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35 rows where devstage_curation = "Larval" and tissue_curation = "Endothelium"

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technology 2

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experiment.library_selection 2

experiment.library_layout 2

tissue_curation_coarse 1

tissue_curation 1

  • Endothelium · 35 ✖

experiment.platform 1

experiment.library_source 1

devstage_curation_coarse 1

devstage_curation 1

  • Larval · 35 ✖
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
40968 40968 SRR3498282 SRX1756828 SRS1433359 SRP074847 PRJNA321312 mRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues GSE81335 Transcriptome Analysis Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages parent bioproject:PRJNA321317 pubmed:28350988;pubmed:33273096   6dpf E1 GSM2150746   source name:Endothelial cell|developmental stage:6 dpf|tissue:Endothelial|stain:GFP 6dpf E1 Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include FPKM values for each Sample . Endothelial cell   Transgenic fish were treated with Liberase to dissociate the cells. post FACS sorting the GFP positive RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473. developmental stage:6 dpf|tissue:Endothelial|stain:GFP GSM2150746 GSM2150746: 6dpf E1; Danio rerio; RNA Seq GSM2150746   1 Transgenic fish were treated with Liberase to dissociate the cells. post FACS sorting the GFP positive RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM2150746 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer   SRP074847     EF_036_004_TGACCA_L002_R1.fastq.gz fastq 446212036.0 5871211.0 GSM2150746 r1 0:76 A:121356950;C:99664887;G:97289960;T:122019647;N:5880592 76       121356950 99664887 97289960 122019647 5880592 SRX1756828 SRS1433359 SRA424807 GEO Internal Medicine, Yale University 1 0.76652   0.13082   0.73985   0.47925   76   B   usable mapping rate illumina early_illumina unknown small_rna trueseq bulk unknown unknown   United States 2016-05-11 Larval Larval Endothelium Cardiovascular System
40969 40969 SRR3498281 SRX1756827 SRS1433358 SRP074847 PRJNA321312 mRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues GSE81335 Transcriptome Analysis Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages parent bioproject:PRJNA321317 pubmed:28350988;pubmed:33273096   72hpf E1 GSM2150745   source name:Endothelial cell|developmental stage:72 hpf|tissue:Endothelial|stain:GFP 72hpf E1 Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include FPKM values for each Sample . Endothelial cell   Transgenic fish were treated with Liberase to dissociate the cells. post FACS sorting the GFP positive RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473. developmental stage:72 hpf|tissue:Endothelial|stain:GFP GSM2150745 GSM2150745: 72hpf E1; Danio rerio; RNA Seq GSM2150745   1 Transgenic fish were treated with Liberase to dissociate the cells. post FACS sorting the GFP positive RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM2150745 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer   SRP074847     EF_035_003_TTAGGC_L002_R1.fastq.gz fastq 533039908.0 7013683.0 GSM2150745 r1 0:76 A:141643030;C:119112106;G:118099940;T:147160011;N:7024821 76       141643030 119112106 118099940 147160011 7024821 SRX1756827 SRS1433358 SRA424807 GEO Internal Medicine, Yale University 1 0.86605   0.1329   0.72253   0.49856   76   B   usable mapping rate illumina early_illumina unknown small_rna trueseq bulk unknown unknown   United States 2016-05-11 Larval Larval Endothelium Cardiovascular System
40972 40972 SRR3498294 SRX1756840 SRS1433371 SRP074848 PRJNA321321 microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues GSE81340 Transcriptome Analysis Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate parent bioproject:PRJNA321317 pubmed:28350988;pubmed:33273096   NoEndo 72hpf E2 GSM2150819   source name:Endothelial cell|developmental stage:72hpf|tissue:Endothelial|stain:GFP NoEndo 72hpf E2 Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ... Endothelial cell   Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473. developmental stage:72hpf|tissue:Endothelial|stain:GFP GSM2150819 GSM2150819: NoEndo 72hpf E2; Danio rerio; miRNA Seq GSM2150819   1 Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM2150819 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer   SRP074848     NoEndo_72hpf_E2.fastq.gz fastq 797509876.0 10493551.0 GSM2150819 r1 0:76 A:182564842;C:199547592;G:199064466;T:216287390;N:45586 76       182564842 199547592 199064466 216287390 45586 SRX1756840 SRS1433371 SRA424808 GEO Internal Medicine, Yale University 1 1e-05   0.0   1.0       76   T   under 1.2% mapping rate illumina early_illumina unknown size_fractionation trueseq bulk unknown unknown   United States 2016-05-11 Larval Larval Endothelium Cardiovascular System
40973 40973 SRR3498293 SRX1756839 SRS1433370 SRP074848 PRJNA321321 microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues GSE81340 Transcriptome Analysis Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate parent bioproject:PRJNA321317 pubmed:28350988;pubmed:33273096   NoEndo 72hpf E1 GSM2150818   source name:Endothelial cell|developmental stage:72hpf|tissue:Endothelial|stain:GFP NoEndo 72hpf E1 Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ... Endothelial cell   Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473. developmental stage:72hpf|tissue:Endothelial|stain:GFP GSM2150818 GSM2150818: NoEndo 72hpf E1; Danio rerio; miRNA Seq GSM2150818   1 Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM2150818 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer   SRP074848     NoEndo_72hpf_E1.fastq.gz fastq 1864172232.0 24528582.0 GSM2150818 r1 0:76 A:426671762;C:469538477;G:458132395;T:509711525;N:118073 76       426671762 469538477 458132395 509711525 118073 SRX1756839 SRS1433370 SRA424808 GEO Internal Medicine, Yale University 1 0.0   0.0   1.0       76   T   under 1.2% mapping rate illumina early_illumina unknown size_fractionation trueseq bulk unknown unknown   United States 2016-05-11 Larval Larval Endothelium Cardiovascular System
40974 40974 SRR3498292 SRX1756838 SRS1433369 SRP074848 PRJNA321321 microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues GSE81340 Transcriptome Analysis Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate parent bioproject:PRJNA321317 pubmed:28350988;pubmed:33273096   NoEndo 6dpf E1 GSM2150817   source name:Endothelial cell|developmental stage:6dpf|tissue:Endothelial|stain:GFP NoEndo 6dpf E1 Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ... Endothelial cell   Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473. developmental stage:6dpf|tissue:Endothelial|stain:GFP GSM2150817 GSM2150817: NoEndo 6dpf E1; Danio rerio; miRNA Seq GSM2150817   1 Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM2150817 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer   SRP074848     NoEndo_6dpf_E1.fastq.gz fastq 1414849364.0 18616439.0 GSM2150817 r1 0:76 A:315250036;C:366906308;G:364673112;T:367938758;N:81150 76       315250036 366906308 364673112 367938758 81150 SRX1756838 SRS1433369 SRA424808 GEO Internal Medicine, Yale University 1 1e-05   0.0   1.0       76   T   under 1.2% mapping rate illumina early_illumina unknown size_fractionation trueseq bulk unknown unknown   United States 2016-05-11 Larval Larval Endothelium Cardiovascular System
40978 40978 SRR3498288 SRX1756834 SRS1433365 SRP074848 PRJNA321321 microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues GSE81340 Transcriptome Analysis Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate parent bioproject:PRJNA321317 pubmed:28350988;pubmed:33273096   Endo 72hpf E2 GSM2150813   source name:Endothelial cell|developmental stage:72hpf|tissue:Endothelial|stain:GFP Endo 72hpf E2 Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ... Endothelial cell   Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473. developmental stage:72hpf|tissue:Endothelial|stain:GFP GSM2150813 GSM2150813: Endo 72hpf E2; Danio rerio; miRNA Seq GSM2150813   1 Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM2150813 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer   SRP074848     Endo_72hpf_E2.fastq.gz fastq 438128980.0 5764855.0 GSM2150813 r1 0:76 A:101851745;C:114159902;G:115733669;T:106360221;N:23443 76       101851745 114159902 115733669 106360221 23443 SRX1756834 SRS1433365 SRA424808 GEO Internal Medicine, Yale University 1 2e-05   1e-05   1.0       76   T   under 1.2% mapping rate illumina early_illumina unknown size_fractionation trueseq bulk unknown unknown   United States 2016-05-11 Larval Larval Endothelium Cardiovascular System
40979 40979 SRR3498287 SRX1756833 SRS1433364 SRP074848 PRJNA321321 microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues GSE81340 Transcriptome Analysis Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate parent bioproject:PRJNA321317 pubmed:28350988;pubmed:33273096   Endo 72hpf E1 GSM2150812   source name:Endothelial cell|developmental stage:72hpf|tissue:Endothelial|stain:GFP Endo 72hpf E1 Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ... Endothelial cell   Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473. developmental stage:72hpf|tissue:Endothelial|stain:GFP GSM2150812 GSM2150812: Endo 72hpf E1; Danio rerio; miRNA Seq GSM2150812   1 Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM2150812 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer   SRP074848     Endo_72hpf_E1.fastq.gz fastq 1267915068.0 16683093.0 GSM2150812 r1 0:76 A:321606522;C:310505837;G:323829249;T:311892892;N:80568 76       321606522 310505837 323829249 311892892 80568 SRX1756833 SRS1433364 SRA424808 GEO Internal Medicine, Yale University 1 0.0   0.0   1.0       76   T   under 1.2% mapping rate illumina early_illumina unknown size_fractionation trueseq bulk unknown unknown   United States 2016-05-11 Larval Larval Endothelium Cardiovascular System
40980 40980 SRR3498286 SRX1756832 SRS1433363 SRP074848 PRJNA321321 microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues GSE81340 Transcriptome Analysis Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate parent bioproject:PRJNA321317 pubmed:28350988;pubmed:33273096   Endo 6dpf E1 GSM2150811   source name:Endothelial cell|developmental stage:6dpf|tissue:Endothelial|stain:GFP Endo 6dpf E1 Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ... Endothelial cell   Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473. developmental stage:6dpf|tissue:Endothelial|stain:GFP GSM2150811 GSM2150811: Endo 6dpf E1; Danio rerio; miRNA Seq GSM2150811   1 Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM2150811 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer   SRP074848     Endo_6dpf_E1.fastq.gz fastq 890474824.0 11716774.0 GSM2150811 r1 0:76 A:230419087;C:212029155;G:232306960;T:215672618;N:47004 76       230419087 212029155 232306960 215672618 47004 SRX1756832 SRS1433363 SRA424808 GEO Internal Medicine, Yale University 1 2e-05   1e-05   1.0       76   T   under 1.2% mapping rate illumina early_illumina unknown size_fractionation trueseq bulk unknown unknown   United States 2016-05-11 Larval Larval Endothelium Cardiovascular System
49040 49040 SRR7633494 SRX4497225 SRS3618225 SRP155992 PRJNA483985 Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA GSE118000 Transcriptome Analysis We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2   pubmed:31158233   G2 endo 03 GSM3317066   tissue:zebrafish endothelium|line:fli:EGFP|treatment:human APOL1 G2 mRNA G2 endo 03 Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2 zebrafish endothelium Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf line:fli:EGFP|treatment:human APOL1 G2 mRNA GSM3317066 GSM3317066: G2 endo 03; Danio rerio; RNA Seq GSM3317066   1 RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech GEO Accession:GSM3317066 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP155992     BA_S18_trimmed.fastq.gz fastq 950344310.0 18847513.0 GSM3317066 r1 0:50.42 1:0 A:270135652;C:209210468;G:202674675;T:268256430;N:67085 50 0     270135652 209210468 202674675 268256430 67085 SRX4497225 SRS3618225 SRA749599 GEO Duke Molecular Physiology Institute, Duke University Medical Center 1 0.89759   0.1428   0.69132   0.4729   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2018-08-01 Larval Larval Endothelium Cardiovascular System
