301544;T:232350598;N:37541 76       238316720 132163709 179301544 232350598 37541 SRX2557162 SRS1974555 SRA537606 Yale University|Genetics Yale University 1 0.7683   0.10712   0.80034   0.55804   76   B   usable mapping rate illumina hiseq_era unknown small_rna lexogen bulk unknown unknown   United States 2017-03-28 Undetermined Embryo Endothelium Cardiovascular System
41837 41837 SRR5251436 SRX2557161 SRS1974554 SRP099466 PRJNA374579 microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos PRJNA374579 Other Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.       QuantSeq mutant miRNAs Mut miR24 B2 nicoli mutmir AG01655   strain:TU/AB|age:51.0|sex:pooled male and female|tissue:endothelial cells|genotype:miR 24 ya324/? ya325/? ya326/? ya327/?|molecule:mRNA|condition:miR 24|replicate:2|BioSampleModel:Model organism or animal                 QuantSeq mutant miRNAs Mut miR24 B2 AG01655.1 AG01655.1 1     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP099466     AG01655.1_R1.fastq.gz fastq 1053946340.0 13867715.0 AG01655.1 R1.fastq.gz 0:76 A:318351311;C:191163031;G:240348413;T:304030367;N:53218 76       318351311 191163031 240348413 304030367 53218 SRX2557161 SRS1974554 SRA537606 Yale University|Genetics Yale University 1 0.77588   0.07983   0.83934   0.56228   76   B   usable mapping rate illumina hiseq_era unknown small_rna lexogen bulk unknown unknown   United States 2017-03-28 Undetermined Embryo Endothelium Cardiovascular System
41838 41838 SRR5251435 SRX2557160 SRS1974553 SRP099466 PRJNA374579 microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos PRJNA374579 Other Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.       QuantSeq mutant miRNAs Mut miR24 B3 nicoli mutmir AG01656   strain:TU/AB|age:51.0|sex:pooled male and female|tissue:endothelial cells|genotype:miR 24 ya324/? ya325/? ya326/? ya327/?|molecule:mRNA|condition:miR 24|replicate:3|BioSampleModel:Model organism or animal                 QuantSeq mutant miRNAs Mut miR24 B3 AG01656.1 AG01656.1 1     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP099466     AG01656.1_R1.fastq.gz fastq 1182467736.0 15558786.0 AG01656.1 R1.fastq.gz 0:76 A:344465226;C:204677242;G:269228338;T:364036735;N:60195 76       344465226 204677242 269228338 364036735 60195 SRX2557160 SRS1974553 SRA537606 Yale University|Genetics Yale University 1 0.78956   0.13495   0.81517   0.56342   76   B   usable mapping rate illumina hiseq_era unknown small_rna lexogen bulk unknown unknown   United States 2017-02-13 Undetermined Embryo Endothelium Cardiovascular System
41839 41839 SRR5251434 SRX2557159 SRS1974552 SRP099466 PRJNA374579 microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos PRJNA374579 Other Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.       QuantSeq mutant miRNAs WT miR223 B1 nicoli mutmir AG01657   strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|molecule:mRNA|condition:miR 223|replicate:1|BioSampleModel:Model organism or animal                 QuantSeq mutant miRNAs WT miR223 B1 AG01657.1 AG01657.1 1     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP099466     AG01657.1_R1.fastq.gz fastq 536336712.0 7057062.0 AG01657.1 R1.fastq.gz 0:76 A:158301607;C:93070120;G:121382262;T:163555487;N:27236 76       158301607 93070120 121382262 163555487 27236 SRX2557159 SRS1974552 SRA537606 Yale University|Genetics Yale University 1 0.76425   0.1278   0.84222   0.55305   76   B   usable mapping rate illumina hiseq_era unknown small_rna lexogen bulk unknown unknown   United States 2017-02-13 Undetermined Embryo Endothelium Cardiovascular System
41840 41840 SRR5251433 SRX2557158 SRS1974551 SRP099466 PRJNA374579 microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos PRJNA374579 Other Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.       QuantSeq mutant miRNAs WT miR223 B2 nicoli mutmir AG01658   strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|molecule:mRNA|condition:miR 223|replicate:2|BioSampleModel:Model organism or animal                 QuantSeq mutant miRNAs WT miR223 B2 AG01658.1 AG01658.1 1     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP099466     AG01658.1_R1.fastq.gz fastq 798581856.0 10507656.0 AG01658.1 R1.fastq.gz 0:76 A:241352089;C:134327379;G:183394123;T:239469845;N:38420 76       241352089 134327379 183394123 239469845 38420 SRX2557158 SRS1974551 SRA537606 Yale University|Genetics Yale University 1 0.76221   0.13398   0.82459   0.55228   76   B   usable mapping rate illumina hiseq_era unknown small_rna lexogen bulk unknown unknown   United States 2017-03-28 Undetermined Embryo Endothelium Cardiovascular System
41841 41841 SRR5251432 SRX2557157 SRS1974550 SRP099466 PRJNA374579 microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos PRJNA374579 Other Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.       QuantSeq mutant miRNAs WT miR223 B3 nicoli mutmir AG01659   strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|molecule:mRNA|condition:miR 223|replicate:3|BioSampleModel:Model organism or animal                 QuantSeq mutant miRNAs WT miR223 B3 AG01659.1 AG01659.1 1     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP099466     AG01659.1_R1.fastq.gz fastq 1093998948.0 14394723.0 AG01659.1 R1.fastq.gz 0:76 A:330741822;C:186325335;G:249557623;T:327320449;N:53719 76       330741822 186325335 249557623 327320449 53719 SRX2557157 SRS1974550 SRA537606 Yale University|Genetics Yale University 1 0.77108   0.14674   0.80955   0.55819   76   B   usable mapping rate illumina hiseq_era unknown small_rna lexogen bulk unknown unknown   United States 2017-03-28 Undetermined Embryo Endothelium Cardiovascular System
41842 41842 SRR5251431 SRX2557156 SRS1974549 SRP099466 PRJNA374579 microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos PRJNA374579 Other Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.       QuantSeq mutant miRNAs Mut miR223 B1 nicoli mutmir AG01660   strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|genotype:miR 223 ya304/ya304|molecule:mRNA|condition:miR 223|replicate:1|BioSampleModel:Model organism or animal                 QuantSeq mutant miRNAs Mut miR223 B1 AG01660.1 AG01660.1 1     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP099466     AG01660.1_R1.fastq.gz fastq 849905492.0 11182967.0 AG01660.1 R1.fastq.gz 0:76 A:250953875;C:146191904;G:190040699;T:262674911;N:44103 76       250953875 146191904 190040699 262674911 44103 SRX2557156 SRS1974549 SRA537606 Yale University|Genetics Yale University 1 0.7687   0.14192   0.82842   0.5344   76   B   usable mapping rate illumina hiseq_era unknown small_rna lexogen bulk unknown unknown   United States 2017-02-13 Undetermined Embryo Endothelium Cardiovascular System
