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126 rows where devstage_curation = "Pharyngula" and tissue_curation = "Endothelium"

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technology 4

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experiment.library_strategy 2

experiment.library_layout 2

tissue_curation_coarse 1

tissue_curation 1

  • Endothelium · 126 ✖

experiment.platform 1

experiment.library_source 1

devstage_curation_coarse 1

devstage_curation 1

  • Pharyngula · 126 ✖
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
38364 38364 SRR1793802 SRX869237 SRS840014 SRP053359 PRJNA274951 Lymphatic vessels arise from a niche of multipotent angioblasts within the floor of the cardinal vein GSE65751 Transcriptome Analysis How cells acquire their fate is a fundamental question in both developmental and regenerative biology. Multipotent progenitors undergo gradual cell fate restriction in response to temporal and positional cues from the microenvironment the nature of which is far from being clear. In the case of the lymphatic system venous endothelial cells are thought to give rise to lymphatic vessels through a process of trans differentiation. Upon expression of a set of transcription factors venous cells acquire a lymphatic fate and bud out to generate the lymphatic vasculature. In this work we challenge this view and show that while lymphatic endothelial cells LECs do arise in the Cardinal Vein CV they do so from a previously uncharacterized pool of multipotent angioblasts. Using lymphatic specific transgenic zebrafish in combination with endothelial photoconvertible reporters and long term live imaging we demonstrate that these multipotent angioblasts can generate not only lymphatic but also arterious and venous fates. We further reveal that the underlying endoderm serves as a source of Wnt5b which acts as a lymphatic inductive signal promoting the angioblast to lymphatic transition. Moreover Wnt5b induced lymphatic specification in human embryonic stem cells derived vascular progenitors suggesting that this process is evolutionary conserved. Our results uncover a novel mechanism of lymphatic vessel formation whereby multipotent angioblasts and not venous endothelial cells give rise to the lymphatic endothelium and provide the first characterization of their inductive niche. More broadly our findings highlight the CV as a plastic and heterogeneous structure containing different cell populations analogous to the hematopoietic niche in the aortic floor. Overall design: Following Kaede photoconversion of dorsal or ventral halves of the PCV in Tgfli1:gal4;uasKaede embryos at 24 hpf 6 embryos per group were used for FACS isolation of Kaede photconverted red ECs.   pubmed:25992545   d red ZF sample 0012 GSM1604058   tissue:Dorsal endothelial cells|strain:Tgfli1:gal4; uasKaede|developmental stage:24hpf d red ZF sample 0012 Libraries were sequenced on the Illumina HiSeq2500 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 20. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et al. 2012 demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations. Reads with the same unique molecular identifiers UMIs were colapsed for transcript counting. Genome build: Zv9 Supplementary files format and content: Tabular expression matrix includes number of transcript molecules. Dorsal endothelial cells   RNA was isolated using TRIzol with addition of ERCC spike ins and GenElute LPA Sigma The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL Seq multiplexing barocdes with slite modification were used. Each CEL Seq primer cointained a barcode and a unique moleculare identifier Teemu et al. 2011 The vPCV vs dPCV endothelial cells were analyzed at 24hpf strain:Tgfli1:gal4;uasKaede|developmental stage:24hpf GSM1604058 GSM1604058: d red ZF sample 0012; Danio rerio; RNA Seq GSM1604058   1 RNA was isolated using TRIzol with addition of ERCC spike ins and GenElute LPA Sigma The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL Seq multiplexing barocdes with slite modification were used. Each CEL Seq primer cointained a barcode and a unique moleculare identifier Teemu et al. 2011 GEO Accession:GSM1604058 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP053359     d_red_ZF_sample_0012.fastq.gz fastq 136949295.0 3912837.0 GSM1604058 r1 0:35 A:38967686;C:29235653;G:29781723;T:38764742;N:199491 35       38967686 29235653 29781723 38764742 199491 SRX869237 SRS840014 SRA236924 GEO Itai Yanai, Biology, Technion - Israel Institute of Technology 1 0.50546   0.22201   0.91524   0.49457   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2015-02-09 Pharyngula Embryo Endothelium Cardiovascular System
38365 38365 SRR1793801 SRX869236 SRS840015 SRP053359 PRJNA274951 Lymphatic vessels arise from a niche of multipotent angioblasts within the floor of the cardinal vein GSE65751 Transcriptome Analysis How cells acquire their fate is a fundamental question in both developmental and regenerative biology. Multipotent progenitors undergo gradual cell fate restriction in response to temporal and positional cues from the microenvironment the nature of which is far from being clear. In the case of the lymphatic system venous endothelial cells are thought to give rise to lymphatic vessels through a process of trans differentiation. Upon expression of a set of transcription factors venous cells acquire a lymphatic fate and bud out to generate the lymphatic vasculature. In this work we challenge this view and show that while lymphatic endothelial cells LECs do arise in the Cardinal Vein CV they do so from a previously uncharacterized pool of multipotent angioblasts. Using lymphatic specific transgenic zebrafish in combination with endothelial photoconvertible reporters and long term live imaging we demonstrate that these multipotent angioblasts can generate not only lymphatic but also arterious and venous fates. We further reveal that the underlying endoderm serves as a source of Wnt5b which acts as a lymphatic inductive signal promoting the angioblast to lymphatic transition. Moreover Wnt5b induced lymphatic specification in human embryonic stem cells derived vascular progenitors suggesting that this process is evolutionary conserved. Our results uncover a novel mechanism of lymphatic vessel formation whereby multipotent angioblasts and not venous endothelial cells give rise to the lymphatic endothelium and provide the first characterization of their inductive niche. More broadly our findings highlight the CV as a plastic and heterogeneous structure containing different cell populations analogous to the hematopoietic niche in the aortic floor. Overall design: Following Kaede photoconversion of dorsal or ventral halves of the PCV in Tgfli1:gal4;uasKaede embryos at 24 hpf 6 embryos per group were used for FACS isolation of Kaede photconverted red ECs.   pubmed:25992545   d red ZF sample 0008 GSM1604057   tissue:Dorsal endothelial cells|strain:Tgfli1:gal4; uasKaede|developmental stage:24hpf d red ZF sample 0008 Libraries were sequenced on the Illumina HiSeq2500 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 20. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et al. 2012 demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations. Reads with the same unique molecular identifiers UMIs were colapsed for transcript counting. Genome build: Zv9 Supplementary files format and content: Tabular expression matrix includes number of transcript molecules. Dorsal endothelial cells   RNA was isolated using TRIzol with addition of ERCC spike ins and GenElute LPA Sigma The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL Seq multiplexing barocdes with slite modification were used. Each CEL Seq primer cointained a barcode and a unique moleculare identifier Teemu et al. 2011 The vPCV vs dPCV endothelial cells were analyzed at 24hpf strain:Tgfli1:gal4;uasKaede|developmental stage:24hpf GSM1604057 GSM1604057: d red ZF sample 0008; Danio rerio; RNA Seq GSM1604057   1 RNA was isolated using TRIzol with addition of ERCC spike ins and GenElute LPA Sigma The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL Seq multiplexing barocdes with slite modification were used. Each CEL Seq primer cointained a barcode and a unique moleculare identifier Teemu et al. 2011 GEO Accession:GSM1604057 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP053359     d_red_ZF_sample_0008.fastq.gz fastq 230204380.0 6577268.0 GSM1604057 r1 0:35 A:63286154;C:49924891;G:50948035;T:65703538;N:341762 35       63286154 49924891 50948035 65703538 341762 SRX869236 SRS840015 SRA236924 GEO Itai Yanai, Biology, Technion - Israel Institute of Technology 1 0.59898   0.14092   0.89073   0.49292   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2015-02-09 Pharyngula Embryo Endothelium Cardiovascular System
38366 38366 SRR1793800 SRX869235 SRS840013 SRP053359 PRJNA274951 Lymphatic vessels arise from a niche of multipotent angioblasts within the floor of the cardinal vein GSE65751 Transcriptome Analysis How cells acquire their fate is a fundamental question in both developmental and regenerative biology. Multipotent progenitors undergo gradual cell fate restriction in response to temporal and positional cues from the microenvironment the nature of which is far from being clear. In the case of the lymphatic system venous endothelial cells are thought to give rise to lymphatic vessels through a process of trans differentiation. Upon expression of a set of transcription factors venous cells acquire a lymphatic fate and bud out to generate the lymphatic vasculature. In this work we challenge this view and show that while lymphatic endothelial cells LECs do arise in the Cardinal Vein CV they do so from a previously uncharacterized pool of multipotent angioblasts. Using lymphatic specific transgenic zebrafish in combination with endothelial photoconvertible reporters and long term live imaging we demonstrate that these multipotent angioblasts can generate not only lymphatic but also arterious and venous fates. We further reveal that the underlying endoderm serves as a source of Wnt5b which acts as a lymphatic inductive signal promoting the angioblast to lymphatic transition. Moreover Wnt5b induced lymphatic specification in human embryonic stem cells derived vascular progenitors suggesting that this process is evolutionary conserved. Our results uncover a novel mechanism of lymphatic vessel formation whereby multipotent angioblasts and not venous endothelial cells give rise to the lymphatic endothelium and provide the first characterization of their inductive niche. More broadly our findings highlight the CV as a plastic and heterogeneous structure containing different cell populations analogous to the hematopoietic niche in the aortic floor. Overall design: Following Kaede photoconversion of dorsal or ventral halves of the PCV in Tgfli1:gal4;uasKaede embryos at 24 hpf 6 embryos per group were used for FACS isolation of Kaede photconverted red ECs.   pubmed:25992545   V red ZF sample 0011 GSM1604056   tissue:Ventral endothelial cells|strain:Tgfli1:gal4; uasKaede|developmental stage:24hpf V red ZF sample 0011 Libraries were sequenced on the Illumina HiSeq2500 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 20. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et al. 2012 demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations. Reads with the same unique molecular identifiers UMIs were colapsed for transcript counting. Genome build: Zv9 Supplementary files format and content: Tabular expression matrix includes number of transcript molecules. Ventral endothelial cells   RNA was isolated using TRIzol with addition of ERCC spike ins and GenElute LPA Sigma The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL Seq multiplexing barocdes with slite modification were used. Each CEL Seq primer cointained a barcode and a unique moleculare identifier Teemu et al. 2011 The vPCV vs dPCV endothelial cells were analyzed at 24hpf strain:Tgfli1:gal4;uasKaede|developmental stage:24hpf GSM1604056 GSM1604056: V red ZF sample 0011; Danio rerio; RNA Seq GSM1604056   1 RNA was isolated using TRIzol with addition of ERCC spike ins and GenElute LPA Sigma The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL Seq multiplexing barocdes with slite modification were used. Each CEL Seq primer cointained a barcode and a unique moleculare identifier Teemu et al. 2011 GEO Accession:GSM1604056 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP053359     V_red_ZF_sample_0011.fastq.gz fastq 146319705.0 4180563.0 GSM1604056 r1 0:35 A:40991954;C:30892087;G:32112709;T:42103782;N:219173 35       40991954 30892087 32112709 42103782 219173 SRX869235 SRS840013 SRA236924 GEO Itai Yanai, Biology, Technion - Israel Institute of Technology 1 0.57038   0.16086   0.89014   0.53016   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2015-02-09 Pharyngula Embryo Endothelium Cardiovascular System
38367 38367 SRR1793799 SRX869234 SRS840016 SRP053359 PRJNA274951 Lymphatic vessels arise from a niche of multipotent angioblasts within the floor of the cardinal vein GSE65751 Transcriptome Analysis How cells acquire their fate is a fundamental question in both developmental and regenerative biology. Multipotent progenitors undergo gradual cell fate restriction in response to temporal and positional cues from the microenvironment the nature of which is far from being clear. In the case of the lymphatic system venous endothelial cells are thought to give rise to lymphatic vessels through a process of trans differentiation. Upon expression of a set of transcription factors venous cells acquire a lymphatic fate and bud out to generate the lymphatic vasculature. In this work we challenge this view and show that while lymphatic endothelial cells LECs do arise in the Cardinal Vein CV they do so from a previously uncharacterized pool of multipotent angioblasts. Using lymphatic specific transgenic zebrafish in combination with endothelial photoconvertible reporters and long term live imaging we demonstrate that these multipotent angioblasts can generate not only lymphatic but also arterious and venous fates. We further reveal that the underlying endoderm serves as a source of Wnt5b which acts as a lymphatic inductive signal promoting the angioblast to lymphatic transition. Moreover Wnt5b induced lymphatic specification in human embryonic stem cells derived vascular progenitors suggesting that this process is evolutionary conserved. Our results uncover a novel mechanism of lymphatic vessel formation whereby multipotent angioblasts and not venous endothelial cells give rise to the lymphatic endothelium and provide the first characterization of their inductive niche. More broadly our findings highlight the CV as a plastic and heterogeneous structure containing different cell populations analogous to the hematopoietic niche in the aortic floor. Overall design: Following Kaede photoconversion of dorsal or ventral halves of the PCV in Tgfli1:gal4;uasKaede embryos at 24 hpf 6 embryos per group were used for FACS isolation of Kaede photconverted red ECs.   pubmed:25992545   V red ZF sample 0007 GSM1604055   tissue:Ventral endothelial cells|strain:Tgfli1:gal4; uasKaede|developmental stage:24hpf V red ZF sample 0007 Libraries were sequenced on the Illumina HiSeq2500 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 20. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et al. 2012 demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations. Reads with the same unique molecular identifiers UMIs were colapsed for transcript counting. Genome build: Zv9 Supplementary files format and content: Tabular expression matrix includes number of transcript molecules. Ventral endothelial cells   RNA was isolated using TRIzol with addition of ERCC spike ins and GenElute LPA Sigma The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL Seq multiplexing barocdes with slite modification were used. Each CEL Seq primer cointained a barcode and a unique moleculare identifier Teemu et al. 2011 The vPCV vs dPCV endothelial cells were analyzed at 24hpf strain:Tgfli1:gal4;uasKaede|developmental stage:24hpf GSM1604055 GSM1604055: V red ZF sample 0007; Danio rerio; RNA Seq GSM1604055   1 RNA was isolated using TRIzol with addition of ERCC spike ins and GenElute LPA Sigma The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL Seq multiplexing barocdes with slite modification were used. Each CEL Seq primer cointained a barcode and a unique moleculare identifier Teemu et al. 2011 GEO Accession:GSM1604055 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP053359     V_red_ZF_sample_0007.fastq.gz fastq 219537045.0 6272487.0 GSM1604055 r1 0:35 A:61562432;C:46586451;G:48274564;T:62792331;N:321267 35       61562432 46586451 48274564 62792331 321267 SRX869234 SRS840016 SRA236924 GEO Itai Yanai, Biology, Technion - Israel Institute of Technology 1 0.57949   0.1659   0.88187   0.51446   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2015-02-09 Pharyngula Embryo Endothelium Cardiovascular System
40971 40971 SRR3498279 SRX1756825 SRS1433356 SRP074847 PRJNA321312 mRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues GSE81335 Transcriptome Analysis Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages parent bioproject:PRJNA321317 pubmed:28350988;pubmed:33273096   24hpf E1 GSM2150743   source name:Endothelial cell|developmental stage:24 hpf|tissue:Endothelial|stain:GFP 24hpf E1 Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include FPKM values for each Sample . Endothelial cell   Transgenic fish were treated with Liberase to dissociate the cells. post FACS sorting the GFP positive RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473. developmental stage:24 hpf|tissue:Endothelial|stain:GFP GSM2150743 GSM2150743: 24hpf E1; Danio rerio; RNA Seq GSM2150743   1 Transgenic fish were treated with Liberase to dissociate the cells. post FACS sorting the GFP positive RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM2150743 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer   SRP074847     EF_033_001_ATCACG_L002_R1.fastq.gz fastq 426238476.0 5608401.0 GSM2150743 r1 0:76 A:113332066;C:95045840;G:93307502;T:118935708;N:5617360 76       113332066 95045840 93307502 118935708 5617360 SRX1756825 SRS1433356 SRA424807 GEO Internal Medicine, Yale University 1 0.88651   0.15752   0.72805   0.48414   76   B   usable mapping rate illumina early_illumina unknown small_rna trueseq bulk unknown unknown   United States 2016-05-11 Pharyngula Embryo Endothelium Cardiovascular System
40977 40977 SRR3498289 SRX1756835 SRS1433366 SRP074848 PRJNA321321 microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues GSE81340 Transcriptome Analysis Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate parent bioproject:PRJNA321317 pubmed:28350988;pubmed:33273096   NoEndo 24hpf E1 GSM2150814   source name:Endothelial cell|developmental stage:24hpf|tissue:Endothelial|stain:GFP NoEndo 24hpf E1 Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ... Endothelial cell   Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473. developmental stage:24hpf|tissue:Endothelial|stain:GFP GSM2150814 GSM2150814: NoEndo 24hpf E1; Danio rerio; miRNA Seq GSM2150814   1 Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM2150814 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer   SRP074848     NoEndo_24hpf_E1.fastq.gz fastq 1422085704.0 18711654.0 GSM2150814 r1 0:76 A:347700492;C:356065333;G:376424133;T:341806001;N:89745 76       347700492 356065333 376424133 341806001 89745 SRX1756835 SRS1433366 SRA424808 GEO Internal Medicine, Yale University 1 0.0   0.0   1.0       76   T   under 1.2% mapping rate illumina early_illumina unknown size_fractionation trueseq bulk unknown unknown   United States 2016-05-11 Pharyngula Embryo Endothelium Cardiovascular System
40983 40983 SRR3498283 SRX1756829 SRS1433360 SRP074848 PRJNA321321 microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues GSE81340 Transcriptome Analysis Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate parent bioproject:PRJNA321317 pubmed:28350988;pubmed:33273096   Endo 24hpf E1 GSM2150808   source name:Endothelial cell|developmental stage:24hpf|tissue:Endothelial|stain:GFP Endo 24hpf E1 Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ... Endothelial cell   Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473. developmental stage:24hpf|tissue:Endothelial|stain:GFP GSM2150808 GSM2150808: Endo 24hpf E1; Danio rerio; miRNA Seq GSM2150808   1 Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM2150808 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer   SRP074848     Endo_24hpf_E1.fastq.gz fastq 1527500440.0 20098690.0 GSM2150808 r1 0:76 A:356712587;C:354608109;G:432977038;T:383106520;N:96186 76       356712587 354608109 432977038 383106520 96186 SRX1756829 SRS1433360 SRA424808 GEO Internal Medicine, Yale University 1 0.0   0.0   1.0       76   T   under 1.2% mapping rate illumina early_illumina unknown size_fractionation trueseq bulk unknown unknown   United States 2016-05-11 Pharyngula Embryo Endothelium Cardiovascular System