49041 49041 SRR7633493 SRX4497224 SRS3618224 SRP155992 PRJNA483985 Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA GSE118000 Transcriptome Analysis We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2   pubmed:31158233   G2 endo 02 GSM3317065   tissue:zebrafish endothelium|line:fli:EGFP|treatment:human APOL1 G2 mRNA G2 endo 02 Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2 zebrafish endothelium Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf line:fli:EGFP|treatment:human APOL1 G2 mRNA GSM3317065 GSM3317065: G2 endo 02; Danio rerio; RNA Seq GSM3317065   1 RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech GEO Accession:GSM3317065 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP155992     BA_S17_trimmed.fastq.gz fastq 1635110054.0 32380584.0 GSM3317065 r1 0:50.50 1:0 A:462134552;C:361057634;G:349465446;T:462337205;N:115217 50 0     462134552 361057634 349465446 462337205 115217 SRX4497224 SRS3618224 SRA749599 GEO Duke Molecular Physiology Institute, Duke University Medical Center 1 0.80201   0.12711   0.70471   0.44427   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2018-08-01 Larval Larval Endothelium Cardiovascular System
49042 49042 SRR7633492 SRX4497223 SRS3618223 SRP155992 PRJNA483985 Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA GSE118000 Transcriptome Analysis We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2   pubmed:31158233   G2 endo 01 GSM3317064   tissue:zebrafish endothelium|line:fli:EGFP|treatment:human APOL1 G2 mRNA G2 endo 01 Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2 zebrafish endothelium Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf line:fli:EGFP|treatment:human APOL1 G2 mRNA GSM3317064 GSM3317064: G2 endo 01; Danio rerio; RNA Seq GSM3317064   1 RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech GEO Accession:GSM3317064 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP155992     BA_S16_trimmed.fastq.gz fastq 1302352614.0 25794210.0 GSM3317064 r1 0:50.49 1:0 A:370194702;C:286011167;G:276758200;T:369297736;N:90809 50 0     370194702 286011167 276758200 369297736 90809 SRX4497223 SRS3618223 SRA749599 GEO Duke Molecular Physiology Institute, Duke University Medical Center 1 0.89468   0.15745   0.69447   0.47938   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2018-08-01 Larval Larval Endothelium Cardiovascular System
49043 49043 SRR7633491 SRX4497222 SRS3618222 SRP155992 PRJNA483985 Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA GSE118000 Transcriptome Analysis We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2   pubmed:31158233   G0 endo 03 GSM3317063   tissue:zebrafish endothelium|line:fli:EGFP|treatment:human APOL1 G0 mRNA G0 endo 03 Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2 zebrafish endothelium Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf line:fli:EGFP|treatment:human APOL1 G0 mRNA GSM3317063 GSM3317063: G0 endo 03; Danio rerio; RNA Seq GSM3317063   1 RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech GEO Accession:GSM3317063 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP155992     BA_S15_trimmed.fastq.gz fastq 1248556473.0 24725241.0 GSM3317063 r1 0:50.50 1:0 A:350256976;C:280431139;G:270771772;T:347009294;N:87292 50 0     350256976 280431139 270771772 347009294 87292 SRX4497222 SRS3618222 SRA749599 GEO Duke Molecular Physiology Institute, Duke University Medical Center 1 0.90514   0.13266   0.69236   0.47977   49   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2018-08-01 Larval Larval Endothelium Cardiovascular System
49044 49044 SRR7633490 SRX4497221 SRS3618221 SRP155992 PRJNA483985 Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA GSE118000 Transcriptome Analysis We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2   pubmed:31158233   G0 endo 02 GSM3317062   tissue:zebrafish endothelium|line:fli:EGFP|treatment:human APOL1 G0 mRNA G0 endo 02 Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2 zebrafish endothelium Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf line:fli:EGFP|treatment:human APOL1 G0 mRNA GSM3317062 GSM3317062: G0 endo 02; Danio rerio; RNA Seq GSM3317062   1 RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech GEO Accession:GSM3317062 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP155992     BA_S14_trimmed.fastq.gz fastq 372093672.0 7456111.0 GSM3317062 r1 0:49.90 1:0 A:113486766;C:74400549;G:71245468;T:112935661;N:25228 49 0     113486766 74400549 71245468 112935661 25228 SRX4497221 SRS3618221 SRA749599 GEO Duke Molecular Physiology Institute, Duke University Medical Center 1 0.89644   0.12968   0.70658   0.47231   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2018-08-01 Larval Larval Endothelium Cardiovascular System
49045 49045 SRR7633489 SRX4497220 SRS3618220 SRP155992 PRJNA483985 Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA GSE118000 Transcriptome Analysis We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2   pubmed:31158233   G0 endo 01 GSM3317061   tissue:zebrafish endothelium|line:fli:EGFP|treatment:human APOL1 G0 mRNA G0 endo 01 Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2 zebrafish endothelium Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf line:fli:EGFP|treatment:human APOL1 G0 mRNA GSM3317061 GSM3317061: G0 endo 01; Danio rerio; RNA Seq GSM3317061   1 RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech GEO Accession:GSM3317061 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP155992     BA_S13_trimmed.fastq.gz fastq 1450133780.0 28705598.0 GSM3317061 r1 0:50.52 1:0 A:407543677;C:323333189;G:313321100;T:405835253;N:100561 50 0     407543677 323333189 313321100 405835253 100561 SRX4497220 SRS3618220 SRA749599 GEO Duke Molecular Physiology Institute, Duke University Medical Center 1 0.8994   0.13347   0.6942   0.47759   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2018-08-01 Larval Larval Endothelium Cardiovascular System
49046 49046 SRR7633488 SRX4497219 SRS3618219 SRP155992 PRJNA483985 Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA GSE118000 Transcriptome Analysis We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2   pubmed:31158233   control endo 03 GSM3317060   tissue:zebrafish endothelium|line:fli:EGFP|treatment:control control endo 03 Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2 zebrafish endothelium Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf line:fli:EGFP|treatment:control GSM3317060 GSM3317060: control endo 03; Danio rerio; RNA Seq GSM3317060   1 RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech GEO Accession:GSM3317060 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP155992     BA_S12_trimmed.fastq.gz fastq 1720199608.0 34019943.0 GSM3317060 r1 0:50.56 1:0 A:474252335;C:393152371;G:382256277;T:470417173;N:121452 50 0     474252335 393152371 382256277 470417173 121452 SRX4497219 SRS3618219 SRA749599 GEO Duke Molecular Physiology Institute, Duke University Medical Center 1 0.90252   0.11709   0.69668   0.47424   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2018-08-01 Larval Larval Endothelium Cardiovascular System
49047 49047 SRR7633487 SRX4497218 SRS3618218 SRP155992 PRJNA483985 Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA GSE118000 Transcriptome Analysis We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2   pubmed:31158233   control endo 02 GSM3317059   tissue:zebrafish endothelium|line:fli:EGFP|treatment:control control endo 02 Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2 zebrafish endothelium Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf line:fli:EGFP|treatment:control GSM3317059 GSM3317059: control endo 02; Danio rerio; RNA Seq GSM3317059   1 RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech GEO Accession:GSM3317059 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP155992     BA_S11_trimmed.fastq.gz fastq 322327295.0 6605687.0 GSM3317059 r1 0:48.80 1:0 A:109722776;C:53179948;G:51091267;T:108312123;N:21181 48 0     109722776 53179948 51091267 108312123 21181 SRX4497218 SRS3618218 SRA749599 GEO Duke Molecular Physiology Institute, Duke University Medical Center 1 0.8922   0.1261   0.72811   0.46128   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2018-08-01 Larval Larval Endothelium Cardiovascular System
49048 49048 SRR7633486 SRX4497217 SRS3618217 SRP155992 PRJNA483985 Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA GSE118000 Transcriptome Analysis We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2   pubmed:31158233   control endo 01 GSM3317058   tissue:zebrafish endothelium|line:fli:EGFP|treatment:control control endo 01 Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2 zebrafish endothelium Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf line:fli:EGFP|treatment:control GSM3317058 GSM3317058: control endo 01; Danio rerio; RNA Seq GSM3317058   1 RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech GEO Accession:GSM3317058 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP155992     BA_S10_trimmed.fastq.gz fastq 1484074935.0 29385409.0 GSM3317058 r1 0:50.50 1:0 A:411414710;C:336260838;G:326730208;T:409563857;N:105322 50 0     411414710 336260838 326730208 409563857 105322 SRX4497217 SRS3618217 SRA749599 GEO Duke Molecular Physiology Institute, Duke University Medical Center 1 0.88777   0.11462   0.70102   0.47353   49   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2018-08-01 Larval Larval Endothelium Cardiovascular System
58567 58567 SRR11420478 SRX7998914 SRS6376277 SRP254020 PRJNA615175 A Zebrafish Based Orthotopic Glioblastoma Xenograft Model for Preclinical Drug Screening and Clinical Drug Sensitivity Prediction GSE147526 Other A reliable animal model that can mimic the GBM intracranial infiltration and Blood brain barrier BBB interaction is necessary for effective therapeutics development. Here we report a zebrafish based orthotopic GBM xenograft model in which GBM cells from different species and even patients can robustly propagate and faithfully reproduce their histological characteristics. Single cell RNA seq indicates a transcriptomic adaption of GBM xenografts to infiltrative phenotype within the zebrafish brains. We also provide evidence that the BBB in zebrafish larva is molecularly and functionally intact and can interact with GBM cells in similar ways as in mammals which together enables this model to accurately identify BBB penetrating drugs. Using GBM patients' samples we further generate zebrafish patient derived orthotopic xenografts z PDOX and proof of concept experiments indicate the short term temozolomide response in z PDOX can predict the long term prognosis of corresponding GBM patients. These together illustrate the value of zebrafish GBM model in drug discovery and precision medicine. Overall design: 1.Single cell RNA seq for endothelial cells of zebrafish 2.Single cell RNA seq for GBM cells implanted in zebrafish brain   pubmed:35199829   Smartseq2 AXL E3 endo Danio GSM4432625   tissue:endothelial cells|strain:flk:GFP|cell tye:endothelial cells Smartseq2 AXL E3 endo Danio ScRNA seq alignment process was completed by STAR 2.6.0a DESeq2 standard workflow Genome build: GRCz10 genome references for Zebrafish and GRCh38 genome references for human Supplementary files format and content: csv files with raw counts and FPKM endothelial cells   1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle. 2. For GBM cells zebrafish were injected with GBM U251 mCherry cells and allowed to form widespread tumor invasion for xxx 5 days. At that point the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the 3’ scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang 2010.   strain:flk:GFP|cell tye:endothelial cells GSM4432625 GSM4432625: Smartseq2 AXL E3 endo Danio; Danio rerio; RNA Seq GSM4432625   1 1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle. 2. For GBM cells zebrafish were injected with GBM U251 mCherry cells and allowed to form widespread tumor invasion for xxx 5 days. At that point the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the three prime scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang 2010. GEO Accession:GSM4432625 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP254020     AXL-E3_HHVK7CCXY_L3_1.clean.fq.gz AXL-E3_HHVK7CCXY_L3_2.clean.fq.gz fastq fastq 1568068200.0 5226894.0 GSM4432625 r1 0:150 1:150 A:437547051;C:305827667;G:317225931;T:507380843;N:86708 150 150     437547051 305827667 317225931 507380843 86708 SRX7998914 SRS6376277 SRA1059261 GEO Chen & Liu Lab, State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University., Sichuan University 2 0.90556 0.91298 0.73969 0.74743 0.94888 0.95061 0.47195 0.48203 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   China 2020-03-25 Larval Larval Endothelium Cardiovascular System