41843 41843 SRR5251430 SRX2557155 SRS1974548 SRP099466 PRJNA374579 microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos PRJNA374579 Other Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.       QuantSeq mutant miRNAs Mut miR223 B2 nicoli mutmir AG01661   strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|genotype:miR 223 ya304/ya304|molecule:mRNA|condition:miR 223|replicate:2|BioSampleModel:Model organism or animal                 QuantSeq mutant miRNAs Mut miR223 B2 AG01661.1 AG01661.1 1     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP099466     AG01661.1_R1.fastq.gz fastq 840115400.0 11054150.0 AG01661.1 R1.fastq.gz 0:76 A:257057495;C:141775085;G:188281166;T:252960590;N:41064 76       257057495 141775085 188281166 252960590 41064 SRX2557155 SRS1974548 SRA537606 Yale University|Genetics Yale University 1 0.74292   0.10759   0.83615   0.55136   76   B   usable mapping rate illumina hiseq_era unknown small_rna lexogen bulk unknown unknown   United States 2017-03-28 Undetermined Embryo Endothelium Cardiovascular System
67022 67022 SRR16973878 SRX13164742 SRS11095945 SRP346708 PRJNA781453 WGBS and RNA seq of Danio rerio in HSPC generation GSE189072 Other In this study we interrogated the role of DNA methylation in HSPC generation by taking advantage of dnmt1 knockout/knockdown embryos in zebrafish. First we generated a comprehensive DNA methylation landscape of EHT which revealed gradually hypermethylated regions associated with vasculogenesis. Taking advantage of dnmt1 deficient embryos we showed that the decreased DNA methylation blocked HSPC emergence. Mechanistically we demonstrated that the decreased DNA methylation increased the expression of arterial genes and Notch signaling thus contributing to defects in the EHT in dnmt1 deficient embryos. Herein we identified that DNA methylation as epigenetic regulator participates in the negative modulation of Notch signaling through inhibiting transcription during HSPC generation in zebrafish. Overall design: WGBS and RNA seq of Danio rerio in EC HE and HSPC.   pubmed:35502759   HE mut rep3 RNA GSM5694252   tissue:hemogenic endothelium cells|developmental stage:HE|genotype:dnmt1 mutant|region:AGM HE mut rep3 RNA Basecalls perfomed using CASAVA2.19 WGBS and RNA seq raw sequencing reads were first trimmed for adapter and low quality sequences. Then mapped to GRCz11 using BS Seeker2v2.1.8 and hisat2v2.2.1 with parameters " t Y m 0.04 bt2 end to end" and " known splicesite infile p 30 k 10 dta t" separately. Student's T test was used to perform DMR analysis for WGBS data. Gene expression level was quantified by HTSeqv0.12.4 and differentially expressed genesDEGs were determined by DESeq2v1.30.1 Genome build: GRCz11 Supplementary files format and content: RNA seq raw count matrix Supplementary files format and content: raw count.txt raw counts Supplementary files format and content: EC sib.bed DMRs of EC sibling compared with HE sibling and HSC sibling Supplementary files format and content: HE sib.bed DMRs of HE sibling compared with EC sibling and HSC sibling Supplementary files format and content: HSC sib.bed DMRs of HSC sibling compared with EC sibling and HE sibling Supplementary files format and content: EC HE sib.bed DMRs of EC and HE sibling Supplementary files format and content: HE HSC sib.bed DMRs of HE and HSC sibling Supplementary files format and content: EC sib mut.bed DMRs of EC sibling and EC mutant Supplementary files format and content: HE sib mut.bed DMRs of HE sibling and HE mutant Supplementary files format and content: HSC sib mut.bed DMRs of HSC sibling and HSC mutant hemogenic endothelium cells   Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3′ biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification   developmental stage:HE|genotype:dnmt1 mutant|region:AGM GSM5694252 GSM5694252: HE mut rep3 RNA; Danio rerio; RNA Seq GSM5694252   1 Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3′ biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification GEO Accession:GSM5694252 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP346708   loader:fastq load.py HE_sib_3_1_RNA.fq.gz HE_sib_3_2_RNA.fq.gz fastq fastq 8484093900.0 28280313.0 GSM5694252 r1 0:150 1:150 A:2396956113;C:1725799170;G:1832630297;T:2528680586;N:27734 150 150     2396956113 1725799170 1832630297 2528680586 27734 SRX13164742 SRS11095945 SRA1331007 GEO Institute of Hematology and Blood Diseases Hospital 2 0.93895 0.93325 0.16467 0.16385 0.76595 0.76895 0.47613 0.46536 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_plate strtseq   China 2021-11-18 Undetermined Embryo Endothelium Cardiovascular System
67023 67023 SRR16973877 SRX13164741 SRS11095944 SRP346708 PRJNA781453 WGBS and RNA seq of Danio rerio in HSPC generation GSE189072 Other In this study we interrogated the role of DNA methylation in HSPC generation by taking advantage of dnmt1 knockout/knockdown embryos in zebrafish. First we generated a comprehensive DNA methylation landscape of EHT which revealed gradually hypermethylated regions associated with vasculogenesis. Taking advantage of dnmt1 deficient embryos we showed that the decreased DNA methylation blocked HSPC emergence. Mechanistically we demonstrated that the decreased DNA methylation increased the expression of arterial genes and Notch signaling thus contributing to defects in the EHT in dnmt1 deficient embryos. Herein we identified that DNA methylation as epigenetic regulator participates in the negative modulation of Notch signaling through inhibiting transcription during HSPC generation in zebrafish. Overall design: WGBS and RNA seq of Danio rerio in EC HE and HSPC.   pubmed:35502759   HE mut rep2 RNA GSM5694251   tissue:hemogenic endothelium cells|developmental stage:HE|genotype:dnmt1 mutant|region:AGM HE mut rep2 RNA Basecalls perfomed using CASAVA2.19 WGBS and RNA seq raw sequencing reads were first trimmed for adapter and low quality sequences. Then