41146 41146 SRR3742564 SRX1896783 SRS1539775 SRP077871 PRJNA327749 Gene expression profiles of endothelial cells from mutants and siblings of tsu3994 GSE83987 Transcriptome Analysis Through RNA seq we report endothelial cells from mutants had 1063 up regulated and 132 down regulated genes >2.0 fold with false discovery rate <0.001 when compared to siblings. Overall design: Examination of gene exprssion profiles of endothelial cells from siblings and mutants of tsu3994   pubmed:28003365   Mt GSM2224910   tissue:kdrl:GFP+ Endothelial cells|genetic background:tsu3994;Tgkdrl;GFP cross|genotype/variation:Morphologically mutant embryo|Stage:44 hpf type:Endothelial cells Mt HCS3.3.20 RTA 2.5.2 and bcl2fastq2 v2.16 were used for basecalling. Sequenced reads were remove reads with adaptors and remove reads in which unknown bases are more than 10% remove reads in which unknown bases are more than 10%.We use Bowtie2 with parameters q phred64 sensitive dpad 0 gbar 99999999 mp 1 1 np 1 score min L 0 0.1 p 16 k 200 to map clean reads to reference gene and use BWA with parameters o 1 e 50 i 50 L k 2 l 31 t 4 q 10 to reference genome Danio rerio.GRCz10.dna.toplevel.fa . RSEM is a quantification tool that computed Maximum likelihood abundance estimates using the Expectation Maximization EM algorithm for its statistical model . FPKM fragment Per Kilobase of gene per Megabase of library size method is used in calculated expression level. Genome build: Zv10 Supplementary files format and content: tab delimited text files include FPKM values for each Sample kdrl:GFP+ Endothelial cells   Morphologically normal siblings and mutant embryos from crosses of Tgkdrl:GFP; gbf1tsu3994/+ at 44 hpf were dechorionated and disintegrated completely to prepare single cell suspension. Then kdrl:GFP+ ECs were sorted by flow cytomer FACSAria BD and MoFlo XDP BeckMan and positive cells were confirmed by microscopy. Total mRNAs were extracted with RNeasy Mini Kit QIAGEN. The total RNA samples are first treated with DNase I to degrade any possible DNA contamination. Then the mRNA is enriched by using the oligo dT magnetic beads. Mixed with the fragmentation buffer the mRNA is fragmented into short fragments. Then the first strand of cDNA is synthesized by using random hexamer primer. Buffer dNTPs RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with magnetic beads. End reparation and 3’ end single nucleotide A adenine addition is then performed. Finally sequencing adaptors are ligated to the fragments. The fragments are enriched by PCR amplification.During the QC step Agilent 2100 Bioanaylzer and ABI StepOnePlus Real Time PCR System are used to qualify and quantify of the sample library. The library products are ready for sequencing via Illumina HiSeqTM 2000 or other sequencer when necessary.   genetic background:tsu3994;Tgkdrl;GFP cross|genotype/variation:Morphologically mutant embryo|Stage:44 hpf type:Endothelial cells GSM2224910 GSM2224910: Mt; Danio rerio; RNA Seq GSM2224910   1 Morphologically normal siblings and mutant embryos from crosses of Tgkdrl:GFP; gbf1tsu3994/+ at 44 hpf were dechorionated and disintegrated completely to prepare single cell suspension. Then kdrl:GFP+ ECs were sorted by flow cytomer FACSAria BD and MoFlo XDP BeckMan and positive cells were confirmed by microscopy. Total mRNAs were extracted with RNeasy Mini Kit QIAGEN. The total RNA samples are first treated with DNase I to degrade any possible DNA contamination. Then the mRNA is enriched by using the oligo dT magnetic beads. Mixed with the fragmentation buffer the mRNA is fragmented into short fragments. Then the first strand of cDNA is synthesized by using random hexamer primer. Buffer dNTPs RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with magnetic beads. End reparation and 3’ end single nucleotide A adenine addition is then performed. Finally sequencing adaptors are ligated to the fragments. The fragments are enriched by PCR amplification.During the QC step Agilent 2100 Bioanaylzer and ABI StepOnePlus Real Time PCR System are used to qualify and quantify of the sample library. The library products are ready for sequencing via Illumina HiSeqTM 2000 or other sequencer when necessary. GEO Accession:GSM2224910 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP077871     160123_I114_FCH52M2BBXX_L2_WHFISoiqRAABRAAPEI-144_1.fq.gz fastq 262444686.0 5356014.0 GSM2224910 r1 0:49 A:66548564;C:63544339;G:66582385;T:65755749;N:13649 49       66548564 63544339 66582385 65755749 13649 SRX1896783 SRS1539775 SRA437681 GEO Anming Meng, School of Lifesciences, Tsinghua University 1 0.92714   0.05568   0.73423   0.48371   49   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2016-07-04 Pharyngula Embryo Endothelium Cardiovascular System
41147 41147 SRR3742565 SRX1896783 SRS1539775 SRP077871 PRJNA327749 Gene expression profiles of endothelial cells from mutants and siblings of tsu3994 GSE83987 Transcriptome Analysis Through RNA seq we report endothelial cells from mutants had 1063 up regulated and 132 down regulated genes >2.0 fold with false discovery rate <0.001 when compared to siblings. Overall design: Examination of gene exprssion profiles of endothelial cells from siblings and mutants of tsu3994   pubmed:28003365   Mt GSM2224910   tissue:kdrl:GFP+ Endothelial cells|genetic background:tsu3994;Tgkdrl;GFP cross|genotype/variation:Morphologically mutant embryo|Stage:44 hpf type:Endothelial cells Mt HCS3.3.20 RTA 2.5.2 and bcl2fastq2 v2.16 were used for basecalling. Sequenced reads were remove reads with adaptors and remove reads in which unknown bases are more than 10% remove reads in which unknown bases are more than 10%.We use Bowtie2 with parameters q phred64 sensitive dpad 0 gbar 99999999 mp 1 1 np 1 score min L 0 0.1 p 16 k 200 to map clean reads to reference gene and use BWA with parameters o 1 e 50 i 50 L k 2 l 31 t 4 q 10 to reference genome Danio rerio.GRCz10.dna.toplevel.fa . RSEM is a quantification tool that computed Maximum likelihood abundance estimates using the Expectation Maximization EM algorithm for its statistical model . FPKM fragment Per Kilobase of gene per Megabase of library size method is used in calculated expression level. Genome build: Zv10 Supplementary files format and content: tab delimited text files include FPKM values for each Sample kdrl:GFP+ Endothelial cells   Morphologically normal siblings and mutant embryos from crosses of Tgkdrl:GFP; gbf1tsu3994/+ at 44 hpf were dechorionated and disintegrated completely to prepare single cell suspension. Then kdrl:GFP+ ECs were sorted by flow cytomer FACSAria BD and MoFlo XDP BeckMan and positive cells were confirmed by microscopy. Total mRNAs were extracted with RNeasy Mini Kit QIAGEN. The total RNA samples are first treated with DNase I to degrade any possible DNA contamination. Then the mRNA is enriched by using the oligo dT magnetic beads. Mixed with the fragmentation buffer the mRNA is fragmented into short fragments. Then the first strand of cDNA is synthesized by using random hexamer primer. Buffer dNTPs RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with magnetic beads. End reparation and 3’ end single nucleotide A adenine addition is then performed. Finally sequencing adaptors are ligated to the fragments. The fragments are enriched by PCR amplification.During the QC step Agilent 2100 Bioanaylzer and ABI StepOnePlus Real Time PCR System are used to qualify and quantify of the sample library. The library products are ready for sequencing via Illumina HiSeqTM 2000 or other sequencer when necessary.   genetic background:tsu3994;Tgkdrl;GFP cross|genotype/variation:Morphologically mutant embryo|Stage:44 hpf type:Endothelial cells GSM2224910 GSM2224910: Mt; Danio rerio; RNA Seq GSM2224910   1 Morphologically normal siblings and mutant embryos from crosses of Tgkdrl:GFP; gbf1tsu3994/+ at 44 hpf were dechorionated and disintegrated completely to prepare single cell suspension. Then kdrl:GFP+ ECs were sorted by flow cytomer FACSAria BD and MoFlo XDP BeckMan and positive cells were confirmed by microscopy. Total mRNAs were extracted with RNeasy Mini Kit QIAGEN. The total RNA samples are first treated with DNase I to degrade any possible DNA contamination. Then the mRNA is enriched by using the oligo dT magnetic beads. Mixed with the fragmentation buffer the mRNA is fragmented into short fragments. Then the first strand of cDNA is synthesized by using random hexamer primer. Buffer dNTPs RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with magnetic beads. End reparation and 3’ end single nucleotide A adenine addition is then performed. Finally sequencing adaptors are ligated to the fragments. The fragments are enriched by PCR amplification.During the QC step Agilent 2100 Bioanaylzer and ABI StepOnePlus Real Time PCR System are used to qualify and quantify of the sample library. The library products are ready for sequencing via Illumina HiSeqTM 2000 or other sequencer when necessary. GEO Accession:GSM2224910 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP077871     160204_I136_FCH55MNBBXX_L6_WHFISoiqRAABRAAPEI-144_1.fq.gz fastq 448147973.0 9145877.0 GSM2224910 r2 0:49 A:113623842;C:108767789;G:113689061;T:112055179;N:12102 49       113623842 108767789 113689061 112055179 12102 SRX1896783 SRS1539775 SRA437681 GEO Anming Meng, School of Lifesciences, Tsinghua University 1 0.91636   0.05377   0.73545   0.48441   49   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2016-07-04 Pharyngula Embryo Endothelium Cardiovascular System
41148 41148 SRR3742562 SRX1896782 SRS1539774 SRP077871 PRJNA327749 Gene expression profiles of endothelial cells from mutants and siblings of tsu3994 GSE83987 Transcriptome Analysis Through RNA seq we report endothelial cells from mutants had 1063 up regulated and 132 down regulated genes >2.0 fold with false discovery rate <0.001 when compared to siblings. Overall design: Examination of gene exprssion profiles of endothelial cells from siblings and mutants of tsu3994   pubmed:28003365   Sib GSM2224909   tissue:kdrl:GFP+ Endothelial cells|genetic background:tsu3994;Tgkdrl;GFP cross|genotype/variation:Morphologically normal siblings embryo|Stage:44 hpf type:Endothelial cells Sib HCS3.3.20 RTA 2.5.2 and bcl2fastq2 v2.16 were used for basecalling. Sequenced reads were remove reads with adaptors and remove reads in which unknown bases are more than 10% remove reads in which unknown bases are more than 10%.We use Bowtie2 with parameters q phred64 sensitive dpad 0 gbar 99999999 mp 1 1 np 1 score min L 0 0.1 p 16 k 200 to map clean reads to reference gene and use BWA with parameters o 1 e 50 i 50 L k 2 l 31 t 4 q 10 to reference genome Danio rerio.GRCz10.dna.toplevel.fa . RSEM is a quantification tool that computed Maximum likelihood abundance estimates using the Expectation Maximization EM algorithm for its statistical model . FPKM fragment Per Kilobase of gene per Megabase of library size method is used in calculated expression level. Genome build: Zv10 Supplementary files format and content: tab delimited text files include FPKM values for each Sample kdrl:GFP+ Endothelial cells   Morphologically normal siblings and mutant embryos from crosses of Tgkdrl:GFP; gbf1tsu3994/+ at 44 hpf were dechorionated and disintegrated completely to prepare single cell suspension. Then kdrl:GFP+ ECs were sorted by flow cytomer FACSAria BD and MoFlo XDP BeckMan and positive cells were confirmed by microscopy. Total mRNAs were extracted with RNeasy Mini Kit QIAGEN. The total RNA samples are first treated with DNase I to degrade any possible DNA contamination. Then the mRNA is enriched by using the oligo dT magnetic beads. Mixed with the fragmentation buffer the mRNA is fragmented into short fragments. Then the first strand of cDNA is synthesized by using random hexamer primer. Buffer dNTPs RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with magnetic beads. End reparation and 3’ end single nucleotide A adenine addition is then performed. Finally sequencing adaptors are ligated to the fragments. The fragments are enriched by PCR amplification.During the QC step Agilent 2100 Bioanaylzer and ABI StepOnePlus Real Time PCR System are used to qualify and quantify of the sample library. The library products are ready for sequencing via Illumina HiSeqTM 2000 or other sequencer when necessary.   genetic background:tsu3994;Tgkdrl;GFP cross|genotype/variation:Morphologically normal siblings embryo|Stage:44 hpf type:Endothelial cells GSM2224909 GSM2224909: Sib; Danio rerio; RNA Seq GSM2224909   1 Morphologically normal siblings and mutant embryos from crosses of Tgkdrl:GFP; gbf1tsu3994/+ at 44 hpf were dechorionated and disintegrated completely to prepare single cell suspension. Then kdrl:GFP+ ECs were sorted by flow cytomer FACSAria BD and MoFlo XDP BeckMan and positive cells were confirmed by microscopy. Total mRNAs were extracted with RNeasy Mini Kit QIAGEN. The total RNA samples are first treated with DNase I to degrade any possible DNA contamination. Then the mRNA is enriched by using the oligo dT magnetic beads. Mixed with the fragmentation buffer the mRNA is fragmented into short fragments. Then the first strand of cDNA is synthesized by using random hexamer primer. Buffer dNTPs RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with magnetic beads. End reparation and 3’ end single nucleotide A adenine addition is then performed. Finally sequencing adaptors are ligated to the fragments. The fragments are enriched by PCR amplification.During the QC step Agilent 2100 Bioanaylzer and ABI StepOnePlus Real Time PCR System are used to qualify and quantify of the sample library. The library products are ready for sequencing via Illumina HiSeqTM 2000 or other sequencer when necessary. GEO Accession:GSM2224909 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP077871     160123_I114_FCH52M2BBXX_L2_WHFISoiqRAAARAAPEI-100_1.fq.gz fastq 180708423.0 3687927.0 GSM2224909 r1 0:49 A:45675389;C:44261209;G:46002295;T:44768361;N:1169 49       45675389 44261209 46002295 44768361 1169 SRX1896782 SRS1539774 SRA437681 GEO Anming Meng, School of Lifesciences, Tsinghua University 1 0.93956   0.0479   0.75276   0.47889   49   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2016-07-04 Pharyngula Embryo Endothelium Cardiovascular System
41149 41149 SRR3742563 SRX1896782 SRS1539774 SRP077871 PRJNA327749 Gene expression profiles of endothelial cells from mutants and siblings of tsu3994 GSE83987 Transcriptome Analysis Through RNA seq we report endothelial cells from mutants had 1063 up regulated and 132 down regulated genes >2.0 fold with false discovery rate <0.001 when compared to siblings. Overall design: Examination of gene exprssion profiles of endothelial cells from siblings and mutants of tsu3994   pubmed:28003365   Sib GSM2224909   tissue:kdrl:GFP+ Endothelial cells|genetic background:tsu3994;Tgkdrl;GFP cross|genotype/variation:Morphologically normal siblings embryo|Stage:44 hpf type:Endothelial cells Sib HCS3.3.20 RTA 2.5.2 and bcl2fastq2 v2.16 were used for basecalling. Sequenced reads were remove reads with adaptors and remove reads in which unknown bases are more than 10% remove reads in which unknown bases are more than 10%.We use Bowtie2 with parameters q phred64 sensitive dpad 0 gbar 99999999 mp 1 1 np 1 score min L 0 0.1 p 16 k 200 to map clean reads to reference gene and use BWA with parameters o 1 e 50 i 50 L k 2 l 31 t 4 q 10 to reference genome Danio rerio.GRCz10.dna.toplevel.fa . RSEM is a quantification tool that computed Maximum likelihood abundance estimates using the Expectation Maximization EM algorithm for its statistical model . FPKM fragment Per Kilobase of gene per Megabase of library size method is used in calculated expression level. Genome build: Zv10 Supplementary files format and content: tab delimited text files include FPKM values for each Sample kdrl:GFP+ Endothelial cells   Morphologically normal siblings and mutant embryos from crosses of Tgkdrl:GFP; gbf1tsu3994/+ at 44 hpf were dechorionated and disintegrated completely to prepare single cell suspension. Then kdrl:GFP+ ECs were sorted by flow cytomer FACSAria BD and MoFlo XDP BeckMan and positive cells were confirmed by microscopy. Total mRNAs were extracted with RNeasy Mini Kit QIAGEN. The total RNA samples are first treated with DNase I to degrade any possible DNA contamination. Then the mRNA is enriched by using the oligo dT magnetic beads. Mixed with the fragmentation buffer the mRNA is fragmented into short fragments. Then the first strand of cDNA is synthesized by using random hexamer primer. Buffer dNTPs RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with magnetic beads. End reparation and 3’ end single nucleotide A adenine addition is then performed. Finally sequencing adaptors are ligated to the fragments. The fragments are enriched by PCR amplification.During the QC step Agilent 2100 Bioanaylzer and ABI StepOnePlus Real Time PCR System are used to qualify and quantify of the sample library. The library products are ready for sequencing via Illumina HiSeqTM 2000 or other sequencer when necessary.   genetic background:tsu3994;Tgkdrl;GFP cross|genotype/variation:Morphologically normal siblings embryo|Stage:44 hpf type:Endothelial cells GSM2224909 GSM2224909: Sib; Danio rerio; RNA Seq GSM2224909   1 Morphologically normal siblings and mutant embryos from crosses of Tgkdrl:GFP; gbf1tsu3994/+ at 44 hpf were dechorionated and disintegrated completely to prepare single cell suspension. Then kdrl:GFP+ ECs were sorted by flow cytomer FACSAria BD and MoFlo XDP BeckMan and positive cells were confirmed by microscopy. Total mRNAs were extracted with RNeasy Mini Kit QIAGEN. The total RNA samples are first treated with DNase I to degrade any possible DNA contamination. Then the mRNA is enriched by using the oligo dT magnetic beads. Mixed with the fragmentation buffer the mRNA is fragmented into short fragments. Then the first strand of cDNA is synthesized by using random hexamer primer. Buffer dNTPs RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with magnetic beads. End reparation and 3’ end single nucleotide A adenine addition is then performed. Finally sequencing adaptors are ligated to the fragments. The fragments are enriched by PCR amplification.During the QC step Agilent 2100 Bioanaylzer and ABI StepOnePlus Real Time PCR System are used to qualify and quantify of the sample library. The library products are ready for sequencing via Illumina HiSeqTM 2000 or other sequencer when necessary. GEO Accession:GSM2224909 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP077871     160204_I136_FCH55MNBBXX_L6_WHFISoiqRAAARAAPEI-100_1.fq.gz fastq 454459418.0 9274682.0 GSM2224909 r2 0:49 A:114982478;C:111450118;G:115561207;T:112452344;N:13271 49       114982478 111450118 115561207 112452344 13271 SRX1896782 SRS1539774 SRA437681 GEO Anming Meng, School of Lifesciences, Tsinghua University 1 0.92536   0.04644   0.75103   0.47559   49   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2016-07-04 Pharyngula Embryo Endothelium Cardiovascular System
50604 50604 SRR8169175 SRX4989831 SRS4025849 SRP168005 PRJNA504385 Endothelial transcriptome of 1dpf Zebrafish empryo PRJNA504385 Other The study aimed to identify endothelial specific transcript isoforms in 24hpf zebrafish embryo. The polyA RNA sequencing was performed on Illumina GA II platform.       Endothelial cells EC   strain:Tgfli1:EGFP gata1a: dsRed|age:1 dpf stage:1 dpf applicable|tissue:Endothelium|cell type:Endothelial|BioSampleModel:Model organism or animal                 Endothelial cells EC EC PolyA RNA Seq     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina Genome Analyzer IIx   SRP168005     EC_R1.fastq EC_R2.fastq fastq fastq 3373890496.0 22196648.0 EC R1.fastq 0:76 1:76 A:984631808;C:769706826;G:812424195;T:790813473;N:16314194 76 76     984631808 769706826 812424195 790813473 16314194 SRX4989831 SRS4025849 SRA805845 CSIR-Institute of Genomics and Integrative Biology|GN Ramachandran Knowledge Center CSIR-Institute of Genomics and Integrative Biology 2 0.92323 0.92543 0.07989 0.0849 0.76842 0.77964 0.46181 0.47429 76 76 B B biological fallback assumption illumina early_illumina unknown poly_a unknown bulk unknown unknown   India 2019-12-06 Pharyngula Embryo Endothelium Cardiovascular System
50605 50605 SRR8169176 SRX4989830 SRS4025850 SRP168005 PRJNA504385 Endothelial transcriptome of 1dpf Zebrafish empryo PRJNA504385 Other The study aimed to identify endothelial specific transcript isoforms in 24hpf zebrafish embryo. The polyA RNA sequencing was performed on Illumina GA II platform.       Non endothelial cells NEC   strain:Tgfli1:EGFP gata1a: dsRed|age:1 dpf stage:1 dpf applicable|tissue:Whole organism devoid of endothelium|BioSampleModel:Model organism or animal                 Non endothelial cells NEC NEC PolyA RNA Seq     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina Genome Analyzer IIx   SRP168005     NEC_R2.fastq NEC_R1.fastq fastq fastq 3903685432.0 25682141.0 NEC R1.fastq 0:76 1:76 A:1078599801;C:913868400;G:942281029;T:950473482;N:18462720 76 76     1078599801 913868400 942281029 950473482 18462720 SRX4989830 SRS4025850 SRA805845 CSIR-Institute of Genomics and Integrative Biology|GN Ramachandran Knowledge Center CSIR-Institute of Genomics and Integrative Biology 2 0.93037 0.92641 0.10373 0.11231 0.72644 0.74081 0.48329 0.48409 76 76 B B biological fallback assumption illumina early_illumina unknown poly_a unknown bulk unknown unknown   India 2019-12-06 Pharyngula Embryo Endothelium Cardiovascular System
52764 52764 SRR9207199 SRX5978265 SRS4884520 SRP200560 PRJNA547066 RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf GSE132259 Transcriptome Analysis The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos. parent bioproject:PRJNA546805 pubmed:31395869   RNA seq MO DP R1hi rep3 GSM3855057   source name:haemogenic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:runx1 morpholino injected RNA seq MO DP R1hi rep3 Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. haemogenic endothelium double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf. age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:runx1 morpholino injected GSM3855057 GSM3855057: MO DP R1hi rep3; Danio rerio; RNA Seq GSM3855057   1 whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. GEO Accession:GSM3855057 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP200560     WTCHG_236896_268_1_pair.fq.gz WTCHG_236896_268_2_pair.fq.gz fastq fastq 1927186907.0 13135764.0 GSM3855057 r1 0:74.85 1:71.86 A:495349382;C:442938837;G:459765161;T:529104158;N:29369 74 71     495349382 442938837 459765161 529104158 29369 SRX5978265 SRS4884520 SRA894667 GEO Oxford University 2 0.9511 0.71957 0.05876 0.04975 0.80322 0.83463 0.41847 0.47909 75 64 B B biological fallback assumption illumina hiseq_era full_length cdna_unspecified smarter bulk unknown unknown   United Kingdom 2019-06-05 Pharyngula Embryo Endothelium Cardiovascular System
52765 52765 SRR9207200 SRX5978265 SRS4884520 SRP200560 PRJNA547066 RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf GSE132259 Transcriptome Analysis The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos. parent bioproject:PRJNA546805 pubmed:31395869   RNA seq MO DP R1hi rep3 GSM3855057   source name:haemogenic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:runx1 morpholino injected RNA seq MO DP R1hi rep3 Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. haemogenic endothelium double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf. age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:runx1 morpholino injected GSM3855057 GSM3855057: MO DP R1hi rep3; Danio rerio; RNA Seq GSM3855057   1 whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. GEO Accession:GSM3855057 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP200560     WTCHG_236897_268_1_pair.fq.gz WTCHG_236897_268_2_pair.fq.gz fastq fastq 1909528693.0 13017658.0 GSM3855057 r2 0:74.82 1:71.87 A:490710971;C:436487071;G:453444216;T:528853285;N:33150 74 71     490710971 436487071 453444216 528853285 33150 SRX5978265 SRS4884520 SRA894667 GEO Oxford University 2 0.94988 0.70903 0.05941 0.04918 0.80346 0.83597 0.42243 0.48127 74 69 B B mate2-mate1 similar by mapping diff illumina hiseq_era full_length cdna_unspecified smarter bulk unknown unknown   United Kingdom 2019-06-05 Pharyngula Embryo Endothelium Cardiovascular System