58568 58568 SRR11420477 SRX7998913 SRS6376276 SRP254020 PRJNA615175 A Zebrafish Based Orthotopic Glioblastoma Xenograft Model for Preclinical Drug Screening and Clinical Drug Sensitivity Prediction GSE147526 Other A reliable animal model that can mimic the GBM intracranial infiltration and Blood brain barrier BBB interaction is necessary for effective therapeutics development. Here we report a zebrafish based orthotopic GBM xenograft model in which GBM cells from different species and even patients can robustly propagate and faithfully reproduce their histological characteristics. Single cell RNA seq indicates a transcriptomic adaption of GBM xenografts to infiltrative phenotype within the zebrafish brains. We also provide evidence that the BBB in zebrafish larva is molecularly and functionally intact and can interact with GBM cells in similar ways as in mammals which together enables this model to accurately identify BBB penetrating drugs. Using GBM patients' samples we further generate zebrafish patient derived orthotopic xenografts z PDOX and proof of concept experiments indicate the short term temozolomide response in z PDOX can predict the long term prognosis of corresponding GBM patients. These together illustrate the value of zebrafish GBM model in drug discovery and precision medicine. Overall design: 1.Single cell RNA seq for endothelial cells of zebrafish 2.Single cell RNA seq for GBM cells implanted in zebrafish brain   pubmed:35199829   Smartseq2 AXL E2 endo Danio GSM4432624   tissue:endothelial cells|strain:flk:GFP|cell tye:endothelial cells Smartseq2 AXL E2 endo Danio ScRNA seq alignment process was completed by STAR 2.6.0a DESeq2 standard workflow Genome build: GRCz10 genome references for Zebrafish and GRCh38 genome references for human Supplementary files format and content: csv files with raw counts and FPKM endothelial cells   1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle. 2. For GBM cells zebrafish were injected with GBM U251 mCherry cells and allowed to form widespread tumor invasion for xxx 5 days. At that point the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the 3’ scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang 2010.   strain:flk:GFP|cell tye:endothelial cells GSM4432624 GSM4432624: Smartseq2 AXL E2 endo Danio; Danio rerio; RNA Seq GSM4432624   1 1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle. 2. For GBM cells zebrafish were injected with GBM U251 mCherry cells and allowed to form widespread tumor invasion for xxx 5 days. At that point the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the three prime scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang 2010. GEO Accession:GSM4432624 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP254020     AXL-E2_HHVK7CCXY_L3_2.clean.fq.gz AXL-E2_HHVK7CCXY_L3_1.clean.fq.gz fastq fastq 1506462600.0 5021542.0 GSM4432624 r1 0:150 1:150 A:419138482;C:294375706;G:306403925;T:486460081;N:84406 150 150     419138482 294375706 306403925 486460081 84406 SRX7998913 SRS6376276 SRA1059261 GEO Chen & Liu Lab, State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University., Sichuan University 2 0.90958 0.91859 0.78806 0.79513 0.96327 0.96477 0.45808 0.46876 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   China 2020-03-25 Larval Larval Endothelium Cardiovascular System
58569 58569 SRR11420476 SRX7998912 SRS6376275 SRP254020 PRJNA615175 A Zebrafish Based Orthotopic Glioblastoma Xenograft Model for Preclinical Drug Screening and Clinical Drug Sensitivity Prediction GSE147526 Other A reliable animal model that can mimic the GBM intracranial infiltration and Blood brain barrier BBB interaction is necessary for effective therapeutics development. Here we report a zebrafish based orthotopic GBM xenograft model in which GBM cells from different species and even patients can robustly propagate and faithfully reproduce their histological characteristics. Single cell RNA seq indicates a transcriptomic adaption of GBM xenografts to infiltrative phenotype within the zebrafish brains. We also provide evidence that the BBB in zebrafish larva is molecularly and functionally intact and can interact with GBM cells in similar ways as in mammals which together enables this model to accurately identify BBB penetrating drugs. Using GBM patients' samples we further generate zebrafish patient derived orthotopic xenografts z PDOX and proof of concept experiments indicate the short term temozolomide response in z PDOX can predict the long term prognosis of corresponding GBM patients. These together illustrate the value of zebrafish GBM model in drug discovery and precision medicine. Overall design: 1.Single cell RNA seq for endothelial cells of zebrafish 2.Single cell RNA seq for GBM cells implanted in zebrafish brain   pubmed:35199829   Smartseq2 AXL E1 endo Danio GSM4432623   tissue:endothelial cells|strain:flk:GFP|cell tye:endothelial cells Smartseq2 AXL E1 endo Danio ScRNA seq alignment process was completed by STAR 2.6.0a DESeq2 standard workflow Genome build: GRCz10 genome references for Zebrafish and GRCh38 genome references for human Supplementary files format and content: csv files with raw counts and FPKM endothelial cells   1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle. 2. For GBM cells zebrafish were injected with GBM U251 mCherry cells and allowed to form widespread tumor invasion for xxx 5 days. At that point the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the 3’ scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang 2010.   strain:flk:GFP|cell tye:endothelial cells GSM4432623 GSM4432623: Smartseq2 AXL E1 endo Danio; Danio rerio; RNA Seq GSM4432623   1 1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle. 2. For GBM cells zebrafish were injected with GBM U251 mCherry cells and allowed to form widespread tumor invasion for xxx 5 days. At that point the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the three prime scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang 2010. GEO Accession:GSM4432623 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP254020     AXL-E1_HHVK7CCXY_L3_1.clean.fq.gz AXL-E1_HHVK7CCXY_L3_2.clean.fq.gz fastq fastq 1583815800.0 5279386.0 GSM4432623 r1 0:150 1:150 A:440756401;C:310619619;G:322228450;T:510122285;N:89045 150 150     440756401 310619619 322228450 510122285 89045 SRX7998912 SRS6376275 SRA1059261 GEO Chen & Liu Lab, State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University., Sichuan University 2 0.91047 0.91678 0.69764 0.70328 0.95217 0.95349 0.46044 0.44698 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   China 2020-03-25 Larval Larval Endothelium Cardiovascular System
58570 58570 SRR11420475 SRX7998911 SRS6376274 SRP254020 PRJNA615175 A Zebrafish Based Orthotopic Glioblastoma Xenograft Model for Preclinical Drug Screening and Clinical Drug Sensitivity Prediction GSE147526 Other A reliable animal model that can mimic the GBM intracranial infiltration and Blood brain barrier BBB interaction is necessary for effective therapeutics development. Here we report a zebrafish based orthotopic GBM xenograft model in which GBM cells from different species and even patients can robustly propagate and faithfully reproduce their histological characteristics. Single cell RNA seq indicates a transcriptomic adaption of GBM xenografts to infiltrative phenotype within the zebrafish brains. We also provide evidence that the BBB in zebrafish larva is molecularly and functionally intact and can interact with GBM cells in similar ways as in mammals which together enables this model to accurately identify BBB penetrating drugs. Using GBM patients' samples we further generate zebrafish patient derived orthotopic xenografts z PDOX and proof of concept experiments indicate the short term temozolomide response in z PDOX can predict the long term prognosis of corresponding GBM patients. These together illustrate the value of zebrafish GBM model in drug discovery and precision medicine. Overall design: 1.Single cell RNA seq for endothelial cells of zebrafish 2.Single cell RNA seq for GBM cells implanted in zebrafish brain   pubmed:35199829   Smartseq2 AXL D3 endo Danio GSM4432622   tissue:endothelial cells|strain:flk:GFP|cell tye:endothelial cells Smartseq2 AXL D3 endo Danio ScRNA seq alignment process was completed by STAR 2.6.0a DESeq2 standard workflow Genome build: GRCz10 genome references for Zebrafish and GRCh38 genome references for human Supplementary files format and content: csv files with raw counts and FPKM endothelial cells   1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle. 2. For GBM cells zebrafish were injected with GBM U251 mCherry cells and allowed to form widespread tumor invasion for xxx 5 days. At that point the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the 3’ scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang 2010.   strain:flk:GFP|cell tye:endothelial cells GSM4432622 GSM4432622: Smartseq2 AXL D3 endo Danio; Danio rerio; RNA Seq GSM4432622   1 1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle. 2. For GBM cells zebrafish were injected with GBM U251 mCherry cells and allowed to form widespread tumor invasion for xxx 5 days. At that point the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the three prime scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang 2010. GEO Accession:GSM4432622 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP254020     AXL-D3_HHVK7CCXY_L3_1.clean.fq.gz AXL-D3_HHVK7CCXY_L3_2.clean.fq.gz fastq fastq 1602725100.0 5342417.0 GSM4432622 r1 0:150 1:150 A:454250175;C:320141617;G:330588624;T:497655411;N:89273 150 150     454250175 320141617 330588624 497655411 89273 SRX7998911 SRS6376274 SRA1059261 GEO Chen & Liu Lab, State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University., Sichuan University 2 0.82435 0.83275 0.22763 0.23084 0.88716 0.89023 0.75529 0.75251 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   China 2020-03-25 Larval Larval Endothelium Cardiovascular System
58571 58571 SRR11420474 SRX7998910 SRS6376273 SRP254020 PRJNA615175 A Zebrafish Based Orthotopic Glioblastoma Xenograft Model for Preclinical Drug Screening and Clinical Drug Sensitivity Prediction GSE147526 Other A reliable animal model that can mimic the GBM intracranial infiltration and Blood brain barrier BBB interaction is necessary for effective therapeutics development. Here we report a zebrafish based orthotopic GBM xenograft model in which GBM cells from different species and even patients can robustly propagate and faithfully reproduce their histological characteristics. Single cell RNA seq indicates a transcriptomic adaption of GBM xenografts to infiltrative phenotype within the zebrafish brains. We also provide evidence that the BBB in zebrafish larva is molecularly and functionally intact and can interact with GBM cells in similar ways as in mammals which together enables this model to accurately identify BBB penetrating drugs. Using GBM patients' samples we further generate zebrafish patient derived orthotopic xenografts z PDOX and proof of concept experiments indicate the short term temozolomide response in z PDOX can predict the long term prognosis of corresponding GBM patients. These together illustrate the value of zebrafish GBM model in drug discovery and precision medicine. Overall design: 1.Single cell RNA seq for endothelial cells of zebrafish 2.Single cell RNA seq for GBM cells implanted in zebrafish brain   pubmed:35199829   Smartseq2 AXL C3 endo Danio GSM4432621   tissue:endothelial cells|strain:flk:GFP|cell tye:endothelial cells Smartseq2 AXL C3 endo Danio ScRNA seq alignment process was completed by STAR 2.6.0a DESeq2 standard workflow Genome build: GRCz10 genome references for Zebrafish and GRCh38 genome references for human Supplementary files format and content: csv files with raw counts and FPKM endothelial cells   1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle. 2. For GBM cells zebrafish were injected with GBM U251 mCherry cells and allowed to form widespread tumor invasion for xxx 5 days. At that point the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the 3’ scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang 2010.   strain:flk:GFP|cell tye:endothelial cells GSM4432621 GSM4432621: Smartseq2 AXL C3 endo Danio; Danio rerio; RNA Seq GSM4432621   1 1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle. 2. For GBM cells zebrafish were injected with GBM U251 mCherry cells and allowed to form widespread tumor invasion for xxx 5 days. At that point the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the three prime scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang 2010. GEO Accession:GSM4432621 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP254020     AXL-C3_HHVK7CCXY_L3_1.clean.fq.gz AXL-C3_HHVK7CCXY_L3_2.clean.fq.gz fastq fastq 1574724600.0 5249082.0 GSM4432621 r1 0:150 1:150 A:435586693;C:313192449;G:325059370;T:500799470;N:86618 150 150     435586693 313192449 325059370 500799470 86618 SRX7998910 SRS6376273 SRA1059261 GEO Chen & Liu Lab, State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University., Sichuan University 2 0.91247 0.91968 0.66959 0.67559 0.94515 0.94734 0.47277 0.49142 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   China 2020-03-25 Larval Larval Endothelium Cardiovascular System