mapped to GRCz11 using BS Seeker2v2.1.8 and hisat2v2.2.1 with parameters " t Y m 0.04 bt2 end to end" and " known splicesite infile p 30 k 10 dta t" separately. Student's T test was used to perform DMR analysis for WGBS data. Gene expression level was quantified by HTSeqv0.12.4 and differentially expressed genesDEGs were determined by DESeq2v1.30.1 Genome build: GRCz11 Supplementary files format and content: RNA seq raw count matrix Supplementary files format and content: raw count.txt raw counts Supplementary files format and content: EC sib.bed DMRs of EC sibling compared with HE sibling and HSC sibling Supplementary files format and content: HE sib.bed DMRs of HE sibling compared with EC sibling and HSC sibling Supplementary files format and content: HSC sib.bed DMRs of HSC sibling compared with EC sibling and HE sibling Supplementary files format and content: EC HE sib.bed DMRs of EC and HE sibling Supplementary files format and content: HE HSC sib.bed DMRs of HE and HSC sibling Supplementary files format and content: EC sib mut.bed DMRs of EC sibling and EC mutant Supplementary files format and content: HE sib mut.bed DMRs of HE sibling and HE mutant Supplementary files format and content: HSC sib mut.bed DMRs of HSC sibling and HSC mutant hemogenic endothelium cells   Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3′ biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification   developmental stage:HE|genotype:dnmt1 mutant|region:AGM GSM5694251 GSM5694251: HE mut rep2 RNA; Danio rerio; RNA Seq GSM5694251   1 Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3′ biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification GEO Accession:GSM5694251 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP346708     HE_sib_2_1_RNA.fq.gz HE_sib_2_2_RNA.fq.gz fastq fastq 3391937700.0 11306459.0 GSM5694251 r1 0:150 1:150 A:981400300;C:664246146;G:716019213;T:1030238113;N:33928 150 150     981400300 664246146 716019213 1030238113 33928 SRX13164741 SRS11095944 SRA1331007 GEO Institute of Hematology and Blood Diseases Hospital 2 0.88669 0.88216 0.25368 0.25155 0.76361 0.76883 0.54578 0.54556 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_plate strtseq   China 2021-11-18 Undetermined Embryo Endothelium Cardiovascular System
67024 67024 SRR16973876 SRX13164740 SRS11095942 SRP346708 PRJNA781453 WGBS and RNA seq of Danio rerio in HSPC generation GSE189072 Other In this study we interrogated the role of DNA methylation in HSPC generation by taking advantage of dnmt1 knockout/knockdown embryos in zebrafish. First we generated a comprehensive DNA methylation landscape of EHT which revealed gradually hypermethylated regions associated with vasculogenesis. Taking advantage of dnmt1 deficient embryos we showed that the decreased DNA methylation blocked HSPC emergence. Mechanistically we demonstrated that the decreased DNA methylation increased the expression of arterial genes and Notch signaling thus contributing to defects in the EHT in dnmt1 deficient embryos. Herein we identified that DNA methylation as epigenetic regulator participates in the negative modulation of Notch signaling through inhibiting transcription during HSPC generation in zebrafish. Overall design: WGBS and RNA seq of Danio rerio in EC HE and HSPC.   pubmed:35502759   HE mut rep1 RNA GSM5694250   tissue:hemogenic endothelium cells|developmental stage:HE|genotype:dnmt1 mutant|region:AGM HE mut rep1 RNA Basecalls perfomed using CASAVA2.19 WGBS and RNA seq raw sequencing reads were first trimmed for adapter and low quality sequences. Then mapped to GRCz11 using BS Seeker2v2.1.8 and hisat2v2.2.1 with parameters " t Y m 0.04 bt2 end to end" and " known splicesite infile p 30 k 10 dta t" separately. Student's T test was used to perform DMR analysis for WGBS data. Gene expression level was quantified by HTSeqv0.12.4 and differentially expressed genesDEGs were determined by DESeq2v1.30.1 Genome build: GRCz11 Supplementary files format and content: RNA seq raw count matrix Supplementary files format and content: raw count.txt raw counts Supplementary files format and content: EC sib.bed DMRs of EC sibling compared with HE sibling and HSC sibling Supplementary files format and content: HE sib.bed DMRs of HE sibling compared with EC sibling and HSC sibling Supplementary files format and content: HSC sib.bed DMRs of HSC sibling compared with EC sibling and HE sibling Supplementary files format and content: EC HE sib.bed DMRs of EC and HE sibling Supplementary files format and content: HE HSC sib.bed DMRs of HE and HSC sibling Supplementary files format and content: EC sib mut.bed DMRs of EC sibling and EC mutant Supplementary files format and content: HE sib mut.bed DMRs of HE sibling and HE mutant Supplementary files format and content: HSC sib mut.bed DMRs of HSC sibling and HSC mutant hemogenic endothelium cells   Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3′ biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification   developmental stage:HE|genotype:dnmt1 mutant|region:AGM GSM5694250 GSM5694250: HE mut rep1 RNA; Danio rerio; RNA Seq GSM5694250   1 Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3′ biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification GEO Accession:GSM5694250 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP346708     HE_sib_1_1_RNA.fq.gz HE_sib_1_2_RNA.fq.gz fastq fastq 3246930300.0 10823101.0 GSM5694250 r1 0:150 1:150 A:938425919;C:639911754;G:671817291;T:996741337;N:33999 150 150     938425919 639911754 671817291 996741337 33999 SRX13164740 SRS11095942 SRA1331007 GEO Institute of Hematology and Blood Diseases Hospital 2 0.93431 0.92139 0.18855 0.18424 0.78886 0.79308 0.52892 0.52798 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_plate strtseq   China 2021-11-18 Undetermined Embryo Endothelium Cardiovascular System