52766 52766 SRR9207197 SRX5978264 SRS4884519 SRP200560 PRJNA547066 RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf GSE132259 Transcriptome Analysis The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos. parent bioproject:PRJNA546805 pubmed:31395869   RNA seq MO DP R1hi rep2 GSM3855056   source name:haemogenic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:runx1 morpholino injected RNA seq MO DP R1hi rep2 Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. haemogenic endothelium double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf. age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:runx1 morpholino injected GSM3855056 GSM3855056: MO DP R1hi rep2; Danio rerio; RNA Seq GSM3855056   1 whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. GEO Accession:GSM3855056 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP200560     WTCHG_236896_253_2_pair.fq.gz WTCHG_236896_253_1_pair.fq.gz fastq fastq 2328318316.0 15846855.0 GSM3855056 r1 0:74.86 1:72.07 A:595900608;C:546479100;G:562297908;T:623605072;N:35628 74 72     595900608 546479100 562297908 623605072 35628 SRX5978264 SRS4884519 SRA894667 GEO Oxford University 2 0.95426 0.78099 0.04531 0.04107 0.79285 0.81738 0.47636 0.47393 74 74 B B biological fallback assumption illumina hiseq_era full_length cdna_unspecified smarter bulk unknown unknown   United Kingdom 2019-06-05 Pharyngula Embryo Endothelium Cardiovascular System
52767 52767 SRR9207198 SRX5978264 SRS4884519 SRP200560 PRJNA547066 RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf GSE132259 Transcriptome Analysis The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos. parent bioproject:PRJNA546805 pubmed:31395869   RNA seq MO DP R1hi rep2 GSM3855056   source name:haemogenic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:runx1 morpholino injected RNA seq MO DP R1hi rep2 Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. haemogenic endothelium double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf. age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:runx1 morpholino injected GSM3855056 GSM3855056: MO DP R1hi rep2; Danio rerio; RNA Seq GSM3855056   1 whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. GEO Accession:GSM3855056 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP200560     WTCHG_236897_253_1_pair.fq.gz WTCHG_236897_253_2_pair.fq.gz fastq fastq 2302889916.0 15678935.0 GSM3855056 r2 0:74.83 1:72.05 A:589414837;C:537423117;G:553631542;T:622379721;N:40699 74 72     589414837 537423117 553631542 622379721 40699 SRX5978264 SRS4884519 SRA894667 GEO Oxford University 2 0.95316 0.76729 0.04543 0.04 0.79368 0.81994 0.4793 0.45619 74 73 B B biological fallback assumption illumina hiseq_era full_length cdna_unspecified smarter bulk unknown unknown   United Kingdom 2019-06-05 Pharyngula Embryo Endothelium Cardiovascular System
52768 52768 SRR9207195 SRX5978263 SRS4884518 SRP200560 PRJNA547066 RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf GSE132259 Transcriptome Analysis The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos. parent bioproject:PRJNA546805 pubmed:31395869   RNA seq MO DP R1hi rep1 GSM3855055   source name:haemogenic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:runx1 morpholino injected RNA seq MO DP R1hi rep1 Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. haemogenic endothelium double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf. age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:runx1 morpholino injected GSM3855055 GSM3855055: MO DP R1hi rep1; Danio rerio; RNA Seq GSM3855055   1 whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. GEO Accession:GSM3855055 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP200560     WTCHG_236896_246_1_pair.fq.gz WTCHG_236896_246_2_pair.fq.gz fastq fastq 2117580563.0 14386411.0 GSM3855055 r1 0:74.87 1:72.33 A:541407670;C:500318189;G:514959635;T:560861522;N:33547 74 72     541407670 500318189 514959635 560861522 33547 SRX5978263 SRS4884518 SRA894667 GEO Oxford University 2 0.95698 0.79806 0.0412 0.03838 0.79683 0.82073 0.4361 0.47246 75 74 B B biological fallback assumption illumina hiseq_era full_length cdna_unspecified smarter bulk unknown unknown   United Kingdom 2019-06-05 Pharyngula Embryo Endothelium Cardiovascular System
52769 52769 SRR9207196 SRX5978263 SRS4884518 SRP200560 PRJNA547066 RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf GSE132259 Transcriptome Analysis The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos. parent bioproject:PRJNA546805 pubmed:31395869   RNA seq MO DP R1hi rep1 GSM3855055   source name:haemogenic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:runx1 morpholino injected RNA seq MO DP R1hi rep1 Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. haemogenic endothelium double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf. age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:runx1 morpholino injected GSM3855055 GSM3855055: MO DP R1hi rep1; Danio rerio; RNA Seq GSM3855055   1 whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. GEO Accession:GSM3855055 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP200560     WTCHG_236897_246_1_pair.fq.gz WTCHG_236897_246_2_pair.fq.gz fastq fastq 2093566860.0 14226227.0 GSM3855055 r2 0:74.83 1:72.33 A:535219614;C:492666345;G:507484718;T:558158640;N:37543 74 72     535219614 492666345 507484718 558158640 37543 SRX5978263 SRS4884518 SRA894667 GEO Oxford University 2 0.95586 0.7889 0.04114 0.03868 0.79689 0.82104 0.43998 0.46953 74 47 B B biological fallback assumption illumina hiseq_era full_length cdna_unspecified smarter bulk unknown unknown   United Kingdom 2019-06-05 Pharyngula Embryo Endothelium Cardiovascular System
52770 52770 SRR9207193 SRX5978262 SRS4884517 SRP200560 PRJNA547066 RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf GSE132259 Transcriptome Analysis The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos. parent bioproject:PRJNA546805 pubmed:31395869   RNA seq MO DN rep3 GSM3855054   source name:non endothelial tissue|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:runx1 morpholino injected RNA seq MO DN rep3 Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. non endothelial tissue double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf. age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:runx1 morpholino injected GSM3855054 GSM3855054: MO DN rep3; Danio rerio; RNA Seq GSM3855054   1 whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. GEO Accession:GSM3855054 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP200560     WTCHG_236896_269_1_pair.fq.gz WTCHG_236896_269_2_pair.fq.gz fastq fastq 2046617161.0 13945847.0 GSM3855054 r1 0:74.83 1:71.93 A:534129043;C:466415284;G:478200001;T:567840465;N:32368 74 71     534129043 466415284 478200001 567840465 32368 SRX5978262 SRS4884517 SRA894667 GEO Oxford University 2 0.94896 0.77373 0.08658 0.07153 0.73519 0.76715 0.49305 0.48341 75 74 B B biological fallback assumption illumina hiseq_era full_length cdna_unspecified smarter bulk unknown unknown   United Kingdom 2019-06-05 Pharyngula Embryo Endothelium Cardiovascular System
52771 52771 SRR9207194 SRX5978262 SRS4884517 SRP200560 PRJNA547066 RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf GSE132259 Transcriptome Analysis The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos. parent bioproject:PRJNA546805 pubmed:31395869   RNA seq MO DN rep3 GSM3855054   source name:non endothelial tissue|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:runx1 morpholino injected RNA seq MO DN rep3 Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. non endothelial tissue double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf. age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:runx1 morpholino injected GSM3855054 GSM3855054: MO DN rep3; Danio rerio; RNA Seq GSM3855054   1 whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. GEO Accession:GSM3855054 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP200560     WTCHG_236897_269_1_pair.fq.gz WTCHG_236897_269_2_pair.fq.gz fastq fastq 2013937570.0 13725739.0 GSM3855054 r2 0:74.79 1:71.93 A:525460437;C:456678849;G:468917277;T:562845673;N:35334 74 71     525460437 456678849 468917277 562845673 35334 SRX5978262 SRS4884517 SRA894667 GEO Oxford University 2 0.94917 0.76456 0.08857 0.07125 0.73541 0.76777 0.49906 0.49093 74 44 B B biological fallback assumption illumina hiseq_era full_length cdna_unspecified smarter bulk unknown unknown   United Kingdom 2019-06-05 Pharyngula Embryo Endothelium Cardiovascular System
52772 52772 SRR9207191 SRX5978261 SRS4884516 SRP200560 PRJNA547066 RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf GSE132259 Transcriptome Analysis The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos. parent bioproject:PRJNA546805 pubmed:31395869   RNA seq MO DN rep2 GSM3855053   source name:non endothelial tissue|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:runx1 morpholino injected RNA seq MO DN rep2 Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. non endothelial tissue double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf. age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:runx1 morpholino injected GSM3855053 GSM3855053: MO DN rep2; Danio rerio; RNA Seq GSM3855053   1 whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. GEO Accession:GSM3855053 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP200560     WTCHG_236896_254_1_pair.fq.gz WTCHG_236896_254_2_pair.fq.gz fastq fastq 2491569443.0 17007413.0 GSM3855053 r1 0:74.84 1:71.66 A:650887336;C:562551977;G:579971830;T:698120812;N:37488 74 71     650887336 562551977 579971830 698120812 37488 SRX5978261 SRS4884516 SRA894667 GEO Oxford University 2 0.95058 0.74758 0.08565 0.06922 0.74817 0.78344 0.49706 0.48533 74 74 B B biological fallback assumption illumina hiseq_era full_length cdna_unspecified smarter bulk unknown unknown   United Kingdom 2019-06-05 Pharyngula Embryo Endothelium Cardiovascular System
52773 52773 SRR9207192 SRX5978261 SRS4884516 SRP200560 PRJNA547066 RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf GSE132259 Transcriptome Analysis The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos. parent bioproject:PRJNA546805 pubmed:31395869   RNA seq MO DN rep2 GSM3855053   source name:non endothelial tissue|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:runx1 morpholino injected RNA seq MO DN rep2 Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. non endothelial tissue double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf. age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:runx1 morpholino injected GSM3855053 GSM3855053: MO DN rep2; Danio rerio; RNA Seq GSM3855053   1 whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. GEO Accession:GSM3855053 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP200560     WTCHG_236897_254_1_pair.fq.gz WTCHG_236897_254_2_pair.fq.gz fastq fastq 2467826388.0 16847563.0 GSM3855053 r2 0:74.80 1:71.67 A:644767348;C:554488060;G:572473532;T:696053759;N:43689 74 71     644767348 554488060 572473532 696053759 43689 SRX5978261 SRS4884516 SRA894667 GEO Oxford University 2 0.95097 0.73759 0.0857 0.0679 0.74805 0.78307 0.50597 0.48761 74 59 B B biological fallback assumption illumina hiseq_era full_length cdna_unspecified smarter bulk unknown unknown   United Kingdom 2019-06-05 Pharyngula Embryo Endothelium Cardiovascular System
52774 52774 SRR9207189 SRX5978260 SRS4884515 SRP200560 PRJNA547066 RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf GSE132259 Transcriptome Analysis The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos. parent bioproject:PRJNA546805 pubmed:31395869   RNA seq MO DN rep1 GSM3855052   source name:non endothelial tissue|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:runx1 morpholino injected RNA seq MO DN rep1 Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. non endothelial tissue double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf. age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:runx1 morpholino injected GSM3855052 GSM3855052: MO DN rep1; Danio rerio; RNA Seq GSM3855052   1 whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. GEO Accession:GSM3855052 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP200560     WTCHG_236896_247_1_pair.fq.gz WTCHG_236896_247_2_pair.fq.gz fastq fastq 1764365530.0 12029530.0 GSM3855052 r1 0:74.84 1:71.83 A:466613214;C:395400217;G:407881798;T:494443051;N:27250 74 71     466613214 395400217 407881798 494443051 27250 SRX5978260 SRS4884515 SRA894667 GEO Oxford University 2 0.95055 0.76043 0.0868 0.07313 0.75436 0.79295 0.51961 0.5131 75 74 B B biological fallback assumption illumina hiseq_era full_length cdna_unspecified smarter bulk unknown unknown   United Kingdom 2019-06-05 Pharyngula Embryo Endothelium Cardiovascular System
52775 52775 SRR9207190 SRX5978260 SRS4884515 SRP200560 PRJNA547066 RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf GSE132259 Transcriptome Analysis The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos. parent bioproject:PRJNA546805 pubmed:31395869   RNA seq MO DN rep1 GSM3855052   source name:non endothelial tissue|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:runx1 morpholino injected RNA seq MO DN rep1 Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. non endothelial tissue double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf. age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:runx1 morpholino injected GSM3855052 GSM3855052: MO DN rep1; Danio rerio; RNA Seq GSM3855052   1 whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. GEO Accession:GSM3855052 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP200560     WTCHG_236897_247_1_pair.fq.gz WTCHG_236897_247_2_pair.fq.gz fastq fastq 1746830974.0 11912737.0 GSM3855052 r2 0:74.80 1:71.83 A:461791276;C:389648653;G:402516938;T:492843307;N:30800 74 71     461791276 389648653 402516938 492843307 30800 SRX5978260 SRS4884515 SRA894667 GEO Oxford University 2 0.94945 0.75002 0.08645 0.07146 0.75564 0.79247 0.52424 0.51007 74 74 B B biological fallback assumption illumina hiseq_era full_length cdna_unspecified smarter bulk unknown unknown   United Kingdom 2019-06-05 Pharyngula Embryo Endothelium Cardiovascular System
52776 52776 SRR9207187 SRX5978259 SRS4884514 SRP200560 PRJNA547066 RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf GSE132259 Transcriptome Analysis The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos. parent bioproject:PRJNA546805 pubmed:31395869   RNA seq Wt DP R1hi rep3 GSM3855051   source name:haemogenic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:non injected RNA seq Wt DP R1hi rep3 Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. haemogenic endothelium double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf. age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:non injected GSM3855051 GSM3855051: Wt DP R1hi rep3; Danio rerio; RNA Seq GSM3855051   1 whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. GEO Accession:GSM3855051 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP200560     WTCHG_236896_256_1_pair.fq.gz WTCHG_236896_256_2_pair.fq.gz fastq fastq 2404346186.0 16361688.0 GSM3855051 r1 0:74.85 1:72.10 A:623840845;C:555338266;G:572145582;T:652983438;N:38055 74 72     623840845 555338266 572145582 652983438 38055 SRX5978259 SRS4884514 SRA894667 GEO Oxford University 2 0.95156 0.77737 0.06227 0.05592 0.78013 0.80811 0.47747 0.46476 75 74 B B biological fallback assumption illumina hiseq_era full_length cdna_unspecified smarter bulk unknown unknown   United Kingdom 2019-06-05 Pharyngula Embryo Endothelium Cardiovascular System
52777 52777 SRR9207188 SRX5978259 SRS4884514 SRP200560 PRJNA547066 RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf GSE132259 Transcriptome Analysis The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos. parent bioproject:PRJNA546805 pubmed:31395869   RNA seq Wt DP R1hi rep3 GSM3855051   source name:haemogenic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:non injected RNA seq Wt DP R1hi rep3 Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. haemogenic endothelium double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf. age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:non injected GSM3855051 GSM3855051: Wt DP R1hi rep3; Danio rerio; RNA Seq GSM3855051   1 whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. GEO Accession:GSM3855051 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP200560     WTCHG_236897_256_1_pair.fq.gz WTCHG_236897_256_2_pair.fq.gz fastq fastq 2376933896.0 16184470.0 GSM3855051 r2 0:74.81 1:72.05 A:616256503;C:545472678;G:562708331;T:652453993;N:42391 74 72     616256503 545472678 562708331 652453993 42391 SRX5978259 SRS4884514 SRA894667 GEO Oxford University 2 0.95009 0.76216 0.06391 0.05506 0.78131 0.81051 0.48169 0.4736 74 74 B B biological fallback assumption illumina hiseq_era full_length cdna_unspecified smarter bulk unknown unknown   United Kingdom 2019-06-05 Pharyngula Embryo Endothelium Cardiovascular System
52778 52778 SRR9207185 SRX5978258 SRS4884513 SRP200560 PRJNA547066 RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf GSE132259 Transcriptome Analysis The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos. parent bioproject:PRJNA546805 pubmed:31395869   RNA seq Wt DP R1hi rep2 GSM3855050   source name:haemogenic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:non injected RNA seq Wt DP R1hi rep2 Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. haemogenic endothelium double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf. age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:non injected GSM3855050 GSM3855050: Wt DP R1hi rep2; Danio rerio; RNA Seq GSM3855050   1 whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. GEO Accession:GSM3855050 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP200560     WTCHG_236896_249_1_pair.fq.gz WTCHG_236896_249_2_pair.fq.gz fastq fastq 2143701223.0 14577609.0 GSM3855050 r1 0:74.85 1:72.21 A:556710384;C:496467692;G:509166690;T:581322427;N:34030 74 72     556710384 496467692 509166690 581322427 34030 SRX5978258 SRS4884513 SRA894667 GEO Oxford University 2 0.94754 0.79028 0.06346 0.05688 0.7811 0.80754 0.47106 0.45364 75 74 B B biological fallback assumption illumina hiseq_era full_length cdna_unspecified smarter bulk unknown unknown   United Kingdom 2019-06-05 Pharyngula Embryo Endothelium Cardiovascular System
52779 52779 SRR9207186 SRX5978258 SRS4884513 SRP200560 PRJNA547066 RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf GSE132259 Transcriptome Analysis The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos. parent bioproject:PRJNA546805 pubmed:31395869   RNA seq Wt DP R1hi rep2 GSM3855050   source name:haemogenic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:non injected RNA seq Wt DP R1hi rep2 Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. haemogenic endothelium double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf. age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:non injected GSM3855050 GSM3855050: Wt DP R1hi rep2; Danio rerio; RNA Seq GSM3855050   1 whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. GEO Accession:GSM3855050 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP200560     WTCHG_236897_249_1_pair.fq.gz WTCHG_236897_249_2_pair.fq.gz fastq fastq 2117035142.0 14401911.0 GSM3855050 r2 0:74.82 1:72.18 A:549829321;C:487941130;G:501062541;T:578164319;N:37831 74 72     549829321 487941130 501062541 578164319 37831 SRX5978258 SRS4884513 SRA894667 GEO Oxford University 2 0.9478 0.78326 0.06392 0.05622 0.78271 0.80764 0.46978 0.44622 74 74 B B biological fallback assumption illumina hiseq_era full_length cdna_unspecified smarter bulk unknown unknown   United Kingdom 2019-06-05 Pharyngula Embryo Endothelium Cardiovascular System
52780 52780 SRR9207183 SRX5978257 SRS4884512 SRP200560 PRJNA547066 RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf GSE132259 Transcriptome Analysis The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos. parent bioproject:PRJNA546805 pubmed:31395869   RNA seq Wt DP R1hi rep1 GSM3855049   source name:haemogenic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:non injected RNA seq Wt DP R1hi rep1 Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. haemogenic endothelium double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf. age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:non injected GSM3855049 GSM3855049: Wt DP R1hi rep1; Danio rerio; RNA Seq GSM3855049   1 whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. GEO Accession:GSM3855049 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP200560     WTCHG_236896_242_1_pair.fq.gz WTCHG_236896_242_2_pair.fq.gz fastq fastq 2095674074.0 14243567.0 GSM3855049 r1 0:74.85 1:72.28 A:541444792;C:489580880;G:501484244;T:563130979;N:33179 74 72     541444792 489580880 501484244 563130979 33179 SRX5978257 SRS4884512 SRA894667 GEO Oxford University 2 0.95275 0.80515 0.0503 0.0447 0.78827 0.81028 0.47691 0.47164 74 74 B B biological fallback assumption illumina hiseq_era full_length cdna_unspecified smarter bulk unknown unknown   United Kingdom 2019-06-05 Pharyngula Embryo Endothelium Cardiovascular System
52781 52781 SRR9207184 SRX5978257 SRS4884512 SRP200560 PRJNA547066 RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf GSE132259 Transcriptome Analysis The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos. parent bioproject:PRJNA546805 pubmed:31395869   RNA seq Wt DP R1hi rep1 GSM3855049   source name:haemogenic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:non injected RNA seq Wt DP R1hi rep1 Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. haemogenic endothelium double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf. age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:non injected GSM3855049 GSM3855049: Wt DP R1hi rep1; Danio rerio; RNA Seq GSM3855049   1 whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. GEO Accession:GSM3855049 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP200560     WTCHG_236897_242_1_pair.fq.gz WTCHG_236897_242_2_pair.fq.gz fastq fastq 2063492969.0 14026048.0 GSM3855049 r2 0:74.82 1:72.30 A:533045811;C:480334040;G:492421855;T:557653783;N:37480 74 72     533045811 480334040 492421855 557653783 37480 SRX5978257 SRS4884512 SRA894667 GEO Oxford University 2 0.95243 0.79788 0.04971 0.04343 0.7878 0.81016 0.48035 0.46512 74 74 B B biological fallback assumption illumina hiseq_era full_length cdna_unspecified smarter bulk unknown unknown   United Kingdom 2019-06-05 Pharyngula Embryo Endothelium Cardiovascular System