58572 58572 SRR11420473 SRX7998909 SRS6376272 SRP254020 PRJNA615175 A Zebrafish Based Orthotopic Glioblastoma Xenograft Model for Preclinical Drug Screening and Clinical Drug Sensitivity Prediction GSE147526 Other A reliable animal model that can mimic the GBM intracranial infiltration and Blood brain barrier BBB interaction is necessary for effective therapeutics development. Here we report a zebrafish based orthotopic GBM xenograft model in which GBM cells from different species and even patients can robustly propagate and faithfully reproduce their histological characteristics. Single cell RNA seq indicates a transcriptomic adaption of GBM xenografts to infiltrative phenotype within the zebrafish brains. We also provide evidence that the BBB in zebrafish larva is molecularly and functionally intact and can interact with GBM cells in similar ways as in mammals which together enables this model to accurately identify BBB penetrating drugs. Using GBM patients' samples we further generate zebrafish patient derived orthotopic xenografts z PDOX and proof of concept experiments indicate the short term temozolomide response in z PDOX can predict the long term prognosis of corresponding GBM patients. These together illustrate the value of zebrafish GBM model in drug discovery and precision medicine. Overall design: 1.Single cell RNA seq for endothelial cells of zebrafish 2.Single cell RNA seq for GBM cells implanted in zebrafish brain   pubmed:35199829   Smartseq2 AXL C2 endo Danio GSM4432620   tissue:endothelial cells|strain:flk:GFP|cell tye:endothelial cells Smartseq2 AXL C2 endo Danio ScRNA seq alignment process was completed by STAR 2.6.0a DESeq2 standard workflow Genome build: GRCz10 genome references for Zebrafish and GRCh38 genome references for human Supplementary files format and content: csv files with raw counts and FPKM endothelial cells   1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle. 2. For GBM cells zebrafish were injected with GBM U251 mCherry cells and allowed to form widespread tumor invasion for xxx 5 days. At that point the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the 3’ scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang 2010.   strain:flk:GFP|cell tye:endothelial cells GSM4432620 GSM4432620: Smartseq2 AXL C2 endo Danio; Danio rerio; RNA Seq GSM4432620   1 1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle. 2. For GBM cells zebrafish were injected with GBM U251 mCherry cells and allowed to form widespread tumor invasion for xxx 5 days. At that point the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the three prime scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang 2010. GEO Accession:GSM4432620 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP254020     AXL-C2_HHVK7CCXY_L3_1.clean.fq.gz AXL-C2_HHVK7CCXY_L3_2.clean.fq.gz fastq fastq 918029400.0 3060098.0 GSM4432620 r1 0:150 1:150 A:247708437;C:197427436;G:203244315;T:269598842;N:50370 150 150     247708437 197427436 203244315 269598842 50370 SRX7998909 SRS6376272 SRA1059261 GEO Chen & Liu Lab, State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University., Sichuan University 2 0.85585 0.86096 0.18376 0.1852 0.91352 0.91571 0.44329 0.55709 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   China 2020-03-25 Larval Larval Endothelium Cardiovascular System
58573 58573 SRR11420472 SRX7998908 SRS6376270 SRP254020 PRJNA615175 A Zebrafish Based Orthotopic Glioblastoma Xenograft Model for Preclinical Drug Screening and Clinical Drug Sensitivity Prediction GSE147526 Other A reliable animal model that can mimic the GBM intracranial infiltration and Blood brain barrier BBB interaction is necessary for effective therapeutics development. Here we report a zebrafish based orthotopic GBM xenograft model in which GBM cells from different species and even patients can robustly propagate and faithfully reproduce their histological characteristics. Single cell RNA seq indicates a transcriptomic adaption of GBM xenografts to infiltrative phenotype within the zebrafish brains. We also provide evidence that the BBB in zebrafish larva is molecularly and functionally intact and can interact with GBM cells in similar ways as in mammals which together enables this model to accurately identify BBB penetrating drugs. Using GBM patients' samples we further generate zebrafish patient derived orthotopic xenografts z PDOX and proof of concept experiments indicate the short term temozolomide response in z PDOX can predict the long term prognosis of corresponding GBM patients. These together illustrate the value of zebrafish GBM model in drug discovery and precision medicine. Overall design: 1.Single cell RNA seq for endothelial cells of zebrafish 2.Single cell RNA seq for GBM cells implanted in zebrafish brain   pubmed:35199829   Smartseq2 AXL C1 endo Danio GSM4432619   tissue:endothelial cells|strain:flk:GFP|cell tye:endothelial cells Smartseq2 AXL C1 endo Danio ScRNA seq alignment process was completed by STAR 2.6.0a DESeq2 standard workflow Genome build: GRCz10 genome references for Zebrafish and GRCh38 genome references for human Supplementary files format and content: csv files with raw counts and FPKM endothelial cells   1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle. 2. For GBM cells zebrafish were injected with GBM U251 mCherry cells and allowed to form widespread tumor invasion for xxx 5 days. At that point the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the 3’ scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang 2010.   strain:flk:GFP|cell tye:endothelial cells GSM4432619 GSM4432619: Smartseq2 AXL C1 endo Danio; Danio rerio; RNA Seq GSM4432619   1 1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle. 2. For GBM cells zebrafish were injected with GBM U251 mCherry cells and allowed to form widespread tumor invasion for xxx 5 days. At that point the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the three prime scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang 2010. GEO Accession:GSM4432619 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP254020     AXL-C1_HHVK7CCXY_L3_1.clean.fq.gz AXL-C1_HHVK7CCXY_L3_2.clean.fq.gz fastq fastq 1500775500.0 5002585.0 GSM4432619 r1 0:150 1:150 A:432671655;C:289434226;G:302125698;T:476460891;N:83030 150 150     432671655 289434226 302125698 476460891 83030 SRX7998908 SRS6376270 SRA1059261 GEO Chen & Liu Lab, State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University., Sichuan University 2 0.67663 0.68022 0.32993 0.33204 0.86841 0.87373 0.55098 0.55286 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   China 2020-03-25 Larval Larval Endothelium Cardiovascular System
58574 58574 SRR11420471 SRX7998907 SRS6376271 SRP254020 PRJNA615175 A Zebrafish Based Orthotopic Glioblastoma Xenograft Model for Preclinical Drug Screening and Clinical Drug Sensitivity Prediction GSE147526 Other A reliable animal model that can mimic the GBM intracranial infiltration and Blood brain barrier BBB interaction is necessary for effective therapeutics development. Here we report a zebrafish based orthotopic GBM xenograft model in which GBM cells from different species and even patients can robustly propagate and faithfully reproduce their histological characteristics. Single cell RNA seq indicates a transcriptomic adaption of GBM xenografts to infiltrative phenotype within the zebrafish brains. We also provide evidence that the BBB in zebrafish larva is molecularly and functionally intact and can interact with GBM cells in similar ways as in mammals which together enables this model to accurately identify BBB penetrating drugs. Using GBM patients' samples we further generate zebrafish patient derived orthotopic xenografts z PDOX and proof of concept experiments indicate the short term temozolomide response in z PDOX can predict the long term prognosis of corresponding GBM patients. These together illustrate the value of zebrafish GBM model in drug discovery and precision medicine. Overall design: 1.Single cell RNA seq for endothelial cells of zebrafish 2.Single cell RNA seq for GBM cells implanted in zebrafish brain   pubmed:35199829   Smartseq2 AXL B2 endo Danio GSM4432618   tissue:endothelial cells|strain:flk:GFP|cell tye:endothelial cells Smartseq2 AXL B2 endo Danio ScRNA seq alignment process was completed by STAR 2.6.0a DESeq2 standard workflow Genome build: GRCz10 genome references for Zebrafish and GRCh38 genome references for human Supplementary files format and content: csv files with raw counts and FPKM endothelial cells   1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle. 2. For GBM cells zebrafish were injected with GBM U251 mCherry cells and allowed to form widespread tumor invasion for xxx 5 days. At that point the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the 3’ scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang 2010.   strain:flk:GFP|cell tye:endothelial cells GSM4432618 GSM4432618: Smartseq2 AXL B2 endo Danio; Danio rerio; RNA Seq GSM4432618   1 1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle. 2. For GBM cells zebrafish were injected with GBM U251 mCherry cells and allowed to form widespread tumor invasion for xxx 5 days. At that point the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the three prime scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang 2010. GEO Accession:GSM4432618 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP254020     AXL-B2_HHVK7CCXY_L3_1.clean.fq.gz AXL-B2_HHVK7CCXY_L3_2.clean.fq.gz fastq fastq 989060100.0 3296867.0 GSM4432618 r1 0:150 1:150 A:274301021;C:196555336;G:203736274;T:314412137;N:55332 150 150     274301021 196555336 203736274 314412137 55332 SRX7998907 SRS6376271 SRA1059261 GEO Chen & Liu Lab, State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University., Sichuan University 2 0.9149 0.92243 0.73373 0.73884 0.95296 0.95426 0.47934 0.47668 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   China 2020-03-25 Larval Larval Endothelium Cardiovascular System