67025 67025 SRR16973875 SRX13164739 SRS11095943 SRP346708 PRJNA781453 WGBS and RNA seq of Danio rerio in HSPC generation GSE189072 Other In this study we interrogated the role of DNA methylation in HSPC generation by taking advantage of dnmt1 knockout/knockdown embryos in zebrafish. First we generated a comprehensive DNA methylation landscape of EHT which revealed gradually hypermethylated regions associated with vasculogenesis. Taking advantage of dnmt1 deficient embryos we showed that the decreased DNA methylation blocked HSPC emergence. Mechanistically we demonstrated that the decreased DNA methylation increased the expression of arterial genes and Notch signaling thus contributing to defects in the EHT in dnmt1 deficient embryos. Herein we identified that DNA methylation as epigenetic regulator participates in the negative modulation of Notch signaling through inhibiting transcription during HSPC generation in zebrafish. Overall design: WGBS and RNA seq of Danio rerio in EC HE and HSPC.   pubmed:35502759   HE sib rep3 RNA GSM5694249   tissue:hemogenic endothelium cells|developmental stage:HE|genotype:sibling|region:AGM HE sib rep3 RNA Basecalls perfomed using CASAVA2.19 WGBS and RNA seq raw sequencing reads were first trimmed for adapter and low quality sequences. Then mapped to GRCz11 using BS Seeker2v2.1.8 and hisat2v2.2.1 with parameters " t Y m 0.04 bt2 end to end" and " known splicesite infile p 30 k 10 dta t" separately. Student's T test was used to perform DMR analysis for WGBS data. Gene expression level was quantified by HTSeqv0.12.4 and differentially expressed genesDEGs were determined by DESeq2v1.30.1 Genome build: GRCz11 Supplementary files format and content: RNA seq raw count matrix Supplementary files format and content: raw count.txt raw counts Supplementary files format and content: EC sib.bed DMRs of EC sibling compared with HE sibling and HSC sibling Supplementary files format and content: HE sib.bed DMRs of HE sibling compared with EC sibling and HSC sibling Supplementary files format and content: HSC sib.bed DMRs of HSC sibling compared with EC sibling and HE sibling Supplementary files format and content: EC HE sib.bed DMRs of EC and HE sibling Supplementary files format and content: HE HSC sib.bed DMRs of HE and HSC sibling Supplementary files format and content: EC sib mut.bed DMRs of EC sibling and EC mutant Supplementary files format and content: HE sib mut.bed DMRs of HE sibling and HE mutant Supplementary files format and content: HSC sib mut.bed DMRs of HSC sibling and HSC mutant hemogenic endothelium cells   Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3′ biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification   developmental stage:HE|genotype:sibling|region:AGM GSM5694249 GSM5694249: HE sib rep3 RNA; Danio rerio; RNA Seq GSM5694249   1 Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3′ biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification GEO Accession:GSM5694249 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP346708   loader:fastq load.py HE_mut_3_1_RNA.fq.gz HE_mut_3_2_RNA.fq.gz fastq fastq 7531062600.0 25103542.0 GSM5694249 r1 0:150 1:150 A:2130133337;C:1522023953;G:1620977746;T:2257902956;N:24608 150 150     2130133337 1522023953 1620977746 2257902956 24608 SRX13164739 SRS11095943 SRA1331007 GEO Institute of Hematology and Blood Diseases Hospital 2 0.93514 0.92906 0.1645 0.16366 0.76706 0.77086 0.4871 0.48732 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_plate strtseq   China 2021-11-18 Undetermined Embryo Endothelium Cardiovascular System
67026 67026 SRR16973874 SRX13164738 SRS11095941 SRP346708 PRJNA781453 WGBS and RNA seq of Danio rerio in HSPC generation GSE189072 Other In this study we interrogated the role of DNA methylation in HSPC generation by taking advantage of dnmt1 knockout/knockdown embryos in zebrafish. First we generated a comprehensive DNA methylation landscape of EHT which revealed gradually hypermethylated regions associated with vasculogenesis. Taking advantage of dnmt1 deficient embryos we showed that the decreased DNA methylation blocked HSPC emergence. Mechanistically we demonstrated that the decreased DNA methylation increased the expression of arterial genes and Notch signaling thus contributing to defects in the EHT in dnmt1 deficient embryos. Herein we identified that DNA methylation as epigenetic regulator participates in the negative modulation of Notch signaling through inhibiting transcription during HSPC generation in zebrafish. Overall design: WGBS and RNA seq of Danio rerio in EC HE and HSPC.   pubmed:35502759   HE sib rep2 RNA GSM5694248   tissue:hemogenic endothelium cells|developmental stage:HE|genotype:sibling|region:AGM HE sib rep2 RNA Basecalls perfomed using CASAVA2.19 WGBS and RNA seq raw sequencing reads were first trimmed for adapter and low quality sequences. Then mapped to GRCz11 using BS Seeker2v2.1.8 and hisat2v2.2.1 with parameters " t Y m 0.04 bt2 end to end" and " known splicesite infile p 30 k 10 dta t" separately. Student's T test was used to perform DMR analysis for WGBS data. Gene expression level was quantified by HTSeqv0.12.4 and differentially expressed genesDEGs were determined by DESeq2v1.30.1 Genome build: GRCz11 Supplementary files format and content: RNA seq raw count matrix Supplementary files format and content: raw count.txt raw counts Supplementary files format and content: EC sib.bed DMRs of EC sibling compared with HE sibling and HSC sibling Supplementary files format and content: HE sib.bed DMRs of HE sibling compared with EC sibling and HSC sibling Supplementary files format and content: HSC sib.bed DMRs of HSC sibling compared with EC sibling and HE sibling Supplementary files format and content: EC HE sib.bed DMRs of EC and HE sibling Supplementary files format and content: HE HSC sib.bed DMRs of HE and HSC sibling Supplementary files format and content: EC sib mut.bed DMRs of EC sibling and EC mutant Supplementary files format and content: HE sib mut.bed DMRs of HE sibling and HE mutant Supplementary files format and content: HSC sib mut.bed DMRs of HSC sibling and HSC mutant hemogenic endothelium cells   Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3′ biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification   developmental stage:HE|genotype:sibling|region:AGM GSM5694248 GSM5694248: HE sib rep2 RNA; Danio rerio; RNA Seq GSM5694248   1 Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3′ biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification GEO Accession:GSM5694248 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP346708     HE_mut_2_1_RNA.fq.gz HE_mut_2_2_RNA.fq.gz fastq fastq 3480792300.0 11602641.0 GSM5694248 r1 0:150 1:150 A:992011776;C:688862509;G:749973391;T:1049913481;N:31143 150 150     992011776 688862509 749973391 1049913481 31143 SRX13164738 SRS11095941 SRA1331007 GEO Institute of Hematology and Blood Diseases Hospital 2 0.92794 0.92305 0.17775 0.17805 0.77159 0.77705 0.51315 0.52162 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_plate strtseq   China 2021-11-18 Undetermined Embryo Endothelium Cardiovascular System