52782 52782 SRR9207181 SRX5978256 SRS4884511 SRP200560 PRJNA547066 RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf GSE132259 Transcriptome Analysis The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos. parent bioproject:PRJNA546805 pubmed:31395869   RNA seq Wt DP R1med rep3 GSM3855048   source name:aortic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected RNA seq Wt DP R1med rep3 Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. aortic endothelium double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf. age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected GSM3855048 GSM3855048: Wt DP R1med rep3; Danio rerio; RNA Seq GSM3855048   1 whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. GEO Accession:GSM3855048 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP200560     WTCHG_236896_265_1_pair.fq.gz WTCHG_236896_265_2_pair.fq.gz fastq fastq 1745443128.0 11892304.0 GSM3855048 r1 0:74.86 1:71.91 A:453150216;C:403838492;G:414952890;T:473474634;N:26896 74 71     453150216 403838492 414952890 473474634 26896 SRX5978256 SRS4884511 SRA894667 GEO Oxford University 2 0.95301 0.78351 0.0658 0.06097 0.78368 0.80941 0.47251 0.4445 75 74 B B biological fallback assumption illumina hiseq_era full_length cdna_unspecified smarter bulk unknown unknown   United Kingdom 2019-06-05 Pharyngula Embryo Endothelium Cardiovascular System
52783 52783 SRR9207182 SRX5978256 SRS4884511 SRP200560 PRJNA547066 RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf GSE132259 Transcriptome Analysis The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos. parent bioproject:PRJNA546805 pubmed:31395869   RNA seq Wt DP R1med rep3 GSM3855048   source name:aortic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected RNA seq Wt DP R1med rep3 Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. aortic endothelium double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf. age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected GSM3855048 GSM3855048: Wt DP R1med rep3; Danio rerio; RNA Seq GSM3855048   1 whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. GEO Accession:GSM3855048 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP200560     WTCHG_236897_265_1_pair.fq.gz WTCHG_236897_265_2_pair.fq.gz fastq fastq 1728817726.0 11782024.0 GSM3855048 r2 0:74.82 1:71.91 A:448845759;C:398200726;G:409703125;T:472037424;N:30692 74 71     448845759 398200726 409703125 472037424 30692 SRX5978256 SRS4884511 SRA894667 GEO Oxford University 2 0.9518 0.77329 0.06602 0.05955 0.78423 0.81051 0.47776 0.46478 74 74 B B biological fallback assumption illumina hiseq_era full_length cdna_unspecified smarter bulk unknown unknown   United Kingdom 2019-06-05 Pharyngula Embryo Endothelium Cardiovascular System
52784 52784 SRR9207179 SRX5978255 SRS4884510 SRP200560 PRJNA547066 RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf GSE132259 Transcriptome Analysis The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos. parent bioproject:PRJNA546805 pubmed:31395869   RNA seq Wt DP R1med rep2 GSM3855047   source name:aortic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected RNA seq Wt DP R1med rep2 Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. aortic endothelium double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf. age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected GSM3855047 GSM3855047: Wt DP R1med rep2; Danio rerio; RNA Seq GSM3855047   1 whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. GEO Accession:GSM3855047 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP200560     WTCHG_236896_250_1_pair.fq.gz WTCHG_236896_250_2_pair.fq.gz fastq fastq 2096576707.0 14262609.0 GSM3855047 r1 0:74.87 1:72.13 A:536583711;C:491572815;G:509433296;T:558953949;N:32936 74 72     536583711 491572815 509433296 558953949 32936 SRX5978255 SRS4884510 SRA894667 GEO Oxford University 2 0.95719 0.76406 0.04256 0.03937 0.7989 0.82856 0.40968 0.4591 75 74 B B biological fallback assumption illumina hiseq_era full_length cdna_unspecified smarter bulk unknown unknown   United Kingdom 2019-06-05 Pharyngula Embryo Endothelium Cardiovascular System
52785 52785 SRR9207180 SRX5978255 SRS4884510 SRP200560 PRJNA547066 RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf GSE132259 Transcriptome Analysis The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos. parent bioproject:PRJNA546805 pubmed:31395869   RNA seq Wt DP R1med rep2 GSM3855047   source name:aortic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected RNA seq Wt DP R1med rep2 Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. aortic endothelium double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf. age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected GSM3855047 GSM3855047: Wt DP R1med rep2; Danio rerio; RNA Seq GSM3855047   1 whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. GEO Accession:GSM3855047 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP200560     WTCHG_236897_250_1_pair.fq.gz WTCHG_236897_250_2_pair.fq.gz fastq fastq 2081468598.0 14169082.0 GSM3855047 r2 0:74.83 1:72.07 A:532025059;C:484883611;G:503099767;T:561423564;N:36597 74 72     532025059 484883611 503099767 561423564 36597 SRX5978255 SRS4884510 SRA894667 GEO Oxford University 2 0.95742 0.74712 0.04275 0.03741 0.79922 0.82866 0.40398 0.46313 74 74 B B biological fallback assumption illumina hiseq_era full_length cdna_unspecified smarter bulk unknown unknown   United Kingdom 2019-06-05 Pharyngula Embryo Endothelium Cardiovascular System
52786 52786 SRR9207177 SRX5978254 SRS4884509 SRP200560 PRJNA547066 RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf GSE132259 Transcriptome Analysis The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos. parent bioproject:PRJNA546805 pubmed:31395869   RNA seq Wt DP R1med rep1 GSM3855046   source name:aortic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected RNA seq Wt DP R1med rep1 Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. aortic endothelium double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf. age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected GSM3855046 GSM3855046: Wt DP R1med rep1; Danio rerio; RNA Seq GSM3855046   1 whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. GEO Accession:GSM3855046 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP200560     WTCHG_236896_243_1_pair.fq.gz WTCHG_236896_243_2_pair.fq.gz fastq fastq 2011950216.0 13680917.0 GSM3855046 r1 0:74.86 1:72.20 A:511635564;C:476475475;G:489688294;T:534119393;N:31490 74 72     511635564 476475475 489688294 534119393 31490 SRX5978254 SRS4884509 SRA894667 GEO Oxford University 2 0.9571 0.78471 0.03658 0.03396 0.80247 0.8268 0.48025 0.46265 74 74 B B biological fallback assumption illumina hiseq_era full_length cdna_unspecified smarter bulk unknown unknown   United Kingdom 2019-06-05 Pharyngula Embryo Endothelium Cardiovascular System
52787 52787 SRR9207178 SRX5978254 SRS4884509 SRP200560 PRJNA547066 RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf GSE132259 Transcriptome Analysis The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos. parent bioproject:PRJNA546805 pubmed:31395869   RNA seq Wt DP R1med rep1 GSM3855046   source name:aortic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected RNA seq Wt DP R1med rep1 Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. aortic endothelium double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf. age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected GSM3855046 GSM3855046: Wt DP R1med rep1; Danio rerio; RNA Seq GSM3855046   1 whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. GEO Accession:GSM3855046 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP200560     WTCHG_236897_243_1_pair.fq.gz WTCHG_236897_243_2_pair.fq.gz fastq fastq 1979368927.0 13461179.0 GSM3855046 r2 0:74.83 1:72.21 A:503539205;C:467446638;G:480794441;T:527553577;N:35066 74 72     503539205 467446638 480794441 527553577 35066 SRX5978254 SRS4884509 SRA894667 GEO Oxford University 2 0.95558 0.78357 0.03711 0.03412 0.80318 0.82664 0.42185 0.46216 74 64 B B biological fallback assumption illumina hiseq_era full_length cdna_unspecified smarter bulk unknown unknown   United Kingdom 2019-06-05 Pharyngula Embryo Endothelium Cardiovascular System
52788 52788 SRR9207175 SRX5978253 SRS4884508 SRP200560 PRJNA547066 RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf GSE132259 Transcriptome Analysis The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos. parent bioproject:PRJNA546805 pubmed:31395869   RNA seq Wt DP R1lo rep3 GSM3855045   source name:aortic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected RNA seq Wt DP R1lo rep3 Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. aortic endothelium double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf. age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected GSM3855045 GSM3855045: Wt DP R1lo rep3; Danio rerio; RNA Seq GSM3855045   1 whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. GEO Accession:GSM3855045 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP200560     WTCHG_236896_266_1_pair.fq.gz WTCHG_236896_266_2_pair.fq.gz fastq fastq 2022090059.0 13752247.0 GSM3855045 r1 0:74.84 1:72.20 A:529671943;C:466470156;G:476864148;T:549051395;N:32417 74 72     529671943 466470156 476864148 549051395 32417 SRX5978253 SRS4884508 SRA894667 GEO Oxford University 2 0.94638 0.80375 0.07924 0.06889 0.76098 0.78636 0.4888 0.46168 74 74 B B biological fallback assumption illumina hiseq_era full_length cdna_unspecified smarter bulk unknown unknown   United Kingdom 2019-06-05 Pharyngula Embryo Endothelium Cardiovascular System
52789 52789 SRR9207176 SRX5978253 SRS4884508 SRP200560 PRJNA547066 RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf GSE132259 Transcriptome Analysis The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos. parent bioproject:PRJNA546805 pubmed:31395869   RNA seq Wt DP R1lo rep3 GSM3855045   source name:aortic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected RNA seq Wt DP R1lo rep3 Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. aortic endothelium double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf. age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected GSM3855045 GSM3855045: Wt DP R1lo rep3; Danio rerio; RNA Seq GSM3855045   1 whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. GEO Accession:GSM3855045 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP200560     WTCHG_236897_266_1_pair.fq.gz WTCHG_236897_266_2_pair.fq.gz fastq fastq 1996491732.0 13581226.0 GSM3855045 r2 0:74.81 1:72.20 A:522970179;C:458424995;G:469211257;T:545848558;N:36743 74 72     522970179 458424995 469211257 545848558 36743 SRX5978253 SRS4884508 SRA894667 GEO Oxford University 2 0.94571 0.7947 0.08062 0.06773 0.76116 0.78591 0.49549 0.46742 74 74 B B biological fallback assumption illumina hiseq_era full_length cdna_unspecified smarter bulk unknown unknown   United Kingdom 2019-06-05 Pharyngula Embryo Endothelium Cardiovascular System
52790 52790 SRR9207173 SRX5978252 SRS4884507 SRP200560 PRJNA547066 RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf GSE132259 Transcriptome Analysis The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos. parent bioproject:PRJNA546805 pubmed:31395869   RNA seq Wt DP R1lo rep2 GSM3855044   source name:aortic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected RNA seq Wt DP R1lo rep2 Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. aortic endothelium double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf. age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected GSM3855044 GSM3855044: Wt DP R1lo rep2; Danio rerio; RNA Seq GSM3855044   1 whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. GEO Accession:GSM3855044 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP200560     WTCHG_236896_251_1_pair.fq.gz WTCHG_236896_251_2_pair.fq.gz fastq fastq 2166575163.0 14709523.0 GSM3855044 r1 0:74.86 1:72.43 A:559933570;C:510454967;G:520888591;T:575264053;N:33982 74 72     559933570 510454967 520888591 575264053 33982 SRX5978252 SRS4884507 SRA894667 GEO Oxford University 2 0.95094 0.8211 0.0594 0.05292 0.76664 0.79253 0.4795 0.4638 74 74 B B biological fallback assumption illumina hiseq_era full_length cdna_unspecified smarter bulk unknown unknown   United Kingdom 2019-06-05 Pharyngula Embryo Endothelium Cardiovascular System
52791 52791 SRR9207174 SRX5978252 SRS4884507 SRP200560 PRJNA547066 RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf GSE132259 Transcriptome Analysis The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos. parent bioproject:PRJNA546805 pubmed:31395869   RNA seq Wt DP R1lo rep2 GSM3855044   source name:aortic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected RNA seq Wt DP R1lo rep2 Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. aortic endothelium double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf. age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected GSM3855044 GSM3855044: Wt DP R1lo rep2; Danio rerio; RNA Seq GSM3855044   1 whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. GEO Accession:GSM3855044 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP200560     WTCHG_236897_251_1_pair.fq.gz WTCHG_236897_251_2_pair.fq.gz fastq fastq 2148630324.0 14593830.0 GSM3855044 r2 0:74.83 1:72.40 A:555362600;C:503529612;G:514542689;T:575156489;N:38934 74 72     555362600 503529612 514542689 575156489 38934 SRX5978252 SRS4884507 SRA894667 GEO Oxford University 2 0.95053 0.81036 0.06102 0.05199 0.76897 0.79354 0.47523 0.46186 74 74 B B biological fallback assumption illumina hiseq_era full_length cdna_unspecified smarter bulk unknown unknown   United Kingdom 2019-06-05 Pharyngula Embryo Endothelium Cardiovascular System
52792 52792 SRR9207171 SRX5978251 SRS4884506 SRP200560 PRJNA547066 RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf GSE132259 Transcriptome Analysis The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos. parent bioproject:PRJNA546805 pubmed:31395869   RNA seq Wt DP R1lo rep1 GSM3855043   source name:aortic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected RNA seq Wt DP R1lo rep1 Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. aortic endothelium double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf. age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected GSM3855043 GSM3855043: Wt DP R1lo rep1; Danio rerio; RNA Seq GSM3855043   1 whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. GEO Accession:GSM3855043 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP200560     WTCHG_236896_244_1_pair.fq.gz WTCHG_236896_244_2_pair.fq.gz fastq fastq 1899807957.0 12921335.0 GSM3855043 r1 0:74.85 1:72.17 A:494455972;C:440267035;G:451386907;T:513668319;N:29724 74 72     494455972 440267035 451386907 513668319 29724 SRX5978251 SRS4884506 SRA894667 GEO Oxford University 2 0.94888 0.79567 0.06354 0.05518 0.77041 0.79837 0.48973 0.47834 75 73 B B biological fallback assumption illumina hiseq_era full_length cdna_unspecified smarter bulk unknown unknown   United Kingdom 2019-06-05 Pharyngula Embryo Endothelium Cardiovascular System
52793 52793 SRR9207172 SRX5978251 SRS4884506 SRP200560 PRJNA547066 RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf GSE132259 Transcriptome Analysis The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos. parent bioproject:PRJNA546805 pubmed:31395869   RNA seq Wt DP R1lo rep1 GSM3855043   source name:aortic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected RNA seq Wt DP R1lo rep1 Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. aortic endothelium double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf. age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected GSM3855043 GSM3855043: Wt DP R1lo rep1; Danio rerio; RNA Seq GSM3855043   1 whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. GEO Accession:GSM3855043 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP200560     WTCHG_236897_244_1_pair.fq.gz WTCHG_236897_244_2_pair.fq.gz fastq fastq 1882109620.0 12807285.0 GSM3855043 r2 0:74.82 1:72.14 A:489932533;C:433346981;G:444869178;T:513927823;N:33105 74 72     489932533 433346981 444869178 513927823 33105 SRX5978251 SRS4884506 SRA894667 GEO Oxford University 2 0.94837 0.78199 0.06553 0.05587 0.77068 0.79967 0.48984 0.47719 74 74 B B biological fallback assumption illumina hiseq_era full_length cdna_unspecified smarter bulk unknown unknown   United Kingdom 2019-06-05 Pharyngula Embryo Endothelium Cardiovascular System
52800 52800 SRR9207163 SRX5978247 SRS4884502 SRP200560 PRJNA547066 RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf GSE132259 Transcriptome Analysis The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos. parent bioproject:PRJNA546805 pubmed:31395869   RNA seq Wt DN rep3 GSM3855039   source name:non endothelial tissue|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:non injected RNA seq Wt DN rep3 Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. non endothelial tissue double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf. age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:non injected GSM3855039 GSM3855039: Wt DN rep3; Danio rerio; RNA Seq GSM3855039   1 whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. GEO Accession:GSM3855039 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP200560     WTCHG_236896_267_1_pair.fq.gz WTCHG_236896_267_2_pair.fq.gz fastq fastq 1812059909.0 12410104.0 GSM3855039 r1 0:74.81 1:71.21 A:491620609;C:383394578;G:398030819;T:538985491;N:28412 74 71     491620609 383394578 398030819 538985491 28412 SRX5978247 SRS4884502 SRA894667 GEO Oxford University 2 0.93321 0.68178 0.15093 0.11867 0.75282 0.79468 0.51285 0.51101 75 74 B B mate2-mate1 similar by mapping diff illumina hiseq_era full_length cdna_unspecified smarter bulk unknown unknown   United Kingdom 2019-06-05 Pharyngula Embryo Endothelium Cardiovascular System
52801 52801 SRR9207164 SRX5978247 SRS4884502 SRP200560 PRJNA547066 RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf GSE132259 Transcriptome Analysis The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos. parent bioproject:PRJNA546805 pubmed:31395869   RNA seq Wt DN rep3 GSM3855039   source name:non endothelial tissue|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:non injected RNA seq Wt DN rep3 Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. non endothelial tissue double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf. age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:non injected GSM3855039 GSM3855039: Wt DN rep3; Danio rerio; RNA Seq GSM3855039   1 whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. GEO Accession:GSM3855039 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP200560     WTCHG_236897_267_1_pair.fq.gz WTCHG_236897_267_2_pair.fq.gz fastq fastq 1798726377.0 12321488.0 GSM3855039 r2 0:74.77 1:71.21 A:487870380;C:378213454;G:393167780;T:539442882;N:31881 74 71     487870380 378213454 393167780 539442882 31881 SRX5978247 SRS4884502 SRA894667 GEO Oxford University 2 0.93183 0.67372 0.15009 0.11547 0.7555 0.79705 0.52465 0.50781 74 54 B B mate2-mate1 similar by mapping diff illumina hiseq_era full_length cdna_unspecified smarter bulk unknown unknown   United Kingdom 2019-06-05 Pharyngula Embryo Endothelium Cardiovascular System
52802 52802 SRR9207161 SRX5978246 SRS4884501 SRP200560 PRJNA547066 RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf GSE132259 Transcriptome Analysis The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos. parent bioproject:PRJNA546805 pubmed:31395869   RNA seq Wt DN rep2 GSM3855038   source name:non endothelial tissue|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:non injected RNA seq Wt DN rep2 Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. non endothelial tissue double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf. age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:non injected GSM3855038 GSM3855038: Wt DN rep2; Danio rerio; RNA Seq GSM3855038   1 whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. GEO Accession:GSM3855038 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP200560     WTCHG_236896_252_1_pair.fq.gz WTCHG_236896_252_2_pair.fq.gz fastq fastq 2146316233.0 14628161.0 GSM3855038 r1 0:74.84 1:71.88 A:566578244;C:489485503;G:504442873;T:585776104;N:33509 74 71     566578244 489485503 504442873 585776104 33509 SRX5978246 SRS4884501 SRA894667 GEO Oxford University 2 0.94696 0.79752 0.10017 0.0872 0.74572 0.78165 0.50212 0.49488 74 74 B B biological fallback assumption illumina hiseq_era full_length cdna_unspecified smarter bulk unknown unknown   United Kingdom 2019-06-05 Pharyngula Embryo Endothelium Cardiovascular System
52803 52803 SRR9207162 SRX5978246 SRS4884501 SRP200560 PRJNA547066 RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf GSE132259 Transcriptome Analysis The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos. parent bioproject:PRJNA546805 pubmed:31395869   RNA seq Wt DN rep2 GSM3855038   source name:non endothelial tissue|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:non injected RNA seq Wt DN rep2 Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. non endothelial tissue double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf. age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:non injected GSM3855038 GSM3855038: Wt DN rep2; Danio rerio; RNA Seq GSM3855038   1 whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. GEO Accession:GSM3855038 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP200560     WTCHG_236897_252_1_pair.fq.gz WTCHG_236897_252_2_pair.fq.gz fastq fastq 2135407349.0 14569323.0 GSM3855038 r2 0:74.81 1:71.76 A:563322304;C:482982247;G:498831126;T:590234332;N:37340 74 71     563322304 482982247 498831126 590234332 37340 SRX5978246 SRS4884501 SRA894667 GEO Oxford University 2 0.94623 0.77703 0.10192 0.08638 0.74582 0.78289 0.50539 0.48024 74 74 B B biological fallback assumption illumina hiseq_era full_length cdna_unspecified smarter bulk unknown unknown   United Kingdom 2019-06-05 Pharyngula Embryo Endothelium Cardiovascular System
52804 52804 SRR9207159 SRX5978245 SRS4884500 SRP200560 PRJNA547066 RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf GSE132259 Transcriptome Analysis The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos. parent bioproject:PRJNA546805 pubmed:31395869   RNA seq Wt DN rep1 GSM3855037   source name:non endothelial tissue|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:non injected RNA seq Wt DN rep1 Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. non endothelial tissue double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf. age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:non injected GSM3855037 GSM3855037: Wt DN rep1; Danio rerio; RNA Seq GSM3855037   1 whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. GEO Accession:GSM3855037 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP200560     WTCHG_236896_245_2_pair.fq.gz WTCHG_236896_245_1_pair.fq.gz fastq fastq 1719181139.0 11738270.0 GSM3855037 r1 0:74.81 1:71.65 A:459579950;C:379670678;G:392006300;T:487897820;N:26391 74 71     459579950 379670678 392006300 487897820 26391 SRX5978245 SRS4884500 SRA894667 GEO Oxford University 2 0.93052 0.73058 0.11005 0.09187 0.7587 0.79375 0.50611 0.48538 75 73 B B biological fallback assumption illumina hiseq_era full_length cdna_unspecified smarter bulk unknown unknown   United Kingdom 2019-06-05 Pharyngula Embryo Endothelium Cardiovascular System