58575 58575 SRR11420470 SRX7998906 SRS6376269 SRP254020 PRJNA615175 A Zebrafish Based Orthotopic Glioblastoma Xenograft Model for Preclinical Drug Screening and Clinical Drug Sensitivity Prediction GSE147526 Other A reliable animal model that can mimic the GBM intracranial infiltration and Blood brain barrier BBB interaction is necessary for effective therapeutics development. Here we report a zebrafish based orthotopic GBM xenograft model in which GBM cells from different species and even patients can robustly propagate and faithfully reproduce their histological characteristics. Single cell RNA seq indicates a transcriptomic adaption of GBM xenografts to infiltrative phenotype within the zebrafish brains. We also provide evidence that the BBB in zebrafish larva is molecularly and functionally intact and can interact with GBM cells in similar ways as in mammals which together enables this model to accurately identify BBB penetrating drugs. Using GBM patients' samples we further generate zebrafish patient derived orthotopic xenografts z PDOX and proof of concept experiments indicate the short term temozolomide response in z PDOX can predict the long term prognosis of corresponding GBM patients. These together illustrate the value of zebrafish GBM model in drug discovery and precision medicine. Overall design: 1.Single cell RNA seq for endothelial cells of zebrafish 2.Single cell RNA seq for GBM cells implanted in zebrafish brain   pubmed:35199829   Smartseq2 AXL B1 endo Danio GSM4432617   tissue:endothelial cells|strain:flk:GFP|cell tye:endothelial cells Smartseq2 AXL B1 endo Danio ScRNA seq alignment process was completed by STAR 2.6.0a DESeq2 standard workflow Genome build: GRCz10 genome references for Zebrafish and GRCh38 genome references for human Supplementary files format and content: csv files with raw counts and FPKM endothelial cells   1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle. 2. For GBM cells zebrafish were injected with GBM U251 mCherry cells and allowed to form widespread tumor invasion for xxx 5 days. At that point the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the 3’ scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang 2010.   strain:flk:GFP|cell tye:endothelial cells GSM4432617 GSM4432617: Smartseq2 AXL B1 endo Danio; Danio rerio; RNA Seq GSM4432617   1 1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle. 2. For GBM cells zebrafish were injected with GBM U251 mCherry cells and allowed to form widespread tumor invasion for xxx 5 days. At that point the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the three prime scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang 2010. GEO Accession:GSM4432617 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP254020     AXL-B1_HHVK7CCXY_L3_1.clean.fq.gz AXL-B1_HHVK7CCXY_L3_2.clean.fq.gz fastq fastq 2099031600.0 6996772.0 GSM4432617 r1 0:150 1:150 A:583452672;C:414863616;G:430728068;T:669871636;N:115608 150 150     583452672 414863616 430728068 669871636 115608 SRX7998906 SRS6376269 SRA1059261 GEO Chen & Liu Lab, State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University., Sichuan University 2 0.82207 0.82952 0.63293 0.64238 0.94602 0.94828 0.49299 0.49862 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   China 2020-03-25 Larval Larval Endothelium Cardiovascular System
58576 58576 SRR11420469 SRX7998905 SRS6376268 SRP254020 PRJNA615175 A Zebrafish Based Orthotopic Glioblastoma Xenograft Model for Preclinical Drug Screening and Clinical Drug Sensitivity Prediction GSE147526 Other A reliable animal model that can mimic the GBM intracranial infiltration and Blood brain barrier BBB interaction is necessary for effective therapeutics development. Here we report a zebrafish based orthotopic GBM xenograft model in which GBM cells from different species and even patients can robustly propagate and faithfully reproduce their histological characteristics. Single cell RNA seq indicates a transcriptomic adaption of GBM xenografts to infiltrative phenotype within the zebrafish brains. We also provide evidence that the BBB in zebrafish larva is molecularly and functionally intact and can interact with GBM cells in similar ways as in mammals which together enables this model to accurately identify BBB penetrating drugs. Using GBM patients' samples we further generate zebrafish patient derived orthotopic xenografts z PDOX and proof of concept experiments indicate the short term temozolomide response in z PDOX can predict the long term prognosis of corresponding GBM patients. These together illustrate the value of zebrafish GBM model in drug discovery and precision medicine. Overall design: 1.Single cell RNA seq for endothelial cells of zebrafish 2.Single cell RNA seq for GBM cells implanted in zebrafish brain   pubmed:35199829   Smartseq2 AXL A3 endo Danio GSM4432616   tissue:endothelial cells|strain:flk:GFP|cell tye:endothelial cells Smartseq2 AXL A3 endo Danio ScRNA seq alignment process was completed by STAR 2.6.0a DESeq2 standard workflow Genome build: GRCz10 genome references for Zebrafish and GRCh38 genome references for human Supplementary files format and content: csv files with raw counts and FPKM endothelial cells   1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle. 2. For GBM cells zebrafish were injected with GBM U251 mCherry cells and allowed to form widespread tumor invasion for xxx 5 days. At that point the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the 3’ scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang 2010.   strain:flk:GFP|cell tye:endothelial cells GSM4432616 GSM4432616: Smartseq2 AXL A3 endo Danio; Danio rerio; RNA Seq GSM4432616   1 1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle. 2. For GBM cells zebrafish were injected with GBM U251 mCherry cells and allowed to form widespread tumor invasion for xxx 5 days. At that point the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the three prime scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang 2010. GEO Accession:GSM4432616 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP254020     AXL-A3_HHVK7CCXY_L3_1.clean.fq.gz AXL-A3_HHVK7CCXY_L3_2.clean.fq.gz fastq fastq 932495100.0 3108317.0 GSM4432616 r1 0:150 1:150 A:258055487;C:185801372;G:192600723;T:295985361;N:52157 150 150     258055487 185801372 192600723 295985361 52157 SRX7998905 SRS6376268 SRA1059261 GEO Chen & Liu Lab, State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University., Sichuan University 2 0.91666 0.92212 0.7484 0.75372 0.94826 0.95018 0.50494 0.50846 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   China 2020-03-25 Larval Larval Endothelium Cardiovascular System
58577 58577 SRR11420468 SRX7998904 SRS6376267 SRP254020 PRJNA615175 A Zebrafish Based Orthotopic Glioblastoma Xenograft Model for Preclinical Drug Screening and Clinical Drug Sensitivity Prediction GSE147526 Other A reliable animal model that can mimic the GBM intracranial infiltration and Blood brain barrier BBB interaction is necessary for effective therapeutics development. Here we report a zebrafish based orthotopic GBM xenograft model in which GBM cells from different species and even patients can robustly propagate and faithfully reproduce their histological characteristics. Single cell RNA seq indicates a transcriptomic adaption of GBM xenografts to infiltrative phenotype within the zebrafish brains. We also provide evidence that the BBB in zebrafish larva is molecularly and functionally intact and can interact with GBM cells in similar ways as in mammals which together enables this model to accurately identify BBB penetrating drugs. Using GBM patients' samples we further generate zebrafish patient derived orthotopic xenografts z PDOX and proof of concept experiments indicate the short term temozolomide response in z PDOX can predict the long term prognosis of corresponding GBM patients. These together illustrate the value of zebrafish GBM model in drug discovery and precision medicine. Overall design: 1.Single cell RNA seq for endothelial cells of zebrafish 2.Single cell RNA seq for GBM cells implanted in zebrafish brain   pubmed:35199829   Smartseq2 AXL A2 endo Danio GSM4432615   tissue:endothelial cells|strain:flk:GFP|cell tye:endothelial cells Smartseq2 AXL A2 endo Danio ScRNA seq alignment process was completed by STAR 2.6.0a DESeq2 standard workflow Genome build: GRCz10 genome references for Zebrafish and GRCh38 genome references for human Supplementary files format and content: csv files with raw counts and FPKM endothelial cells   1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle. 2. For GBM cells zebrafish were injected with GBM U251 mCherry cells and allowed to form widespread tumor invasion for xxx 5 days. At that point the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the 3’ scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang 2010.   strain:flk:GFP|cell tye:endothelial cells GSM4432615 GSM4432615: Smartseq2 AXL A2 endo Danio; Danio rerio; RNA Seq GSM4432615   1 1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle. 2. For GBM cells zebrafish were injected with GBM U251 mCherry cells and allowed to form widespread tumor invasion for xxx 5 days. At that point the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the three prime scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang 2010. GEO Accession:GSM4432615 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP254020     AXL-A2_HHVK7CCXY_L3_1.clean.fq.gz AXL-A2_HHVK7CCXY_L3_2.clean.fq.gz fastq fastq 1474053600.0 4913512.0 GSM4432615 r1 0:150 1:150 A:409235463;C:294510014;G:304366926;T:465858337;N:82860 150 150     409235463 294510014 304366926 465858337 82860 SRX7998904 SRS6376267 SRA1059261 GEO Chen & Liu Lab, State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University., Sichuan University 2 0.89481 0.90098 0.57187 0.57596 0.91045 0.91366 0.46573 0.46566 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   China 2020-03-25 Larval Larval Endothelium Cardiovascular System
58578 58578 SRR11420467 SRX7998903 SRS6376266 SRP254020 PRJNA615175 A Zebrafish Based Orthotopic Glioblastoma Xenograft Model for Preclinical Drug Screening and Clinical Drug Sensitivity Prediction GSE147526 Other A reliable animal model that can mimic the GBM intracranial infiltration and Blood brain barrier BBB interaction is necessary for effective therapeutics development. Here we report a zebrafish based orthotopic GBM xenograft model in which GBM cells from different species and even patients can robustly propagate and faithfully reproduce their histological characteristics. Single cell RNA seq indicates a transcriptomic adaption of GBM xenografts to infiltrative phenotype within the zebrafish brains. We also provide evidence that the BBB in zebrafish larva is molecularly and functionally intact and can interact with GBM cells in similar ways as in mammals which together enables this model to accurately identify BBB penetrating drugs. Using GBM patients' samples we further generate zebrafish patient derived orthotopic xenografts z PDOX and proof of concept experiments indicate the short term temozolomide response in z PDOX can predict the long term prognosis of corresponding GBM patients. These together illustrate the value of zebrafish GBM model in drug discovery and precision medicine. Overall design: 1.Single cell RNA seq for endothelial cells of zebrafish 2.Single cell RNA seq for GBM cells implanted in zebrafish brain   pubmed:35199829   Smartseq2 AXL A1 endo Danio GSM4432614   tissue:endothelial cells|strain:flk:GFP|cell tye:endothelial cells Smartseq2 AXL A1 endo Danio ScRNA seq alignment process was completed by STAR 2.6.0a DESeq2 standard workflow Genome build: GRCz10 genome references for Zebrafish and GRCh38 genome references for human Supplementary files format and content: csv files with raw counts and FPKM endothelial cells   1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle. 2. For GBM cells zebrafish were injected with GBM U251 mCherry cells and allowed to form widespread tumor invasion for xxx 5 days. At that point the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the 3’ scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang 2010.   strain:flk:GFP|cell tye:endothelial cells GSM4432614 GSM4432614: Smartseq2 AXL A1 endo Danio; Danio rerio; RNA Seq GSM4432614   1 1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle. 2. For GBM cells zebrafish were injected with GBM U251 mCherry cells and allowed to form widespread tumor invasion for xxx 5 days. At that point the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the three prime scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang 2010. GEO Accession:GSM4432614 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP254020     AXL-A1_HHVK7CCXY_L3_1.clean.fq.gz AXL-A1_HHVK7CCXY_L3_2.clean.fq.gz fastq fastq 1017985800.0 3393286.0 GSM4432614 r1 0:150 1:150 A:297904574;C:190252853;G:199665607;T:330106549;N:56217 150 150     297904574 190252853 199665607 330106549 56217 SRX7998903 SRS6376266 SRA1059261 GEO Chen & Liu Lab, State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University., Sichuan University 2 0.82827 0.84942 0.55392 0.56701 0.89029 0.89394 0.61422 0.61422 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   China 2020-03-25 Larval Larval Endothelium Cardiovascular System