67027 67027 SRR16973873 SRX13164737 SRS11095940 SRP346708 PRJNA781453 WGBS and RNA seq of Danio rerio in HSPC generation GSE189072 Other In this study we interrogated the role of DNA methylation in HSPC generation by taking advantage of dnmt1 knockout/knockdown embryos in zebrafish. First we generated a comprehensive DNA methylation landscape of EHT which revealed gradually hypermethylated regions associated with vasculogenesis. Taking advantage of dnmt1 deficient embryos we showed that the decreased DNA methylation blocked HSPC emergence. Mechanistically we demonstrated that the decreased DNA methylation increased the expression of arterial genes and Notch signaling thus contributing to defects in the EHT in dnmt1 deficient embryos. Herein we identified that DNA methylation as epigenetic regulator participates in the negative modulation of Notch signaling through inhibiting transcription during HSPC generation in zebrafish. Overall design: WGBS and RNA seq of Danio rerio in EC HE and HSPC.   pubmed:35502759   HE sib rep1 RNA GSM5694247   tissue:hemogenic endothelium cells|developmental stage:HE|genotype:sibling|region:AGM HE sib rep1 RNA Basecalls perfomed using CASAVA2.19 WGBS and RNA seq raw sequencing reads were first trimmed for adapter and low quality sequences. Then mapped to GRCz11 using BS Seeker2v2.1.8 and hisat2v2.2.1 with parameters " t Y m 0.04 bt2 end to end" and " known splicesite infile p 30 k 10 dta t" separately. Student's T test was used to perform DMR analysis for WGBS data. Gene expression level was quantified by HTSeqv0.12.4 and differentially expressed genesDEGs were determined by DESeq2v1.30.1 Genome build: GRCz11 Supplementary files format and content: RNA seq raw count matrix Supplementary files format and content: raw count.txt raw counts Supplementary files format and content: EC sib.bed DMRs of EC sibling compared with HE sibling and HSC sibling Supplementary files format and content: HE sib.bed DMRs of HE sibling compared with EC sibling and HSC sibling Supplementary files format and content: HSC sib.bed DMRs of HSC sibling compared with EC sibling and HE sibling Supplementary files format and content: EC HE sib.bed DMRs of EC and HE sibling Supplementary files format and content: HE HSC sib.bed DMRs of HE and HSC sibling Supplementary files format and content: EC sib mut.bed DMRs of EC sibling and EC mutant Supplementary files format and content: HE sib mut.bed DMRs of HE sibling and HE mutant Supplementary files format and content: HSC sib mut.bed DMRs of HSC sibling and HSC mutant hemogenic endothelium cells   Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3′ biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification   developmental stage:HE|genotype:sibling|region:AGM GSM5694247 GSM5694247: HE sib rep1 RNA; Danio rerio; RNA Seq GSM5694247   1 Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3′ biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification GEO Accession:GSM5694247 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP346708     HE_mut_1_1_RNA.fq.gz HE_mut_1_2_RNA.fq.gz fastq fastq 4147333500.0 13824445.0 GSM5694247 r1 0:150 1:150 A:1182622375;C:805503602;G:885424962;T:1273741037;N:41524 150 150     1182622375 805503602 885424962 1273741037 41524 SRX13164737 SRS11095940 SRA1331007 GEO Institute of Hematology and Blood Diseases Hospital 2 0.92289 0.91984 0.22715 0.22596 0.77926 0.78644 0.54161 0.53476 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_plate strtseq   China 2021-11-18 Undetermined Embryo Endothelium Cardiovascular System
67028 67028 SRR16973872 SRX13164736 SRS11095939 SRP346708 PRJNA781453 WGBS and RNA seq of Danio rerio in HSPC generation GSE189072 Other In this study we interrogated the role of DNA methylation in HSPC generation by taking advantage of dnmt1 knockout/knockdown embryos in zebrafish. First we generated a comprehensive DNA methylation landscape of EHT which revealed gradually hypermethylated regions associated with vasculogenesis. Taking advantage of dnmt1 deficient embryos we showed that the decreased DNA methylation blocked HSPC emergence. Mechanistically we demonstrated that the decreased DNA methylation increased the expression of arterial genes and Notch signaling thus contributing to defects in the EHT in dnmt1 deficient embryos. Herein we identified that DNA methylation as epigenetic regulator participates in the negative modulation of Notch signaling through inhibiting transcription during HSPC generation in zebrafish. Overall design: WGBS and RNA seq of Danio rerio in EC HE and HSPC.   pubmed:35502759   EC mut rep3 RNA GSM5694246   tissue:endothelial cells|developmental stage:EC|genotype:dnmt1 mutant|region:AGM EC mut rep3 RNA Basecalls perfomed using CASAVA2.19 WGBS and RNA seq raw sequencing reads were first trimmed for adapter and low quality sequences. Then mapped to GRCz11 using BS Seeker2v2.1.8 and hisat2v2.2.1 with parameters " t Y m 0.04 bt2 end to end" and " known splicesite infile p 30 k 10 dta t" separately. Student's T test was used to perform DMR analysis for WGBS data. Gene expression level was quantified by HTSeqv0.12.4 and differentially expressed genesDEGs were determined by DESeq2v1.30.1 Genome build: GRCz11 Supplementary files format and content: RNA seq raw count matrix Supplementary files format and content: raw count.txt raw counts Supplementary files format and content: EC sib.bed DMRs of EC sibling compared with HE sibling and HSC sibling Supplementary files format and content: HE sib.bed DMRs of HE sibling compared with EC sibling and HSC sibling Supplementary files format and content: HSC sib.bed DMRs of HSC sibling compared with EC sibling and HE sibling Supplementary files format and content: EC HE sib.bed DMRs of EC and HE sibling Supplementary files format and content: HE HSC sib.bed DMRs of HE and HSC sibling Supplementary files format and content: EC sib mut.bed DMRs of EC sibling and EC mutant Supplementary files format and content: HE sib mut.bed DMRs of HE sibling and HE mutant Supplementary files format and content: HSC sib mut.bed DMRs of HSC sibling and HSC mutant endothelial cells   Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3′ biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification   developmental stage:EC|genotype:dnmt1 mutant|region:AGM GSM5694246 GSM5694246: EC mut rep3 RNA; Danio rerio; RNA Seq GSM5694246   1 Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3′ biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification GEO Accession:GSM5694246 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP346708   loader:fastq load.py EC_sib_3_1_RNA.fq.gz EC_sib_3_2_RNA.fq.gz fastq fastq 5197238700.0 17324129.0 GSM5694246 r1 0:150 1:150 A:1518447950;C:1011812171;G:1095102019;T:1571846375;N:30185 150 150     1518447950 1011812171 1095102019 1571846375 30185 SRX13164736 SRS11095939 SRA1331007 GEO Institute of Hematology and Blood Diseases Hospital 2 0.91741 0.90997 0.30958 0.30583 0.78573 0.79243 0.44787 0.56503 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_plate strtseq   China 2021-11-18 Undetermined Embryo Endothelium Cardiovascular System
67029 67029 SRR16973871 SRX13164735 SRS11095938 SRP346708 PRJNA781453 WGBS and RNA seq of Danio rerio in HSPC generation GSE189072 Other In this study we interrogated the role of DNA methylation in HSPC generation by taking advantage of dnmt1 knockout/knockdown embryos in zebrafish. First we generated a comprehensive DNA methylation landscape of EHT which revealed gradually hypermethylated regions associated with vasculogenesis. Taking advantage of dnmt1 deficient embryos we showed that the decreased DNA methylation blocked HSPC emergence. Mechanistically we demonstrated that the decreased DNA methylation increased the expression of arterial genes and Notch signaling thus contributing to defects in the EHT in dnmt1 deficient embryos. Herein we identified that DNA methylation as epigenetic regulator participates in the negative modulation of Notch signaling through inhibiting transcription during HSPC generation in zebrafish. Overall design: WGBS and RNA seq of Danio rerio in EC HE and HSPC.   pubmed:35502759   EC mut rep2 RNA GSM5694245   tissue:endothelial cells|developmental stage:EC|genotype:dnmt1 mutant|region:AGM EC mut rep2 RNA Basecalls perfomed using CASAVA2.19 WGBS and RNA seq raw sequencing reads were first trimmed for adapter and low quality sequences. Then mapped to GRCz11 using BS Seeker2v2.1.8 and hisat2v2.2.1 with parameters " t Y m 0.04 bt2 end to end" and " known splicesite infile p 30 k 10 dta t" separately. Student's T test was used to perform DMR analysis for WGBS data. Gene expression level was quantified by HTSeqv0.12.4 and differentially expressed genesDEGs were determined by DESeq2v1.30.1 Genome build: GRCz11 Supplementary files format and content: RNA seq raw count matrix Supplementary files format and content: raw count.txt raw counts Supplementary files format and content: EC sib.bed DMRs of EC sibling compared with HE sibling and HSC sibling Supplementary files format and content: HE sib.bed DMRs of HE sibling compared with EC sibling and HSC sibling Supplementary files format and content: HSC sib.bed DMRs of HSC sibling compared with EC sibling and HE sibling Supplementary files format and content: EC HE sib.bed DMRs of EC and HE sibling Supplementary files format and content: HE HSC sib.bed DMRs of HE and HSC sibling Supplementary files format and content: EC sib mut.bed DMRs of EC sibling and EC mutant Supplementary files format and content: HE sib mut.bed DMRs of HE sibling and HE mutant Supplementary files format and content: HSC sib mut.bed DMRs of HSC sibling and HSC mutant endothelial cells   Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3′ biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification   developmental stage:EC|genotype:dnmt1 mutant|region:AGM GSM5694245 GSM5694245: EC mut rep2 RNA; Danio rerio; RNA Seq GSM5694245   1 Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3′ biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification GEO Accession:GSM5694245 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP346708     EC_sib_2_1_RNA.fq.gz EC_sib_2_2_RNA.fq.gz fastq fastq 3166511400.0 10555038.0 GSM5694245 r1 0:150 1:150 A:953416270;C:589683319;G:624608777;T:998770674;N:32360 150 150     953416270 589683319 624608777 998770674 32360 SRX13164735 SRS11095938 SRA1331007 GEO Institute of Hematology and Blood Diseases Hospital 2 0.90602 0.89266 0.283 0.28004 0.78804 0.79259 0.46429 0.58332 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_plate strtseq   China 2021-11-18 Undetermined Embryo Endothelium Cardiovascular System
67030 67030 SRR16973870 SRX13164734 SRS11095937 SRP346708 PRJNA781453 WGBS and RNA seq of Danio rerio in HSPC generation GSE189072 Other In this study we interrogated the role of DNA methylation in HSPC generation by taking advantage of dnmt1 knockout/knockdown embryos in zebrafish. First we generated a comprehensive DNA methylation landscape of EHT which revealed gradually hypermethylated regions associated with vasculogenesis. Taking advantage of dnmt1 deficient embryos we showed that the decreased DNA methylation blocked HSPC emergence. Mechanistically we demonstrated that the decreased DNA methylation increased the expression of arterial genes and Notch signaling thus contributing to defects in the EHT in dnmt1 deficient embryos. Herein we identified that DNA methylation as epigenetic regulator participates in the negative modulation of Notch signaling through inhibiting transcription during HSPC generation in zebrafish. Overall design: WGBS and RNA seq of Danio rerio in EC HE and HSPC.   pubmed:35502759   EC mut rep1 RNA GSM5694244   tissue:endothelial cells|developmental stage:EC|genotype:dnmt1 mutant|region:AGM EC mut rep1 RNA Basecalls perfomed using CASAVA2.19 WGBS and RNA seq raw sequencing reads were first trimmed for adapter and low quality sequences. Then mapped to GRCz11 using BS Seeker2v2.1.8 and hisat2v2.2.1 with parameters " t Y m 0.04 bt2 end to end" and " known splicesite infile p 30 k 10 dta t" separately. Student's T test was used to perform DMR analysis for WGBS data. Gene expression level was quantified by HTSeqv0.12.4 and differentially expressed genesDEGs were