52805 52805 SRR9207160 SRX5978245 SRS4884500 SRP200560 PRJNA547066 RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf GSE132259 Transcriptome Analysis The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos. parent bioproject:PRJNA546805 pubmed:31395869   RNA seq Wt DN rep1 GSM3855037   source name:non endothelial tissue|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:non injected RNA seq Wt DN rep1 Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. non endothelial tissue double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf. age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:non injected GSM3855037 GSM3855037: Wt DN rep1; Danio rerio; RNA Seq GSM3855037   1 whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA. GEO Accession:GSM3855037 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP200560     WTCHG_236897_245_1_pair.fq.gz WTCHG_236897_245_2_pair.fq.gz fastq fastq 1710103502.0 11683422.0 GSM3855037 r2 0:74.77 1:71.60 A:456758769;C:375069094;G:387904698;T:490340725;N:30216 74 71     456758769 375069094 387904698 490340725 30216 SRX5978245 SRS4884500 SRA894667 GEO Oxford University 2 0.93089 0.71617 0.1094 0.08897 0.75879 0.79667 0.51735 0.49687 74 74 B B biological fallback assumption illumina hiseq_era full_length cdna_unspecified smarter bulk unknown unknown   United Kingdom 2019-06-05 Pharyngula Embryo Endothelium Cardiovascular System
55379 55379 SRR10323881 SRX7034716 SRS5554730 SRP226614 PRJNA578896 Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence PRJNA578896 Other In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.         danRer10 raw data   strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal                 RNA seq control for lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2 10 10 NEBNext Low Input RNA Library Prep Kit     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 3000   SRP226614     RNA_seq control for lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R1.fastq.gz RNA_seq control for lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R2.fastq.gz fastq fastq 3356658750.0 22377725.0 RNA seq control for lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2 R1.fastq.gz 0:75 1:75 A:875300673;C:782517555;G:796855605;T:901672776;N:312141 75 75     875300673 782517555 796855605 901672776 312141 SRX7034716 SRS5554730 SRA983011 Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany 2 0.68437 0.73326 0.04743 0.05194 0.80241 0.80517 0.51875 0.52196 75 75 B B biological fallback assumption illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   Germany 2019-10-24 Pharyngula Embryo Endothelium Cardiovascular System
55380 55380 SRR10323882 SRX7034715 SRS5554730 SRP226614 PRJNA578896 Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence PRJNA578896 Other In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.         danRer10 raw data   strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal                 RNA seq control for lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1 9 9 NEBNext Low Input RNA Library Prep Kit     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 3000   SRP226614     RNA_seq control for lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R2.fastq.gz RNA_seq control for lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R1.fastq.gz fastq fastq 3459242400.0 23061616.0 RNA seq control for lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1 R1.fastq.gz 0:75 1:75 A:924400584;C:762078140;G:779330250;T:993109509;N:323917 75 75     924400584 762078140 779330250 993109509 323917 SRX7034715 SRS5554730 SRA983011 Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany 2 0.67032 0.73764 0.07629 0.08303 0.80856 0.80748 0.52094 0.52695 75 75 B B biological fallback assumption illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   Germany 2019-10-24 Pharyngula Embryo Endothelium Cardiovascular System
55381 55381 SRR10323883 SRX7034714 SRS5554730 SRP226614 PRJNA578896 Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence PRJNA578896 Other In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.         danRer10 raw data   strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal                 RNA seq mda5 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2 8 8 NEBNext Low Input RNA Library Prep Kit     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 3000   SRP226614     RNA_seq mda5 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R1.fastq.gz RNA_seq mda5 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R2.fastq.gz fastq fastq 3238312500.0 21588750.0 RNA seq mda5 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2 R1.fastq.gz 0:75 1:75 A:881635390;C:656958401;G:673596788;T:1025824968;N:296953 75 75     881635390 656958401 673596788 1025824968 296953 SRX7034714 SRS5554730 SRA983011 Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany 2 0.59623 0.72377 0.07781 0.08944 0.80608 0.8016 0.53277 0.53095 75 75 B B biological fallback assumption illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   Germany 2019-10-24 Pharyngula Embryo Endothelium Cardiovascular System
55382 55382 SRR10323884 SRX7034713 SRS5554730 SRP226614 PRJNA578896 Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence PRJNA578896 Other In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.         danRer10 raw data   strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal                 RNA seq mda5 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1 7 7 NEBNext Low Input RNA Library Prep Kit     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 3000   SRP226614     RNA_seq mda5 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R1.fastq.gz RNA_seq mda5 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R2.fastq.gz fastq fastq 3255021150.0 21700141.0 RNA seq mda5 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1 R1.fastq.gz 0:75 1:75 A:858912760;C:733048670;G:750496371;T:912263495;N:299854 75 75     858912760 733048670 750496371 912263495 299854 SRX7034713 SRS5554730 SRA983011 Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany 2 0.65481 0.71883 0.05477 0.05995 0.7903 0.7921 0.51367 0.51188 75 75 B B biological fallback assumption illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   Germany 2019-10-24 Pharyngula Embryo Endothelium Cardiovascular System
55383 55383 SRR10323885 SRX7034712 SRS5554730 SRP226614 PRJNA578896 Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence PRJNA578896 Other In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.         danRer10 raw data   strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal                 RNA seq control for mda5 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2 6 6 NEBNext Low Input RNA Library Prep Kit     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 3000   SRP226614     RNA_seq control for mda5 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R2.fastq.gz RNA_seq control for mda5 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R1.fastq.gz fastq fastq 2413394850.0 16089299.0 RNA seq control for mda5 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2 R1.fastq.gz 0:75 1:75 A:660807483;C:490677840;G:505039519;T:756646234;N:223774 75 75     660807483 490677840 505039519 756646234 223774 SRX7034712 SRS5554730 SRA983011 Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany 2 0.60009 0.72319 0.09185 0.10528 0.82175 0.81815 0.5234 0.51725 75 75 B B biological fallback assumption illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   Germany 2019-10-24 Pharyngula Embryo Endothelium Cardiovascular System
55384 55384 SRR10323886 SRX7034711 SRS5554730 SRP226614 PRJNA578896 Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence PRJNA578896 Other In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.         danRer10 raw data   strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal                 RNA seq control for mda5 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1 5 5 NEBNext Low Input RNA Library Prep Kit     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 3000   SRP226614     RNA_seq control for mda5 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R1.fastq.gz RNA_seq control for mda5 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R2.fastq.gz fastq fastq 3124357200.0 20829048.0 RNA seq control for mda5 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1 R1.fastq.gz 0:75 1:75 A:844721216;C:673572690;G:689308705;T:916479849;N:274740 75 75     844721216 673572690 689308705 916479849 274740 SRX7034711 SRS5554730 SRA983011 Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany 2 0.66396 0.73861 0.09392 0.10351 0.80856 0.80797 0.53225 0.5369 75 75 B B biological fallback assumption illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   Germany 2019-10-24 Pharyngula Embryo Endothelium Cardiovascular System
55385 55385 SRR10323891 SRX7034706 SRS5554730 SRP226614 PRJNA578896 Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence PRJNA578896 Other In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.         danRer10 raw data   strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal                 RNA seq rig 1 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2 4 4 NEBNext Low Input RNA Library Prep Kit     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 3000   SRP226614     RNA_seq rig_1 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R2.fastq.gz RNA_seq rig_1 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R1.fastq.gz fastq fastq 2812593000.0 18750620.0 RNA seq rig 1 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2 R1.fastq.gz 0:75 1:75 A:759189725;C:611361876;G:625876145;T:815905469;N:259785 75 75     759189725 611361876 625876145 815905469 259785 SRX7034706 SRS5554730 SRA983011 Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany 2 0.63609 0.70403 0.08285 0.0932 0.79847 0.79959 0.52487 0.52941 75 75 B B biological fallback assumption illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   Germany 2019-10-24 Pharyngula Embryo Endothelium Cardiovascular System
55386 55386 SRR10323898 SRX7034699 SRS5554730 SRP226614 PRJNA578896 Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence PRJNA578896 Other In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.         danRer10 raw data   strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal                 RNA seq decitabine treatment in hemogenic endothelial cell 26hpf replicate 2 24 24 NEBNext Low Input RNA Library Prep Kit     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 3000   SRP226614     RNA_seq decitabine treatment in hemogenic endothelial cell 26hpf replicate 2_R2.fastq.gz RNA_seq decitabine treatment in hemogenic endothelial cell 26hpf replicate 2_R1.fastq.gz fastq fastq 5849571450.0 38997143.0 RNA seq decitabine treatment in hemogenic endothelial cell 26hpf replicate 2 R1.fastq.gz 0:75 1:75 A:1574421853;C:1316832574;G:1315527058;T:1642305644;N:484321 75 75     1574421853 1316832574 1315527058 1642305644 484321 SRX7034699 SRS5554730 SRA983011 Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany 2 0.78221 0.84034 0.0684 0.07089 0.76607 0.77025 0.50712 0.50772 75 75 B B biological fallback assumption illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   Germany 2019-10-24 Pharyngula Embryo Endothelium Cardiovascular System
55387 55387 SRR10323899 SRX7034698 SRS5554730 SRP226614 PRJNA578896 Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence PRJNA578896 Other In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.         danRer10 raw data   strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal                 RNA seq decitabine treatment in hemogenic endothelial cell 26hpf replicate 1 23 23 NEBNext Low Input RNA Library Prep Kit     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 3000   SRP226614     RNA_seq decitabine treatment in hemogenic endothelial cell 26hpf replicate 1_R1.fastq.gz RNA_seq decitabine treatment in hemogenic endothelial cell 26hpf replicate 1_R2.fastq.gz fastq fastq 5656815000.0 37712100.0 RNA seq decitabine treatment in hemogenic endothelial cell 26hpf replicate 1 R1.fastq.gz 0:75 1:75 A:1487198866;C:1332723090;G:1275197163;T:1514410765;N:47285116 75 75     1487198866 1332723090 1275197163 1514410765 47285116 SRX7034698 SRS5554730 SRA983011 Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany 2 0.86399 0.76012 0.0587 0.05779 0.76461 0.9105 0.49754 0.51037 75 75 B B biological fallback assumption illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   Germany 2019-10-24 Pharyngula Embryo Endothelium Cardiovascular System
55388 55388 SRR10323900 SRX7034697 SRS5554730 SRP226614 PRJNA578896 Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence PRJNA578896 Other In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.         danRer10 raw data   strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal                 RNA seq VPA treatment in hemogenic endothelial cell 26hpf replicate 2 22 22 NEBNext Low Input RNA Library Prep Kit     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 3000   SRP226614     RNA_seq VPA treatment in hemogenic endothelial cell 26hpf replicate 2_R2.fastq.gz RNA_seq VPA treatment in hemogenic endothelial cell 26hpf replicate 2_R1.fastq.gz fastq fastq 5978780250.0 39858535.0 RNA seq VPA treatment in hemogenic endothelial cell 26hpf replicate 2 R1.fastq.gz 0:75 1:75 A:1580804547;C:1404640964;G:1399714637;T:1593586843;N:33259 75 75     1580804547 1404640964 1399714637 1593586843 33259 SRX7034697 SRS5554730 SRA983011 Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany 2 0.92216 0.92477 0.04155 0.04126 0.74537 0.7512 0.48148 0.49049 75 75 B B biological fallback assumption illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   Germany 2019-10-24 Pharyngula Embryo Endothelium Cardiovascular System
55389 55389 SRR10323901 SRX7034696 SRS5554730 SRP226614 PRJNA578896 Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence PRJNA578896 Other In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.         danRer10 raw data   strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal                 RNA seq VPA or decitabine treatment in hemogenic endothelial cell 26hpf replicate 1 21 21 NEBNext Low Input RNA Library Prep Kit     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 3000   SRP226614     RNA_seq VPA treatment in hemogenic endothelial cell 26hpf replicate 1_R1.fastq.gz RNA_seq VPA treatment in hemogenic endothelial cell 26hpf replicate 1_R2.fastq.gz fastq fastq 8777730900.0 58518206.0 RNA seq VPA treatment in hemogenic endothelial cell 26hpf replicate 1 R1.fastq.gz 0:75 1:75 A:2331650285;C:2053244561;G:2042022053;T:2350762388;N:51613 75 75     2331650285 2053244561 2042022053 2350762388 51613 SRX7034696 SRS5554730 SRA983011 Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany 2 0.92143 0.92455 0.04604 0.04567 0.73361 0.73923 0.4802 0.48613 75 75 B B biological fallback assumption illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   Germany 2019-10-24 Pharyngula Embryo Endothelium Cardiovascular System
55390 55390 SRR10323902 SRX7034695 SRS5554730 SRP226614 PRJNA578896 Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence PRJNA578896 Other In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.         danRer10 raw data   strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal                 RNA seq rig 1 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1 3 3 NEBNext Low Input RNA Library Prep Kit     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 3000   SRP226614     RNA_seq rig_1 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R1.fastq.gz RNA_seq rig_1 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R2.fastq.gz fastq fastq 3613041150.0 24086941.0 RNA seq rig 1 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1 R1.fastq.gz 0:75 1:75 A:972417798;C:795483066;G:808300399;T:1036510724;N:329163 75 75     972417798 795483066 808300399 1036510724 329163 SRX7034695 SRS5554730 SRA983011 Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany 2 0.66853 0.7231 0.08329 0.0907 0.78953 0.79131 0.51481 0.52637 75 75 B B biological fallback assumption illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   Germany 2019-10-24 Pharyngula Embryo Endothelium Cardiovascular System
55391 55391 SRR10323903 SRX7034694 SRS5554730 SRP226614 PRJNA578896 Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence PRJNA578896 Other In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.         danRer10 raw data   strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal                 RNA seq control for VPA or decitabine treatment in hemogenic endothelial cell 26hpf replicate 2 20 20 NEBNext Low Input RNA Library Prep Kit     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 3000   SRP226614     RNA_seq control for VPA_or_decitabine treatment in hemogenic endothelial cell 26hpf replicate 2_R1.fastq.gz RNA_seq control for VPA_or_decitabine treatment in hemogenic endothelial cell 26hpf replicate 2_R2.fastq.gz fastq fastq 7211828100.0 48078854.0 RNA seq control for VPA or decitabine treatment in hemogenic endothelial cell 26hpf replicate 2 R1.fastq.gz 0:75 1:75 A:1904350731;C:1693709371;G:1687946675;T:1925778331;N:42992 75 75     1904350731 1693709371 1687946675 1925778331 42992 SRX7034694 SRS5554730 SRA983011 Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany 2 0.91819 0.92224 0.03958 0.03841 0.75584 0.76161 0.46923 0.46415 75 75 B B biological fallback assumption illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   Germany 2019-10-24 Pharyngula Embryo Endothelium Cardiovascular System
55392 55392 SRR10323904 SRX7034693 SRS5554730 SRP226614 PRJNA578896 Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence PRJNA578896 Other In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.         danRer10 raw data   strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal                 RNA seq control for VPA treatment in hemogenic endothelial cell 26hpf replicate 1 19 19 NEBNext Low Input RNA Library Prep Kit     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 3000   SRP226614     RNA_seq control for VPA_or_decitabine treatment in hemogenic endothelial cell 26hpf replicate 1_R1.fastq.gz RNA_seq control for VPA_or_decitabine treatment in hemogenic endothelial cell 26hpf replicate 1_R2.fastq.gz fastq fastq 8021297850.0 53475319.0 RNA seq control for VPA or decitabine treatment in hemogenic endothelial cell 26hpf replicate 1 R1.fastq.gz 0:75 1:75 A:2121666298;C:1880005094;G:1872358379;T:2147221627;N:46452 75 75     2121666298 1880005094 1872358379 2147221627 46452 SRX7034693 SRS5554730 SRA983011 Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany 2 0.91273 0.91897 0.0437 0.04345 0.75485 0.76037 0.46259 0.47199 75 75 B B biological fallback assumption illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   Germany 2019-10-24 Pharyngula Embryo Endothelium Cardiovascular System
55393 55393 SRR10323905 SRX7034692 SRS5554730 SRP226614 PRJNA578896 Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence PRJNA578896 Other In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.         danRer10 raw data   strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal                 RNA seq mda5 lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2 18 18 TruSeq stranded mRNA     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 3000   SRP226614     RNA_seq mda5_lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R1.fastq.gz RNA_seq mda5_lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R2.fastq.gz fastq fastq 4925792850.0 32838619.0 RNA seq mda5 lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2 R1.fastq.gz 0:75 1:75 A:1327496924;C:1143172265;G:1121827107;T:1332765205;N:531349 75 75     1327496924 1143172265 1121827107 1332765205 531349 SRX7034692 SRS5554730 SRA983011 Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany 2 0.9235 0.923 0.07189 0.07157 0.74576 0.7486 0.46424 0.46997 75 75 B B biological fallback assumption illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2019-10-24 Pharyngula Embryo Endothelium Cardiovascular System
55394 55394 SRR10323906 SRX7034691 SRS5554730 SRP226614 PRJNA578896 Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence PRJNA578896 Other In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.         danRer10 raw data   strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal                 RNA seq mda5 lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1 17 17 TruSeq stranded mRNA     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 3000   SRP226614     RNA_seq mda5_lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R1.fastq.gz RNA_seq mda5_lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R2.fastq.gz fastq fastq 4481194200.0 29874628.0 RNA seq mda5 lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1 R1.fastq.gz 0:75 1:75 A:1207561849;C:1040055195;G:1022613796;T:1210492037;N:471323 75 75     1207561849 1040055195 1022613796 1210492037 471323 SRX7034691 SRS5554730 SRA983011 Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany 2 0.92094 0.92157 0.07292 0.07281 0.74704 0.75067 0.47205 0.47416 75 75 B B biological fallback assumption illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2019-10-24 Pharyngula Embryo Endothelium Cardiovascular System
55395 55395 SRR10323907 SRX7034690 SRS5554730 SRP226614 PRJNA578896 Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence PRJNA578896 Other In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.         danRer10 raw data   strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal                 RNA seq rig 1 lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2 16 16 TruSeq stranded mRNA     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 3000   SRP226614     RNA_seq rig_1_lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R2.fastq.gz RNA_seq rig_1_lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R1.fastq.gz fastq fastq 2071385250.0 13809235.0 RNA seq rig 1 lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2 R1.fastq.gz 0:75 1:75 A:497024628;C:535934066;G:538798491;T:499539772;N:88293 75 75     497024628 535934066 538798491 499539772 88293 SRX7034690 SRS5554730 SRA983011 Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany 2 0.92507 0.92563 0.0745 0.07106 0.74148 0.74186 0.5137 0.52923 75 75 B B biological fallback assumption illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2019-10-24 Pharyngula Embryo Endothelium Cardiovascular System