74899 74899 SRR24112510 SRX19911927 SRS17265414 SRP431649 PRJNA953763 Low input RNA seq of endothelial cells sorted from tail of zebrafish larvae GSE229261 Transcriptome Analysis To characterize the mechanism by which AML derived extracellular vesiclesEV impaired the vascular architecture and function EV or PBS injected flk:GFP zebrafish larvae were used for sorting endothelial cells and performing RNA Seq. Vascular niches sustain hematopoietic stem and progenitor cells HSPC and are drastically remodeled in myeloid leukemia to support pathological progression. By utilizing the leukemia xenografted zebrafish model we identified that myeloid leukemia secreted extracellular vesicles EVs to impair HSPC proliferation survival and differentiation towards lymphoid/erythroid lineages. The leukemia EVs delivered arginase 1 into venous vasculature to deplete L arginine and cause NOS uncoupling which catalyzes production of ROS instead of NO. The oxidative stress caused endothelial cell loss vascular constriction and failure of secreting niche factors and supporting hematopoiesis. Our findings indicate that myeloid leukemia impaired the vascular function of supporting hematopoiesis by delivering arginase in EVs and arginase inhibition has the potential to improve normal hematopoiesis in myeloid leukemia. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells sorted from tails of MV4 11 derived EV or PBS injected flk:GFP zebrafish larvae.       flk:GFP injected with MV4 11 derived Evs 3 GSM7157754   tissue:endothelial cells|cell type:endothelial cells|genotype:WT|treatment:injected with MV4 11 derived EVs sorting|geo loc name:missing|collection date:missing flk:GFP injected with MV4 11 derived Evs 3 post removing low quality reads and trimming the adaptor sequences by Trim Galore v0.5.0 Babraham Bioinformatics RNA Seq reads were aligned to zebrafish genome GRCz11 by Salmon v0.03.1 COMBINE lab with ENCODE options and genes were annotated by Ensembl database. For expression quantification the uniquely mapped reads were transformed to counts by Salmon and normalized to counts per million CPM or log2CPM+1 by edgeR v3.40.1 Bioconductor. The batch effect was removed by sva v3.46.0 Bioconductor. Three replicates of PBS or EV treated ECs were aligned by Principal ComponentAnalysis PCA and one replicate that was diverged from the other two was removed for the following analysis. Assembly: GRCz11 Supplementary files format and content: Zebrafish Raw Counts.tar with raw counts matrices endothelial cells   Five hundred of Tgflk:GFP larvae were injected with PBS control or EVs and three replicates were prepared for each treatment. The larvae were then anesthetized at 24 h post injection hpi before cutting tails on ice. The tails were collected and gently triturated in 1.5 mL cold trypsin solution 0.5 g/L; T3924; Sigma with 1 000 μL pipette tip for 20 min. The dissociated cells were then filtered with a 70 μm filter BD Transduction Laboratories to remove the undissociated tissue and washed twice with cold PBS. Cells were then resuspended in 2.5 mL PBS and stained with 7 AAD 5 μg/mL BD Transduction Laboratories on ice for 30 min. About 1X10^5 GFP+ cells were sorted by FACS MoFlo XDP Beckman and total RNA was extracted with Trizol 15596 Invitrogen according to the manufacturer’s instructions. Low input RNA Seq was performed according to the published protocol with modifications . Briefly mRNAs were purified by VAHTS RNA Clean Beads N412 Vayzme in RNase free H2O with reverse transcription mix amplified for 15 cycles and reverse transcribed for cDNAs before purifying with VAHTS DNA Clean Beads N411 Vazyme. Enriched cDNA was quantified using Qubit dsDNA HS Assay Kit Q3285 Guangzhou IGE biotechnology ltd and verified by DNA gel electrophoresis 1.5 2 kb. Libraries were prepared by using TruePrep DNA library Prep Kit V2 for Illumina TD503 Vazyme and adaptor ligated DNAs 400 bp were selected by VAHTS DNA Clean Beads N411 Vazyme. Libraries were sequenced by using NovaSeq PE150 as 150 bp paired end.   cell type:endothelial cells|genotype:WT|treatment:injected with MV4 11 derived EVs sorting GSM7157754 GSM7157754: flk:GFP injected with MV4 11 derived Evs 3; Danio rerio; RNA Seq GSM7157754 r1 GSM7157754 1 Five hundred of Tgflk:GFP larvae were injected with PBS control or EVs and three replicates were prepared for each treatment. The larvae were then anesthetized at 24 h post injection hpi before cutting tails on ice. The tails were collected and gently triturated in 1.5 mL cold trypsin solution 0.5 g/L; T3924; Sigma with 1 000 μL pipette tip for 20 min. The dissociated cells were then filtered with a 70 μm filter BD Transduction Laboratories to remove the undissociated tissue and washed twice with cold PBS. Cells were then resuspended in 2.5 mL PBS and stained with 7 AAD 5 μg/mL BD Transduction Laboratories on ice for 30 min. About 1X10^5 GFP+ cells were sorted by FACS MoFlo XDP Beckman and total RNA was extracted with Trizol 15596 Invitrogen according to the manufacturer's instructions. Low input RNA Seq was performed according to the published protocol with modifications . Briefly mRNAs were purified by VAHTS RNA Clean Beads N412 Vayzme in RNase free H2O with reverse transcription mix amplified for 15 cycles and reverse transcribed for cDNAs before purifying with VAHTS DNA Clean Beads N411 Vazyme. Enriched cDNA was quantified using Qubit dsDNA HS Assay Kit Q3285 Guangzhou IGE biotechnology ltd and verified by DNA gel electrophoresis 1.5 2 kb. Libraries were prepared by using TruePrep DNA library Prep Kit V2 for Illumina TD503 Vazyme and adaptor ligated DNAs 400 bp were selected by VAHTS DNA Clean Beads N411 Vazyme. Libraries were sequenced by using NovaSeq PE150 as 150 bp paired end.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP431649   loader:fastq load.py EC-EVs-3_L4_Q803602.R1.fastq.gz EC-EVs-3_L4_Q803602.R2.fastq.gz fastq fastq 6010992300.0 20036641.0 GSM7157754 r1 0:150 1:150 A:1551150109;C:1411943134;G:1418582790;T:1629299477;N:16790 150 150     1551150109 1411943134 1418582790 1629299477 16790 SRX19911927 SRS17265414 SRA1622779 Jianglinjia Lab, SUN YAT-SEN MEMORIAL HOSPITAL Jianglinjia Lab, SUN YAT-SEN MEMORIAL HOSPITAL 2 0.91791 0.92553 0.05853 0.05906 0.82609 0.82509 0.59566 0.59001 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2023-04-09 Larval Larval Endothelium Cardiovascular System
74900 74900 SRR24112511 SRX19911926 SRS17265413 SRP431649 PRJNA953763 Low input RNA seq of endothelial cells sorted from tail of zebrafish larvae GSE229261 Transcriptome Analysis To characterize the mechanism by which AML derived extracellular vesiclesEV impaired the vascular architecture and function EV or PBS injected flk:GFP zebrafish larvae were used for sorting endothelial cells and performing RNA Seq. Vascular niches sustain hematopoietic stem and progenitor cells HSPC and are drastically remodeled in myeloid leukemia to support pathological progression. By utilizing the leukemia xenografted zebrafish model we identified that myeloid leukemia secreted extracellular vesicles EVs to impair HSPC proliferation survival and differentiation towards lymphoid/erythroid lineages. The leukemia EVs delivered arginase 1 into venous vasculature to deplete L arginine and cause NOS uncoupling which catalyzes production of ROS instead of NO. The oxidative stress caused endothelial cell loss vascular constriction and failure of secreting niche factors and supporting hematopoiesis. Our findings indicate that myeloid leukemia impaired the vascular function of supporting hematopoiesis by delivering arginase in EVs and arginase inhibition has the potential to improve normal hematopoiesis in myeloid leukemia. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells sorted from tails of MV4 11 derived EV or PBS injected flk:GFP zebrafish larvae.       flk:GFP injected with MV4 11 derived Evs 2 GSM7157753   tissue:endothelial cells|cell type:endothelial cells|genotype:WT|treatment:injected with MV4 11 derived EVs sorting|geo loc name:missing|collection date:missing flk:GFP injected with MV4 11 derived Evs 2 post removing low quality reads and trimming the adaptor sequences by Trim Galore v0.5.0 Babraham Bioinformatics RNA Seq reads were aligned to zebrafish genome GRCz11 by Salmon v0.03.1 COMBINE lab with ENCODE options and genes were annotated by Ensembl database. For expression quantification the uniquely mapped reads were transformed to counts by Salmon and normalized to counts per million CPM or log2CPM+1 by edgeR v3.40.1 Bioconductor. The batch effect was removed by sva v3.46.0 Bioconductor. Three replicates of PBS or EV treated ECs were aligned by Principal ComponentAnalysis PCA and one replicate that was diverged from the other two was removed for the following analysis. Assembly: GRCz11 Supplementary files format and content: Zebrafish Raw Counts.tar with raw counts matrices endothelial cells   Five hundred of Tgflk:GFP larvae were injected with PBS control or EVs and three replicates were prepared for each treatment. The larvae were then anesthetized at 24 h post injection hpi before cutting tails on ice. The tails were collected and gently triturated in 1.5 mL cold trypsin solution 0.5 g/L; T3924; Sigma with 1 000 μL pipette tip for 20 min. The dissociated cells were then filtered with a 70 μm filter BD Transduction Laboratories to remove the undissociated tissue and washed twice with cold PBS. Cells were then resuspended in 2.5 mL PBS and stained with 7 AAD 5 μg/mL BD Transduction Laboratories on ice for 30 min. About 1X10^5 GFP+ cells were sorted by FACS MoFlo XDP Beckman and total RNA was extracted with Trizol 15596 Invitrogen according to the manufacturer’s instructions. Low input RNA Seq was performed according to the published protocol with modifications . Briefly mRNAs were purified by VAHTS RNA Clean Beads N412 Vayzme in RNase free H2O with reverse transcription mix amplified for 15 cycles and reverse transcribed for cDNAs before purifying with VAHTS DNA Clean Beads N411 Vazyme. Enriched cDNA was quantified using Qubit dsDNA HS Assay Kit Q3285 Guangzhou IGE biotechnology ltd and verified by DNA gel electrophoresis 1.5 2 kb. Libraries were prepared by using TruePrep DNA library Prep Kit V2 for Illumina TD503 Vazyme and adaptor ligated DNAs 400 bp were selected by VAHTS DNA Clean Beads N411 Vazyme. Libraries were sequenced by using NovaSeq PE150 as 150 bp paired end.   cell type:endothelial cells|genotype:WT|treatment:injected with MV4 11 derived EVs sorting GSM7157753 GSM7157753: flk:GFP injected with MV4 11 derived Evs 2; Danio rerio; RNA Seq GSM7157753 r1 GSM7157753 1 Five hundred of Tgflk:GFP larvae were injected with PBS control or EVs and three replicates were prepared for each treatment. The larvae were then anesthetized at 24 h post injection hpi before cutting tails on ice. The tails were collected and gently triturated in 1.5 mL cold trypsin solution 0.5 g/L; T3924; Sigma with 1 000 μL pipette tip for 20 min. The dissociated cells were then filtered with a 70 μm filter BD Transduction Laboratories to remove the undissociated tissue and washed twice with cold PBS. Cells were then resuspended in 2.5 mL PBS and stained with 7 AAD 5 μg/mL BD Transduction Laboratories on ice for 30 min. About 1X10^5 GFP+ cells were sorted by FACS MoFlo XDP Beckman and total RNA was extracted with Trizol 15596 Invitrogen according to the manufacturer's instructions. Low input RNA Seq was performed according to the published protocol with modifications . Briefly mRNAs were purified by VAHTS RNA Clean Beads N412 Vayzme in RNase free H2O with reverse transcription mix amplified for 15 cycles and reverse transcribed for cDNAs before purifying with VAHTS DNA Clean Beads N411 Vazyme. Enriched cDNA was quantified using Qubit dsDNA HS Assay Kit Q3285 Guangzhou IGE biotechnology ltd and verified by DNA gel electrophoresis 1.5 2 kb. Libraries were prepared by using TruePrep DNA library Prep Kit V2 for Illumina TD503 Vazyme and adaptor ligated DNAs 400 bp were selected by VAHTS DNA Clean Beads N411 Vazyme. Libraries were sequenced by using NovaSeq PE150 as 150 bp paired end.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP431649   loader:fastq load.py EC-EVs-2_L4_Q802602.R1.fastq.gz EC-EVs-2_L4_Q802602.R2.fastq.gz fastq fastq 3675908400.0 12253028.0 GSM7157753 r1 0:150 1:150 A:931683447;C:903366506;G:833017525;T:1007830319;N:10603 150 150     931683447 903366506 833017525 1007830319 10603 SRX19911926 SRS17265413 SRA1622779 Jianglinjia Lab, SUN YAT-SEN MEMORIAL HOSPITAL Jianglinjia Lab, SUN YAT-SEN MEMORIAL HOSPITAL 2 0.95122 0.95594 0.04379 0.04429 0.79655 0.79543 0.52293 0.52953 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2023-04-09 Larval Larval Endothelium Cardiovascular System