determined by DESeq2v1.30.1 Genome build: GRCz11 Supplementary files format and content: RNA seq raw count matrix Supplementary files format and content: raw count.txt raw counts Supplementary files format and content: EC sib.bed DMRs of EC sibling compared with HE sibling and HSC sibling Supplementary files format and content: HE sib.bed DMRs of HE sibling compared with EC sibling and HSC sibling Supplementary files format and content: HSC sib.bed DMRs of HSC sibling compared with EC sibling and HE sibling Supplementary files format and content: EC HE sib.bed DMRs of EC and HE sibling Supplementary files format and content: HE HSC sib.bed DMRs of HE and HSC sibling Supplementary files format and content: EC sib mut.bed DMRs of EC sibling and EC mutant Supplementary files format and content: HE sib mut.bed DMRs of HE sibling and HE mutant Supplementary files format and content: HSC sib mut.bed DMRs of HSC sibling and HSC mutant endothelial cells   Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3′ biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification   developmental stage:EC|genotype:dnmt1 mutant|region:AGM GSM5694244 GSM5694244: EC mut rep1 RNA; Danio rerio; RNA Seq GSM5694244   1 Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3′ biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification GEO Accession:GSM5694244 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP346708     EC_sib_1_1_RNA.fq.gz EC_sib_1_2_RNA.fq.gz fastq fastq 3962208600.0 13207362.0 GSM5694244 r1 0:150 1:150 A:1157734424;C:769637879;G:815215301;T:1219572479;N:48517 150 150     1157734424 769637879 815215301 1219572479 48517 SRX13164734 SRS11095937 SRA1331007 GEO Institute of Hematology and Blood Diseases Hospital 2 0.9138 0.90509 0.21931 0.21725 0.77479 0.77741 0.5314 0.53073 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_plate strtseq   China 2021-11-18 Undetermined Embryo Endothelium Cardiovascular System
67031 67031 SRR16973869 SRX13164733 SRS11095936 SRP346708 PRJNA781453 WGBS and RNA seq of Danio rerio in HSPC generation GSE189072 Other In this study we interrogated the role of DNA methylation in HSPC generation by taking advantage of dnmt1 knockout/knockdown embryos in zebrafish. First we generated a comprehensive DNA methylation landscape of EHT which revealed gradually hypermethylated regions associated with vasculogenesis. Taking advantage of dnmt1 deficient embryos we showed that the decreased DNA methylation blocked HSPC emergence. Mechanistically we demonstrated that the decreased DNA methylation increased the expression of arterial genes and Notch signaling thus contributing to defects in the EHT in dnmt1 deficient embryos. Herein we identified that DNA methylation as epigenetic regulator participates in the negative modulation of Notch signaling through inhibiting transcription during HSPC generation in zebrafish. Overall design: WGBS and RNA seq of Danio rerio in EC HE and HSPC.   pubmed:35502759   EC sib rep3 RNA GSM5694243   tissue:endothelial cells|developmental stage:EC|genotype:sibling|region:AGM EC sib rep3 RNA Basecalls perfomed using CASAVA2.19 WGBS and RNA seq raw sequencing reads were first trimmed for adapter and low quality sequences. Then mapped to GRCz11 using BS Seeker2v2.1.8 and hisat2v2.2.1 with parameters " t Y m 0.04 bt2 end to end" and " known splicesite infile p 30 k 10 dta t" separately. Student's T test was used to perform DMR analysis for WGBS data. Gene expression level was quantified by HTSeqv0.12.4 and differentially expressed genesDEGs were determined by DESeq2v1.30.1 Genome build: GRCz11 Supplementary files format and content: RNA seq raw count matrix Supplementary files format and content: raw count.txt raw counts Supplementary files format and content: EC sib.bed DMRs of EC sibling compared with HE sibling and HSC sibling Supplementary files format and content: HE sib.bed DMRs of HE sibling compared with EC sibling and HSC sibling Supplementary files format and content: HSC sib.bed DMRs of HSC sibling compared with EC sibling and HE sibling Supplementary files format and content: EC HE sib.bed DMRs of EC and HE sibling Supplementary files format and content: HE HSC sib.bed DMRs of HE and HSC sibling Supplementary files format and content: EC sib mut.bed DMRs of EC sibling and EC mutant Supplementary files format and content: HE sib mut.bed DMRs of HE sibling and HE mutant Supplementary files format and content: HSC sib mut.bed DMRs of HSC sibling and HSC mutant endothelial cells   Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3′ biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification   developmental stage:EC|genotype:sibling|region:AGM GSM5694243 GSM5694243: EC sib rep3 RNA; Danio rerio; RNA Seq GSM5694243   1 Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3′ biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification GEO Accession:GSM5694243 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP346708   loader:fastq load.py EC_mut_3_1_RNA.fq.gz EC_mut_3_2_RNA.fq.gz fastq fastq 5214231600.0 17380772.0 GSM5694243 r1 0:150 1:150 A:1518201912;C:1020669101;G:1094674332;T:1580669249;N:17006 150 150     1518201912 1020669101 1094674332 1580669249 17006 SRX13164733 SRS11095936 SRA1331007 GEO Institute of Hematology and Blood Diseases Hospital 2 0.91916 0.91501 0.28949 0.28875 0.77536 0.77749 0.54408 0.54439 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_plate strtseq   China 2021-11-18 Undetermined Embryo Endothelium Cardiovascular System