55396 55396 SRR10323908 SRX7034689 SRS5554730 SRP226614 PRJNA578896 Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence PRJNA578896 Other In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.         danRer10 raw data   strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal                 RNA seq rig 1 lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1 15 15 TruSeq stranded mRNA     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 3000   SRP226614     RNA_seq rig_1_lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R1.fastq.gz RNA_seq rig_1_lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R2.fastq.gz fastq fastq 1708336800.0 11388912.0 RNA seq rig 1 lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1 R1.fastq.gz 0:75 1:75 A:413739883;C:438115098;G:440441368;T:415968029;N:72422 75 75     413739883 438115098 440441368 415968029 72422 SRX7034689 SRS5554730 SRA983011 Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany 2 0.92948 0.93123 0.08112 0.07757 0.7472 0.74921 0.49384 0.502 75 75 B B biological fallback assumption illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2019-10-24 Pharyngula Embryo Endothelium Cardiovascular System
55397 55397 SRR10323909 SRX7034688 SRS5554730 SRP226614 PRJNA578896 Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence PRJNA578896 Other In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.         danRer10 raw data   strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal                 RNA seq control for double morphants endothelial hemogenic endothelial cell 26hpf replicate 2 14 14 TruSeq stranded mRNA     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 3000   SRP226614     RNA_seq control for double morphants endothelial_hemogenic endothelial cell 26hpf replicate 2_R1.fastq.gz RNA_seq control for double morphants endothelial_hemogenic endothelial cell 26hpf replicate 2_R2.fastq.gz fastq fastq 2742841800.0 18285612.0 RNA seq control for double morphants endothelial hemogenic endothelial cell 26hpf replicate 2 R1.fastq.gz 0:75 1:75 A:771268784;C:600759252;G:605972112;T:764554978;N:286674 75 75     771268784 600759252 605972112 764554978 286674 SRX7034688 SRS5554730 SRA983011 Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany 2 0.91195 0.91276 0.15552 0.15531 0.7191 0.7247 0.487 0.47379 75 75 B B biological fallback assumption illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2019-10-24 Pharyngula Embryo Endothelium Cardiovascular System
55398 55398 SRR10323910 SRX7034687 SRS5554730 SRP226614 PRJNA578896 Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence PRJNA578896 Other In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.         danRer10 raw data   strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal                 RNA seq control for double morphants endothelial hemogenic endothelial cell 26hpf replicate 1 13 13 TruSeq stranded mRNA     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 3000   SRP226614     RNA_seq control for double morphants endothelial_hemogenic endothelial cell 26hpf replicate 1_R1.fastq.gz RNA_seq control for double morphants endothelial_hemogenic endothelial cell 26hpf replicate 1_R2.fastq.gz fastq fastq 1909021350.0 12726809.0 RNA seq control for double morphants endothelial hemogenic endothelial cell 26hpf replicate 1 R1.fastq.gz 0:75 1:75 A:536542827;C:420010389;G:423642042;T:528630203;N:195889 75 75     536542827 420010389 423642042 528630203 195889 SRX7034687 SRS5554730 SRA983011 Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany 2 0.91535 0.91534 0.11578 0.11457 0.73705 0.74373 0.47609 0.47115 75 75 B B biological fallback assumption illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2019-10-24 Pharyngula Embryo Endothelium Cardiovascular System
55399 55399 SRR10323911 SRX7034686 SRS5554730 SRP226614 PRJNA578896 Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence PRJNA578896 Other In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.         danRer10 raw data   strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal                 RNA seq lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2 12 12 NEBNext Low Input RNA Library Prep Kit     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 3000   SRP226614     RNA_seq lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R1.fastq.gz RNA_seq lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R2.fastq.gz fastq fastq 5135290500.0 34235270.0 RNA seq lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2 R1.fastq.gz 0:75 1:75 A:1339180940;C:1202946694;G:1230552771;T:1362120185;N:489910 75 75     1339180940 1202946694 1230552771 1362120185 489910 SRX7034686 SRS5554730 SRA983011 Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany 2 0.66031 0.70687 0.04575 0.04896 0.81075 0.81195 0.50951 0.47552 75 75 B B biological fallback assumption illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   Germany 2019-10-24 Pharyngula Embryo Endothelium Cardiovascular System
55400 55400 SRR10323912 SRX7034685 SRS5554730 SRP226614 PRJNA578896 Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence PRJNA578896 Other In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.         danRer10 raw data   strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal                 RNA seq lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1 11 11 NEBNext Low Input RNA Library Prep Kit     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 3000   SRP226614     RNA_seq lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R1.fastq.gz RNA_seq lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R2.fastq.gz fastq fastq 3890046300.0 25933642.0 RNA seq lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1 R1.fastq.gz 0:75 1:75 A:1020376762;C:903218301;G:916043426;T:1050047618;N:360193 75 75     1020376762 903218301 916043426 1050047618 360193 SRX7034685 SRS5554730 SRA983011 Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany 2 0.70733 0.75223 0.05929 0.06271 0.80807 0.81071 0.48475 0.49323 75 75 B B biological fallback assumption illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   Germany 2019-10-24 Pharyngula Embryo Endothelium Cardiovascular System
55401 55401 SRR10323913 SRX7034684 SRS5554730 SRP226614 PRJNA578896 Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence PRJNA578896 Other In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.         danRer10 raw data   strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal                 RNA seq control for rig 1 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2 2 2 NEBNext Low Input RNA Library Prep Kit     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 3000   SRP226614     RNA_seq control for rig_1 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R1.fastq.gz RNA_seq control for rig_1 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R2.fastq.gz fastq fastq 2547796350.0 16985309.0 RNA seq control for rig 1 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2 R1.fastq.gz 0:75 1:75 A:686259539;C:560800822;G:567842650;T:732652800;N:240539 75 75     686259539 560800822 567842650 732652800 240539 SRX7034684 SRS5554730 SRA983011 Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany 2 0.70188 0.75886 0.08072 0.08833 0.8034 0.80649 0.51507 0.5194 75 75 B B biological fallback assumption illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   Germany 2019-10-24 Pharyngula Embryo Endothelium Cardiovascular System
55402 55402 SRR10323914 SRX7034683 SRS5554730 SRP226614 PRJNA578896 Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence PRJNA578896 Other In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.         danRer10 raw data   strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal                 RNA seq control for rig 1 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1 1 1 NEBNext Low Input RNA Library Prep Kit     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 3000   SRP226614     RNA_seq control for rig_1 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R1.fastq.gz RNA_seq control for rig_1 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R2.fastq.gz fastq fastq 2438070600.0 16253804.0 RNA seq control for rig 1 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1 R1.fastq.gz 0:75 1:75 A:654282012;C:534555119;G:543878428;T:705130425;N:224616 75 75     654282012 534555119 543878428 705130425 224616 SRX7034683 SRS5554730 SRA983011 Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany 2 0.69336 0.75626 0.09168 0.09896 0.80166 0.80253 0.51795 0.52538 75 75 B B biological fallback assumption illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   Germany 2019-10-24 Pharyngula Embryo Endothelium Cardiovascular System
59850 59850 SRR12045008 SRX8573978 SRS6865977 SRP267842 PRJNA640350 Bulk RNA seq data to assess an improved zebrafish transcriptome annotation GSE152759 Transcriptome Analysis oligo dT and random primed RNA seq libraries were used to test an improved annotation of the zebrafish transcriptome Overall design: RNA seq was performed on transgene positive cells isolated by FACS   pubmed:32831172   Nr2f2andY1 positive rep3 GSM4625929   tissue:venous endothelial cells|Stage:38 hpf isolated cells Nr2f2andY1 positive rep3 Raw HiSeq2000 data files were processed with CASAVA 1.8.2 Illumina to generate fastq files for inserts and index sequences. Demultiplexing of index sequences was done with CASAVA. For both samples if index sequences were non redundant we allowed for 1 mismatch or N in the index. Paired end reads were mapped to the zebrafish genome GRCz11 using STAR Mapped reads were quantified using Ensembl v95 RefSeq GCF 000002035.6 or a custom annotation V4.3.gtf included as processed file using RSEM Differentially expressed genes were identified using DEseq2 RNAseq pipeline was run in the DolphinNext environment Genome build: GRz11 Supplementary files format and content: CSV formatted output from DEseq2 for differential gene expression and normalized expression values quantified with 3 different annotations; GTF file for customized V4.3 annotation venous endothelial cells embryos were dissociated into single cell suspensions immunostained with Nr2fantibody and secondary fluorescent tagged antibody; EGFP and Nr2f2 positive cells were isolated by fluorescence activated cell sorting. total RNA was treated with Ribogone and libraries constructed using the SMARTer Stranded RNA Seq Kit Clontech   Stage:38 hpf isolated cells GSM4625929 GSM4625929: Nr2f2andY1 positive rep3; Danio rerio; RNA Seq GSM4625929   1 total RNA was treated with Ribogone and libraries constructed using the SMARTer Stranded RNA Seq Kit Clontech GEO Accession:GSM4625929 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP267842     Nr2f2_y1_WT3.R1.fastq Nr2f2_y1_WT3.R2.fastq fastq fastq 4563696700.0 45636967.0 GSM4625929 r1 0:50 1:50 A:1065004679;C:1130434821;G:1255426694;T:1110932954;N:1897552 50 50     1065004679 1130434821 1255426694 1110932954 1897552 SRX8573978 SRS6865977 SRA1088645 GEO Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School 2 0.82873 0.84247 0.30011 0.31275 0.76952 0.7713 0.70461 0.5211 50 50 B B biological fallback assumption illumina hiseq_era full_length poly_a smarter bulk bulk bulk   United States 2020-06-18 Pharyngula Embryo Endothelium Cardiovascular System
59851 59851 SRR12045007 SRX8573977 SRS6865975 SRP267842 PRJNA640350 Bulk RNA seq data to assess an improved zebrafish transcriptome annotation GSE152759 Transcriptome Analysis oligo dT and random primed RNA seq libraries were used to test an improved annotation of the zebrafish transcriptome Overall design: RNA seq was performed on transgene positive cells isolated by FACS   pubmed:32831172   Nr2f2andY1 positive rep2 GSM4625928   tissue:venous endothelial cells|Stage:38 hpf isolated cells Nr2f2andY1 positive rep2 Raw HiSeq2000 data files were processed with CASAVA 1.8.2 Illumina to generate fastq files for inserts and index sequences. Demultiplexing of index sequences was done with CASAVA. For both samples if index sequences were non redundant we allowed for 1 mismatch or N in the index. Paired end reads were mapped to the zebrafish genome GRCz11 using STAR Mapped reads were quantified using Ensembl v95 RefSeq GCF 000002035.6 or a custom annotation V4.3.gtf included as processed file using RSEM Differentially expressed genes were identified using DEseq2 RNAseq pipeline was run in the DolphinNext environment Genome build: GRz11 Supplementary files format and content: CSV formatted output from DEseq2 for differential gene expression and normalized expression values quantified with 3 different annotations; GTF file for customized V4.3 annotation venous endothelial cells embryos were dissociated into single cell suspensions immunostained with Nr2fantibody and secondary fluorescent tagged antibody; EGFP and Nr2f2 positive cells were isolated by fluorescence activated cell sorting. total RNA was treated with Ribogone and libraries constructed using the SMARTer Stranded RNA Seq Kit Clontech   Stage:38 hpf isolated cells GSM4625928 GSM4625928: Nr2f2andY1 positive rep2; Danio rerio; RNA Seq GSM4625928   1 total RNA was treated with Ribogone and libraries constructed using the SMARTer Stranded RNA Seq Kit Clontech GEO Accession:GSM4625928 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP267842     Nr2f2_y1_WT2.R1.fastq Nr2f2_y1_WT2.R2.fastq fastq fastq 5035288300.0 50352883.0 GSM4625928 r1 0:50 1:50 A:1193841347;C:1228803073;G:1365132247;T:1245428530;N:2083103 50 50     1193841347 1228803073 1365132247 1245428530 2083103 SRX8573977 SRS6865975 SRA1088645 GEO Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School 2 0.81964 0.83355 0.31676 0.32935 0.77394 0.77179 0.69865 0.54887 50 50 B B biological fallback assumption illumina hiseq_era full_length poly_a smarter bulk bulk bulk   United States 2020-06-18 Pharyngula Embryo Endothelium Cardiovascular System
59852 59852 SRR12045006 SRX8573976 SRS6865974 SRP267842 PRJNA640350 Bulk RNA seq data to assess an improved zebrafish transcriptome annotation GSE152759 Transcriptome Analysis oligo dT and random primed RNA seq libraries were used to test an improved annotation of the zebrafish transcriptome Overall design: RNA seq was performed on transgene positive cells isolated by FACS   pubmed:32831172   Nr2f2andY1 positive rep1 GSM4625927   tissue:venous endothelial cells|Stage:38 hpf isolated cells Nr2f2andY1 positive rep1 Raw HiSeq2000 data files were processed with CASAVA 1.8.2 Illumina to generate fastq files for inserts and index sequences. Demultiplexing of index sequences was done with CASAVA. For both samples if index sequences were non redundant we allowed for 1 mismatch or N in the index. Paired end reads were mapped to the zebrafish genome GRCz11 using STAR Mapped reads were quantified using Ensembl v95 RefSeq GCF 000002035.6 or a custom annotation V4.3.gtf included as processed file using RSEM Differentially expressed genes were identified using DEseq2 RNAseq pipeline was run in the DolphinNext environment Genome build: GRz11 Supplementary files format and content: CSV formatted output from DEseq2 for differential gene expression and normalized expression values quantified with 3 different annotations; GTF file for customized V4.3 annotation venous endothelial cells embryos were dissociated into single cell suspensions immunostained with Nr2fantibody and secondary fluorescent tagged antibody; EGFP and Nr2f2 positive cells were isolated by fluorescence activated cell sorting. total RNA was treated with Ribogone and libraries constructed using the SMARTer Stranded RNA Seq Kit Clontech   Stage:38 hpf isolated cells GSM4625927 GSM4625927: Nr2f2andY1 positive rep1; Danio rerio; RNA Seq GSM4625927   1 total RNA was treated with Ribogone and libraries constructed using the SMARTer Stranded RNA Seq Kit Clontech GEO Accession:GSM4625927 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP267842     Nr2f2_y1_WT1.R1.fastq Nr2f2_y1_WT1.R2.fastq fastq fastq 4790242000.0 47902420.0 GSM4625927 r1 0:50 1:50 A:1058654389;C:1248085905;G:1387245634;T:1094388168;N:1867904 50 50     1058654389 1248085905 1387245634 1094388168 1867904 SRX8573976 SRS6865974 SRA1088645 GEO Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School 2 0.83369 0.84436 0.23642 0.24601 0.77788 0.77977 0.73738 0.55719 50 50 B B biological fallback assumption illumina hiseq_era full_length poly_a smarter bulk bulk bulk   United States 2020-06-18 Pharyngula Embryo Endothelium Cardiovascular System
70234 70234 SRR19638155 SRX15688388 SRS13384795 SRP379921 PRJNA848797 RNA seq of endothelial cells from 28 hpf sf3b1 mutant and sibling zebrafish GSE206017 Transcriptome Analysis The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of splicing factor 3b subunit 1 Sf3b1 are lowered in embryonic zebrafish. Results provide insight the role of Sf3b1 in hematopoietic development. Overall design: mRNA profiling of kdrl positive endothelial cells isolated from 28 hpf sf3b1 mutant and sibling zebrafish using Illumina HiSeq4000. Four sibling control samples and Four mutant samples were sequenced. parent bioproject:PRJNA848802 pubmed:36516770   Sib4 GSM6238953   tissue:endothelial cells|time:28 hpf Sib4 basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq220 and EdgeR21 Bioconductor packages. To calculate FPKM Cufflinks version 2.2.1 was used. Assembly: GRcz10 Supplementary files format and content: tab delimited text file includes raw counts for each sample endothelial cells   kdrl positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.   time:28 hpf GSM6238953 GSM6238953: Sib4; Danio rerio; RNA Seq GSM6238953 r1 GSM6238953 1 kdrl positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP379921     SIB4_FCH5WC7BBXX_L2_CHKPEI85216020032_1.fq.gz SIB4_FCH5WC7BBXX_L2_CHKPEI85216020032_2.fq.gz fastq fastq 6126485800.0 30632429.0 GSM6238953 r1 0:100 1:100 A:1285365875;C:1727125042;G:1794776070;T:1318660165;N:558648 100 100     1285365875 1727125042 1794776070 1318660165 558648 SRX15688388 SRS13384795 SRA1436858 Albert Einstein College of Medicine Albert Einstein College of Medicine 2 0.87384 0.88683 0.14413 0.14766 0.76617 0.77015 0.7288 0.6223 100 100 B B biological fallback assumption illumina hiseq_era full_length rrna_depletion smarter bulk unknown unknown   United States 2022-06-13 Pharyngula Embryo Endothelium Cardiovascular System
70235 70235 SRR19638156 SRX15688387 SRS13384794 SRP379921 PRJNA848797 RNA seq of endothelial cells from 28 hpf sf3b1 mutant and sibling zebrafish GSE206017 Transcriptome Analysis The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of splicing factor 3b subunit 1 Sf3b1 are lowered in embryonic zebrafish. Results provide insight the role of Sf3b1 in hematopoietic development. Overall design: mRNA profiling of kdrl positive endothelial cells isolated from 28 hpf sf3b1 mutant and sibling zebrafish using Illumina HiSeq4000. Four sibling control samples and Four mutant samples were sequenced. parent bioproject:PRJNA848802 pubmed:36516770   Sib3 GSM6238952   tissue:endothelial cells|time:28 hpf Sib3 basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq220 and EdgeR21 Bioconductor packages. To calculate FPKM Cufflinks version 2.2.1 was used. Assembly: GRcz10 Supplementary files format and content: tab delimited text file includes raw counts for each sample endothelial cells   kdrl positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.   time:28 hpf GSM6238952 GSM6238952: Sib3; Danio rerio; RNA Seq GSM6238952 r1 GSM6238952 1 kdrl positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP379921     SIB3_FCH5WC7BBXX_L2_CHKPEI85216020030_1.fq.gz SIB3_FCH5WC7BBXX_L2_CHKPEI85216020030_2.fq.gz fastq fastq 6297899800.0 31489499.0 GSM6238952 r1 0:100 1:100 A:1299893326;C:1802214016;G:1871542594;T:1323664459;N:585405 100 100     1299893326 1802214016 1871542594 1323664459 585405 SRX15688387 SRS13384794 SRA1436858 Albert Einstein College of Medicine Albert Einstein College of Medicine 2 0.86882 0.879 0.13327 0.13465 0.76976 0.77273 0.73674 0.61341 100 100 B B biological fallback assumption illumina hiseq_era full_length rrna_depletion smarter bulk unknown unknown   United States 2022-06-13 Pharyngula Embryo Endothelium Cardiovascular System
70236 70236 SRR19638157 SRX15688386 SRS13384792 SRP379921 PRJNA848797 RNA seq of endothelial cells from 28 hpf sf3b1 mutant and sibling zebrafish GSE206017 Transcriptome Analysis The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of splicing factor 3b subunit 1 Sf3b1 are lowered in embryonic zebrafish. Results provide insight the role of Sf3b1 in hematopoietic development. Overall design: mRNA profiling of kdrl positive endothelial cells isolated from 28 hpf sf3b1 mutant and sibling zebrafish using Illumina HiSeq4000. Four sibling control samples and Four mutant samples were sequenced. parent bioproject:PRJNA848802 pubmed:36516770   Sib2 GSM6238951   tissue:endothelial cells|time:28 hpf Sib2 basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq220 and EdgeR21 Bioconductor packages. To calculate FPKM Cufflinks version 2.2.1 was used. Assembly: GRcz10 Supplementary files format and content: tab delimited text file includes raw counts for each sample endothelial cells   kdrl positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.   time:28 hpf GSM6238951 GSM6238951: Sib2; Danio rerio; RNA Seq GSM6238951 r1 GSM6238951 1 kdrl positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP379921     SIB2_FCH5WC7BBXX_L2_CHKPEI85216020028_1.fq.gz SIB2_FCH5WC7BBXX_L2_CHKPEI85216020028_2.fq.gz fastq fastq 5653026200.0 28265131.0 GSM6238951 r1 0:100 1:100 A:1180973101;C:1594686967;G:1664673771;T:1212177547;N:514814 100 100     1180973101 1594686967 1664673771 1212177547 514814 SRX15688386 SRS13384792 SRA1436858 Albert Einstein College of Medicine Albert Einstein College of Medicine 2 0.85973 0.86666 0.13276 0.13789 0.78287 0.78575 0.74425 0.6456 100 100 B B biological fallback assumption illumina hiseq_era full_length rrna_depletion smarter bulk unknown unknown   United States 2022-06-13 Pharyngula Embryo Endothelium Cardiovascular System
70237 70237 SRR19638158 SRX15688385 SRS13384793 SRP379921 PRJNA848797 RNA seq of endothelial cells from 28 hpf sf3b1 mutant and sibling zebrafish GSE206017 Transcriptome Analysis The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of splicing factor 3b subunit 1 Sf3b1 are lowered in embryonic zebrafish. Results provide insight the role of Sf3b1 in hematopoietic development. Overall design: mRNA profiling of kdrl positive endothelial cells isolated from 28 hpf sf3b1 mutant and sibling zebrafish using Illumina HiSeq4000. Four sibling control samples and Four mutant samples were sequenced. parent bioproject:PRJNA848802 pubmed:36516770   Sib1 GSM6238950   tissue:endothelial cells|time:28 hpf Sib1 basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq220 and EdgeR21 Bioconductor packages. To calculate FPKM Cufflinks version 2.2.1 was used. Assembly: GRcz10 Supplementary files format and content: tab delimited text file includes raw counts for each sample endothelial cells   kdrl positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.   time:28 hpf GSM6238950 GSM6238950: Sib1; Danio rerio; RNA Seq GSM6238950 r1 GSM6238950 1 kdrl positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP379921     SIB1_FCH5WC7BBXX_L2_CHKPEI85216020026_1.fq.gz SIB1_FCH5WC7BBXX_L2_CHKPEI85216020026_2.fq.gz fastq fastq 5012776400.0 25063882.0 GSM6238950 r1 0:100 1:100 A:1070464314;C:1393173433;G:1467580233;T:1081106314;N:452106 100 100     1070464314 1393173433 1467580233 1081106314 452106 SRX15688385 SRS13384793 SRA1436858 Albert Einstein College of Medicine Albert Einstein College of Medicine 2 0.87448 0.88469 0.14439 0.14674 0.77264 0.77504 0.72109 0.60233 100 100 B B biological fallback assumption illumina hiseq_era full_length rrna_depletion smarter bulk unknown unknown   United States 2022-06-13 Pharyngula Embryo Endothelium Cardiovascular System