74901 74901 SRR24112512 SRX19911925 SRS17265412 SRP431649 PRJNA953763 Low input RNA seq of endothelial cells sorted from tail of zebrafish larvae GSE229261 Transcriptome Analysis To characterize the mechanism by which AML derived extracellular vesiclesEV impaired the vascular architecture and function EV or PBS injected flk:GFP zebrafish larvae were used for sorting endothelial cells and performing RNA Seq. Vascular niches sustain hematopoietic stem and progenitor cells HSPC and are drastically remodeled in myeloid leukemia to support pathological progression. By utilizing the leukemia xenografted zebrafish model we identified that myeloid leukemia secreted extracellular vesicles EVs to impair HSPC proliferation survival and differentiation towards lymphoid/erythroid lineages. The leukemia EVs delivered arginase 1 into venous vasculature to deplete L arginine and cause NOS uncoupling which catalyzes production of ROS instead of NO. The oxidative stress caused endothelial cell loss vascular constriction and failure of secreting niche factors and supporting hematopoiesis. Our findings indicate that myeloid leukemia impaired the vascular function of supporting hematopoiesis by delivering arginase in EVs and arginase inhibition has the potential to improve normal hematopoiesis in myeloid leukemia. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells sorted from tails of MV4 11 derived EV or PBS injected flk:GFP zebrafish larvae.       flk:GFP injected with MV4 11 derived Evs 1 GSM7157752   tissue:endothelial cells|cell type:endothelial cells|genotype:WT|treatment:injected with MV4 11 derived EVs sorting|geo loc name:missing|collection date:missing flk:GFP injected with MV4 11 derived Evs 1 post removing low quality reads and trimming the adaptor sequences by Trim Galore v0.5.0 Babraham Bioinformatics RNA Seq reads were aligned to zebrafish genome GRCz11 by Salmon v0.03.1 COMBINE lab with ENCODE options and genes were annotated by Ensembl database. For expression quantification the uniquely mapped reads were transformed to counts by Salmon and normalized to counts per million CPM or log2CPM+1 by edgeR v3.40.1 Bioconductor. The batch effect was removed by sva v3.46.0 Bioconductor. Three replicates of PBS or EV treated ECs were aligned by Principal ComponentAnalysis PCA and one replicate that was diverged from the other two was removed for the following analysis. Assembly: GRCz11 Supplementary files format and content: Zebrafish Raw Counts.tar with raw counts matrices endothelial cells   Five hundred of Tgflk:GFP larvae were injected with PBS control or EVs and three replicates were prepared for each treatment. The larvae were then anesthetized at 24 h post injection hpi before cutting tails on ice. The tails were collected and gently triturated in 1.5 mL cold trypsin solution 0.5 g/L; T3924; Sigma with 1 000 μL pipette tip for 20 min. The dissociated cells were then filtered with a 70 μm filter BD Transduction Laboratories to remove the undissociated tissue and washed twice with cold PBS. Cells were then resuspended in 2.5 mL PBS and stained with 7 AAD 5 μg/mL BD Transduction Laboratories on ice for 30 min. About 1X10^5 GFP+ cells were sorted by FACS MoFlo XDP Beckman and total RNA was extracted with Trizol 15596 Invitrogen according to the manufacturer’s instructions. Low input RNA Seq was performed according to the published protocol with modifications . Briefly mRNAs were purified by VAHTS RNA Clean Beads N412 Vayzme in RNase free H2O with reverse transcription mix amplified for 15 cycles and reverse transcribed for cDNAs before purifying with VAHTS DNA Clean Beads N411 Vazyme. Enriched cDNA was quantified using Qubit dsDNA HS Assay Kit Q3285 Guangzhou IGE biotechnology ltd and verified by DNA gel electrophoresis 1.5 2 kb. Libraries were prepared by using TruePrep DNA library Prep Kit V2 for Illumina TD503 Vazyme and adaptor ligated DNAs 400 bp were selected by VAHTS DNA Clean Beads N411 Vazyme. Libraries were sequenced by using NovaSeq PE150 as 150 bp paired end.   cell type:endothelial cells|genotype:WT|treatment:injected with MV4 11 derived EVs sorting GSM7157752 GSM7157752: flk:GFP injected with MV4 11 derived Evs 1; Danio rerio; RNA Seq GSM7157752 r1 GSM7157752 1 Five hundred of Tgflk:GFP larvae were injected with PBS control or EVs and three replicates were prepared for each treatment. The larvae were then anesthetized at 24 h post injection hpi before cutting tails on ice. The tails were collected and gently triturated in 1.5 mL cold trypsin solution 0.5 g/L; T3924; Sigma with 1 000 μL pipette tip for 20 min. The dissociated cells were then filtered with a 70 μm filter BD Transduction Laboratories to remove the undissociated tissue and washed twice with cold PBS. Cells were then resuspended in 2.5 mL PBS and stained with 7 AAD 5 μg/mL BD Transduction Laboratories on ice for 30 min. About 1X10^5 GFP+ cells were sorted by FACS MoFlo XDP Beckman and total RNA was extracted with Trizol 15596 Invitrogen according to the manufacturer's instructions. Low input RNA Seq was performed according to the published protocol with modifications . Briefly mRNAs were purified by VAHTS RNA Clean Beads N412 Vayzme in RNase free H2O with reverse transcription mix amplified for 15 cycles and reverse transcribed for cDNAs before purifying with VAHTS DNA Clean Beads N411 Vazyme. Enriched cDNA was quantified using Qubit dsDNA HS Assay Kit Q3285 Guangzhou IGE biotechnology ltd and verified by DNA gel electrophoresis 1.5 2 kb. Libraries were prepared by using TruePrep DNA library Prep Kit V2 for Illumina TD503 Vazyme and adaptor ligated DNAs 400 bp were selected by VAHTS DNA Clean Beads N411 Vazyme. Libraries were sequenced by using NovaSeq PE150 as 150 bp paired end.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP431649   loader:fastq load.py EC-EVs-1_L4_Q801602.R1.fastq.gz EC-EVs-1_L4_Q801602.R2.fastq.gz fastq fastq 4820555400.0 16068518.0 GSM7157752 r1 0:150 1:150 A:1275378736;C:1124561736;G:1042716939;T:1377884919;N:13070 150 150     1275378736 1124561736 1042716939 1377884919 13070 SRX19911925 SRS17265412 SRA1622779 Jianglinjia Lab, SUN YAT-SEN MEMORIAL HOSPITAL Jianglinjia Lab, SUN YAT-SEN MEMORIAL HOSPITAL 2 0.94253 0.94901 0.05444 0.05513 0.79608 0.79476 0.55764 0.55254 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2023-04-09 Larval Larval Endothelium Cardiovascular System
74902 74902 SRR24112513 SRX19911924 SRS17265411 SRP431649 PRJNA953763 Low input RNA seq of endothelial cells sorted from tail of zebrafish larvae GSE229261 Transcriptome Analysis To characterize the mechanism by which AML derived extracellular vesiclesEV impaired the vascular architecture and function EV or PBS injected flk:GFP zebrafish larvae were used for sorting endothelial cells and performing RNA Seq. Vascular niches sustain hematopoietic stem and progenitor cells HSPC and are drastically remodeled in myeloid leukemia to support pathological progression. By utilizing the leukemia xenografted zebrafish model we identified that myeloid leukemia secreted extracellular vesicles EVs to impair HSPC proliferation survival and differentiation towards lymphoid/erythroid lineages. The leukemia EVs delivered arginase 1 into venous vasculature to deplete L arginine and cause NOS uncoupling which catalyzes production of ROS instead of NO. The oxidative stress caused endothelial cell loss vascular constriction and failure of secreting niche factors and supporting hematopoiesis. Our findings indicate that myeloid leukemia impaired the vascular function of supporting hematopoiesis by delivering arginase in EVs and arginase inhibition has the potential to improve normal hematopoiesis in myeloid leukemia. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells sorted from tails of MV4 11 derived EV or PBS injected flk:GFP zebrafish larvae.       flk:GFP injected with PBS 3 GSM7157751   tissue:endothelial cells|cell type:endothelial cells|genotype:WT|treatment:injected with PBS sorting|geo loc name:missing|collection date:missing flk:GFP injected with PBS 3 post removing low quality reads and trimming the adaptor sequences by Trim Galore v0.5.0 Babraham Bioinformatics RNA Seq reads were aligned to zebrafish genome GRCz11 by Salmon v0.03.1 COMBINE lab with ENCODE options and genes were annotated by Ensembl database. For expression quantification the uniquely mapped reads were transformed to counts by Salmon and normalized to counts per million CPM or log2CPM+1 by edgeR v3.40.1 Bioconductor. The batch effect was removed by sva v3.46.0 Bioconductor. Three replicates of PBS or EV treated ECs were aligned by Principal ComponentAnalysis PCA and one replicate that was diverged from the other two was removed for the following analysis. Assembly: GRCz11 Supplementary files format and content: Zebrafish Raw Counts.tar with raw counts matrices endothelial cells   Five hundred of Tgflk:GFP larvae were injected with PBS control or EVs and three replicates were prepared for each treatment. The larvae were then anesthetized at 24 h post injection hpi before cutting tails on ice. The tails were collected and gently triturated in 1.5 mL cold trypsin solution 0.5 g/L; T3924; Sigma with 1 000 μL pipette tip for 20 min. The dissociated cells were then filtered with a 70 μm filter BD Transduction Laboratories to remove the undissociated tissue and washed twice with cold PBS. Cells were then resuspended in 2.5 mL PBS and stained with 7 AAD 5 μg/mL BD Transduction Laboratories on ice for 30 min. About 1X10^5 GFP+ cells were sorted by FACS MoFlo XDP Beckman and total RNA was extracted with Trizol 15596 Invitrogen according to the manufacturer’s instructions. Low input RNA Seq was performed according to the published protocol with modifications . Briefly mRNAs were purified by VAHTS RNA Clean Beads N412 Vayzme in RNase free H2O with reverse transcription mix amplified for 15 cycles and reverse transcribed for cDNAs before purifying with VAHTS DNA Clean Beads N411 Vazyme. Enriched cDNA was quantified using Qubit dsDNA HS Assay Kit Q3285 Guangzhou IGE biotechnology ltd and verified by DNA gel electrophoresis 1.5 2 kb. Libraries were prepared by using TruePrep DNA library Prep Kit V2 for Illumina TD503 Vazyme and adaptor ligated DNAs 400 bp were selected by VAHTS DNA Clean Beads N411 Vazyme. Libraries were sequenced by using NovaSeq PE150 as 150 bp paired end.   cell type:endothelial cells|genotype:WT|treatment:injected with PBS sorting GSM7157751 GSM7157751: flk:GFP injected with PBS 3; Danio rerio; RNA Seq GSM7157751 r1 GSM7157751 1 Five hundred of Tgflk:GFP larvae were injected with PBS control or EVs and three replicates were prepared for each treatment. The larvae were then anesthetized at 24 h post injection hpi before cutting tails on ice. The tails were collected and gently triturated in 1.5 mL cold trypsin solution 0.5 g/L; T3924; Sigma with 1 000 μL pipette tip for 20 min. The dissociated cells were then filtered with a 70 μm filter BD Transduction Laboratories to remove the undissociated tissue and washed twice with cold PBS. Cells were then resuspended in 2.5 mL PBS and stained with 7 AAD 5 μg/mL BD Transduction Laboratories on ice for 30 min. About 1X10^5 GFP+ cells were sorted by FACS MoFlo XDP Beckman and total RNA was extracted with Trizol 15596 Invitrogen according to the manufacturer's instructions. Low input RNA Seq was performed according to the published protocol with modifications . Briefly mRNAs were purified by VAHTS RNA Clean Beads N412 Vayzme in RNase free H2O with reverse transcription mix amplified for 15 cycles and reverse transcribed for cDNAs before purifying with VAHTS DNA Clean Beads N411 Vazyme. Enriched cDNA was quantified using Qubit dsDNA HS Assay Kit Q3285 Guangzhou IGE biotechnology ltd and verified by DNA gel electrophoresis 1.5 2 kb. Libraries were prepared by using TruePrep DNA library Prep Kit V2 for Illumina TD503 Vazyme and adaptor ligated DNAs 400 bp were selected by VAHTS DNA Clean Beads N411 Vazyme. Libraries were sequenced by using NovaSeq PE150 as 150 bp paired end.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP431649   loader:fastq load.py EC-Ctrl-3_L1_Q803601.R1.fastq.gz EC-Ctrl-3_L1_Q803601.R2.fastq.gz fastq fastq 7876493100.0 26254977.0 GSM7157751 r1 0:150 1:150 A:2089536762;C:1833918006;G:1831681778;T:2121319352;N:37202 150 150     2089536762 1833918006 1831681778 2121319352 37202 SRX19911924 SRS17265411 SRA1622779 Jianglinjia Lab, SUN YAT-SEN MEMORIAL HOSPITAL Jianglinjia Lab, SUN YAT-SEN MEMORIAL HOSPITAL 2 0.92206 0.92521 0.10775 0.10806 0.83577 0.8356 0.62745 0.62603 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2023-04-09 Larval Larval Endothelium Cardiovascular System