67032 67032 SRR16973868 SRX13164732 SRS11095935 SRP346708 PRJNA781453 WGBS and RNA seq of Danio rerio in HSPC generation GSE189072 Other In this study we interrogated the role of DNA methylation in HSPC generation by taking advantage of dnmt1 knockout/knockdown embryos in zebrafish. First we generated a comprehensive DNA methylation landscape of EHT which revealed gradually hypermethylated regions associated with vasculogenesis. Taking advantage of dnmt1 deficient embryos we showed that the decreased DNA methylation blocked HSPC emergence. Mechanistically we demonstrated that the decreased DNA methylation increased the expression of arterial genes and Notch signaling thus contributing to defects in the EHT in dnmt1 deficient embryos. Herein we identified that DNA methylation as epigenetic regulator participates in the negative modulation of Notch signaling through inhibiting transcription during HSPC generation in zebrafish. Overall design: WGBS and RNA seq of Danio rerio in EC HE and HSPC.   pubmed:35502759   EC sib rep2 RNA GSM5694242   tissue:endothelial cells|developmental stage:EC|genotype:sibling|region:AGM EC sib rep2 RNA Basecalls perfomed using CASAVA2.19 WGBS and RNA seq raw sequencing reads were first trimmed for adapter and low quality sequences. Then mapped to GRCz11 using BS Seeker2v2.1.8 and hisat2v2.2.1 with parameters " t Y m 0.04 bt2 end to end" and " known splicesite infile p 30 k 10 dta t" separately. Student's T test was used to perform DMR analysis for WGBS data. Gene expression level was quantified by HTSeqv0.12.4 and differentially expressed genesDEGs were determined by DESeq2v1.30.1 Genome build: GRCz11 Supplementary files format and content: RNA seq raw count matrix Supplementary files format and content: raw count.txt raw counts Supplementary files format and content: EC sib.bed DMRs of EC sibling compared with HE sibling and HSC sibling Supplementary files format and content: HE sib.bed DMRs of HE sibling compared with EC sibling and HSC sibling Supplementary files format and content: HSC sib.bed DMRs of HSC sibling compared with EC sibling and HE sibling Supplementary files format and content: EC HE sib.bed DMRs of EC and HE sibling Supplementary files format and content: HE HSC sib.bed DMRs of HE and HSC sibling Supplementary files format and content: EC sib mut.bed DMRs of EC sibling and EC mutant Supplementary files format and content: HE sib mut.bed DMRs of HE sibling and HE mutant Supplementary files format and content: HSC sib mut.bed DMRs of HSC sibling and HSC mutant endothelial cells   Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3′ biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification   developmental stage:EC|genotype:sibling|region:AGM GSM5694242 GSM5694242: EC sib rep2 RNA; Danio rerio; RNA Seq GSM5694242   1 Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3′ biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification GEO Accession:GSM5694242 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP346708     EC_mut_2_1_RNA.fq.gz EC_mut_2_2_RNA.fq.gz fastq fastq 3551728200.0 11839094.0 GSM5694242 r1 0:150 1:150 A:1033665824;C:697141333;G:748608593;T:1072309959;N:2491 150 150     1033665824 697141333 748608593 1072309959 2491 SRX13164732 SRS11095935 SRA1331007 GEO Institute of Hematology and Blood Diseases Hospital 2 0.91086 0.91055 0.22761 0.22617 0.76611 0.77388 0.54742 0.54539 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_plate strtseq   China 2021-11-18 Undetermined Embryo Endothelium Cardiovascular System
67033 67033 SRR16973867 SRX13164731 SRS11095934 SRP346708 PRJNA781453 WGBS and RNA seq of Danio rerio in HSPC generation GSE189072 Other In this study we interrogated the role of DNA methylation in HSPC generation by taking advantage of dnmt1 knockout/knockdown embryos in zebrafish. First we generated a comprehensive DNA methylation landscape of EHT which revealed gradually hypermethylated regions associated with vasculogenesis. Taking advantage of dnmt1 deficient embryos we showed that the decreased DNA methylation blocked HSPC emergence. Mechanistically we demonstrated that the decreased DNA methylation increased the expression of arterial genes and Notch signaling thus contributing to defects in the EHT in dnmt1 deficient embryos. Herein we identified that DNA methylation as epigenetic regulator participates in the negative modulation of Notch signaling through inhibiting transcription during HSPC generation in zebrafish. Overall design: WGBS and RNA seq of Danio rerio in EC HE and HSPC.   pubmed:35502759   EC sib rep1 RNA GSM5694241   tissue:endothelial cells|developmental stage:EC|genotype:sibling|region:AGM EC sib rep1 RNA Basecalls perfomed using CASAVA2.19 WGBS and RNA seq raw sequencing reads were first trimmed for adapter and low quality sequences. Then mapped to GRCz11 using BS Seeker2v2.1.8 and hisat2v2.2.1 with parameters " t Y m 0.04 bt2 end to end" and " known splicesite infile p 30 k 10 dta t" separately. Student's T test was used to perform DMR analysis for WGBS data. Gene expression level was quantified by HTSeqv0.12.4 and differentially expressed genesDEGs were determined by DESeq2v1.30.1 Genome build: GRCz11 Supplementary files format and content: RNA seq raw count matrix Supplementary files format and content: raw count.txt raw counts Supplementary files format and content: EC sib.bed DMRs of EC sibling compared with HE sibling and HSC sibling Supplementary files format and content: HE sib.bed DMRs of HE sibling compared with EC sibling and HSC sibling Supplementary files format and content: HSC sib.bed DMRs of HSC sibling compared with EC sibling and HE sibling Supplementary files format and content: EC HE sib.bed DMRs of EC and HE sibling Supplementary files format and content: HE HSC sib.bed DMRs of HE and HSC sibling Supplementary files format and content: EC sib mut.bed DMRs of EC sibling and EC mutant Supplementary files format and content: HE sib mut.bed DMRs of HE sibling and HE mutant Supplementary files format and content: HSC sib mut.bed DMRs of HSC sibling and HSC mutant endothelial cells   Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3′ biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification   developmental stage:EC|genotype:sibling|region:AGM GSM5694241 GSM5694241: EC sib rep1 RNA; Danio rerio; RNA Seq GSM5694241   1 Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3′ biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification GEO Accession:GSM5694241 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP346708     EC_mut_1_1_RNA.fq.gz EC_mut_1_2_RNA.fq.gz fastq fastq 4174024500.0 13913415.0 GSM5694241 r1 0:150 1:150 A:1198561312;C:807832743;G:886085495;T:1281504164;N:40786 150 150     1198561312 807832743 886085495 1281504164 40786 SRX13164731 SRS11095934 SRA1331007 GEO Institute of Hematology and Blood Diseases Hospital 2 0.9162 0.91249 0.25639 0.25487 0.7767 0.78186 0.45792 0.43528 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_plate strtseq   China 2021-11-18 Undetermined Embryo Endothelium Cardiovascular System

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;