70238 70238 SRR19638159 SRX15688384 SRS13384791 SRP379921 PRJNA848797 RNA seq of endothelial cells from 28 hpf sf3b1 mutant and sibling zebrafish GSE206017 Transcriptome Analysis The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of splicing factor 3b subunit 1 Sf3b1 are lowered in embryonic zebrafish. Results provide insight the role of Sf3b1 in hematopoietic development. Overall design: mRNA profiling of kdrl positive endothelial cells isolated from 28 hpf sf3b1 mutant and sibling zebrafish using Illumina HiSeq4000. Four sibling control samples and Four mutant samples were sequenced. parent bioproject:PRJNA848802 pubmed:36516770   Mut4 GSM6238949   tissue:endothelial cells|time:28 hpf Mut4 basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq220 and EdgeR21 Bioconductor packages. To calculate FPKM Cufflinks version 2.2.1 was used. Assembly: GRcz10 Supplementary files format and content: tab delimited text file includes raw counts for each sample endothelial cells   kdrl positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.   time:28 hpf GSM6238949 GSM6238949: Mut4; Danio rerio; RNA Seq GSM6238949 r1 GSM6238949 1 kdrl positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP379921     Mut4_FCH5WC7BBXX_L2_CHKPEI85216020033_1.fq.gz Mut4_FCH5WC7BBXX_L2_CHKPEI85216020033_2.fq.gz fastq fastq 6178035600.0 30890178.0 GSM6238949 r1 0:100 1:100 A:1301433799;C:1722730513;G:1838039624;T:1315260969;N:570695 100 100     1301433799 1722730513 1838039624 1315260969 570695 SRX15688384 SRS13384791 SRA1436858 Albert Einstein College of Medicine Albert Einstein College of Medicine 2 0.85693 0.86454 0.13476 0.1354 0.77871 0.78104 0.74736 0.6453 100 100 B B biological fallback assumption illumina hiseq_era full_length rrna_depletion smarter bulk unknown unknown   United States 2022-06-13 Pharyngula Embryo Endothelium Cardiovascular System
70239 70239 SRR19638160 SRX15688383 SRS13384790 SRP379921 PRJNA848797 RNA seq of endothelial cells from 28 hpf sf3b1 mutant and sibling zebrafish GSE206017 Transcriptome Analysis The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of splicing factor 3b subunit 1 Sf3b1 are lowered in embryonic zebrafish. Results provide insight the role of Sf3b1 in hematopoietic development. Overall design: mRNA profiling of kdrl positive endothelial cells isolated from 28 hpf sf3b1 mutant and sibling zebrafish using Illumina HiSeq4000. Four sibling control samples and Four mutant samples were sequenced. parent bioproject:PRJNA848802 pubmed:36516770   Mut3 GSM6238948   tissue:endothelial cells|time:28 hpf Mut3 basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq220 and EdgeR21 Bioconductor packages. To calculate FPKM Cufflinks version 2.2.1 was used. Assembly: GRcz10 Supplementary files format and content: tab delimited text file includes raw counts for each sample endothelial cells   kdrl positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.   time:28 hpf GSM6238948 GSM6238948: Mut3; Danio rerio; RNA Seq GSM6238948 r1 GSM6238948 1 kdrl positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP379921     Mut3_FCH5WC7BBXX_L2_CHKPEI85216020031_1.fq.gz Mut3_FCH5WC7BBXX_L2_CHKPEI85216020031_2.fq.gz fastq fastq 6125024800.0 30625124.0 GSM6238948 r1 0:100 1:100 A:1217442139;C:1804787053;G:1859202272;T:1243027936;N:565400 100 100     1217442139 1804787053 1859202272 1243027936 565400 SRX15688383 SRS13384790 SRA1436858 Albert Einstein College of Medicine Albert Einstein College of Medicine 2 0.87443 0.88838 0.13718 0.1382 0.77881 0.7807 0.77832 0.63387 100 100 B B biological fallback assumption illumina hiseq_era full_length rrna_depletion smarter bulk unknown unknown   United States 2022-06-13 Pharyngula Embryo Endothelium Cardiovascular System
70240 70240 SRR19638161 SRX15688382 SRS13384789 SRP379921 PRJNA848797 RNA seq of endothelial cells from 28 hpf sf3b1 mutant and sibling zebrafish GSE206017 Transcriptome Analysis The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of splicing factor 3b subunit 1 Sf3b1 are lowered in embryonic zebrafish. Results provide insight the role of Sf3b1 in hematopoietic development. Overall design: mRNA profiling of kdrl positive endothelial cells isolated from 28 hpf sf3b1 mutant and sibling zebrafish using Illumina HiSeq4000. Four sibling control samples and Four mutant samples were sequenced. parent bioproject:PRJNA848802 pubmed:36516770   Mut2 GSM6238947   tissue:endothelial cells|time:28 hpf Mut2 basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq220 and EdgeR21 Bioconductor packages. To calculate FPKM Cufflinks version 2.2.1 was used. Assembly: GRcz10 Supplementary files format and content: tab delimited text file includes raw counts for each sample endothelial cells   kdrl positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.   time:28 hpf GSM6238947 GSM6238947: Mut2; Danio rerio; RNA Seq GSM6238947 r1 GSM6238947 1 kdrl positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP379921     Mut2_FCH5WC7BBXX_L2_CHKPEI85216020029_1.fq.gz Mut2_FCH5WC7BBXX_L2_CHKPEI85216020029_2.fq.gz fastq fastq 6632897600.0 33164488.0 GSM6238947 r1 0:100 1:100 A:1361386521;C:1895045269;G:1980517948;T:1395337449;N:610413 100 100     1361386521 1895045269 1980517948 1395337449 610413 SRX15688382 SRS13384789 SRA1436858 Albert Einstein College of Medicine Albert Einstein College of Medicine 2 0.88177 0.89115 0.14252 0.14378 0.76568 0.77076 0.66945 0.67015 100 100 B B biological fallback assumption illumina hiseq_era full_length rrna_depletion smarter bulk unknown unknown   United States 2022-06-13 Pharyngula Embryo Endothelium Cardiovascular System
70241 70241 SRR19638162 SRX15688381 SRS13384788 SRP379921 PRJNA848797 RNA seq of endothelial cells from 28 hpf sf3b1 mutant and sibling zebrafish GSE206017 Transcriptome Analysis The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of splicing factor 3b subunit 1 Sf3b1 are lowered in embryonic zebrafish. Results provide insight the role of Sf3b1 in hematopoietic development. Overall design: mRNA profiling of kdrl positive endothelial cells isolated from 28 hpf sf3b1 mutant and sibling zebrafish using Illumina HiSeq4000. Four sibling control samples and Four mutant samples were sequenced. parent bioproject:PRJNA848802 pubmed:36516770   Mut1 GSM6238946   tissue:endothelial cells|time:28 hpf Mut1 basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq220 and EdgeR21 Bioconductor packages. To calculate FPKM Cufflinks version 2.2.1 was used. Assembly: GRcz10 Supplementary files format and content: tab delimited text file includes raw counts for each sample endothelial cells   kdrl positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.   time:28 hpf GSM6238946 GSM6238946: Mut1; Danio rerio; RNA Seq GSM6238946 r1 GSM6238946 1 kdrl positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP379921     Mut1_FCH5WC7BBXX_L2_CHKPEI85216020027_1.fq.gz Mut1_FCH5WC7BBXX_L2_CHKPEI85216020027_2.fq.gz fastq fastq 6970229200.0 34851146.0 GSM6238946 r1 0:100 1:100 A:1444391713;C:1979835747;G:2079119278;T:1466246347;N:636115 100 100     1444391713 1979835747 2079119278 1466246347 636115 SRX15688381 SRS13384788 SRA1436858 Albert Einstein College of Medicine Albert Einstein College of Medicine 2 0.87681 0.88555 0.13764 0.14221 0.77254 0.77717 0.76933 0.59943 100 100 B B biological fallback assumption illumina hiseq_era full_length rrna_depletion smarter bulk unknown unknown   United States 2022-06-13 Pharyngula Embryo Endothelium Cardiovascular System
70242 70242 SRR19638110 SRX15688350 SRS13384757 SRP379896 PRJNA848804 RNA seq of endothelial cells from 28 hpf sf3b1 mutant and sibling zebrafish with Stat3 overexpression GSE206019 Transcriptome Analysis The purpose of the experiment was to define the gene expression and splicing alterations occurring when wildtype or consitutively active Stat3 are expressed in embryonic zebrafish endothelial cells with low levels of splicing factor 3b subunit 1 Sf3b1. Results provide insight the interplay of Sf3b1 and Stat3 in hematopoietic development. Overall design: mRNA profiling of kdrl positive endothelial cells isolated from 28 hpf wildtype sf3b1 mutant and sibling zebrafish with wildtype or constitutively active Stat3 overexpression using the Novogene 6000 platform. A total of 15 samples were sequenced. parent bioproject:PRJNA848802 pubmed:36516770   mut WTstat3 2 GSM6238974   tissue:endothelial cells|time:28 hpf mut WTstat3 2 basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq2 via DEApp. FeatureCounts was used to calculate reads per gene. Assembly: GRcz10 Supplementary files format and content: tab delimited text file includes feature count values for each sample endothelial cells   kdrl positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Poly A RNA was selected by oligo dT primer with low input library generation by Novogene. Libraries were made following the low input library prep and sequenced on a Novoseq 6000   time:28 hpf GSM6238974 GSM6238974: mut WTstat3 2; Danio rerio; RNA Seq GSM6238974 r1 GSM6238974 1 kdrl positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Poly A RNA was selected by oligo dT primer with low input library generation by Novogene. Libraries were made following the low input library prep and sequenced on a Novoseq 6000   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP379896   loader:fastq load.py Exp4_3_S165_L008_R1_001.fastq.gz Exp4_3_S165_L008_R2_001.fastq.gz fastq fastq 10384277550.0 34385025.0 GSM6238974 r1 0:151 1:151 A:1840956361;C:3324376728;G:3454424636;T:1763548987;N:970838 151 151     1840956361 3324376728 3454424636 1763548987 970838 SRX15688350 SRS13384757 SRA1436901 Albert Einstein College of Medicine Albert Einstein College of Medicine 2 0.96136 0.95918 0.25636 0.21064 0.89333 0.89737 0.73541 0.92169 151 151 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2022-06-13 Pharyngula Embryo Endothelium Cardiovascular System
70243 70243 SRR19638111 SRX15688349 SRS13384756 SRP379896 PRJNA848804 RNA seq of endothelial cells from 28 hpf sf3b1 mutant and sibling zebrafish with Stat3 overexpression GSE206019 Transcriptome Analysis The purpose of the experiment was to define the gene expression and splicing alterations occurring when wildtype or consitutively active Stat3 are expressed in embryonic zebrafish endothelial cells with low levels of splicing factor 3b subunit 1 Sf3b1. Results provide insight the interplay of Sf3b1 and Stat3 in hematopoietic development. Overall design: mRNA profiling of kdrl positive endothelial cells isolated from 28 hpf wildtype sf3b1 mutant and sibling zebrafish with wildtype or constitutively active Stat3 overexpression using the Novogene 6000 platform. A total of 15 samples were sequenced. parent bioproject:PRJNA848802 pubmed:36516770   mut CAstat3 3 GSM6238973   tissue:endothelial cells|time:28 hpf mut CAstat3 3 basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq2 via DEApp. FeatureCounts was used to calculate reads per gene. Assembly: GRcz10 Supplementary files format and content: tab delimited text file includes feature count values for each sample endothelial cells   kdrl positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Poly A RNA was selected by oligo dT primer with low input library generation by Novogene. Libraries were made following the low input library prep and sequenced on a Novoseq 6000   time:28 hpf GSM6238973 GSM6238973: mut CAstat3 3; Danio rerio; RNA Seq GSM6238973 r1 GSM6238973 1 kdrl positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Poly A RNA was selected by oligo dT primer with low input library generation by Novogene. Libraries were made following the low input library prep and sequenced on a Novoseq 6000   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP379896   loader:fastq load.py Exp3_6_S164_L008_R1_001.fastq.gz Exp3_6_S164_L008_R2_001.fastq.gz fastq fastq 9225055080.0 30546540.0 GSM6238973 r1 0:151 1:151 A:1794708559;C:2796827335;G:2913010322;T:1719636920;N:871944 151 151     1794708559 2796827335 2913010322 1719636920 871944 SRX15688349 SRS13384756 SRA1436901 Albert Einstein College of Medicine Albert Einstein College of Medicine 2 0.95396 0.95556 0.25122 0.21157 0.84342 0.84837 0.67946 0.89344 151 151 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2022-06-13 Pharyngula Embryo Endothelium Cardiovascular System
70244 70244 SRR19638112 SRX15688348 SRS13384755 SRP379896 PRJNA848804 RNA seq of endothelial cells from 28 hpf sf3b1 mutant and sibling zebrafish with Stat3 overexpression GSE206019 Transcriptome Analysis The purpose of the experiment was to define the gene expression and splicing alterations occurring when wildtype or consitutively active Stat3 are expressed in embryonic zebrafish endothelial cells with low levels of splicing factor 3b subunit 1 Sf3b1. Results provide insight the interplay of Sf3b1 and Stat3 in hematopoietic development. Overall design: mRNA profiling of kdrl positive endothelial cells isolated from 28 hpf wildtype sf3b1 mutant and sibling zebrafish with wildtype or constitutively active Stat3 overexpression using the Novogene 6000 platform. A total of 15 samples were sequenced. parent bioproject:PRJNA848802 pubmed:36516770   sib CAstat3 3 GSM6238972   tissue:endothelial cells|time:28 hpf sib CAstat3 3 basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq2 via DEApp. FeatureCounts was used to calculate reads per gene. Assembly: GRcz10 Supplementary files format and content: tab delimited text file includes feature count values for each sample endothelial cells   kdrl positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Poly A RNA was selected by oligo dT primer with low input library generation by Novogene. Libraries were made following the low input library prep and sequenced on a Novoseq 6000   time:28 hpf GSM6238972 GSM6238972: sib CAstat3 3; Danio rerio; RNA Seq GSM6238972 r1 GSM6238972 1 kdrl positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Poly A RNA was selected by oligo dT primer with low input library generation by Novogene. Libraries were made following the low input library prep and sequenced on a Novoseq 6000   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP379896   loader:fastq load.py Exp3_5_S163_L008_R1_001.fastq.gz Exp3_5_S163_L008_R2_001.fastq.gz fastq fastq 8443820340.0 27959670.0 GSM6238972 r1 0:151 1:151 A:1635898103;C:2566335412;G:2683417484;T:1557364204;N:805137 151 151     1635898103 2566335412 2683417484 1557364204 805137 SRX15688348 SRS13384755 SRA1436901 Albert Einstein College of Medicine Albert Einstein College of Medicine 2 0.96024 0.96118 0.23563 0.18711 0.84058 0.84532 0.64798 0.8526 151 151 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2022-06-13 Pharyngula Embryo Endothelium Cardiovascular System
70245 70245 SRR19638113 SRX15688347 SRS13384754 SRP379896 PRJNA848804 RNA seq of endothelial cells from 28 hpf sf3b1 mutant and sibling zebrafish with Stat3 overexpression GSE206019 Transcriptome Analysis The purpose of the experiment was to define the gene expression and splicing alterations occurring when wildtype or consitutively active Stat3 are expressed in embryonic zebrafish endothelial cells with low levels of splicing factor 3b subunit 1 Sf3b1. Results provide insight the interplay of Sf3b1 and Stat3 in hematopoietic development. Overall design: mRNA profiling of kdrl positive endothelial cells isolated from 28 hpf wildtype sf3b1 mutant and sibling zebrafish with wildtype or constitutively active Stat3 overexpression using the Novogene 6000 platform. A total of 15 samples were sequenced. parent bioproject:PRJNA848802 pubmed:36516770   wt CAstat3 3 GSM6238971   tissue:endothelial cells|time:28 hpf wt CAstat3 3 basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq2 via DEApp. FeatureCounts was used to calculate reads per gene. Assembly: GRcz10 Supplementary files format and content: tab delimited text file includes feature count values for each sample endothelial cells   kdrl positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Poly A RNA was selected by oligo dT primer with low input library generation by Novogene. Libraries were made following the low input library prep and sequenced on a Novoseq 6000   time:28 hpf GSM6238971 GSM6238971: wt CAstat3 3; Danio rerio; RNA Seq GSM6238971 r1 GSM6238971 1 kdrl positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Poly A RNA was selected by oligo dT primer with low input library generation by Novogene. Libraries were made following the low input library prep and sequenced on a Novoseq 6000   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP379896   loader:fastq load.py Exp3_4_S162_L008_R1_001.fastq.gz Exp3_4_S162_L008_R2_001.fastq.gz fastq fastq 10864901490.0 35976495.0 GSM6238971 r1 0:151 1:151 A:2111796980;C:3293914187;G:3427480639;T:2030687904;N:1021780 151 151     2111796980 3293914187 3427480639 2030687904 1021780 SRX15688347 SRS13384754 SRA1436901 Albert Einstein College of Medicine Albert Einstein College of Medicine 2 0.95271 0.95311 0.2466 0.201 0.83015 0.83573 0.61277 0.86761 151 151 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2022-06-13 Pharyngula Embryo Endothelium Cardiovascular System
70246 70246 SRR19638114 SRX15688346 SRS13384753 SRP379896 PRJNA848804 RNA seq of endothelial cells from 28 hpf sf3b1 mutant and sibling zebrafish with Stat3 overexpression GSE206019 Transcriptome Analysis The purpose of the experiment was to define the gene expression and splicing alterations occurring when wildtype or consitutively active Stat3 are expressed in embryonic zebrafish endothelial cells with low levels of splicing factor 3b subunit 1 Sf3b1. Results provide insight the interplay of Sf3b1 and Stat3 in hematopoietic development. Overall design: mRNA profiling of kdrl positive endothelial cells isolated from 28 hpf wildtype sf3b1 mutant and sibling zebrafish with wildtype or constitutively active Stat3 overexpression using the Novogene 6000 platform. A total of 15 samples were sequenced. parent bioproject:PRJNA848802 pubmed:36516770   mut WTstat3 1 GSM6238970   tissue:endothelial cells|time:28 hpf mut WTstat3 1 basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq2 via DEApp. FeatureCounts was used to calculate reads per gene. Assembly: GRcz10 Supplementary files format and content: tab delimited text file includes feature count values for each sample endothelial cells   kdrl positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Poly A RNA was selected by oligo dT primer with low input library generation by Novogene. Libraries were made following the low input library prep and sequenced on a Novoseq 6000   time:28 hpf GSM6238970 GSM6238970: mut WTstat3 1; Danio rerio; RNA Seq GSM6238970 r1 GSM6238970 1 kdrl positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Poly A RNA was selected by oligo dT primer with low input library generation by Novogene. Libraries were made following the low input library prep and sequenced on a Novoseq 6000   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP379896   loader:fastq load.py Exp3_3_S161_L008_R1_001.fastq.gz Exp3_3_S161_L008_R2_001.fastq.gz fastq fastq 8915043020.0 29520010.0 GSM6238970 r1 0:151 1:151 A:1693745824;C:2745718166;G:2860082435;T:1614658018;N:838577 151 151     1693745824 2745718166 2860082435 1614658018 838577 SRX15688346 SRS13384753 SRA1436901 Albert Einstein College of Medicine Albert Einstein College of Medicine 2 0.95689 0.95798 0.2496 0.20922 0.85389 0.85809 0.7267 0.87895 151 151 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2022-06-13 Pharyngula Embryo Endothelium Cardiovascular System
70247 70247 SRR19638115 SRX15688345 SRS13384752 SRP379896 PRJNA848804 RNA seq of endothelial cells from 28 hpf sf3b1 mutant and sibling zebrafish with Stat3 overexpression GSE206019 Transcriptome Analysis The purpose of the experiment was to define the gene expression and splicing alterations occurring when wildtype or consitutively active Stat3 are expressed in embryonic zebrafish endothelial cells with low levels of splicing factor 3b subunit 1 Sf3b1. Results provide insight the interplay of Sf3b1 and Stat3 in hematopoietic development. Overall design: mRNA profiling of kdrl positive endothelial cells isolated from 28 hpf wildtype sf3b1 mutant and sibling zebrafish with wildtype or constitutively active Stat3 overexpression using the Novogene 6000 platform. A total of 15 samples were sequenced. parent bioproject:PRJNA848802 pubmed:36516770   sib WTstat3 2 GSM6238969   tissue:endothelial cells|time:28 hpf sib WTstat3 2 basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq2 via DEApp. FeatureCounts was used to calculate reads per gene. Assembly: GRcz10 Supplementary files format and content: tab delimited text file includes feature count values for each sample endothelial cells   kdrl positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Poly A RNA was selected by oligo dT primer with low input library generation by Novogene. Libraries were made following the low input library prep and sequenced on a Novoseq 6000   time:28 hpf GSM6238969 GSM6238969: sib WTstat3 2; Danio rerio; RNA Seq GSM6238969 r1 GSM6238969 1 kdrl positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Poly A RNA was selected by oligo dT primer with low input library generation by Novogene. Libraries were made following the low input library prep and sequenced on a Novoseq 6000   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP379896   loader:fastq load.py Exp3_2_S160_L008_R1_001.fastq.gz Exp3_2_S160_L008_R2_001.fastq.gz fastq fastq 9196710870.0 30452685.0 GSM6238969 r1 0:151 1:151 A:1745094025;C:2828440030;G:2954522954;T:1667802845;N:851016 151 151     1745094025 2828440030 2954522954 1667802845 851016 SRX15688345 SRS13384752 SRA1436901 Albert Einstein College of Medicine Albert Einstein College of Medicine 2 0.96068 0.95883 0.23379 0.1919 0.84098 0.84526 0.64523 0.89056 151 151 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2022-06-13 Pharyngula Embryo Endothelium Cardiovascular System