74903 74903 SRR24112514 SRX19911923 SRS17265409 SRP431649 PRJNA953763 Low input RNA seq of endothelial cells sorted from tail of zebrafish larvae GSE229261 Transcriptome Analysis To characterize the mechanism by which AML derived extracellular vesiclesEV impaired the vascular architecture and function EV or PBS injected flk:GFP zebrafish larvae were used for sorting endothelial cells and performing RNA Seq. Vascular niches sustain hematopoietic stem and progenitor cells HSPC and are drastically remodeled in myeloid leukemia to support pathological progression. By utilizing the leukemia xenografted zebrafish model we identified that myeloid leukemia secreted extracellular vesicles EVs to impair HSPC proliferation survival and differentiation towards lymphoid/erythroid lineages. The leukemia EVs delivered arginase 1 into venous vasculature to deplete L arginine and cause NOS uncoupling which catalyzes production of ROS instead of NO. The oxidative stress caused endothelial cell loss vascular constriction and failure of secreting niche factors and supporting hematopoiesis. Our findings indicate that myeloid leukemia impaired the vascular function of supporting hematopoiesis by delivering arginase in EVs and arginase inhibition has the potential to improve normal hematopoiesis in myeloid leukemia. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells sorted from tails of MV4 11 derived EV or PBS injected flk:GFP zebrafish larvae.       flk:GFP injected with PBS 2 GSM7157750   tissue:endothelial cells|cell type:endothelial cells|genotype:WT|treatment:injected with PBS sorting|geo loc name:missing|collection date:missing flk:GFP injected with PBS 2 post removing low quality reads and trimming the adaptor sequences by Trim Galore v0.5.0 Babraham Bioinformatics RNA Seq reads were aligned to zebrafish genome GRCz11 by Salmon v0.03.1 COMBINE lab with ENCODE options and genes were annotated by Ensembl database. For expression quantification the uniquely mapped reads were transformed to counts by Salmon and normalized to counts per million CPM or log2CPM+1 by edgeR v3.40.1 Bioconductor. The batch effect was removed by sva v3.46.0 Bioconductor. Three replicates of PBS or EV treated ECs were aligned by Principal ComponentAnalysis PCA and one replicate that was diverged from the other two was removed for the following analysis. Assembly: GRCz11 Supplementary files format and content: Zebrafish Raw Counts.tar with raw counts matrices endothelial cells   Five hundred of Tgflk:GFP larvae were injected with PBS control or EVs and three replicates were prepared for each treatment. The larvae were then anesthetized at 24 h post injection hpi before cutting tails on ice. The tails were collected and gently triturated in 1.5 mL cold trypsin solution 0.5 g/L; T3924; Sigma with 1 000 μL pipette tip for 20 min. The dissociated cells were then filtered with a 70 μm filter BD Transduction Laboratories to remove the undissociated tissue and washed twice with cold PBS. Cells were then resuspended in 2.5 mL PBS and stained with 7 AAD 5 μg/mL BD Transduction Laboratories on ice for 30 min. About 1X10^5 GFP+ cells were sorted by FACS MoFlo XDP Beckman and total RNA was extracted with Trizol 15596 Invitrogen according to the manufacturer’s instructions. Low input RNA Seq was performed according to the published protocol with modifications . Briefly mRNAs were purified by VAHTS RNA Clean Beads N412 Vayzme in RNase free H2O with reverse transcription mix amplified for 15 cycles and reverse transcribed for cDNAs before purifying with VAHTS DNA Clean Beads N411 Vazyme. Enriched cDNA was quantified using Qubit dsDNA HS Assay Kit Q3285 Guangzhou IGE biotechnology ltd and verified by DNA gel electrophoresis 1.5 2 kb. Libraries were prepared by using TruePrep DNA library Prep Kit V2 for Illumina TD503 Vazyme and adaptor ligated DNAs 400 bp were selected by VAHTS DNA Clean Beads N411 Vazyme. Libraries were sequenced by using NovaSeq PE150 as 150 bp paired end.   cell type:endothelial cells|genotype:WT|treatment:injected with PBS sorting GSM7157750 GSM7157750: flk:GFP injected with PBS 2; Danio rerio; RNA Seq GSM7157750 r1 GSM7157750 1 Five hundred of Tgflk:GFP larvae were injected with PBS control or EVs and three replicates were prepared for each treatment. The larvae were then anesthetized at 24 h post injection hpi before cutting tails on ice. The tails were collected and gently triturated in 1.5 mL cold trypsin solution 0.5 g/L; T3924; Sigma with 1 000 μL pipette tip for 20 min. The dissociated cells were then filtered with a 70 μm filter BD Transduction Laboratories to remove the undissociated tissue and washed twice with cold PBS. Cells were then resuspended in 2.5 mL PBS and stained with 7 AAD 5 μg/mL BD Transduction Laboratories on ice for 30 min. About 1X10^5 GFP+ cells were sorted by FACS MoFlo XDP Beckman and total RNA was extracted with Trizol 15596 Invitrogen according to the manufacturer's instructions. Low input RNA Seq was performed according to the published protocol with modifications . Briefly mRNAs were purified by VAHTS RNA Clean Beads N412 Vayzme in RNase free H2O with reverse transcription mix amplified for 15 cycles and reverse transcribed for cDNAs before purifying with VAHTS DNA Clean Beads N411 Vazyme. Enriched cDNA was quantified using Qubit dsDNA HS Assay Kit Q3285 Guangzhou IGE biotechnology ltd and verified by DNA gel electrophoresis 1.5 2 kb. Libraries were prepared by using TruePrep DNA library Prep Kit V2 for Illumina TD503 Vazyme and adaptor ligated DNAs 400 bp were selected by VAHTS DNA Clean Beads N411 Vazyme. Libraries were sequenced by using NovaSeq PE150 as 150 bp paired end.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP431649   loader:fastq load.py EC-Ctrl-2_L1_Q802601.R1.fastq.gz EC-Ctrl-2_L1_Q802601.R2.fastq.gz fastq fastq 5854627800.0 19515426.0 GSM7157750 r1 0:150 1:150 A:1445169159;C:1483296417;G:1424223070;T:1501912158;N:26996 150 150     1445169159 1483296417 1424223070 1501912158 26996 SRX19911923 SRS17265409 SRA1622779 Jianglinjia Lab, SUN YAT-SEN MEMORIAL HOSPITAL Jianglinjia Lab, SUN YAT-SEN MEMORIAL HOSPITAL 2 0.96858 0.96892 0.01876 0.01871 0.83031 0.82923 0.49748 0.5099 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2023-04-09 Larval Larval Endothelium Cardiovascular System
74904 74904 SRR24112515 SRX19911922 SRS17265410 SRP431649 PRJNA953763 Low input RNA seq of endothelial cells sorted from tail of zebrafish larvae GSE229261 Transcriptome Analysis To characterize the mechanism by which AML derived extracellular vesiclesEV impaired the vascular architecture and function EV or PBS injected flk:GFP zebrafish larvae were used for sorting endothelial cells and performing RNA Seq. Vascular niches sustain hematopoietic stem and progenitor cells HSPC and are drastically remodeled in myeloid leukemia to support pathological progression. By utilizing the leukemia xenografted zebrafish model we identified that myeloid leukemia secreted extracellular vesicles EVs to impair HSPC proliferation survival and differentiation towards lymphoid/erythroid lineages. The leukemia EVs delivered arginase 1 into venous vasculature to deplete L arginine and cause NOS uncoupling which catalyzes production of ROS instead of NO. The oxidative stress caused endothelial cell loss vascular constriction and failure of secreting niche factors and supporting hematopoiesis. Our findings indicate that myeloid leukemia impaired the vascular function of supporting hematopoiesis by delivering arginase in EVs and arginase inhibition has the potential to improve normal hematopoiesis in myeloid leukemia. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells sorted from tails of MV4 11 derived EV or PBS injected flk:GFP zebrafish larvae.       flk:GFP injected with PBS 1 GSM7157749   tissue:endothelial cells|cell type:endothelial cells|genotype:WT|treatment:injected with PBS sorting|geo loc name:missing|collection date:missing flk:GFP injected with PBS 1 post removing low quality reads and trimming the adaptor sequences by Trim Galore v0.5.0 Babraham Bioinformatics RNA Seq reads were aligned to zebrafish genome GRCz11 by Salmon v0.03.1 COMBINE lab with ENCODE options and genes were annotated by Ensembl database. For expression quantification the uniquely mapped reads were transformed to counts by Salmon and normalized to counts per million CPM or log2CPM+1 by edgeR v3.40.1 Bioconductor. The batch effect was removed by sva v3.46.0 Bioconductor. Three replicates of PBS or EV treated ECs were aligned by Principal ComponentAnalysis PCA and one replicate that was diverged from the other two was removed for the following analysis. Assembly: GRCz11 Supplementary files format and content: Zebrafish Raw Counts.tar with raw counts matrices endothelial cells   Five hundred of Tgflk:GFP larvae were injected with PBS control or EVs and three replicates were prepared for each treatment. The larvae were then anesthetized at 24 h post injection hpi before cutting tails on ice. The tails were collected and gently triturated in 1.5 mL cold trypsin solution 0.5 g/L; T3924; Sigma with 1 000 μL pipette tip for 20 min. The dissociated cells were then filtered with a 70 μm filter BD Transduction Laboratories to remove the undissociated tissue and washed twice with cold PBS. Cells were then resuspended in 2.5 mL PBS and stained with 7 AAD 5 μg/mL BD Transduction Laboratories on ice for 30 min. About 1X10^5 GFP+ cells were sorted by FACS MoFlo XDP Beckman and total RNA was extracted with Trizol 15596 Invitrogen according to the manufacturer’s instructions. Low input RNA Seq was performed according to the published protocol with modifications . Briefly mRNAs were purified by VAHTS RNA Clean Beads N412 Vayzme in RNase free H2O with reverse transcription mix amplified for 15 cycles and reverse transcribed for cDNAs before purifying with VAHTS DNA Clean Beads N411 Vazyme. Enriched cDNA was quantified using Qubit dsDNA HS Assay Kit Q3285 Guangzhou IGE biotechnology ltd and verified by DNA gel electrophoresis 1.5 2 kb. Libraries were prepared by using TruePrep DNA library Prep Kit V2 for Illumina TD503 Vazyme and adaptor ligated DNAs 400 bp were selected by VAHTS DNA Clean Beads N411 Vazyme. Libraries were sequenced by using NovaSeq PE150 as 150 bp paired end.   cell type:endothelial cells|genotype:WT|treatment:injected with PBS sorting GSM7157749 GSM7157749: flk:GFP injected with PBS 1; Danio rerio; RNA Seq GSM7157749 r1 GSM7157749 1 Five hundred of Tgflk:GFP larvae were injected with PBS control or EVs and three replicates were prepared for each treatment. The larvae were then anesthetized at 24 h post injection hpi before cutting tails on ice. The tails were collected and gently triturated in 1.5 mL cold trypsin solution 0.5 g/L; T3924; Sigma with 1 000 μL pipette tip for 20 min. The dissociated cells were then filtered with a 70 μm filter BD Transduction Laboratories to remove the undissociated tissue and washed twice with cold PBS. Cells were then resuspended in 2.5 mL PBS and stained with 7 AAD 5 μg/mL BD Transduction Laboratories on ice for 30 min. About 1X10^5 GFP+ cells were sorted by FACS MoFlo XDP Beckman and total RNA was extracted with Trizol 15596 Invitrogen according to the manufacturer's instructions. Low input RNA Seq was performed according to the published protocol with modifications . Briefly mRNAs were purified by VAHTS RNA Clean Beads N412 Vayzme in RNase free H2O with reverse transcription mix amplified for 15 cycles and reverse transcribed for cDNAs before purifying with VAHTS DNA Clean Beads N411 Vazyme. Enriched cDNA was quantified using Qubit dsDNA HS Assay Kit Q3285 Guangzhou IGE biotechnology ltd and verified by DNA gel electrophoresis 1.5 2 kb. Libraries were prepared by using TruePrep DNA library Prep Kit V2 for Illumina TD503 Vazyme and adaptor ligated DNAs 400 bp were selected by VAHTS DNA Clean Beads N411 Vazyme. Libraries were sequenced by using NovaSeq PE150 as 150 bp paired end.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP431649   loader:fastq load.py EC-Ctrl-1_L1_Q801601.R1.fastq.gz EC-Ctrl-1_L1_Q801601.R2.fastq.gz fastq fastq 8619243000.0 28730810.0 GSM7157749 r1 0:150 1:150 A:2216862162;C:2063188245;G:2036562936;T:2302587656;N:42001 150 150     2216862162 2063188245 2036562936 2302587656 42001 SRX19911922 SRS17265410 SRA1622779 Jianglinjia Lab, SUN YAT-SEN MEMORIAL HOSPITAL Jianglinjia Lab, SUN YAT-SEN MEMORIAL HOSPITAL 2 0.94822 0.94707 0.05974 0.05972 0.8015 0.8006 0.53046 0.52886 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2023-04-09 Larval Larval 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");;