70248 70248 SRR19638116 SRX15688344 SRS13384751 SRP379896 PRJNA848804 RNA seq of endothelial cells from 28 hpf sf3b1 mutant and sibling zebrafish with Stat3 overexpression GSE206019 Transcriptome Analysis The purpose of the experiment was to define the gene expression and splicing alterations occurring when wildtype or consitutively active Stat3 are expressed in embryonic zebrafish endothelial cells with low levels of splicing factor 3b subunit 1 Sf3b1. Results provide insight the interplay of Sf3b1 and Stat3 in hematopoietic development. Overall design: mRNA profiling of kdrl positive endothelial cells isolated from 28 hpf wildtype sf3b1 mutant and sibling zebrafish with wildtype or constitutively active Stat3 overexpression using the Novogene 6000 platform. A total of 15 samples were sequenced. parent bioproject:PRJNA848802 pubmed:36516770   wt WTstat3 2 GSM6238968   tissue:endothelial cells|time:28 hpf wt WTstat3 2 basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq2 via DEApp. FeatureCounts was used to calculate reads per gene. Assembly: GRcz10 Supplementary files format and content: tab delimited text file includes feature count values for each sample endothelial cells   kdrl positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Poly A RNA was selected by oligo dT primer with low input library generation by Novogene. Libraries were made following the low input library prep and sequenced on a Novoseq 6000   time:28 hpf GSM6238968 GSM6238968: wt WTstat3 2; Danio rerio; RNA Seq GSM6238968 r1 GSM6238968 1 kdrl positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Poly A RNA was selected by oligo dT primer with low input library generation by Novogene. Libraries were made following the low input library prep and sequenced on a Novoseq 6000   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP379896   loader:fastq load.py Exp3_1_S159_L008_R1_001.fastq.gz Exp3_1_S159_L008_R2_001.fastq.gz fastq fastq 10005583744.0 33131072.0 GSM6238968 r1 0:151 1:151 A:1893830644;C:3081644105;G:3197422762;T:1831747681;N:938552 151 151     1893830644 3081644105 3197422762 1831747681 938552 SRX15688344 SRS13384751 SRA1436901 Albert Einstein College of Medicine Albert Einstein College of Medicine 2 0.95618 0.95612 0.24678 0.20613 0.83684 0.8408 0.70056 0.83001 151 151 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2022-06-13 Pharyngula Embryo Endothelium Cardiovascular System
70249 70249 SRR19638117 SRX15688343 SRS13384750 SRP379896 PRJNA848804 RNA seq of endothelial cells from 28 hpf sf3b1 mutant and sibling zebrafish with Stat3 overexpression GSE206019 Transcriptome Analysis The purpose of the experiment was to define the gene expression and splicing alterations occurring when wildtype or consitutively active Stat3 are expressed in embryonic zebrafish endothelial cells with low levels of splicing factor 3b subunit 1 Sf3b1. Results provide insight the interplay of Sf3b1 and Stat3 in hematopoietic development. Overall design: mRNA profiling of kdrl positive endothelial cells isolated from 28 hpf wildtype sf3b1 mutant and sibling zebrafish with wildtype or constitutively active Stat3 overexpression using the Novogene 6000 platform. A total of 15 samples were sequenced. parent bioproject:PRJNA848802 pubmed:36516770   mut CAstat3 2 GSM6238967   tissue:endothelial cells|time:28 hpf mut CAstat3 2 basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq2 via DEApp. FeatureCounts was used to calculate reads per gene. Assembly: GRcz10 Supplementary files format and content: tab delimited text file includes feature count values for each sample endothelial cells   kdrl positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Poly A RNA was selected by oligo dT primer with low input library generation by Novogene. Libraries were made following the low input library prep and sequenced on a Novoseq 6000   time:28 hpf GSM6238967 GSM6238967: mut CAstat3 2; Danio rerio; RNA Seq GSM6238967 r1 GSM6238967 1 kdrl positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Poly A RNA was selected by oligo dT primer with low input library generation by Novogene. Libraries were made following the low input library prep and sequenced on a Novoseq 6000   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP379896   loader:fastq load.py Exp2_6_S158_L008_R1_001.fastq.gz Exp2_6_S158_L008_R2_001.fastq.gz fastq fastq 9462358526.0 31332313.0 GSM6238967 r1 0:151 1:151 A:1751113648;C:2955540673;G:3070646771;T:1684170095;N:887339 151 151     1751113648 2955540673 3070646771 1684170095 887339 SRX15688343 SRS13384750 SRA1436901 Albert Einstein College of Medicine Albert Einstein College of Medicine 2 0.96928 0.9695 0.2371 0.20224 0.8576 0.86202 0.68544 0.86709 151 151 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2022-06-13 Pharyngula Embryo Endothelium Cardiovascular System
70250 70250 SRR19638118 SRX15688342 SRS13384749 SRP379896 PRJNA848804 RNA seq of endothelial cells from 28 hpf sf3b1 mutant and sibling zebrafish with Stat3 overexpression GSE206019 Transcriptome Analysis The purpose of the experiment was to define the gene expression and splicing alterations occurring when wildtype or consitutively active Stat3 are expressed in embryonic zebrafish endothelial cells with low levels of splicing factor 3b subunit 1 Sf3b1. Results provide insight the interplay of Sf3b1 and Stat3 in hematopoietic development. Overall design: mRNA profiling of kdrl positive endothelial cells isolated from 28 hpf wildtype sf3b1 mutant and sibling zebrafish with wildtype or constitutively active Stat3 overexpression using the Novogene 6000 platform. A total of 15 samples were sequenced. parent bioproject:PRJNA848802 pubmed:36516770   sib CAstat3 2 GSM6238966   tissue:endothelial cells|time:28 hpf sib CAstat3 2 basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq2 via DEApp. FeatureCounts was used to calculate reads per gene. Assembly: GRcz10 Supplementary files format and content: tab delimited text file includes feature count values for each sample endothelial cells   kdrl positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Poly A RNA was selected by oligo dT primer with low input library generation by Novogene. Libraries were made following the low input library prep and sequenced on a Novoseq 6000   time:28 hpf GSM6238966 GSM6238966: sib CAstat3 2; Danio rerio; RNA Seq GSM6238966 r1 GSM6238966 1 kdrl positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Poly A RNA was selected by oligo dT primer with low input library generation by Novogene. Libraries were made following the low input library prep and sequenced on a Novoseq 6000   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP379896   loader:fastq load.py Exp2_5_S157_L008_R1_001.fastq.gz Exp2_5_S157_L008_R2_001.fastq.gz fastq fastq 11265435030.0 37302765.0 GSM6238966 r1 0:151 1:151 A:2133158433;C:3471482468;G:3606423466;T:2053300841;N:1069822 151 151     2133158433 3471482468 3606423466 2053300841 1069822 SRX15688342 SRS13384749 SRA1436901 Albert Einstein College of Medicine Albert Einstein College of Medicine 2 0.96617 0.96674 0.23123 0.18413 0.83938 0.84392 0.67197 0.82759 151 151 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2022-06-13 Pharyngula Embryo Endothelium Cardiovascular System
70251 70251 SRR19638119 SRX15688341 SRS13384748 SRP379896 PRJNA848804 RNA seq of endothelial cells from 28 hpf sf3b1 mutant and sibling zebrafish with Stat3 overexpression GSE206019 Transcriptome Analysis The purpose of the experiment was to define the gene expression and splicing alterations occurring when wildtype or consitutively active Stat3 are expressed in embryonic zebrafish endothelial cells with low levels of splicing factor 3b subunit 1 Sf3b1. Results provide insight the interplay of Sf3b1 and Stat3 in hematopoietic development. Overall design: mRNA profiling of kdrl positive endothelial cells isolated from 28 hpf wildtype sf3b1 mutant and sibling zebrafish with wildtype or constitutively active Stat3 overexpression using the Novogene 6000 platform. A total of 15 samples were sequenced. parent bioproject:PRJNA848802 pubmed:36516770   wt CAstat3 2 GSM6238965   tissue:endothelial cells|time:28 hpf wt CAstat3 2 basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq2 via DEApp. FeatureCounts was used to calculate reads per gene. Assembly: GRcz10 Supplementary files format and content: tab delimited text file includes feature count values for each sample endothelial cells   kdrl positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Poly A RNA was selected by oligo dT primer with low input library generation by Novogene. Libraries were made following the low input library prep and sequenced on a Novoseq 6000   time:28 hpf GSM6238965 GSM6238965: wt CAstat3 2; Danio rerio; RNA Seq GSM6238965 r1 GSM6238965 1 kdrl positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Poly A RNA was selected by oligo dT primer with low input library generation by Novogene. Libraries were made following the low input library prep and sequenced on a Novoseq 6000   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP379896   loader:fastq load.py Exp2_4_S156_L008_R1_001.fastq.gz Exp2_4_S156_L008_R2_001.fastq.gz fastq fastq 11615176398.0 38460849.0 GSM6238965 r1 0:151 1:151 A:2248659834;C:3530304055;G:3658345359;T:2176781681;N:1085469 151 151     2248659834 3530304055 3658345359 2176781681 1085469 SRX15688341 SRS13384748 SRA1436901 Albert Einstein College of Medicine Albert Einstein College of Medicine 2 0.96128 0.96057 0.24177 0.19571 0.82637 0.83197 0.67165 0.83592 151 151 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2022-06-13 Pharyngula Embryo Endothelium Cardiovascular System
70252 70252 SRR19638120 SRX15688340 SRS13384747 SRP379896 PRJNA848804 RNA seq of endothelial cells from 28 hpf sf3b1 mutant and sibling zebrafish with Stat3 overexpression GSE206019 Transcriptome Analysis The purpose of the experiment was to define the gene expression and splicing alterations occurring when wildtype or consitutively active Stat3 are expressed in embryonic zebrafish endothelial cells with low levels of splicing factor 3b subunit 1 Sf3b1. Results provide insight the interplay of Sf3b1 and Stat3 in hematopoietic development. Overall design: mRNA profiling of kdrl positive endothelial cells isolated from 28 hpf wildtype sf3b1 mutant and sibling zebrafish with wildtype or constitutively active Stat3 overexpression using the Novogene 6000 platform. A total of 15 samples were sequenced. parent bioproject:PRJNA848802 pubmed:36516770   mut CAstat3 1 GSM6238964   tissue:endothelial cells|time:28 hpf mut CAstat3 1 basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq2 via DEApp. FeatureCounts was used to calculate reads per gene. Assembly: GRcz10 Supplementary files format and content: tab delimited text file includes feature count values for each sample endothelial cells   kdrl positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Poly A RNA was selected by oligo dT primer with low input library generation by Novogene. Libraries were made following the low input library prep and sequenced on a Novoseq 6000   time:28 hpf GSM6238964 GSM6238964: mut CAstat3 1; Danio rerio; RNA Seq GSM6238964 r1 GSM6238964 1 kdrl positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Poly A RNA was selected by oligo dT primer with low input library generation by Novogene. Libraries were made following the low input library prep and sequenced on a Novoseq 6000   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP379896   loader:fastq load.py Exp1_6_S155_L008_R1_001.fastq.gz Exp1_6_S155_L008_R2_001.fastq.gz fastq fastq 10399177022.0 34434361.0 GSM6238964 r1 0:151 1:151 A:2034691390;C:3140596200;G:3259410466;T:1963496672;N:982294 151 151     2034691390 3140596200 3259410466 1963496672 982294 SRX15688340 SRS13384747 SRA1436901 Albert Einstein College of Medicine Albert Einstein College of Medicine 2 0.95531 0.95521 0.25078 0.21192 0.83071 0.83583 0.66724 0.84646 151 151 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2022-06-13 Pharyngula Embryo Endothelium Cardiovascular System
70253 70253 SRR19638121 SRX15688339 SRS13384745 SRP379896 PRJNA848804 RNA seq of endothelial cells from 28 hpf sf3b1 mutant and sibling zebrafish with Stat3 overexpression GSE206019 Transcriptome Analysis The purpose of the experiment was to define the gene expression and splicing alterations occurring when wildtype or consitutively active Stat3 are expressed in embryonic zebrafish endothelial cells with low levels of splicing factor 3b subunit 1 Sf3b1. Results provide insight the interplay of Sf3b1 and Stat3 in hematopoietic development. Overall design: mRNA profiling of kdrl positive endothelial cells isolated from 28 hpf wildtype sf3b1 mutant and sibling zebrafish with wildtype or constitutively active Stat3 overexpression using the Novogene 6000 platform. A total of 15 samples were sequenced. parent bioproject:PRJNA848802 pubmed:36516770   sib CAstat3 1 GSM6238963   tissue:endothelial cells|time:28 hpf sib CAstat3 1 basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq2 via DEApp. FeatureCounts was used to calculate reads per gene. Assembly: GRcz10 Supplementary files format and content: tab delimited text file includes feature count values for each sample endothelial cells   kdrl positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Poly A RNA was selected by oligo dT primer with low input library generation by Novogene. Libraries were made following the low input library prep and sequenced on a Novoseq 6000   time:28 hpf GSM6238963 GSM6238963: sib CAstat3 1; Danio rerio; RNA Seq GSM6238963 r1 GSM6238963 1 kdrl positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Poly A RNA was selected by oligo dT primer with low input library generation by Novogene. Libraries were made following the low input library prep and sequenced on a Novoseq 6000   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP379896   loader:fastq load.py Exp1_5_S154_L008_R1_001.fastq.gz Exp1_5_S154_L008_R2_001.fastq.gz fastq fastq 11919087756.0 39467178.0 GSM6238963 r1 0:151 1:151 A:2313106016;C:3618768272;G:3747933413;T:2238165241;N:1114814 151 151     2313106016 3618768272 3747933413 2238165241 1114814 SRX15688339 SRS13384745 SRA1436901 Albert Einstein College of Medicine Albert Einstein College of Medicine 2 0.96055 0.96095 0.23199 0.18734 0.83195 0.83619 0.63431 0.82346 151 151 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2022-06-13 Pharyngula Embryo Endothelium Cardiovascular System
70254 70254 SRR19638122 SRX15688338 SRS13384746 SRP379896 PRJNA848804 RNA seq of endothelial cells from 28 hpf sf3b1 mutant and sibling zebrafish with Stat3 overexpression GSE206019 Transcriptome Analysis The purpose of the experiment was to define the gene expression and splicing alterations occurring when wildtype or consitutively active Stat3 are expressed in embryonic zebrafish endothelial cells with low levels of splicing factor 3b subunit 1 Sf3b1. Results provide insight the interplay of Sf3b1 and Stat3 in hematopoietic development. Overall design: mRNA profiling of kdrl positive endothelial cells isolated from 28 hpf wildtype sf3b1 mutant and sibling zebrafish with wildtype or constitutively active Stat3 overexpression using the Novogene 6000 platform. A total of 15 samples were sequenced. parent bioproject:PRJNA848802 pubmed:36516770   wt CAstat3 1 GSM6238962   tissue:endothelial cells|time:28 hpf wt CAstat3 1 basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq2 via DEApp. FeatureCounts was used to calculate reads per gene. Assembly: GRcz10 Supplementary files format and content: tab delimited text file includes feature count values for each sample endothelial cells   kdrl positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Poly A RNA was selected by oligo dT primer with low input library generation by Novogene. Libraries were made following the low input library prep and sequenced on a Novoseq 6000   time:28 hpf GSM6238962 GSM6238962: wt CAstat3 1; Danio rerio; RNA Seq GSM6238962 r1 GSM6238962 1 kdrl positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Poly A RNA was selected by oligo dT primer with low input library generation by Novogene. Libraries were made following the low input library prep and sequenced on a Novoseq 6000   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP379896   loader:fastq load.py Exp1_4_S153_L008_R1_001.fastq.gz Exp1_4_S153_L008_R2_001.fastq.gz fastq fastq 11497964460.0 38072730.0 GSM6238962 r1 0:151 1:151 A:2250612304;C:3475043015;G:3607086823;T:2164152816;N:1069502 151 151     2250612304 3475043015 3607086823 2164152816 1069502 SRX15688338 SRS13384746 SRA1436901 Albert Einstein College of Medicine Albert Einstein College of Medicine 2 0.95894 0.95831 0.23718 0.19205 0.83104 0.83514 0.67708 0.8305 151 151 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2022-06-13 Pharyngula Embryo Endothelium Cardiovascular System
70255 70255 SRR19638123 SRX15688337 SRS13384744 SRP379896 PRJNA848804 RNA seq of endothelial cells from 28 hpf sf3b1 mutant and sibling zebrafish with Stat3 overexpression GSE206019 Transcriptome Analysis The purpose of the experiment was to define the gene expression and splicing alterations occurring when wildtype or consitutively active Stat3 are expressed in embryonic zebrafish endothelial cells with low levels of splicing factor 3b subunit 1 Sf3b1. Results provide insight the interplay of Sf3b1 and Stat3 in hematopoietic development. Overall design: mRNA profiling of kdrl positive endothelial cells isolated from 28 hpf wildtype sf3b1 mutant and sibling zebrafish with wildtype or constitutively active Stat3 overexpression using the Novogene 6000 platform. A total of 15 samples were sequenced. parent bioproject:PRJNA848802 pubmed:36516770   sib WTstat3 1 GSM6238961   tissue:endothelial cells|time:28 hpf sib WTstat3 1 basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq2 via DEApp. FeatureCounts was used to calculate reads per gene. Assembly: GRcz10 Supplementary files format and content: tab delimited text file includes feature count values for each sample endothelial cells   kdrl positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Poly A RNA was selected by oligo dT primer with low input library generation by Novogene. Libraries were made following the low input library prep and sequenced on a Novoseq 6000   time:28 hpf GSM6238961 GSM6238961: sib WTstat3 1; Danio rerio; RNA Seq GSM6238961 r1 GSM6238961 1 kdrl positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Poly A RNA was selected by oligo dT primer with low input library generation by Novogene. Libraries were made following the low input library prep and sequenced on a Novoseq 6000   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP379896   loader:fastq load.py Exp1_2_S152_L008_R1_001.fastq.gz Exp1_2_S152_L008_R2_001.fastq.gz fastq fastq 11337560784.0 37541592.0 GSM6238961 r1 0:151 1:151 A:2267901503;C:3373840182;G:3494902299;T:2199847509;N:1069291 151 151     2267901503 3373840182 3494902299 2199847509 1069291 SRX15688337 SRS13384744 SRA1436901 Albert Einstein College of Medicine Albert Einstein College of Medicine 2 0.94635 0.9457 0.25659 0.21796 0.82668 0.83096 0.70895 0.84151 151 151 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2022-06-13 Pharyngula Embryo Endothelium Cardiovascular System
70256 70256 SRR19638124 SRX15688336 SRS13384743 SRP379896 PRJNA848804 RNA seq of endothelial cells from 28 hpf sf3b1 mutant and sibling zebrafish with Stat3 overexpression GSE206019 Transcriptome Analysis The purpose of the experiment was to define the gene expression and splicing alterations occurring when wildtype or consitutively active Stat3 are expressed in embryonic zebrafish endothelial cells with low levels of splicing factor 3b subunit 1 Sf3b1. Results provide insight the interplay of Sf3b1 and Stat3 in hematopoietic development. Overall design: mRNA profiling of kdrl positive endothelial cells isolated from 28 hpf wildtype sf3b1 mutant and sibling zebrafish with wildtype or constitutively active Stat3 overexpression using the Novogene 6000 platform. A total of 15 samples were sequenced. parent bioproject:PRJNA848802 pubmed:36516770   wt WTstat3 1 GSM6238960   tissue:endothelial cells|time:28 hpf wt WTstat3 1 basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq2 via DEApp. FeatureCounts was used to calculate reads per gene. Assembly: GRcz10 Supplementary files format and content: tab delimited text file includes feature count values for each sample endothelial cells   kdrl positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Poly A RNA was selected by oligo dT primer with low input library generation by Novogene. Libraries were made following the low input library prep and sequenced on a Novoseq 6000   time:28 hpf GSM6238960 GSM6238960: wt WTstat3 1; Danio rerio; RNA Seq GSM6238960 r1 GSM6238960 1 kdrl positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Poly A RNA was selected by oligo dT primer with low input library generation by Novogene. Libraries were made following the low input library prep and sequenced on a Novoseq 6000   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP379896   loader:fastq load.py Exp1_1_S151_L008_R1_001.fastq.gz Exp1_1_S151_L008_R2_001.fastq.gz fastq fastq 12110767458.0 40101879.0 GSM6238960 r1 0:151 1:151 A:2374851845;C:3648786741;G:3800016692;T:2285963576;N:1148604 151 151     2374851845 3648786741 3800016692 2285963576 1148604 SRX15688336 SRS13384743 SRA1436901 Albert Einstein College of Medicine Albert Einstein College of Medicine 2 0.95385 0.95362 0.24549 0.20304 0.83063 0.83524 0.62301 0.83616 151 151 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2022-06-13 Pharyngula Embryo Endothelium Cardiovascular System
71628 71628 SRR21849082 SRX17837648 SRS15359799 SRP401744 PRJNA888821 The RNA binding protein CSDE1 promotes hematopoietic stem and progenitor cell generation via translational control of Wnt signaling PRJNA888821 Other We identified RBP as an important post transcriptional regulator of HSPC generation and elucidated the underlying molecular mechanisms. The study also provides helpful insights into designing novel strategies for HSPC generation in vitro.       33 hpf Zebrafish trunk region Bulk RNA seq.Sibling2 Zebrafish 33 hpf.Bulk RNA seq.Sibling2   breed:Zebrafish|age:33 hpf|dev stage:HSPC generation|sex:pooled male and female|tissue:endothelial cells|treatment:4|BioSampleModel:Model organism or animal                 33 hpf Zebrafish trunk region Bulk RNA seq.Sibling2 Sibling2 Sibling2 RNA Seq     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP401744     Sibling2_1.fq.gz Sibling2_2.fq.gz fastq fastq 8355719700.0 27852399.0 Sibling2 1.fq.gz 0:150 1:150 A:2334078708;C:1842634378;G:1847518409;T:2331414647;N:73558 150 150     2334078708 1842634378 1847518409 2331414647 73558 SRX17837648 SRS15359799 SRA1516844 Institute of Hematology &amp; Blood Diseases Hospital|State Key Laboratory of Experimental Hematology Institute of Hematology & Blood Diseases Hospital 2 0.92166 0.92002 0.15953 0.15792 0.75162 0.75116 0.51255 0.54267 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2022-10-09 Pharyngula Embryo Endothelium Cardiovascular System

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